--- _id: '15179' abstract: - lang: eng text: The fungal bioluminescence pathway can be reconstituted in other organisms allowing luminescence imaging without exogenously supplied substrate. The pathway starts from hispidin biosynthesis—a step catalyzed by a large fungal polyketide synthase that requires a posttranslational modification for activity. Here, we report identification of alternative compact hispidin synthases encoded by a phylogenetically diverse group of plants. A hybrid bioluminescence pathway that combines plant and fungal genes is more compact, not dependent on availability of machinery for posttranslational modifications, and confers autonomous bioluminescence in yeast, mammalian, and plant hosts. The compact size of plant hispidin synthases enables additional modes of delivery of autoluminescence, such as delivery with viral vectors. acknowledgement: "We thank Milaboratory (milaboratory.com) for the access to computing and storage infrastructure. We thank J. Petrasek for providing the BY-2 cell culture line. We thank Konstantin Lukyanov laboratory and Sergey Deyev laboratory for assistance with experiments.\r\nThis study was partially funded by Light Bio and Planta. The Synthetic biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0). Cloning and luminescent assays performed in BY-2 were partially supported by RSF, project number 22-14-00400, https://rscf.ru/project/22-14-00400/. Plant transformations were funded by RFBR and MOST, project number 21-54-52004. Plant imaging experiments were funded by RSF, project number 22-74-00124, https://rscf.ru/project/22-74-00124/. Viral delivery experiments were funded by the grant PID2019-108203RB-I00 Plan Nacional I + D from the Ministerio de Ciencia e Innovación (Spain) through the Agencia Estatal de Investigación (cofinanced by the European Regional Development Fund)." article_number: adk1992 article_processing_charge: Yes article_type: original author: - first_name: Kseniia A. full_name: Palkina, Kseniia A. last_name: Palkina - first_name: Tatiana A. full_name: Karataeva, Tatiana A. last_name: Karataeva - first_name: Maxim M. full_name: Perfilov, Maxim M. last_name: Perfilov - first_name: Liliia I. full_name: Fakhranurova, Liliia I. last_name: Fakhranurova - first_name: Nadezhda M. full_name: Markina, Nadezhda M. last_name: Markina - first_name: Louisa full_name: Gonzalez Somermeyer, Louisa id: 4720D23C-F248-11E8-B48F-1D18A9856A87 last_name: Gonzalez Somermeyer orcid: 0000-0001-9139-5383 - first_name: Elena full_name: Garcia-Perez, Elena last_name: Garcia-Perez - first_name: Marta full_name: Vazquez-Vilar, Marta last_name: Vazquez-Vilar - first_name: Marta full_name: Rodriguez-Rodriguez, Marta last_name: Rodriguez-Rodriguez - first_name: Victor full_name: Vazquez-Vilriales, Victor last_name: Vazquez-Vilriales - first_name: Ekaterina S. full_name: Shakhova, Ekaterina S. last_name: Shakhova - first_name: Tatiana full_name: Mitiouchkina, Tatiana last_name: Mitiouchkina - first_name: Olga A. full_name: Belozerova, Olga A. last_name: Belozerova - first_name: Sergey I. full_name: Kovalchuk, Sergey I. last_name: Kovalchuk - first_name: Anna full_name: Alekberova, Anna last_name: Alekberova - first_name: Alena K. full_name: Malyshevskaia, Alena K. last_name: Malyshevskaia - first_name: Evgenia N. full_name: Bugaeva, Evgenia N. last_name: Bugaeva - first_name: Elena B. full_name: Guglya, Elena B. last_name: Guglya - first_name: Anastasia full_name: Balakireva, Anastasia last_name: Balakireva - first_name: Nikita full_name: Sytov, Nikita last_name: Sytov - first_name: Anastasia full_name: Bezlikhotnova, Anastasia last_name: Bezlikhotnova - first_name: Daria I. full_name: Boldyreva, Daria I. last_name: Boldyreva - first_name: Vladislav V. full_name: Babenko, Vladislav V. last_name: Babenko - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Vladimir V. full_name: Choob, Vladimir V. last_name: Choob - first_name: Diego full_name: Orzaez, Diego last_name: Orzaez - first_name: Ilia V. full_name: Yampolsky, Ilia V. last_name: Yampolsky - first_name: Alexander S. full_name: Mishin, Alexander S. last_name: Mishin - first_name: Karen S. full_name: Sarkisyan, Karen S. last_name: Sarkisyan citation: ama: Palkina KA, Karataeva TA, Perfilov MM, et al. A hybrid pathway for self-sustained luminescence. Science Advances. 2024;10(10). doi:10.1126/sciadv.adk1992 apa: Palkina, K. A., Karataeva, T. A., Perfilov, M. M., Fakhranurova, L. I., Markina, N. M., Gonzalez Somermeyer, L., … Sarkisyan, K. S. (2024). A hybrid pathway for self-sustained luminescence. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adk1992 chicago: Palkina, Kseniia A., Tatiana A. Karataeva, Maxim M. Perfilov, Liliia I. Fakhranurova, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, Elena Garcia-Perez, et al. “A Hybrid Pathway for Self-Sustained Luminescence.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adk1992. ieee: K. A. Palkina et al., “A hybrid pathway for self-sustained luminescence,” Science Advances, vol. 10, no. 10. American Association for the Advancement of Science, 2024. ista: Palkina KA, Karataeva TA, Perfilov MM, Fakhranurova LI, Markina NM, Gonzalez Somermeyer L, Garcia-Perez E, Vazquez-Vilar M, Rodriguez-Rodriguez M, Vazquez-Vilriales V, Shakhova ES, Mitiouchkina T, Belozerova OA, Kovalchuk SI, Alekberova A, Malyshevskaia AK, Bugaeva EN, Guglya EB, Balakireva A, Sytov N, Bezlikhotnova A, Boldyreva DI, Babenko VV, Kondrashov F, Choob VV, Orzaez D, Yampolsky IV, Mishin AS, Sarkisyan KS. 2024. A hybrid pathway for self-sustained luminescence. Science Advances. 10(10), adk1992. mla: Palkina, Kseniia A., et al. “A Hybrid Pathway for Self-Sustained Luminescence.” Science Advances, vol. 10, no. 10, adk1992, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adk1992. short: K.A. Palkina, T.A. Karataeva, M.M. Perfilov, L.I. Fakhranurova, N.M. Markina, L. Gonzalez Somermeyer, E. Garcia-Perez, M. Vazquez-Vilar, M. Rodriguez-Rodriguez, V. Vazquez-Vilriales, E.S. Shakhova, T. Mitiouchkina, O.A. Belozerova, S.I. Kovalchuk, A. Alekberova, A.K. Malyshevskaia, E.N. Bugaeva, E.B. Guglya, A. Balakireva, N. Sytov, A. Bezlikhotnova, D.I. Boldyreva, V.V. Babenko, F. Kondrashov, V.V. Choob, D. Orzaez, I.V. Yampolsky, A.S. Mishin, K.S. Sarkisyan, Science Advances 10 (2024). date_created: 2024-03-25T08:54:33Z date_published: 2024-03-01T00:00:00Z date_updated: 2024-03-25T09:44:53Z day: '01' ddc: - '580' department: - _id: FyKo doi: 10.1126/sciadv.adk1992 file: - access_level: open_access checksum: a19c43b260ea0bbaf895a29712e3153c content_type: application/pdf creator: dernst date_created: 2024-03-25T09:42:10Z date_updated: 2024-03-25T09:42:10Z file_id: '15185' file_name: 2024_ScienceAdv_Palkina.pdf file_size: 1499302 relation: main_file success: 1 file_date_updated: 2024-03-25T09:42:10Z has_accepted_license: '1' intvolume: ' 10' issue: '10' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Science Advances publication_identifier: issn: - 2375-2548 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: A hybrid pathway for self-sustained luminescence tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2024' ... --- _id: '12758' abstract: - lang: eng text: AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is “solved”. However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted the pLDDT and metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the same AlphaFold pLDDT metrics with the impact of a single mutation on structure using a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold may not be immediately applied to other problems or applications in protein folding. acknowledgement: The authors acknowledge the use of Zhores supercomputer [28] for obtaining the results presented in this paper.The authors thank Zimin Foundation and Petrovax for support of the presented study at the School of Molecular and Theoretical Biology 2021. article_number: e0282689 article_processing_charge: No article_type: original author: - first_name: Marina A. full_name: Pak, Marina A. last_name: Pak - first_name: Karina A. full_name: Markhieva, Karina A. last_name: Markhieva - first_name: Mariia S. full_name: Novikova, Mariia S. last_name: Novikova - first_name: Dmitry S. full_name: Petrov, Dmitry S. last_name: Petrov - first_name: Ilya S. full_name: Vorobyev, Ilya S. last_name: Vorobyev - first_name: Ekaterina full_name: Maksimova, Ekaterina id: 2FBE0DE4-F248-11E8-B48F-1D18A9856A87 last_name: Maksimova - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Dmitry N. full_name: Ivankov, Dmitry N. last_name: Ivankov citation: ama: Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 2023;18(3). doi:10.1371/journal.pone.0282689 apa: Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I. S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0282689 chicago: Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov, Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0282689. ieee: M. A. Pak et al., “Using AlphaFold to predict the impact of single mutations on protein stability and function,” PLoS ONE, vol. 18, no. 3. Public Library of Science, 2023. ista: Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 18(3), e0282689. mla: Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” PLoS ONE, vol. 18, no. 3, e0282689, Public Library of Science, 2023, doi:10.1371/journal.pone.0282689. short: M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova, F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023). date_created: 2023-03-26T22:01:07Z date_published: 2023-03-16T00:00:00Z date_updated: 2023-08-01T13:47:14Z day: '16' ddc: - '570' department: - _id: FyKo - _id: MaRo doi: 10.1371/journal.pone.0282689 external_id: isi: - '000985134400106' file: - access_level: open_access checksum: 0281bdfccf8d76c4e08dd011c603f6b6 content_type: application/pdf creator: dernst date_created: 2023-03-27T07:09:08Z date_updated: 2023-03-27T07:09:08Z file_id: '12771' file_name: 2023_PLoSOne_Pak.pdf file_size: 856625 relation: main_file success: 1 file_date_updated: 2023-03-27T07:09:08Z has_accepted_license: '1' intvolume: ' 18' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: PLoS ONE publication_identifier: eissn: - 1932-6203 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Using AlphaFold to predict the impact of single mutations on protein stability and function tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 18 year: '2023' ... --- _id: '13164' abstract: - lang: eng text: Molecular compatibility between gametes is a prerequisite for successful fertilization. As long as a sperm and egg can recognize and bind each other via their surface proteins, gamete fusion may occur even between members of separate species, resulting in hybrids that can impact speciation. The egg membrane protein Bouncer confers species specificity to gamete interactions between medaka and zebrafish, preventing their cross-fertilization. Here, we leverage this specificity to uncover distinct amino acid residues and N-glycosylation patterns that differentially influence the function of medaka and zebrafish Bouncer and contribute to cross-species incompatibility. Curiously, in contrast to the specificity observed for medaka and zebrafish Bouncer, seahorse and fugu Bouncer are compatible with both zebrafish and medaka sperm, in line with the pervasive purifying selection that dominates Bouncer’s evolution. The Bouncer-sperm interaction is therefore the product of seemingly opposing evolutionary forces that, for some species, restrict fertilization to closely related fish, and for others, allow broad gamete compatibility that enables hybridization. acknowledgement: We thank Manfred Schartl for sharing RNA-seq data from medaka ovaries and testes prior to publication; Maria Novatchkova for help with RNA-seq analysis; Katharina Lust for advice on medaka techniques; Milan Malinsky for input on Lake Malawi cichlid Bouncer sequences; Felicia Spitzer, Mirjam Binner, and Anna Bandura for help with genotyping; Friedrich Puhl, Kerstin Rattner, Julia Koenig, and Dijana Sunjic for taking care of zebrafish and medaka; and the Pauli lab for helpful discussions about the project and feedback on the manuscript. K.R.B.G. was supported by a DOC Fellowship from the Austrian Academy of Sciences. Work in the Pauli lab was supported by the FWF START program (Y 1031-B28 to A.P.), the ERC CoG 101044495/GaMe, the HFSP Career Development Award (CDA00066/2015 to A.P.), a HFSP Young Investigator Award (RGY0079/2020 to A.P.) and the FWF SFB RNA-Deco (project number F80). The IMP receives institutional funding from Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936). Work by J.S. and Y.M. in this project was supported by the Israel Science Foundation grant 636/21 to Y.M. Work by L.J. was supported by the Swedish Research Council grant 2020-04936 and the Knut and Alice Wallenberg Foundation grant 2018.0042. For the purpose of Open Access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript (AAM) version arising from this submission. article_number: '3506' article_processing_charge: No article_type: original author: - first_name: Krista R.B. full_name: Gert, Krista R.B. last_name: Gert - first_name: Karin full_name: Panser, Karin last_name: Panser - first_name: Joachim full_name: Surm, Joachim last_name: Surm - first_name: Benjamin S. full_name: Steinmetz, Benjamin S. last_name: Steinmetz - first_name: Alexander full_name: Schleiffer, Alexander last_name: Schleiffer - first_name: Luca full_name: Jovine, Luca last_name: Jovine - first_name: Yehu full_name: Moran, Yehu last_name: Moran - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Andrea full_name: Pauli, Andrea last_name: Pauli citation: ama: Gert KRB, Panser K, Surm J, et al. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. 2023;14. doi:10.1038/s41467-023-39317-4 apa: Gert, K. R. B., Panser, K., Surm, J., Steinmetz, B. S., Schleiffer, A., Jovine, L., … Pauli, A. (2023). Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-39317-4 chicago: Gert, Krista R.B., Karin Panser, Joachim Surm, Benjamin S. Steinmetz, Alexander Schleiffer, Luca Jovine, Yehu Moran, Fyodor Kondrashov, and Andrea Pauli. “Divergent Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-39317-4. ieee: K. R. B. Gert et al., “Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Gert KRB, Panser K, Surm J, Steinmetz BS, Schleiffer A, Jovine L, Moran Y, Kondrashov F, Pauli A. 2023. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. 14, 3506. mla: Gert, Krista R. B., et al. “Divergent Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.” Nature Communications, vol. 14, 3506, Springer Nature, 2023, doi:10.1038/s41467-023-39317-4. short: K.R.B. Gert, K. Panser, J. Surm, B.S. Steinmetz, A. Schleiffer, L. Jovine, Y. Moran, F. Kondrashov, A. Pauli, Nature Communications 14 (2023). date_created: 2023-06-25T22:00:45Z date_published: 2023-06-14T00:00:00Z date_updated: 2023-12-13T11:26:34Z day: '14' ddc: - '570' department: - _id: FyKo doi: 10.1038/s41467-023-39317-4 external_id: isi: - '001048208600023' file: - access_level: open_access checksum: d6165f41c7f1c2c04b04256ec9f003fb content_type: application/pdf creator: dernst date_created: 2023-06-26T10:26:04Z date_updated: 2023-06-26T10:26:04Z file_id: '13172' file_name: 2023_NatureComm_Gert.pdf file_size: 1555006 relation: main_file success: 1 file_date_updated: 2023-06-26T10:26:04Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '13976' abstract: - lang: eng text: Conflicts and natural disasters affect entire populations of the countries involved and, in addition to the thousands of lives destroyed, have a substantial negative impact on the scientific advances these countries provide. The unprovoked invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria, and the ongoing conflicts in the Middle East are just a few examples. Millions of people have been killed or displaced, their futures uncertain. These events have resulted in extensive infrastructure collapse, with loss of electricity, transportation, and access to services. Schools, universities, and research centers have been destroyed along with decades’ worth of data, samples, and findings. Scholars in disaster areas face short- and long-term problems in terms of what they can accomplish now for obtaining grants and for employment in the long run. In our interconnected world, conflicts and disasters are no longer a local problem but have wide-ranging impacts on the entire world, both now and in the future. Here, we focus on the current and ongoing impact of war on the scientific community within Ukraine and from this draw lessons that can be applied to all affected countries where scientists at risk are facing hardship. We present and classify examples of effective and feasible mechanisms used to support researchers in countries facing hardship and discuss how these can be implemented with help from the international scientific community and what more is desperately needed. Reaching out, providing accessible training opportunities, and developing collaborations should increase inclusion and connectivity, support scientific advancements within affected communities, and expedite postwar and disaster recovery. acknowledgement: "Our article is dedicated to all freedom-loving people around the world and to the people of Ukraine who fight for our freedom. Special thanks to Anita Bandrowski, Oleksandra V. Ivashchenko, and Sanita Reinsone for the helpful review, valuable criticism, and useful suggestions while preparing this manuscript, and to Tetiana Yes'kova for helping with Ukrainian translation.\r\nAll authors volunteered their time. No funding supported work on this article." article_processing_charge: Yes article_type: original author: - first_name: Walter full_name: Wolfsberger, Walter last_name: Wolfsberger - first_name: Karishma full_name: Chhugani, Karishma last_name: Chhugani - first_name: Khrystyna full_name: Shchubelka, Khrystyna last_name: Shchubelka - first_name: Alina full_name: Frolova, Alina last_name: Frolova - first_name: Yuriy full_name: Salyha, Yuriy last_name: Salyha - first_name: Oksana full_name: Zlenko, Oksana last_name: Zlenko - first_name: Mykhailo full_name: Arych, Mykhailo last_name: Arych - first_name: Dmytro full_name: Dziuba, Dmytro last_name: Dziuba - first_name: Andrii full_name: Parkhomenko, Andrii last_name: Parkhomenko - first_name: Volodymyr full_name: Smolanka, Volodymyr last_name: Smolanka - first_name: Zeynep H. full_name: Gümüş, Zeynep H. last_name: Gümüş - first_name: Efe full_name: Sezgin, Efe last_name: Sezgin - first_name: Alondra full_name: Diaz-Lameiro, Alondra last_name: Diaz-Lameiro - first_name: Viktor R. full_name: Toth, Viktor R. last_name: Toth - first_name: Megi full_name: Maci, Megi last_name: Maci - first_name: Eric full_name: Bortz, Eric last_name: Bortz - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Patricia M. full_name: Morton, Patricia M. last_name: Morton - first_name: Paweł P. full_name: Łabaj, Paweł P. last_name: Łabaj - first_name: Veronika full_name: Romero, Veronika last_name: Romero - first_name: Jakub full_name: Hlávka, Jakub last_name: Hlávka - first_name: Serghei full_name: Mangul, Serghei last_name: Mangul - first_name: Taras K. full_name: Oleksyk, Taras K. last_name: Oleksyk citation: ama: 'Wolfsberger W, Chhugani K, Shchubelka K, et al. Scientists without borders: Lessons from Ukraine. GigaScience. 2023;12. doi:10.1093/gigascience/giad045' apa: 'Wolfsberger, W., Chhugani, K., Shchubelka, K., Frolova, A., Salyha, Y., Zlenko, O., … Oleksyk, T. K. (2023). Scientists without borders: Lessons from Ukraine. GigaScience. Oxford Academic. https://doi.org/10.1093/gigascience/giad045' chicago: 'Wolfsberger, Walter, Karishma Chhugani, Khrystyna Shchubelka, Alina Frolova, Yuriy Salyha, Oksana Zlenko, Mykhailo Arych, et al. “Scientists without Borders: Lessons from Ukraine.” GigaScience. Oxford Academic, 2023. https://doi.org/10.1093/gigascience/giad045.' ieee: 'W. Wolfsberger et al., “Scientists without borders: Lessons from Ukraine,” GigaScience, vol. 12. Oxford Academic, 2023.' ista: 'Wolfsberger W, Chhugani K, Shchubelka K, Frolova A, Salyha Y, Zlenko O, Arych M, Dziuba D, Parkhomenko A, Smolanka V, Gümüş ZH, Sezgin E, Diaz-Lameiro A, Toth VR, Maci M, Bortz E, Kondrashov F, Morton PM, Łabaj PP, Romero V, Hlávka J, Mangul S, Oleksyk TK. 2023. Scientists without borders: Lessons from Ukraine. GigaScience. 12.' mla: 'Wolfsberger, Walter, et al. “Scientists without Borders: Lessons from Ukraine.” GigaScience, vol. 12, Oxford Academic, 2023, doi:10.1093/gigascience/giad045.' short: W. Wolfsberger, K. Chhugani, K. Shchubelka, A. Frolova, Y. Salyha, O. Zlenko, M. Arych, D. Dziuba, A. Parkhomenko, V. Smolanka, Z.H. Gümüş, E. Sezgin, A. Diaz-Lameiro, V.R. Toth, M. Maci, E. Bortz, F. Kondrashov, P.M. Morton, P.P. Łabaj, V. Romero, J. Hlávka, S. Mangul, T.K. Oleksyk, GigaScience 12 (2023). date_created: 2023-08-06T22:01:13Z date_published: 2023-07-27T00:00:00Z date_updated: 2023-12-13T12:01:46Z day: '27' department: - _id: FyKo doi: 10.1093/gigascience/giad045 external_id: isi: - '001081086100001' pmid: - '37496156' intvolume: ' 12' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/gigascience/giad045 month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: GigaScience publication_identifier: eissn: - 2047-217X publication_status: epub_ahead publisher: Oxford Academic quality_controlled: '1' scopus_import: '1' status: public title: 'Scientists without borders: Lessons from Ukraine' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2023' ... --- _id: '14862' article_number: ckad160.597 article_processing_charge: No author: - first_name: Simon full_name: Rella, Simon id: B4765ACA-AA38-11E9-AC9A-0930E6697425 last_name: Rella - first_name: Y full_name: Kulikova, Y last_name: Kulikova - first_name: Aygul full_name: Minnegalieva, Aygul id: 87DF77F0-1D9A-11EA-B6AE-CE443DDC885E last_name: Minnegalieva - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: 'Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. Complex vaccination strategies prevent the emergence of vaccine resistance. In: European Journal of Public Health. Vol 33. Oxford University Press; 2023. doi:10.1093/eurpub/ckad160.597' apa: Rella, S., Kulikova, Y., Minnegalieva, A., & Kondrashov, F. (2023). Complex vaccination strategies prevent the emergence of vaccine resistance. In European Journal of Public Health (Vol. 33). Oxford University Press. https://doi.org/10.1093/eurpub/ckad160.597 chicago: Rella, Simon, Y Kulikova, Aygul Minnegalieva, and Fyodor Kondrashov. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” In European Journal of Public Health, Vol. 33. Oxford University Press, 2023. https://doi.org/10.1093/eurpub/ckad160.597. ieee: S. Rella, Y. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination strategies prevent the emergence of vaccine resistance,” in European Journal of Public Health, 2023, vol. 33, no. Supplement_2. ista: Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. 2023. Complex vaccination strategies prevent the emergence of vaccine resistance. European Journal of Public Health. vol. 33, ckad160.597. mla: Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” European Journal of Public Health, vol. 33, no. Supplement_2, ckad160.597, Oxford University Press, 2023, doi:10.1093/eurpub/ckad160.597. short: S. Rella, Y. Kulikova, A. Minnegalieva, F. Kondrashov, in:, European Journal of Public Health, Oxford University Press, 2023. date_created: 2024-01-22T12:02:28Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-01-24T11:16:09Z day: '01' ddc: - '570' department: - _id: GaTk doi: 10.1093/eurpub/ckad160.597 file: - access_level: open_access checksum: 98706755bb4cc5d553818ade7660a7d2 content_type: application/pdf creator: dernst date_created: 2024-01-24T11:12:33Z date_updated: 2024-01-24T11:12:33Z file_id: '14882' file_name: 2023_EurJourPublicHealth_Rella.pdf file_size: 71057 relation: main_file success: 1 file_date_updated: 2024-01-24T11:12:33Z has_accepted_license: '1' intvolume: ' 33' issue: Supplement_2 keyword: - Public Health - Environmental and Occupational Health language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: European Journal of Public Health publication_identifier: eissn: - 1464-360X issn: - 1101-1262 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Complex vaccination strategies prevent the emergence of vaccine resistance tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2023' ... --- _id: '11187' abstract: - lang: eng text: During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific and organizational challenges. Here, we discuss the application of genomic and computational methods for efficient data-driven COVID-19 response, the advantages of the democratization of viral sequencing around the world and the challenges associated with viral genome data collection and processing. acknowledgement: 'Our paper is dedicated to all freedom-loving people around the world, and to the people of Ukraine who fight for our freedom. We thank William M. Switzer and Ellsworth M. Campbell from the Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA, for discussions and suggestions. We thank Jason Ladner from the Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, for providing suggestions and feedback. S.M. was partially supported by National Science Foundation grants 2041984. T.L. is supported by the NSFC Excellent Young Scientists Fund (Hong Kong and Macau; 31922087), Research Grants Council (RGC) Collaborative Research Fund (C7144-20GF), RGC Research Impact Fund (R7021-20), Innovation and Technology Commission’s InnoHK funding (D24H) and Health and Medical Research Fund (COVID190223). P.S. was supported by US National Institutes of Health (NIH) grant 1R01EB025022 and National Science Foundation (NSF) grant 2047828. M.A. acknowledges King Abdulaziz City for Science and Technology and the Saudi Human Genome Project for technical and financial support (https://shgp.kacst.edu.sa) N.W. was supported by US NIH grants R00 AI139445, DP2 AT011966 and R01 AI167910. A.S. acknowledge funding from NSF grant no. 2029025. A.Z. has been partially supported by NIH grants 1R01EB025022-01 and 1R21CA241044-01A1. S. Knyazev has been partly supported by Molecular Basis of Disease at Georgia State University and NIH awards R01 HG009120, R01 MH115676, R01 AI153827 and U01 HG011715. A.W. has been supported by the CAMS Innovation Fund for Medical Sciences (2021-I2M-1-061). R.K. was supported by NSF project 2038509, RAPID: Improving QIIME 2 and UniFrac for Viruses to Respond to COVID-19, CDC project 30055281 with Scripps led by Kristian Andersen, Genomic sequencing of SARS-CoV-2 to investigate local and cross-border emergence and spread. J.O.W. was supported by NIH–National Institute of Allergy and Infectious Diseases (NIAID) R01 AI135992 and receives funding from the CDC unrelated to this work. T.I.V. is supported by the Branco Weiss Fellowship. Y.P. was supported by the Ministry of Science and Higher Education of the Russian Federation within the framework of state support for the creation and development of World-Class Research Centers “Digital biodesign and personalized healthcare” N◦075-15-2020-926. E.B. was supported by a US National Institute of General Medical Sciences IDeA Alaska INBRE (P20GM103395) and NIAID CEIRR (75N93019R00028). C.E.M. thanks Testing for America (501c3), OpenCovidScreen Foundation, Igor Tulchinsky and the WorldQuant Foundation, Bill Ackman and Olivia Flatto and the Pershing Square Foundation, Ken Griffin and Citadel, the US National Institutes of Health (R01AI125416, R01AI151059, R21AI129851, U01DA053941), and the Alfred P. Sloan Foundation (G-2015-13964). C.Y.C. is supported by US CDC Epidemiology and Laboratory Capacity (ELC) for Infectious Diseases grant 6NU50CK000539 to the California Department of Public Health, the Innovative Genomics Institute (IGI) at the University of California, Berkeley, and University of California, San Francisco, NIH grant R33AI12945 and US CDC contract 75D30121C10991. A.K. was partly supported by RFBR grant 20-515-80017. P.L. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. ~725422 - ReservoirDOCS), the Wellcome Trust through project 206298/Z/17/Z (Artic Network) and NIH grants R01 AI153044 and U19 AI135995. K.C. acknowledges support from the US NSF award EEID-IOS-2109688. F.K.’s work was supported by an ERC Consolidator grant to F.K. (771209–CharFL).' article_processing_charge: No article_type: letter_note author: - first_name: Sergey full_name: Knyazev, Sergey last_name: Knyazev - first_name: Karishma full_name: Chhugani, Karishma last_name: Chhugani - first_name: Varuni full_name: Sarwal, Varuni last_name: Sarwal - first_name: Ram full_name: Ayyala, Ram last_name: Ayyala - first_name: Harman full_name: Singh, Harman last_name: Singh - first_name: Smruthi full_name: Karthikeyan, Smruthi last_name: Karthikeyan - first_name: Dhrithi full_name: Deshpande, Dhrithi last_name: Deshpande - first_name: Pelin Icer full_name: Baykal, Pelin Icer last_name: Baykal - first_name: Zoia full_name: Comarova, Zoia last_name: Comarova - first_name: Angela full_name: Lu, Angela last_name: Lu - first_name: Yuri full_name: Porozov, Yuri last_name: Porozov - first_name: Tetyana I. full_name: Vasylyeva, Tetyana I. last_name: Vasylyeva - first_name: Joel O. full_name: Wertheim, Joel O. last_name: Wertheim - first_name: Braden T. full_name: Tierney, Braden T. last_name: Tierney - first_name: Charles Y. full_name: Chiu, Charles Y. last_name: Chiu - first_name: Ren full_name: Sun, Ren last_name: Sun - first_name: Aiping full_name: Wu, Aiping last_name: Wu - first_name: Malak S. full_name: Abedalthagafi, Malak S. last_name: Abedalthagafi - first_name: Victoria M. full_name: Pak, Victoria M. last_name: Pak - first_name: Shivashankar H. full_name: Nagaraj, Shivashankar H. last_name: Nagaraj - first_name: Adam L. full_name: Smith, Adam L. last_name: Smith - first_name: Pavel full_name: Skums, Pavel last_name: Skums - first_name: Bogdan full_name: Pasaniuc, Bogdan last_name: Pasaniuc - first_name: Andrey full_name: Komissarov, Andrey last_name: Komissarov - first_name: Christopher E. full_name: Mason, Christopher E. last_name: Mason - first_name: Eric full_name: Bortz, Eric last_name: Bortz - first_name: Philippe full_name: Lemey, Philippe last_name: Lemey - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Niko full_name: Beerenwinkel, Niko last_name: Beerenwinkel - first_name: Tommy Tsan Yuk full_name: Lam, Tommy Tsan Yuk last_name: Lam - first_name: Nicholas C. full_name: Wu, Nicholas C. last_name: Wu - first_name: Alex full_name: Zelikovsky, Alex last_name: Zelikovsky - first_name: Rob full_name: Knight, Rob last_name: Knight - first_name: Keith A. full_name: Crandall, Keith A. last_name: Crandall - first_name: Serghei full_name: Mangul, Serghei last_name: Mangul citation: ama: Knyazev S, Chhugani K, Sarwal V, et al. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods. 2022;19(4):374-380. doi:10.1038/s41592-022-01444-z apa: Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan, S., … Mangul, S. (2022). Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-022-01444-z chicago: Knyazev, Sergey, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, et al. “Unlocking Capacities of Genomics for the COVID-19 Response and Future Pandemics.” Nature Methods. Springer Nature, 2022. https://doi.org/10.1038/s41592-022-01444-z. ieee: S. Knyazev et al., “Unlocking capacities of genomics for the COVID-19 response and future pandemics,” Nature Methods, vol. 19, no. 4. Springer Nature, pp. 374–380, 2022. ista: Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. 2022. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods. 19(4), 374–380. mla: Knyazev, Sergey, et al. “Unlocking Capacities of Genomics for the COVID-19 Response and Future Pandemics.” Nature Methods, vol. 19, no. 4, Springer Nature, 2022, pp. 374–80, doi:10.1038/s41592-022-01444-z. short: S. Knyazev, K. Chhugani, V. Sarwal, R. Ayyala, H. Singh, S. Karthikeyan, D. Deshpande, P.I. Baykal, Z. Comarova, A. Lu, Y. Porozov, T.I. Vasylyeva, J.O. Wertheim, B.T. Tierney, C.Y. Chiu, R. Sun, A. Wu, M.S. Abedalthagafi, V.M. Pak, S.H. Nagaraj, A.L. Smith, P. Skums, B. Pasaniuc, A. Komissarov, C.E. Mason, E. Bortz, P. Lemey, F. Kondrashov, N. Beerenwinkel, T.T.Y. Lam, N.C. Wu, A. Zelikovsky, R. Knight, K.A. Crandall, S. Mangul, Nature Methods 19 (2022) 374–380. date_created: 2022-04-17T22:01:48Z date_published: 2022-04-08T00:00:00Z date_updated: 2023-08-03T06:46:09Z day: '08' department: - _id: FyKo doi: 10.1038/s41592-022-01444-z ec_funded: 1 external_id: isi: - '000781199600011' pmid: - '35396471' intvolume: ' 19' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41592-022-01444-z month: '04' oa: 1 oa_version: Published Version page: 374-380 pmid: 1 project: - _id: 26580278-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771209' name: Characterizing the fitness landscape on population and global scales publication: Nature Methods publication_identifier: eissn: - 1548-7105 issn: - 1548-7091 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Unlocking capacities of genomics for the COVID-19 response and future pandemics type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 19 year: '2022' ... --- _id: '11344' abstract: - lang: eng text: Until recently, Shigella and enteroinvasive Escherichia coli were thought to be primate-restricted pathogens. The base of their pathogenicity is the type 3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates host cell invasion and subsequent proliferation. A large family of T3SS effectors, E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella pathogenicity through the modulation of cellular ubiquitination that degrades host proteins. However, recent genomic studies identified ipaH genes in the genomes of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted from fecal samples of bovine calves, suggesting that non-human hosts may also be infected by these strains, potentially pathogenic to humans. We performed a comparative genomic study of the functional repertoires in the ipaH gene family in Shigella and enteroinvasive Escherichia from human and predicted non-human hosts. We found that fewer than half of Shigella genomes had a complete set of ipaH genes, with frequent gene losses and duplications that were not consistent with the species tree and nomenclature. Non-human host IpaH proteins had a diverse set of substrate-binding domains and, in contrast to the Shigella proteins, two variants of the NEL C-terminal domain. Inconsistencies between strains phylogeny and composition of effectors indicate horizontal gene transfer between E. coli adapted to different hosts. These results provide a framework for understanding of ipaH-mediated host-pathogens interactions and suggest a need for a genomic study of fecal samples from diseased animals. acknowledgement: 'The project was initiated with Aygul Minnegalieva and Yulia Yakovleva at the Summer School of Molecular and Theoretical Biology (SMTB-2020), supported by the Zimin Foundation. We thank Inna Shapovalenko, Daria Abuzova, Elizaveta Kaminskaya, and Dmitriy Zvezdin for their contribution to the project during SMTB-2020. We also thank Peter Vlasov for fruitful discussions.This study was supported by the Russian Foundation for Basic Research (RFBR), Grant # 20-54-14005 and Fonds zur Förderung der wissenschaftlichen Forschung (FWF), Grant # I5127-B. The work of OB is supported by the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. ' article_number: '6868' article_processing_charge: No article_type: original author: - first_name: NO full_name: Dranenko, NO last_name: Dranenko - first_name: MN full_name: Tutukina, MN last_name: Tutukina - first_name: MS full_name: Gelfand, MS last_name: Gelfand - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 citation: ama: Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific Reports. 2022;12. doi:10.1038/s41598-022-10827-3 apa: Dranenko, N., Tutukina, M., Gelfand, M., Kondrashov, F., & Bochkareva, O. (2022). Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-10827-3 chicago: Dranenko, NO, MN Tutukina, MS Gelfand, Fyodor Kondrashov, and Olga Bochkareva. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.” Scientific Reports. Springer Nature, 2022. https://doi.org/10.1038/s41598-022-10827-3. ieee: N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, and O. Bochkareva, “Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia,” Scientific Reports, vol. 12. Springer Nature, 2022. ista: Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. 2022. Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific Reports. 12, 6868. mla: Dranenko, NO, et al. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.” Scientific Reports, vol. 12, 6868, Springer Nature, 2022, doi:10.1038/s41598-022-10827-3. short: N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, O. Bochkareva, Scientific Reports 12 (2022). date_created: 2022-05-02T07:08:42Z date_published: 2022-04-27T00:00:00Z date_updated: 2023-08-03T06:59:49Z day: '27' ddc: - '570' department: - _id: FyKo doi: 10.1038/s41598-022-10827-3 ec_funded: 1 external_id: isi: - '000788639400032' pmid: - '35477739' file: - access_level: open_access checksum: 12601b8a5c6b83bb618f92bcb963ecc9 content_type: application/pdf creator: dernst date_created: 2022-05-02T09:05:20Z date_updated: 2022-05-02T09:05:20Z file_id: '11349' file_name: 2022_ScientificReports_Dranenko.pdf file_size: 3564155 relation: main_file success: 1 file_date_updated: 2022-05-02T09:05:20Z has_accepted_license: '1' intvolume: ' 12' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: c098eddd-5a5b-11eb-8a69-abe27170a68f grant_number: I05127 name: Evolutionary analysis of gene regulation - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Scientific Reports publication_identifier: issn: - 2045-2322 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2022' ... --- _id: '11448' abstract: - lang: eng text: Studies of protein fitness landscapes reveal biophysical constraints guiding protein evolution and empower prediction of functional proteins. However, generalisation of these findings is limited due to scarceness of systematic data on fitness landscapes of proteins with a defined evolutionary relationship. We characterized the fitness peaks of four orthologous fluorescent proteins with a broad range of sequence divergence. While two of the four studied fitness peaks were sharp, the other two were considerably flatter, being almost entirely free of epistatic interactions. Mutationally robust proteins, characterized by a flat fitness peak, were not optimal templates for machine-learning-driven protein design – instead, predictions were more accurate for fragile proteins with epistatic landscapes. Our work paves insights for practical application of fitness landscape heterogeneity in protein engineering. acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: "We thank Ondřej Draganov, Rodrigo Redondo, Bor Kavčič, Mia Juračić and Andrea Pauli for discussion and technical advice. We thank Anita Testa Salmazo for advice on resin protein purification, Dmitry Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure, and Josef Houser and Eva Fujdiarova for technical assistance and data interpretation. Core facility Biomolecular Interactions and Crystallization of CEITEC Masaryk University is gratefully acknowledged for the obtaining of the scientific data presented in this paper. This research was supported by the Scientific Service Units (SSU) of IST-Austria\r\nthrough resources provided by the Bioimaging Facility (BIF), and the Life Science Facility (LSF). MiSeq and HiSeq NGS sequencing was performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Austria. FACS was performed at the BioOptics Facility of the Institute of Molecular Pathology (IMP), Austria. We also thank the Biomolecular Crystallography Facility in the Vanderbilt University Center for Structural Biology. We are grateful to Joel M Harp for help with X-ray data collection. This work was supported by the ERC Consolidator grant to FAK (771209—CharFL). KSS acknowledges support by President’s Grant МК–5405.2021.1.4, the Imperial College Research Fellowship and the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0).\r\nAF is supported by the Marie Skłodowska-Curie Fellowship (H2020-MSCA-IF-2019, Grant Agreement No. 898203, Project acronym \"FLINDIP\"). Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy of Sciences Сore Facility (CKP IBCH). This work was supported by a Russian Science Foundation grant 19-74-10102.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665,385." article_number: '75842' article_processing_charge: No article_type: original author: - first_name: Louisa full_name: Gonzalez Somermeyer, Louisa id: 4720D23C-F248-11E8-B48F-1D18A9856A87 last_name: Gonzalez Somermeyer orcid: 0000-0001-9139-5383 - first_name: Aubin full_name: Fleiss, Aubin last_name: Fleiss - first_name: Alexander S full_name: Mishin, Alexander S last_name: Mishin - first_name: Nina G full_name: Bozhanova, Nina G last_name: Bozhanova - first_name: Anna A full_name: Igolkina, Anna A last_name: Igolkina - first_name: Jens full_name: Meiler, Jens last_name: Meiler - first_name: Maria-Elisenda full_name: Alaball Pujol, Maria-Elisenda last_name: Alaball Pujol - first_name: Ekaterina V full_name: Putintseva, Ekaterina V last_name: Putintseva - first_name: Karen S full_name: Sarkisyan, Karen S last_name: Sarkisyan - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP fitness landscape and data-driven protein design. eLife. 2022;11. doi:10.7554/elife.75842 apa: Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina, A. A., Meiler, J., … Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape and data-driven protein design. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.75842 chicago: Gonzalez Somermeyer, Louisa, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova, Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva, Karen S Sarkisyan, and Fyodor Kondrashov. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/elife.75842. ieee: L. Gonzalez Somermeyer et al., “Heterogeneity of the GFP fitness landscape and data-driven protein design,” eLife, vol. 11. eLife Sciences Publications, 2022. ista: Gonzalez Somermeyer L, Fleiss A, Mishin AS, Bozhanova NG, Igolkina AA, Meiler J, Alaball Pujol M-E, Putintseva EV, Sarkisyan KS, Kondrashov F. 2022. Heterogeneity of the GFP fitness landscape and data-driven protein design. eLife. 11, 75842. mla: Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” ELife, vol. 11, 75842, eLife Sciences Publications, 2022, doi:10.7554/elife.75842. short: L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina, J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov, ELife 11 (2022). date_created: 2022-06-18T09:06:59Z date_published: 2022-05-05T00:00:00Z date_updated: 2023-08-03T07:20:15Z day: '05' ddc: - '570' department: - _id: GradSch - _id: FyKo doi: 10.7554/elife.75842 ec_funded: 1 external_id: isi: - '000799197200001' file: - access_level: open_access checksum: 7573c28f44028ab0cc81faef30039e44 content_type: application/pdf creator: dernst date_created: 2022-06-20T07:44:19Z date_updated: 2022-06-20T07:44:19Z file_id: '11454' file_name: 2022_eLife_Somermeyer.pdf file_size: 5297213 relation: main_file success: 1 file_date_updated: 2022-06-20T07:44:19Z has_accepted_license: '1' intvolume: ' 11' isi: 1 keyword: - General Immunology and Microbiology - General Biochemistry - Genetics and Molecular Biology - General Medicine - General Neuroscience language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 26580278-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771209' name: Characterizing the fitness landscape on population and global scales - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Heterogeneity of the GFP fitness landscape and data-driven protein design tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2022' ... --- _id: '11447' abstract: - lang: eng text: Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks. acknowledgement: We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful discussions. Open access funding provided by Austrian Science Fund (FWF). Partially supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund (I5127-B) grants to FAK. article_number: '74' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Raimundo J full_name: Saona Urmeneta, Raimundo J id: BD1DF4C4-D767-11E9-B658-BC13E6697425 last_name: Saona Urmeneta orcid: 0000-0001-5103-038X - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Kseniia full_name: Khudiakova, Kseniia id: 4E6DC800-AE37-11E9-AC72-31CAE5697425 last_name: Khudiakova orcid: 0000-0002-6246-1465 citation: ama: Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 2022;84(8). doi:10.1007/s11538-022-01029-z apa: Saona Urmeneta, R. J., Kondrashov, F., & Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. Springer Nature. https://doi.org/10.1007/s11538-022-01029-z chicago: Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical Biology. Springer Nature, 2022. https://doi.org/10.1007/s11538-022-01029-z. ieee: R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” Bulletin of Mathematical Biology, vol. 84, no. 8. Springer Nature, 2022. ista: Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 84(8), 74. mla: Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical Biology, vol. 84, no. 8, 74, Springer Nature, 2022, doi:10.1007/s11538-022-01029-z. short: R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022). date_created: 2022-06-17T16:16:15Z date_published: 2022-06-17T00:00:00Z date_updated: 2023-08-03T07:20:53Z day: '17' ddc: - '510' - '570' department: - _id: GradSch - _id: NiBa - _id: JaMa doi: 10.1007/s11538-022-01029-z ec_funded: 1 external_id: isi: - '000812509800001' file: - access_level: open_access checksum: 05a1fe7d10914a00c2bca9b447993a65 content_type: application/pdf creator: dernst date_created: 2022-06-20T07:51:32Z date_updated: 2022-06-20T07:51:32Z file_id: '11455' file_name: 2022_BulletinMathBiology_Saona.pdf file_size: 463025 relation: main_file success: 1 file_date_updated: 2022-06-20T07:51:32Z has_accepted_license: '1' intvolume: ' 84' isi: 1 issue: '8' keyword: - Computational Theory and Mathematics - General Agricultural and Biological Sciences - Pharmacology - General Environmental Science - General Biochemistry - Genetics and Molecular Biology - General Mathematics - Immunology - General Neuroscience language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 26580278-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771209' name: Characterizing the fitness landscape on population and global scales - _id: c098eddd-5a5b-11eb-8a69-abe27170a68f grant_number: I05127 name: Evolutionary analysis of gene regulation publication: Bulletin of Mathematical Biology publication_identifier: eissn: - 1522-9602 issn: - 0092-8240 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1007/s11538-022-01118-z scopus_import: '1' status: public title: Relation between the number of peaks and the number of reciprocal sign epistatic interactions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 84 year: '2022' ... --- _id: '12116' abstract: - lang: eng text: Russia’s unprovoked attack on Ukraine has destroyed civilian infrastructure, including universities, research centers, and other academic infrastructure (1). Many Ukrainian scholars and researchers remain in Ukraine, and their work has suffered from major setbacks (2–4). We call on international scientists and institutions to support them. article_processing_charge: No article_type: letter_note author: - first_name: Karishma full_name: Chhugani, Karishma last_name: Chhugani - first_name: Alina full_name: Frolova, Alina last_name: Frolova - first_name: Yuriy full_name: Salyha, Yuriy last_name: Salyha - first_name: Andrada full_name: Fiscutean, Andrada last_name: Fiscutean - first_name: Oksana full_name: Zlenko, Oksana last_name: Zlenko - first_name: Sanita full_name: Reinsone, Sanita last_name: Reinsone - first_name: Walter W. full_name: Wolfsberger, Walter W. last_name: Wolfsberger - first_name: Oleksandra V. full_name: Ivashchenko, Oleksandra V. last_name: Ivashchenko - first_name: Megi full_name: Maci, Megi last_name: Maci - first_name: Dmytro full_name: Dziuba, Dmytro last_name: Dziuba - first_name: Andrii full_name: Parkhomenko, Andrii last_name: Parkhomenko - first_name: Eric full_name: Bortz, Eric last_name: Bortz - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Paweł P. full_name: Łabaj, Paweł P. last_name: Łabaj - first_name: Veronika full_name: Romero, Veronika last_name: Romero - first_name: Jakub full_name: Hlávka, Jakub last_name: Hlávka - first_name: Taras K. full_name: Oleksyk, Taras K. last_name: Oleksyk - first_name: Serghei full_name: Mangul, Serghei last_name: Mangul citation: ama: Chhugani K, Frolova A, Salyha Y, et al. Remote opportunities for scholars in Ukraine. Science. 2022;378(6626):1285-1286. doi:10.1126/science.adg0797 apa: Chhugani, K., Frolova, A., Salyha, Y., Fiscutean, A., Zlenko, O., Reinsone, S., … Mangul, S. (2022). Remote opportunities for scholars in Ukraine. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adg0797 chicago: Chhugani, Karishma, Alina Frolova, Yuriy Salyha, Andrada Fiscutean, Oksana Zlenko, Sanita Reinsone, Walter W. Wolfsberger, et al. “Remote Opportunities for Scholars in Ukraine.” Science. American Association for the Advancement of Science, 2022. https://doi.org/10.1126/science.adg0797. ieee: K. Chhugani et al., “Remote opportunities for scholars in Ukraine,” Science, vol. 378, no. 6626. American Association for the Advancement of Science, pp. 1285–1286, 2022. ista: Chhugani K, Frolova A, Salyha Y, Fiscutean A, Zlenko O, Reinsone S, Wolfsberger WW, Ivashchenko OV, Maci M, Dziuba D, Parkhomenko A, Bortz E, Kondrashov F, Łabaj PP, Romero V, Hlávka J, Oleksyk TK, Mangul S. 2022. Remote opportunities for scholars in Ukraine. Science. 378(6626), 1285–1286. mla: Chhugani, Karishma, et al. “Remote Opportunities for Scholars in Ukraine.” Science, vol. 378, no. 6626, American Association for the Advancement of Science, 2022, pp. 1285–86, doi:10.1126/science.adg0797. short: K. Chhugani, A. Frolova, Y. Salyha, A. Fiscutean, O. Zlenko, S. Reinsone, W.W. Wolfsberger, O.V. Ivashchenko, M. Maci, D. Dziuba, A. Parkhomenko, E. Bortz, F. Kondrashov, P.P. Łabaj, V. Romero, J. Hlávka, T.K. Oleksyk, S. Mangul, Science 378 (2022) 1285–1286. date_created: 2023-01-12T11:56:30Z date_published: 2022-12-22T00:00:00Z date_updated: 2023-10-03T11:01:06Z day: '22' department: - _id: FyKo doi: 10.1126/science.adg0797 external_id: isi: - '000963463700023' intvolume: ' 378' isi: 1 issue: '6626' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1126/science.adg0797 month: '12' oa: 1 oa_version: Published Version page: 1285-1286 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Remote opportunities for scholars in Ukraine type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 378 year: '2022' ... --- _id: '9910' abstract: - lang: eng text: Adult height inspired the first biometrical and quantitative genetic studies and is a test-case trait for understanding heritability. The studies of height led to formulation of the classical polygenic model, that has a profound influence on the way we view and analyse complex traits. An essential part of the classical model is an assumption of additivity of effects and normality of the distribution of the residuals. However, it may be expected that the normal approximation will become insufficient in bigger studies. Here, we demonstrate that when the height of hundreds of thousands of individuals is analysed, the model complexity needs to be increased to include non-additive interactions between sex, environment and genes. Alternatively, the use of log-normal approximation allowed us to still use the additive effects model. These findings are important for future genetic and methodologic studies that make use of adult height as an exemplar trait. acknowledgement: "We are grateful to Marianna Bevova and Pavel Borodin for fruitful discussion and help with conceptualising our findings and to Lennart C. Karssen for help with handling the UK Biobank data.\r\n\r\nFunding\r\nThis research has been conducted using the UK Biobank Resource (project # 41601, “Non-additive effects in control of complex human traits”). The work of SAS, IAK, and TIS were supported by Russian Ministry of Science and Education under the 5–100 Excellence Programme. The work of YSA and TIA was supported by the Ministry of Education and Science of the RF via the Institute of Cytology and Genetics SB RAS (project number 0324-2019-0040-C-01/AAAA-A17-117092070032-4). FAK is supported by the ERC Consolidator Grant (ChrFL: 771209)." article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Sergei A. full_name: Slavskii, Sergei A. last_name: Slavskii - first_name: Ivan A. full_name: Kuznetsov, Ivan A. last_name: Kuznetsov - first_name: Tatiana I. full_name: Shashkova, Tatiana I. last_name: Shashkova - first_name: Georgii A. full_name: Bazykin, Georgii A. last_name: Bazykin - first_name: Tatiana I. full_name: Axenovich, Tatiana I. last_name: Axenovich - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Yurii S. full_name: Aulchenko, Yurii S. last_name: Aulchenko citation: ama: Slavskii SA, Kuznetsov IA, Shashkova TI, et al. The limits of normal approximation for adult height. European Journal of Human Genetics. 2021;29(7):1082-1091. doi:10.1038/s41431-021-00836-7 apa: Slavskii, S. A., Kuznetsov, I. A., Shashkova, T. I., Bazykin, G. A., Axenovich, T. I., Kondrashov, F., & Aulchenko, Y. S. (2021). The limits of normal approximation for adult height. European Journal of Human Genetics. Springer Nature. https://doi.org/10.1038/s41431-021-00836-7 chicago: Slavskii, Sergei A., Ivan A. Kuznetsov, Tatiana I. Shashkova, Georgii A. Bazykin, Tatiana I. Axenovich, Fyodor Kondrashov, and Yurii S. Aulchenko. “The Limits of Normal Approximation for Adult Height.” European Journal of Human Genetics. Springer Nature, 2021. https://doi.org/10.1038/s41431-021-00836-7. ieee: S. A. Slavskii et al., “The limits of normal approximation for adult height,” European Journal of Human Genetics, vol. 29, no. 7. Springer Nature, pp. 1082–1091, 2021. ista: Slavskii SA, Kuznetsov IA, Shashkova TI, Bazykin GA, Axenovich TI, Kondrashov F, Aulchenko YS. 2021. The limits of normal approximation for adult height. European Journal of Human Genetics. 29(7), 1082–1091. mla: Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.” European Journal of Human Genetics, vol. 29, no. 7, Springer Nature, 2021, pp. 1082–91, doi:10.1038/s41431-021-00836-7. short: S.A. Slavskii, I.A. Kuznetsov, T.I. Shashkova, G.A. Bazykin, T.I. Axenovich, F. Kondrashov, Y.S. Aulchenko, European Journal of Human Genetics 29 (2021) 1082–1091. date_created: 2021-08-15T22:01:28Z date_published: 2021-07-01T00:00:00Z date_updated: 2023-08-11T10:33:42Z day: '01' ddc: - '576' department: - _id: FyKo doi: 10.1038/s41431-021-00836-7 ec_funded: 1 external_id: isi: - '000625853200001' pmid: - '33664501' file: - access_level: open_access checksum: a676d76f91b0dbe0504c63e469129c2a content_type: application/pdf creator: asandaue date_created: 2021-08-16T09:14:36Z date_updated: 2021-08-16T09:14:36Z file_id: '9921' file_name: 2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf file_size: 1079395 relation: main_file success: 1 file_date_updated: 2021-08-16T09:14:36Z has_accepted_license: '1' intvolume: ' 29' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1082-1091 pmid: 1 project: - _id: 26580278-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771209' name: Characterizing the fitness landscape on population and global scales publication: European Journal of Human Genetics publication_identifier: eissn: - '14765438' issn: - '10184813' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: The limits of normal approximation for adult height tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 29 year: '2021' ... --- _id: '9905' abstract: - lang: eng text: Vaccines are thought to be the best available solution for controlling the ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains may come too rapidly for current vaccine developments to alleviate the health, economic and social consequences of the pandemic. To quantify and characterize the risk of such a scenario, we created a SIR-derived model with initial stochastic dynamics of the vaccine-resistant strain to study the probability of its emergence and establishment. Using parameters realistically resembling SARS-CoV-2 transmission, we model a wave-like pattern of the pandemic and consider the impact of the rate of vaccination and the strength of non-pharmaceutical intervention measures on the probability of emergence of a resistant strain. As expected, we found that a fast rate of vaccination decreases the probability of emergence of a resistant strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions happened at a time when most individuals of the population have already been vaccinated the probability of emergence of a resistant strain was greatly increased. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment. Our results suggest that policymakers and individuals should consider maintaining non-pharmaceutical interventions and transmission-reducing behaviours throughout the entire vaccination period. acknowledgement: We thank Alexey Kondrashov, Nick Machnik, Raimundo Julian Saona Urmeneta, Gasper Tkacik and Nick Barton for fruitful discussions. We also thank participants of EvoLunch seminar at IST Austria and the internal seminar at the Banco de España for useful comments. The opinions expressed in this document are exclusively of the authors and, therefore, do not necessarily coincide with those of the Banco de España or the Eurosystem. ETD is supported by the Swiss National Science and Louis Jeantet Foundation. The work of FAK was in part supported by the ERC Consolidator Grant (771209-CharFL). article_number: '15729' article_processing_charge: Yes article_type: original author: - first_name: Simon full_name: Rella, Simon id: B4765ACA-AA38-11E9-AC9A-0930E6697425 last_name: Rella - first_name: Yuliya A. full_name: Kulikova, Yuliya A. last_name: Kulikova - first_name: Emmanouil T. full_name: Dermitzakis, Emmanouil T. last_name: Dermitzakis - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 2021;11(1). doi:10.1038/s41598-021-95025-3 apa: Rella, S., Kulikova, Y. A., Dermitzakis, E. T., & Kondrashov, F. (2021). Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-95025-3 chicago: Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-95025-3. ieee: S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,” Scientific Reports, vol. 11, no. 1. Springer Nature, 2021. ista: Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 11(1), 15729. mla: Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” Scientific Reports, vol. 11, no. 1, 15729, Springer Nature, 2021, doi:10.1038/s41598-021-95025-3. short: S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports 11 (2021). date_created: 2021-08-15T22:01:26Z date_published: 2021-07-30T00:00:00Z date_updated: 2023-08-11T10:42:58Z day: '30' ddc: - '570' - '610' department: - _id: FyKo doi: 10.1038/s41598-021-95025-3 ec_funded: 1 external_id: isi: - '000683329100001' pmid: - '34330988' file: - access_level: open_access checksum: ac86892ed17e6724c7251844da5cef5c content_type: application/pdf creator: asandaue date_created: 2021-08-16T11:36:49Z date_updated: 2021-08-16T11:36:49Z file_id: '9927' file_name: 2021_ScientificReports_Rella.pdf file_size: 3432001 relation: main_file success: 1 file_date_updated: 2021-08-16T11:36:49Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26580278-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771209' name: Characterizing the fitness landscape on population and global scales publication: Scientific Reports publication_identifier: eissn: - '20452322' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Website relation: press_release url: https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/ scopus_import: '1' status: public title: Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2021' ... --- _id: '8151' abstract: - lang: eng text: The main idea behind the Core Project is to teach first year students at IST scientific communication skills and let them practice by presenting their research within an interdisciplinary environment. Over the course of the first semester, students participated in seminars, where they shared their results with the colleagues from other fields and took part in discussions on relevant subjects. The main focus during this sessions was on delivering the information in a simplified and comprehensible way, going into the very basics of a subject if necessary. At the end, the students were asked to present their research in the written form to exercise their writing skills. The reports were gathered in this document. All of them were reviewed by the teaching assistants and write-ups illustrating unique stylistic features and, in general, an outstanding level of writing skills, were honorably mentioned in the section "Selected Reports". article_processing_charge: No author: - first_name: Mikhail full_name: Maslov, Mikhail id: 2E65BB0E-F248-11E8-B48F-1D18A9856A87 last_name: Maslov orcid: 0000-0003-4074-2570 - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Christina full_name: Artner, Christina id: 45DF286A-F248-11E8-B48F-1D18A9856A87 last_name: Artner - first_name: Mike full_name: Hennessey-Wesen, Mike id: 3F338C72-F248-11E8-B48F-1D18A9856A87 last_name: Hennessey-Wesen - first_name: Bor full_name: Kavcic, Bor id: 350F91D2-F248-11E8-B48F-1D18A9856A87 last_name: Kavcic orcid: 0000-0001-6041-254X - first_name: Nick N full_name: Machnik, Nick N id: 3591A0AA-F248-11E8-B48F-1D18A9856A87 last_name: Machnik - first_name: Roshan K full_name: Satapathy, Roshan K id: 46046B7A-F248-11E8-B48F-1D18A9856A87 last_name: Satapathy - first_name: Isabella full_name: Tomanek, Isabella id: 3981F020-F248-11E8-B48F-1D18A9856A87 last_name: Tomanek orcid: 0000-0001-6197-363X citation: ama: Maslov M, Kondrashov F, Artner C, et al. Core Project Proceedings. IST Austria; 2020. apa: Maslov, M., Kondrashov, F., Artner, C., Hennessey-Wesen, M., Kavcic, B., Machnik, N. N., … Tomanek, I. (2020). Core Project Proceedings. IST Austria. chicago: Maslov, Mikhail, Fyodor Kondrashov, Christina Artner, Mike Hennessey-Wesen, Bor Kavcic, Nick N Machnik, Roshan K Satapathy, and Isabella Tomanek. Core Project Proceedings. IST Austria, 2020. ieee: M. Maslov et al., Core Project Proceedings. IST Austria, 2020. ista: Maslov M, Kondrashov F, Artner C, Hennessey-Wesen M, Kavcic B, Machnik NN, Satapathy RK, Tomanek I. 2020. Core Project Proceedings, IST Austria, 425p. mla: Maslov, Mikhail, et al. Core Project Proceedings. IST Austria, 2020. short: M. Maslov, F. Kondrashov, C. Artner, M. Hennessey-Wesen, B. Kavcic, N.N. Machnik, R.K. Satapathy, I. Tomanek, Core Project Proceedings, IST Austria, 2020. date_created: 2020-07-22T14:48:14Z date_published: 2020-06-01T00:00:00Z date_updated: 2023-02-23T13:26:00Z day: '01' ddc: - '510' - '530' - '570' extern: '1' file: - access_level: local content_type: application/pdf creator: dernst date_created: 2020-07-22T14:45:07Z date_updated: 2020-07-22T14:45:07Z file_id: '8152' file_name: Core_Project_Proceedings_mod.pdf file_size: 169620437 relation: main_file file_date_updated: 2020-07-22T14:45:07Z has_accepted_license: '1' language: - iso: eng month: '06' oa_version: None page: '425' publication_status: published publisher: IST Austria status: public title: Core Project Proceedings type: report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '7931' abstract: - lang: eng text: In the course of sample preparation for Next Generation Sequencing (NGS), DNA is fragmented by various methods. Fragmentation shows a persistent bias with regard to the cleavage rates of various dinucleotides. With the exception of CpG dinucleotides the previously described biases were consistent with results of the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides including the methylated CpG and unmethylated CpG dinucleotides using data of the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides. Using this information, we developed a classifier for distinguishing cancer and healthy tissues based on their CpG islands statuses of the fragmentation. A simple Support Vector Machine classifier based on this algorithm shows an accuracy of 84%. The proposed method allows the detection of epigenetic markers purely based on mechanochemical DNA fragmentation, which can be detected by a simple analysis of the NGS sequencing data. article_number: '8635' article_processing_charge: No article_type: original author: - first_name: Leonid A. full_name: Uroshlev, Leonid A. last_name: Uroshlev - first_name: Eldar T. full_name: Abdullaev, Eldar T. last_name: Abdullaev - first_name: Iren R. full_name: Umarova, Iren R. last_name: Umarova - first_name: Irina A. full_name: Il’Icheva, Irina A. last_name: Il’Icheva - first_name: Larisa A. full_name: Panchenko, Larisa A. last_name: Panchenko - first_name: Robert V. full_name: Polozov, Robert V. last_name: Polozov - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Yury D. full_name: Nechipurenko, Yury D. last_name: Nechipurenko - first_name: Sergei L. full_name: Grokhovsky, Sergei L. last_name: Grokhovsky citation: ama: Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 2020;10. doi:10.1038/s41598-020-65406-1 apa: Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko, L. A., Polozov, R. V., … Grokhovsky, S. L. (2020). A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-65406-1 chicago: Uroshlev, Leonid A., Eldar T. Abdullaev, Iren R. Umarova, Irina A. Il’Icheva, Larisa A. Panchenko, Robert V. Polozov, Fyodor Kondrashov, Yury D. Nechipurenko, and Sergei L. Grokhovsky. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-65406-1. ieee: L. A. Uroshlev et al., “A method for identification of the methylation level of CpG islands from NGS data,” Scientific Reports, vol. 10. Springer Nature, 2020. ista: Uroshlev LA, Abdullaev ET, Umarova IR, Il’Icheva IA, Panchenko LA, Polozov RV, Kondrashov F, Nechipurenko YD, Grokhovsky SL. 2020. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 10, 8635. mla: Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” Scientific Reports, vol. 10, 8635, Springer Nature, 2020, doi:10.1038/s41598-020-65406-1. short: L.A. Uroshlev, E.T. Abdullaev, I.R. Umarova, I.A. Il’Icheva, L.A. Panchenko, R.V. Polozov, F. Kondrashov, Y.D. Nechipurenko, S.L. Grokhovsky, Scientific Reports 10 (2020). date_created: 2020-06-07T22:00:51Z date_published: 2020-05-25T00:00:00Z date_updated: 2023-08-21T07:00:17Z day: '25' ddc: - '570' department: - _id: FyKo doi: 10.1038/s41598-020-65406-1 external_id: isi: - '000560774200007' file: - access_level: open_access checksum: 099e51611a5b7ca04244d03b2faddf33 content_type: application/pdf creator: dernst date_created: 2020-06-08T06:27:32Z date_updated: 2020-07-14T12:48:05Z file_id: '7947' file_name: 2020_ScientificReports_Uroshlev.pdf file_size: 1001724 relation: main_file file_date_updated: 2020-07-14T12:48:05Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Scientific Reports publication_identifier: eissn: - '20452322' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A method for identification of the methylation level of CpG islands from NGS data tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2020' ... --- _id: '8645' abstract: - lang: eng text: 'Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a ‘combinatorially complete dataset’. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199 847 053 unique combinatorially complete genotype combinations of dimensionality ranging from 2 to 12. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data.' acknowledgement: 'This work was supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013, ERC grant agreement 335980_EinME) and Startup package to the Ivankov laboratory at Skolkovo Institute of Science and Technology. The work was started at the School of Molecular and Theoretical Biology 2017 supported by the Zimin Foundation. N.S.B. was supported by the Woman Scientists Support Grant in Centre for Genomic Regulation (CRG). ' article_processing_charge: No article_type: original author: - first_name: Laura A full_name: Esteban, Laura A last_name: Esteban - first_name: Lyubov R full_name: Lonishin, Lyubov R last_name: Lonishin - first_name: Daniil M full_name: Bobrovskiy, Daniil M last_name: Bobrovskiy - first_name: Gregory full_name: Leleytner, Gregory last_name: Leleytner - first_name: Natalya S full_name: Bogatyreva, Natalya S last_name: Bogatyreva - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: 'Dmitry N ' full_name: 'Ivankov, Dmitry N ' last_name: Ivankov citation: ama: 'Esteban LA, Lonishin LR, Bobrovskiy DM, et al. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 2020;36(6):1960-1962. doi:10.1093/bioinformatics/btz841' apa: 'Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva, N. S., Kondrashov, F., & Ivankov, D. N. (2020). HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btz841' chicago: 'Esteban, Laura A, Lyubov R Lonishin, Daniil M Bobrovskiy, Gregory Leleytner, Natalya S Bogatyreva, Fyodor Kondrashov, and Dmitry N Ivankov. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics. Oxford Academic, 2020. https://doi.org/10.1093/bioinformatics/btz841.' ieee: 'L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially complete datasets from a single experiment,” Bioinformatics, vol. 36, no. 6. Oxford Academic, pp. 1960–1962, 2020.' ista: 'Esteban LA, Lonishin LR, Bobrovskiy DM, Leleytner G, Bogatyreva NS, Kondrashov F, Ivankov DN. 2020. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 36(6), 1960–1962.' mla: 'Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics, vol. 36, no. 6, Oxford Academic, 2020, pp. 1960–62, doi:10.1093/bioinformatics/btz841.' short: L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva, F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962. date_created: 2020-10-11T22:01:14Z date_published: 2020-03-15T00:00:00Z date_updated: 2023-08-22T09:57:29Z day: '15' ddc: - '000' - '570' department: - _id: FyKo doi: 10.1093/bioinformatics/btz841 ec_funded: 1 external_id: isi: - '000538696800054' pmid: - '31742320' file: - access_level: open_access checksum: 21d6f71839deb3b83e4a356193f72767 content_type: application/pdf creator: dernst date_created: 2020-10-12T12:02:09Z date_updated: 2020-10-12T12:02:09Z file_id: '8649' file_name: 2020_Bioinformatics_Esteban.pdf file_size: 308341 relation: main_file success: 1 file_date_updated: 2020-10-12T12:02:09Z has_accepted_license: '1' intvolume: ' 36' isi: 1 issue: '6' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 1960-1962 pmid: 1 project: - _id: 26120F5C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '335980' name: Systematic investigation of epistasis in molecular evolution publication: Bioinformatics publication_identifier: eissn: - 1460-2059 issn: - 1367-4803 publication_status: published publisher: Oxford Academic quality_controlled: '1' scopus_import: '1' status: public title: 'HypercubeME: Two hundred million combinatorially complete datasets from a single experiment' tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 36 year: '2020' ... --- _id: '7889' abstract: - lang: eng text: Autoluminescent plants engineered to express a bacterial bioluminescence gene cluster in plastids have not been widely adopted because of low light output. We engineered tobacco plants with a fungal bioluminescence system that converts caffeic acid (present in all plants) into luciferin and report self-sustained luminescence that is visible to the naked eye. Our findings could underpin development of a suite of imaging tools for plants. acknowledgement: "This study was designed, performed and funded by Planta LLC. We thank K. Wood for assisting in manuscript development. Planta acknowledges support from the Skolkovo Innovation Centre. We thank D. Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure. We thank S. Shakhov for providing\r\nphotography equipment. The Synthetic Biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0, K.S.S.). K.S.S. is supported by an Imperial College Research Fellowship. Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy\r\nof Sciences Сore Facility (CKP IBCH; supported by the Russian Ministry of Education and Science Grant RFMEFI62117X0018). The F.A.K. lab is supported by ERC grant agreement 771209—CharFL. This project received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie\r\nGrant Agreement 665385. K.S.S. acknowledges support by President’s Grant 075-15-2019-411. Design and assembly of some of the plasmids was supported by Russian Science Foundation grant 19-74-10102. Imaging experiments were partially supported by Russian Science Foundation grant 17-14-01169p. LC-MS/MS analyses of extracts were\r\nsupported by Russian Science Foundation grant 16-14-00052p. Design and assembly of plasmids was partially supported by grant 075-15-2019-1789 from the Ministry of Science and Higher Education of the Russian Federation allocated to the Center for Precision Genome Editing and Genetic Technologies for Biomedicine. The authors\r\nwould like to acknowledge the work of Genomics Core Facility of the Skolkovo Institute of Science and Technology, which performed the sequencing and bioinformatic analysis." article_processing_charge: No article_type: original author: - first_name: Tatiana full_name: Mitiouchkina, Tatiana last_name: Mitiouchkina - first_name: Alexander S. full_name: Mishin, Alexander S. last_name: Mishin - first_name: Louisa full_name: Gonzalez Somermeyer, Louisa id: 4720D23C-F248-11E8-B48F-1D18A9856A87 last_name: Gonzalez Somermeyer orcid: 0000-0001-9139-5383 - first_name: Nadezhda M. full_name: Markina, Nadezhda M. last_name: Markina - first_name: Tatiana V. full_name: Chepurnyh, Tatiana V. last_name: Chepurnyh - first_name: Elena B. full_name: Guglya, Elena B. last_name: Guglya - first_name: Tatiana A. full_name: Karataeva, Tatiana A. last_name: Karataeva - first_name: Kseniia A. full_name: Palkina, Kseniia A. last_name: Palkina - first_name: Ekaterina S. full_name: Shakhova, Ekaterina S. last_name: Shakhova - first_name: Liliia I. full_name: Fakhranurova, Liliia I. last_name: Fakhranurova - first_name: Sofia V. full_name: Chekova, Sofia V. last_name: Chekova - first_name: Aleksandra S. full_name: Tsarkova, Aleksandra S. last_name: Tsarkova - first_name: Yaroslav V. full_name: Golubev, Yaroslav V. last_name: Golubev - first_name: Vadim V. full_name: Negrebetsky, Vadim V. last_name: Negrebetsky - first_name: Sergey A. full_name: Dolgushin, Sergey A. last_name: Dolgushin - first_name: Pavel V. full_name: Shalaev, Pavel V. last_name: Shalaev - first_name: Dmitry full_name: Shlykov, Dmitry last_name: Shlykov - first_name: Olesya A. full_name: Melnik, Olesya A. last_name: Melnik - first_name: Victoria O. full_name: Shipunova, Victoria O. last_name: Shipunova - first_name: Sergey M. full_name: Deyev, Sergey M. last_name: Deyev - first_name: Andrey I. full_name: Bubyrev, Andrey I. last_name: Bubyrev - first_name: Alexander S. full_name: Pushin, Alexander S. last_name: Pushin - first_name: Vladimir V. full_name: Choob, Vladimir V. last_name: Choob - first_name: Sergey V. full_name: Dolgov, Sergey V. last_name: Dolgov - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Ilia V. full_name: Yampolsky, Ilia V. last_name: Yampolsky - first_name: Karen S. full_name: Sarkisyan, Karen S. last_name: Sarkisyan citation: ama: Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, et al. Plants with genetically encoded autoluminescence. Nature Biotechnology. 2020;38:944-946. doi:10.1038/s41587-020-0500-9 apa: Mitiouchkina, T., Mishin, A. S., Gonzalez Somermeyer, L., Markina, N. M., Chepurnyh, T. V., Guglya, E. B., … Sarkisyan, K. S. (2020). Plants with genetically encoded autoluminescence. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-020-0500-9 chicago: Mitiouchkina, Tatiana, Alexander S. Mishin, Louisa Gonzalez Somermeyer, Nadezhda M. Markina, Tatiana V. Chepurnyh, Elena B. Guglya, Tatiana A. Karataeva, et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology. Springer Nature, 2020. https://doi.org/10.1038/s41587-020-0500-9. ieee: T. Mitiouchkina et al., “Plants with genetically encoded autoluminescence,” Nature Biotechnology, vol. 38. Springer Nature, pp. 944–946, 2020. ista: Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, Markina NM, Chepurnyh TV, Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV, Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D, Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV, Kondrashov F, Yampolsky IV, Sarkisyan KS. 2020. Plants with genetically encoded autoluminescence. Nature Biotechnology. 38, 944–946. mla: Mitiouchkina, Tatiana, et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology, vol. 38, Springer Nature, 2020, pp. 944–46, doi:10.1038/s41587-020-0500-9. short: T. Mitiouchkina, A.S. Mishin, L. Gonzalez Somermeyer, N.M. Markina, T.V. Chepurnyh, E.B. Guglya, T.A. Karataeva, K.A. Palkina, E.S. Shakhova, L.I. Fakhranurova, S.V. Chekova, A.S. Tsarkova, Y.V. Golubev, V.V. Negrebetsky, S.A. Dolgushin, P.V. Shalaev, D. Shlykov, O.A. Melnik, V.O. Shipunova, S.M. Deyev, A.I. Bubyrev, A.S. Pushin, V.V. Choob, S.V. Dolgov, F. Kondrashov, I.V. Yampolsky, K.S. Sarkisyan, Nature Biotechnology 38 (2020) 944–946. date_created: 2020-05-25T15:02:00Z date_published: 2020-04-27T00:00:00Z date_updated: 2023-09-05T15:30:34Z day: '27' ddc: - '570' department: - _id: FyKo doi: 10.1038/s41587-020-0500-9 ec_funded: 1 external_id: isi: - '000529298800003' pmid: - '32341562' file: - access_level: open_access checksum: 1b30467500ec6277229a875b06e196d0 content_type: application/pdf creator: dernst date_created: 2020-08-28T08:57:07Z date_updated: 2021-03-02T23:30:03Z embargo: 2021-03-01 file_id: '8316' file_name: 2020_NatureBiotech_Mitiouchkina.pdf file_size: 1180086 relation: main_file file_date_updated: 2021-03-02T23:30:03Z has_accepted_license: '1' intvolume: ' 38' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 944-946 pmid: 1 project: - _id: 26580278-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771209' name: Characterizing the fitness landscape on population and global scales publication: Nature Biotechnology publication_identifier: eissn: - 1546-1696 issn: - 1087-0156 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41587-020-0578-0 scopus_import: '1' status: public title: Plants with genetically encoded autoluminescence type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 38 year: '2020' ... --- _id: '6419' abstract: - lang: eng text: Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible. article_number: e1008079 article_processing_charge: No author: - first_name: Victoria full_name: Pokusaeva, Victoria id: 3184041C-F248-11E8-B48F-1D18A9856A87 last_name: Pokusaeva orcid: 0000-0001-7660-444X - first_name: Dinara R. full_name: Usmanova, Dinara R. last_name: Usmanova - first_name: Ekaterina V. full_name: Putintseva, Ekaterina V. last_name: Putintseva - first_name: Lorena full_name: Espinar, Lorena last_name: Espinar - first_name: Karen full_name: Sarkisyan, Karen id: 39A7BF80-F248-11E8-B48F-1D18A9856A87 last_name: Sarkisyan orcid: 0000-0002-5375-6341 - first_name: Alexander S. full_name: Mishin, Alexander S. last_name: Mishin - first_name: Natalya S. full_name: Bogatyreva, Natalya S. last_name: Bogatyreva - first_name: Dmitry full_name: Ivankov, Dmitry id: 49FF1036-F248-11E8-B48F-1D18A9856A87 last_name: Ivankov - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Sergey full_name: Avvakumov, Sergey id: 3827DAC8-F248-11E8-B48F-1D18A9856A87 last_name: Avvakumov - first_name: Inna S. full_name: Povolotskaya, Inna S. last_name: Povolotskaya - first_name: Guillaume J. full_name: Filion, Guillaume J. last_name: Filion - first_name: Lucas B. full_name: Carey, Lucas B. last_name: Carey - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 2019;15(4). doi:10.1371/journal.pgen.1008079 apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079 chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics. Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079. ieee: V. Pokusaeva et al., “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS Genetics, vol. 15, no. 4. Public Library of Science, 2019. ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 15(4), e1008079. mla: Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079. short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019). date_created: 2019-05-13T07:58:38Z date_published: 2019-04-10T00:00:00Z date_updated: 2023-08-25T10:30:37Z day: '10' ddc: - '570' department: - _id: FyKo doi: 10.1371/journal.pgen.1008079 ec_funded: 1 external_id: isi: - '000466866000029' file: - access_level: open_access checksum: cf3889c8a8a16053dacf9c3776cbe217 content_type: application/pdf creator: dernst date_created: 2019-05-14T08:26:08Z date_updated: 2020-07-14T12:47:30Z file_id: '6445' file_name: 2019_PLOSGenetics_Pokusaeva.pdf file_size: 3726017 relation: main_file file_date_updated: 2020-07-14T12:47:30Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: PLoS Genetics publication_identifier: eissn: - '15537404' publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '9789' relation: research_data status: public - id: '9790' relation: research_data status: public - id: '9797' relation: research_data status: public scopus_import: '1' status: public title: An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 15 year: '2019' ... --- _id: '9790' article_processing_charge: No author: - first_name: Victoria full_name: Pokusaeva, Victoria id: 3184041C-F248-11E8-B48F-1D18A9856A87 last_name: Pokusaeva orcid: 0000-0001-7660-444X - first_name: Dinara R. full_name: Usmanova, Dinara R. last_name: Usmanova - first_name: Ekaterina V. full_name: Putintseva, Ekaterina V. last_name: Putintseva - first_name: Lorena full_name: Espinar, Lorena last_name: Espinar - first_name: Karen full_name: Sarkisyan, Karen id: 39A7BF80-F248-11E8-B48F-1D18A9856A87 last_name: Sarkisyan orcid: 0000-0002-5375-6341 - first_name: Alexander S. full_name: Mishin, Alexander S. last_name: Mishin - first_name: Natalya S. full_name: Bogatyreva, Natalya S. last_name: Bogatyreva - first_name: Dmitry full_name: Ivankov, Dmitry id: 49FF1036-F248-11E8-B48F-1D18A9856A87 last_name: Ivankov - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Sergey full_name: Avvakumov, Sergey id: 3827DAC8-F248-11E8-B48F-1D18A9856A87 last_name: Avvakumov - first_name: Inna S. full_name: Povolotskaya, Inna S. last_name: Povolotskaya - first_name: Guillaume J. full_name: Filion, Guillaume J. last_name: Filion - first_name: Lucas B. full_name: Carey, Lucas B. last_name: Carey - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011 apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011 chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A Statistical Summary of Segment Libraries and Sequencing Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011. ieee: V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019. ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing results, Public Library of Science, 10.1371/journal.pgen.1008079.s011. mla: Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011. short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019). date_created: 2021-08-06T08:50:15Z date_published: 2019-04-10T00:00:00Z date_updated: 2023-08-25T10:30:36Z day: '10' department: - _id: FyKo doi: 10.1371/journal.pgen.1008079.s011 month: '04' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '6419' relation: used_in_publication status: public status: public title: A statistical summary of segment libraries and sequencing results type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9797' article_processing_charge: No author: - first_name: Victoria full_name: Pokusaeva, Victoria id: 3184041C-F248-11E8-B48F-1D18A9856A87 last_name: Pokusaeva orcid: 0000-0001-7660-444X - first_name: Dinara R. full_name: Usmanova, Dinara R. last_name: Usmanova - first_name: Ekaterina V. full_name: Putintseva, Ekaterina V. last_name: Putintseva - first_name: Lorena full_name: Espinar, Lorena last_name: Espinar - first_name: Karen full_name: Sarkisyan, Karen id: 39A7BF80-F248-11E8-B48F-1D18A9856A87 last_name: Sarkisyan orcid: 0000-0002-5375-6341 - first_name: Alexander S. full_name: Mishin, Alexander S. last_name: Mishin - first_name: Natalya S. full_name: Bogatyreva, Natalya S. last_name: Bogatyreva - first_name: Dmitry full_name: Ivankov, Dmitry id: 49FF1036-F248-11E8-B48F-1D18A9856A87 last_name: Ivankov - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Inna S. full_name: Povolotskaya, Inna S. last_name: Povolotskaya - first_name: Guillaume J. full_name: Filion, Guillaume J. last_name: Filion - first_name: Lucas B. full_name: Carey, Lucas B. last_name: Carey - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011 apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011 chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A Statistical Summary of Segment Libraries and Sequencing Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011. ieee: V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019. ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing results, Public Library of Science, 10.1371/journal.pgen.1008079.s011. mla: Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011. short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019). date_created: 2021-08-06T11:08:20Z date_published: 2019-04-10T00:00:00Z date_updated: 2023-08-25T10:30:36Z day: '10' department: - _id: FyKo doi: 10.1371/journal.pgen.1008079.s011 month: '04' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '6419' relation: used_in_publication status: public status: public title: A statistical summary of segment libraries and sequencing results type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9789' article_processing_charge: No author: - first_name: Victoria full_name: Pokusaeva, Victoria id: 3184041C-F248-11E8-B48F-1D18A9856A87 last_name: Pokusaeva orcid: 0000-0001-7660-444X - first_name: Dinara R. full_name: Usmanova, Dinara R. last_name: Usmanova - first_name: Ekaterina V. full_name: Putintseva, Ekaterina V. last_name: Putintseva - first_name: Lorena full_name: Espinar, Lorena last_name: Espinar - first_name: Karen full_name: Sarkisyan, Karen id: 39A7BF80-F248-11E8-B48F-1D18A9856A87 last_name: Sarkisyan orcid: 0000-0002-5375-6341 - first_name: Alexander S. full_name: Mishin, Alexander S. last_name: Mishin - first_name: Natalya S. full_name: Bogatyreva, Natalya S. last_name: Bogatyreva - first_name: Dmitry full_name: Ivankov, Dmitry id: 49FF1036-F248-11E8-B48F-1D18A9856A87 last_name: Ivankov - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Sergey full_name: Avvakumov, Sergey id: 3827DAC8-F248-11E8-B48F-1D18A9856A87 last_name: Avvakumov - first_name: Inna S. full_name: Povolotskaya, Inna S. last_name: Povolotskaya - first_name: Guillaume J. full_name: Filion, Guillaume J. last_name: Filion - first_name: Lucas B. full_name: Carey, Lucas B. last_name: Carey - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. Multiple alignment of His3 orthologues. 2019. doi:10.1371/journal.pgen.1008079.s010 apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). Multiple alignment of His3 orthologues. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s010 chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “Multiple Alignment of His3 Orthologues.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s010. ieee: V. Pokusaeva et al., “Multiple alignment of His3 orthologues.” Public Library of Science, 2019. ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. Multiple alignment of His3 orthologues, Public Library of Science, 10.1371/journal.pgen.1008079.s010. mla: Pokusaeva, Victoria, et al. Multiple Alignment of His3 Orthologues. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s010. short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019). date_created: 2021-08-06T08:38:50Z date_published: 2019-04-10T00:00:00Z date_updated: 2023-08-25T10:30:36Z day: '10' department: - _id: FyKo doi: 10.1371/journal.pgen.1008079.s010 month: '04' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '6419' relation: used_in_publication status: public status: public title: Multiple alignment of His3 orthologues type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '7181' abstract: - lang: eng text: Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy declines substantially as the number of sequences is scaled up5. We introduce a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard workstation and substantially improves accuracy on datasets larger than 10,000 sequences. Our regressive algorithm works the other way around to the progressive algorithm and begins by aligning the most dissimilar sequences. It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their original complexity. Our approach will enable analyses of extremely large genomic datasets such as the recently announced Earth BioGenome Project, which comprises 1.5 million eukaryotic genomes6. article_processing_charge: No article_type: original author: - first_name: Edgar full_name: Garriga, Edgar last_name: Garriga - first_name: Paolo full_name: Di Tommaso, Paolo last_name: Di Tommaso - first_name: Cedrik full_name: Magis, Cedrik last_name: Magis - first_name: Ionas full_name: Erb, Ionas last_name: Erb - first_name: Leila full_name: Mansouri, Leila last_name: Mansouri - first_name: Athanasios full_name: Baltzis, Athanasios last_name: Baltzis - first_name: Hafid full_name: Laayouni, Hafid last_name: Laayouni - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Evan full_name: Floden, Evan last_name: Floden - first_name: Cedric full_name: Notredame, Cedric last_name: Notredame citation: ama: Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 2019;37(12):1466-1470. doi:10.1038/s41587-019-0333-6 apa: Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-019-0333-6 chicago: Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41587-019-0333-6. ieee: E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf regressive method,” Nature Biotechnology, vol. 37, no. 12. Springer Nature, pp. 1466–1470, 2019. ista: Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2019. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 37(12), 1466–1470. mla: Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology, vol. 37, no. 12, Springer Nature, 2019, pp. 1466–70, doi:10.1038/s41587-019-0333-6. short: E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019) 1466–1470. date_created: 2019-12-15T23:00:43Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-09-06T14:32:52Z day: '01' department: - _id: FyKo doi: 10.1038/s41587-019-0333-6 ec_funded: 1 external_id: isi: - '000500748900021' pmid: - '31792410' intvolume: ' 37' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/ month: '12' oa: 1 oa_version: Submitted Version page: 1466-1470 pmid: 1 project: - _id: 26580278-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771209' name: Characterizing the fitness landscape on population and global scales publication: Nature Biotechnology publication_identifier: eissn: - '15461696' issn: - '10870156' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '13059' relation: research_data status: public scopus_import: '1' status: public title: Large multiple sequence alignments with a root-to-leaf regressive method type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 37 year: '2019' ... --- _id: '13059' abstract: - lang: eng text: "This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript.\r\nThe repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee)." article_processing_charge: No author: - first_name: Edgar full_name: Garriga, Edgar last_name: Garriga - first_name: Paolo full_name: di Tommaso, Paolo last_name: di Tommaso - first_name: Cedrik full_name: Magis, Cedrik last_name: Magis - first_name: Ionas full_name: Erb, Ionas last_name: Erb - first_name: Leila full_name: Mansouri, Leila last_name: Mansouri - first_name: Athanasios full_name: Baltzis, Athanasios last_name: Baltzis - first_name: Hafid full_name: Laayouni, Hafid last_name: Laayouni - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Evan full_name: Floden, Evan last_name: Floden - first_name: Cedric full_name: Notredame, Cedric last_name: Notredame citation: ama: Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. 2018. doi:10.5281/ZENODO.2025846 apa: Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo. https://doi.org/10.5281/ZENODO.2025846 chicago: Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.2025846. ieee: E. Garriga et al., “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018. ista: Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method, Zenodo, 10.5281/ZENODO.2025846. mla: Garriga, Edgar, et al. Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method. Zenodo, 2018, doi:10.5281/ZENODO.2025846. short: E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018). date_created: 2023-05-23T16:08:20Z date_published: 2018-12-07T00:00:00Z date_updated: 2023-09-06T14:32:51Z day: '07' ddc: - '570' department: - _id: FyKo doi: 10.5281/ZENODO.2025846 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.3271452 month: '12' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '7181' relation: used_in_publication status: public status: public title: Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '5780' abstract: - lang: eng text: Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in full, which is found only in bacteria. Here, we report identification of the fungal luciferase and three other key enzymes that together form the biosynthetic cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite. Introduction of the identified genes into the genome of the yeast Pichia pastoris along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis cycle and found that fungal bioluminescence emerged through a series of events that included two independent gene duplications. The retention of the duplicated enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication was followed by functional sequence divergence of enzymes of at least one gene in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence proceeded through several closely related stepping stone nonluminescent biochemical reactions with adaptive roles. The availability of a complete eukaryotic luciferin biosynthesis pathway provides several applications in biomedicine and bioengineering. article_processing_charge: No author: - first_name: Alexey A. full_name: Kotlobay, Alexey A. last_name: Kotlobay - first_name: Karen full_name: Sarkisyan, Karen id: 39A7BF80-F248-11E8-B48F-1D18A9856A87 last_name: Sarkisyan orcid: 0000-0002-5375-6341 - first_name: Yuliana A. full_name: Mokrushina, Yuliana A. last_name: Mokrushina - first_name: Marina full_name: Marcet-Houben, Marina last_name: Marcet-Houben - first_name: Ekaterina O. full_name: Serebrovskaya, Ekaterina O. last_name: Serebrovskaya - first_name: Nadezhda M. full_name: Markina, Nadezhda M. last_name: Markina - first_name: Louisa full_name: Gonzalez Somermeyer, Louisa id: 4720D23C-F248-11E8-B48F-1D18A9856A87 last_name: Gonzalez Somermeyer orcid: 0000-0001-9139-5383 - first_name: Andrey Y. full_name: Gorokhovatsky, Andrey Y. last_name: Gorokhovatsky - first_name: Andrey full_name: Vvedensky, Andrey last_name: Vvedensky - first_name: Konstantin V. full_name: Purtov, Konstantin V. last_name: Purtov - first_name: Valentin N. full_name: Petushkov, Valentin N. last_name: Petushkov - first_name: Natalja S. full_name: Rodionova, Natalja S. last_name: Rodionova - first_name: Tatiana V. full_name: Chepurnyh, Tatiana V. last_name: Chepurnyh - first_name: Liliia full_name: Fakhranurova, Liliia last_name: Fakhranurova - first_name: Elena B. full_name: Guglya, Elena B. last_name: Guglya - first_name: Rustam full_name: Ziganshin, Rustam last_name: Ziganshin - first_name: Aleksandra S. full_name: Tsarkova, Aleksandra S. last_name: Tsarkova - first_name: Zinaida M. full_name: Kaskova, Zinaida M. last_name: Kaskova - first_name: Victoria full_name: Shender, Victoria last_name: Shender - first_name: Maxim full_name: Abakumov, Maxim last_name: Abakumov - first_name: Tatiana O. full_name: Abakumova, Tatiana O. last_name: Abakumova - first_name: Inna S. full_name: Povolotskaya, Inna S. last_name: Povolotskaya - first_name: Fedor M. full_name: Eroshkin, Fedor M. last_name: Eroshkin - first_name: Andrey G. full_name: Zaraisky, Andrey G. last_name: Zaraisky - first_name: Alexander S. full_name: Mishin, Alexander S. last_name: Mishin - first_name: Sergey V. full_name: Dolgov, Sergey V. last_name: Dolgov - first_name: Tatiana Y. full_name: Mitiouchkina, Tatiana Y. last_name: Mitiouchkina - first_name: Eugene P. full_name: Kopantzev, Eugene P. last_name: Kopantzev - first_name: Hans E. full_name: Waldenmaier, Hans E. last_name: Waldenmaier - first_name: Anderson G. full_name: Oliveira, Anderson G. last_name: Oliveira - first_name: Yuichi full_name: Oba, Yuichi last_name: Oba - first_name: Ekaterina full_name: Barsova, Ekaterina last_name: Barsova - first_name: Ekaterina A. full_name: Bogdanova, Ekaterina A. last_name: Bogdanova - first_name: Toni full_name: Gabaldón, Toni last_name: Gabaldón - first_name: Cassius V. full_name: Stevani, Cassius V. last_name: Stevani - first_name: Sergey full_name: Lukyanov, Sergey last_name: Lukyanov - first_name: Ivan V. full_name: Smirnov, Ivan V. last_name: Smirnov - first_name: Josef I. full_name: Gitelson, Josef I. last_name: Gitelson - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Ilia V. full_name: Yampolsky, Ilia V. last_name: Yampolsky citation: ama: Kotlobay AA, Sarkisyan K, Mokrushina YA, et al. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(50):12728-12732. doi:10.1073/pnas.1803615115 apa: Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya, E. O., Markina, N. M., … Yampolsky, I. V. (2018). Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1803615115 chicago: Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben, Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1803615115. ieee: A. A. Kotlobay et al., “Genetically encodable bioluminescent system from fungi,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50. National Academy of Sciences, pp. 12728–12732, 2018. ista: Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 115(50), 12728–12732. mla: Kotlobay, Alexey A., et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50, National Academy of Sciences, 2018, pp. 12728–32, doi:10.1073/pnas.1803615115. short: A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya, N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov, V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya, R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova, I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y. Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova, E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson, F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 12728–12732. date_created: 2018-12-23T22:59:18Z date_published: 2018-12-11T00:00:00Z date_updated: 2023-09-11T14:04:05Z day: '11' ddc: - '580' department: - _id: FyKo doi: 10.1073/pnas.1803615115 external_id: isi: - '000452866000068' file: - access_level: open_access checksum: 46b2c12185eb2ddb598f4c7b4bd267bf content_type: application/pdf creator: dernst date_created: 2019-02-05T15:21:40Z date_updated: 2020-07-14T12:47:11Z file_id: '5926' file_name: 2018_PNAS_Kotlobay.pdf file_size: 1271988 relation: main_file file_date_updated: 2020-07-14T12:47:11Z has_accepted_license: '1' intvolume: ' 115' isi: 1 issue: '50' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '12' oa: 1 oa_version: Published Version page: 12728-12732 publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: issn: - '00278424' publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Genetically encodable bioluminescent system from fungi tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 115 year: '2018' ... --- _id: '279' abstract: - lang: eng text: 'Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments.' article_number: '67' article_processing_charge: No author: - first_name: Luis full_name: Zapata, Luis last_name: Zapata - first_name: Oriol full_name: Pich, Oriol last_name: Pich - first_name: Luis full_name: Serrano, Luis last_name: Serrano - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Stephan full_name: Ossowski, Stephan last_name: Ossowski - first_name: Martin full_name: Schaefer, Martin last_name: Schaefer citation: ama: Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 2018;19. doi:10.1186/s13059-018-1434-0 apa: Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1434-0 chicago: Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1434-0. ieee: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” Genome Biology, vol. 19. BioMed Central, 2018. ista: Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19, 67. mla: Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology, vol. 19, 67, BioMed Central, 2018, doi:10.1186/s13059-018-1434-0. short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018). date_created: 2018-12-11T11:45:35Z date_published: 2018-05-31T00:00:00Z date_updated: 2023-09-13T09:01:32Z day: '31' ddc: - '570' department: - _id: FyKo doi: 10.1186/s13059-018-1434-0 ec_funded: 1 external_id: isi: - '000433986200001' file: - access_level: open_access checksum: f3e4922486bd9bf1483271bdbed394a7 content_type: application/pdf creator: dernst date_created: 2018-12-17T14:05:01Z date_updated: 2020-07-14T12:45:47Z file_id: '5708' file_name: 2018_GenomeBiology_Zapata.pdf file_size: 1414722 relation: main_file file_date_updated: 2020-07-14T12:45:47Z has_accepted_license: '1' intvolume: ' 19' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 26120F5C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '335980' name: Systematic investigation of epistasis in molecular evolution publication: Genome Biology publication_status: published publisher: BioMed Central publist_id: '7620' quality_controlled: '1' related_material: record: - id: '9811' relation: research_data status: public - id: '9812' relation: research_data status: public scopus_import: '1' status: public title: Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 19 year: '2018' ... --- _id: '9812' abstract: - lang: eng text: This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb) article_processing_charge: No author: - first_name: Luis full_name: Zapata, Luis last_name: Zapata - first_name: Oriol full_name: Pich, Oriol last_name: Pich - first_name: Luis full_name: Serrano, Luis last_name: Serrano - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Stephan full_name: Ossowski, Stephan last_name: Ossowski - first_name: Martin full_name: Schaefer, Martin last_name: Schaefer citation: ama: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401414.v1' apa: 'Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401414.v1' chicago: 'Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401414.v1.' ieee: 'L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.' ista: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401414.v1.' mla: 'Zapata, Luis, et al. Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1.' short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018). date_created: 2021-08-06T12:58:25Z date_published: 2018-05-31T00:00:00Z date_updated: 2023-09-13T09:01:31Z day: '31' department: - _id: FyKo doi: 10.6084/m9.figshare.6401414.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.6401414.v1 month: '05' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '279' relation: used_in_publication status: public status: public title: 'Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2018' ... --- _id: '9811' abstract: - lang: eng text: This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb) article_processing_charge: No author: - first_name: Luis full_name: Zapata, Luis last_name: Zapata - first_name: Oriol full_name: Pich, Oriol last_name: Pich - first_name: Luis full_name: Serrano, Luis last_name: Serrano - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Stephan full_name: Ossowski, Stephan last_name: Ossowski - first_name: Martin full_name: Schaefer, Martin last_name: Schaefer citation: ama: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401390.v1' apa: 'Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401390.v1' chicago: 'Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401390.v1.' ieee: 'L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.' ista: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401390.v1.' mla: 'Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1.' short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018). date_created: 2021-08-06T12:53:49Z date_published: 2018-05-31T00:00:00Z date_updated: 2023-09-13T09:01:31Z day: '31' department: - _id: FyKo doi: 10.6084/m9.figshare.6401390.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.6401390.v1 month: '05' oa: 1 oa_version: Preprint publisher: Springer Nature related_material: record: - id: '279' relation: used_in_publication status: public status: public title: 'Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2018' ... --- _id: '5995' abstract: - lang: eng text: "Motivation\r\nComputational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic shift of the predicted change of stability, has been noted as an issue for several methods, but has not been investigated systematically. Presence of the bias may lead to misleading results especially when exploring the effects of combination of different mutations.\r\n\r\nResults\r\nHere we use a protocol to measure the bias as a function of the number of introduced mutations. It is based on a self-consistency test of the reciprocity the effect of a mutation. An advantage of the used approach is that it relies solely on crystal structures without experimentally measured stability values. We applied the protocol to four popular algorithms predicting change of protein stability upon mutation, FoldX, Eris, Rosetta and I-Mutant, and found an inherent bias. For one program, FoldX, we manage to substantially reduce the bias using additional relaxation by Modeller. Authors using algorithms for predicting effects of mutations should be aware of the bias described here." article_processing_charge: No author: - first_name: Dinara R full_name: Usmanova, Dinara R last_name: Usmanova - first_name: Natalya S full_name: Bogatyreva, Natalya S last_name: Bogatyreva - first_name: Joan full_name: Ariño Bernad, Joan last_name: Ariño Bernad - first_name: Aleksandra A full_name: Eremina, Aleksandra A last_name: Eremina - first_name: Anastasiya A full_name: Gorshkova, Anastasiya A last_name: Gorshkova - first_name: German M full_name: Kanevskiy, German M last_name: Kanevskiy - first_name: Lyubov R full_name: Lonishin, Lyubov R last_name: Lonishin - first_name: Alexander V full_name: Meister, Alexander V last_name: Meister - first_name: Alisa G full_name: Yakupova, Alisa G last_name: Yakupova - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Dmitry full_name: Ivankov, Dmitry id: 49FF1036-F248-11E8-B48F-1D18A9856A87 last_name: Ivankov citation: ama: Usmanova DR, Bogatyreva NS, Ariño Bernad J, et al. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 2018;34(21):3653-3658. doi:10.1093/bioinformatics/bty340 apa: Usmanova, D. R., Bogatyreva, N. S., Ariño Bernad, J., Eremina, A. A., Gorshkova, A. A., Kanevskiy, G. M., … Ivankov, D. (2018). Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. Oxford University Press . https://doi.org/10.1093/bioinformatics/bty340 chicago: Usmanova, Dinara R, Natalya S Bogatyreva, Joan Ariño Bernad, Aleksandra A Eremina, Anastasiya A Gorshkova, German M Kanevskiy, Lyubov R Lonishin, et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics. Oxford University Press , 2018. https://doi.org/10.1093/bioinformatics/bty340. ieee: D. R. Usmanova et al., “Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation,” Bioinformatics, vol. 34, no. 21. Oxford University Press , pp. 3653–3658, 2018. ista: Usmanova DR, Bogatyreva NS, Ariño Bernad J, Eremina AA, Gorshkova AA, Kanevskiy GM, Lonishin LR, Meister AV, Yakupova AG, Kondrashov F, Ivankov D. 2018. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 34(21), 3653–3658. mla: Usmanova, Dinara R., et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics, vol. 34, no. 21, Oxford University Press , 2018, pp. 3653–58, doi:10.1093/bioinformatics/bty340. short: D.R. Usmanova, N.S. Bogatyreva, J. Ariño Bernad, A.A. Eremina, A.A. Gorshkova, G.M. Kanevskiy, L.R. Lonishin, A.V. Meister, A.G. Yakupova, F. Kondrashov, D. Ivankov, Bioinformatics 34 (2018) 3653–3658. date_created: 2019-02-14T12:48:00Z date_published: 2018-11-01T00:00:00Z date_updated: 2023-09-19T14:31:13Z day: '01' ddc: - '570' department: - _id: FyKo doi: 10.1093/bioinformatics/bty340 ec_funded: 1 external_id: isi: - '000450038900008' pmid: - '29722803' file: - access_level: open_access checksum: 7e0495153f44211479674601d7f6ee03 content_type: application/pdf creator: kschuh date_created: 2019-02-14T13:00:55Z date_updated: 2020-07-14T12:47:15Z file_id: '5997' file_name: 2018_Oxford_Usmanova.pdf file_size: 291969 relation: main_file file_date_updated: 2020-07-14T12:47:15Z has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '21' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 3653-3658 pmid: 1 project: - _id: 26120F5C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '335980' name: Systematic investigation of epistasis in molecular evolution publication: Bioinformatics publication_identifier: issn: - 1367-4803 - 1460-2059 publication_status: published publisher: 'Oxford University Press ' quality_controlled: '1' scopus_import: '1' status: public title: Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 34 year: '2018' ... --- _id: '850' abstract: - lang: eng text: Fitness landscapes depict how genotypes manifest at the phenotypic level and form the basis of our understanding of many areas of biology, yet their properties remain elusive. Previous studies have analysed specific genes, often using their function as a proxy for fitness, experimentally assessing the effect on function of single mutations and their combinations in a specific sequence or in different sequences. However, systematic high-throughput studies of the local fitness landscape of an entire protein have not yet been reported. Here we visualize an extensive region of the local fitness landscape of the green fluorescent protein from Aequorea Victoria (avGFP) by measuring the native function (fluorescence) of tens of thousands of derivative genotypes of avGFP. We show that the fitness landscape of avGFP is narrow, with 3/4 of the derivatives with a single mutation showing reduced fluorescence and half of the derivatives with four mutations being completely non-fluorescent. The narrowness is enhanced by epistasis, which was detected in up to 30% of genotypes with multiple mutations and mostly occurred through the cumulative effect of slightly deleterious mutations causing a threshold-like decrease in protein stability and a concomitant loss of fluorescence. A model of orthologous sequence divergence spanning hundreds of millions of years predicted the extent of epistasis in our data, indicating congruence between the fitness landscape properties at the local and global scales. The characterization of the local fitness landscape of avGFP has important implications for several fields including molecular evolution, population genetics and protein design. acknowledgement: We thank Y. Kulikova and G. Filion for discussion on statistical analysis and I. Osterman, R. Moretti and J. Meiler for technical assistance and M. Friesen for a critical reading of the manuscript. We thank H. Himmelbauer, CRG Genomic Unit and the Russian Science Foundation project (14-50-00150) for sequencing. Experiments were partially carried out using the equipment provided by the IBCH core facility (CKP IBCH). The work was supported by HHMI International Early Career Scientist Program (55007424), the EMBO Young Investigator Programme, MINECO (BFU2012-31329), Spanish Ministry of Economy and Competitiveness Centro de Excelencia Severo Ochoa 2013-2017 grant (SEV-2012-0208), Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat's AGAUR program (2014 SGR 0974), Russian Science Foundation (14-25-00129) and the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013, ERC grant agreement, 335980-EinME). author: - first_name: Karen full_name: Karen Sarkisyan id: 39A7BF80-F248-11E8-B48F-1D18A9856A87 last_name: Sarkisyan orcid: 0000-0002-5375-6341 - first_name: Dmitry full_name: Bolotin, Dmitry A last_name: Bolotin - first_name: Margarita full_name: Meer, Margarita V last_name: Meer - first_name: Dinara full_name: Usmanova, Dinara R last_name: Usmanova - first_name: Alexander full_name: Mishin, Alexander S last_name: Mishin - first_name: George full_name: Sharonov, George V last_name: Sharonov - first_name: Dmitry full_name: Ivankov, Dmitry N last_name: Ivankov - first_name: Nina full_name: Bozhanova, Nina G last_name: Bozhanova - first_name: Mikhail full_name: Baranov, Mikhail S last_name: Baranov - first_name: Onuralp full_name: Soylemez, Onuralp last_name: Soylemez - first_name: Natalya full_name: Bogatyreva, Natalya S last_name: Bogatyreva - first_name: Peter full_name: Vlasov, Peter K last_name: Vlasov - first_name: Evgeny full_name: Egorov, Evgeny S last_name: Egorov - first_name: Maria full_name: Logacheva, Maria D last_name: Logacheva - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov - first_name: Dmitriy full_name: Chudakov, Dmitriy M last_name: Chudakov - first_name: Ekaterina full_name: Putintseva, Ekaterina V last_name: Putintseva - first_name: Ilgar full_name: Mamedov, Ilgar Z last_name: Mamedov - first_name: Dan full_name: Tawfik, Dan S last_name: Tawfik - first_name: Konstantin full_name: Lukyanov, Konstantin A last_name: Lukyanov - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Sarkisyan K, Bolotin D, Meer M, et al. Local fitness landscape of the green fluorescent protein. Nature. 2016;533:397-401. doi:10.1038/nature17995 apa: Sarkisyan, K., Bolotin, D., Meer, M., Usmanova, D., Mishin, A., Sharonov, G., … Kondrashov, F. (2016). Local fitness landscape of the green fluorescent protein. Nature. Nature Publishing Group. https://doi.org/10.1038/nature17995 chicago: Sarkisyan, Karen, Dmitry Bolotin, Margarita Meer, Dinara Usmanova, Alexander Mishin, George Sharonov, Dmitry Ivankov, et al. “Local Fitness Landscape of the Green Fluorescent Protein.” Nature. Nature Publishing Group, 2016. https://doi.org/10.1038/nature17995. ieee: K. Sarkisyan et al., “Local fitness landscape of the green fluorescent protein,” Nature, vol. 533. Nature Publishing Group, pp. 397–401, 2016. ista: Sarkisyan K, Bolotin D, Meer M, Usmanova D, Mishin A, Sharonov G, Ivankov D, Bozhanova N, Baranov M, Soylemez O, Bogatyreva N, Vlasov P, Egorov E, Logacheva M, Kondrashov A, Chudakov D, Putintseva E, Mamedov I, Tawfik D, Lukyanov K, Kondrashov F. 2016. Local fitness landscape of the green fluorescent protein. Nature. 533, 397–401. mla: Sarkisyan, Karen, et al. “Local Fitness Landscape of the Green Fluorescent Protein.” Nature, vol. 533, Nature Publishing Group, 2016, pp. 397–401, doi:10.1038/nature17995. short: K. Sarkisyan, D. Bolotin, M. Meer, D. Usmanova, A. Mishin, G. Sharonov, D. Ivankov, N. Bozhanova, M. Baranov, O. Soylemez, N. Bogatyreva, P. Vlasov, E. Egorov, M. Logacheva, A. Kondrashov, D. Chudakov, E. Putintseva, I. Mamedov, D. Tawfik, K. Lukyanov, F. Kondrashov, Nature 533 (2016) 397–401. date_created: 2018-12-11T11:48:50Z date_published: 2016-05-11T00:00:00Z date_updated: 2021-01-12T08:19:42Z day: '11' doi: 10.1038/nature17995 extern: 1 intvolume: ' 533' month: '05' page: 397 - 401 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6799' quality_controlled: 0 status: public title: Local fitness landscape of the green fluorescent protein type: journal_article volume: 533 year: '2016' ... --- _id: '896' abstract: - lang: eng text: Multicellular eukaryotes have evolved a range of mechanisms for immune recognition. A widespread family involved in innate immunity are the NACHT-domain and leucine-rich-repeat-containing (NLR) proteins.Mammals have small numbers of NLR proteins, whereas in some species, mostly those without adaptive immune systems, NLRs have expanded into very large families.We describe a family of nearly 400NLR proteins encoded in the zebrafish genome. The proteins share a defining overall structure, which arose in fishes after a fusion of the core NLR domains with a B30.2 domain, but can be subdivided into four groups based on their NACHT domains. Gene conversion acting differentially on the NACHT and B30.2 domains has shaped the family and created the groups. Evidence of positive selection in the B30.2 domain indicates that this domain rather than the leucine-rich repeats acts as the pathogen recognition module. In an unusual chromosomal organization, the majority of the genes are located on one chromosome arm, interspersed with other large multigene families, including a new family encoding zinc-finger proteins. The NLR-B30.2 proteins represent a new family with diversity in the specific recognition module that is present in fishes in spite of the parallel existence of an adaptive immune system. acknowledgement: Financial support was provided by EMBO and the DFG SFB 670 'Zellautonome Immunität' to M.L., DFG SFB 680 'Molecular basis of evolutionary innovation' to T.W., DFG SPP1819 to M.L. and T.W., the HHMI International Early Career Scientist Programme (55007424), MINECO (Sev-2012-0208), AGAUR programme (2014 SGR 0974), and an ERC Starting Grant (335980-EinME) to F.K., the European Molecular Biology Laboratory to J.M., the Wellcome Trust to K.H. (zebrafish genome sequencing project) and the National Human Genome Research Institute (NHGRI) grant HG002659 to G.K.L. (gene annotation), and a grant from the Volkswagen Foundation to P.H.S. We thank the CHEOPS support team and the Bundesland Nordrhein Westfalen for making HPC applications freely available at the University of Cologne. author: - first_name: Kerstin full_name: Howe, Kerstin L last_name: Howe - first_name: Philipp full_name: Schiffer, Philipp H last_name: Schiffer - first_name: Julia full_name: Zielinski, Julia G last_name: Zielinski - first_name: Thomas full_name: Wiehe, Thomas H last_name: Wiehe - first_name: Gavin full_name: Laird, Gavin K last_name: Laird - first_name: John full_name: Marioni, John C last_name: Marioni - first_name: Onuralp full_name: Soylemez, Onuralp last_name: Soylemez - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Maria full_name: Leptin, Maria last_name: Leptin citation: ama: Howe K, Schiffer P, Zielinski J, et al. Structure and evolutionary history of a large family of NLR proteins in the zebrafish. Open Biology. 2016;6(4). doi:10.1098/rsob.160009 apa: Howe, K., Schiffer, P., Zielinski, J., Wiehe, T., Laird, G., Marioni, J., … Leptin, M. (2016). Structure and evolutionary history of a large family of NLR proteins in the zebrafish. Open Biology. Royal Society, The. https://doi.org/10.1098/rsob.160009 chicago: Howe, Kerstin, Philipp Schiffer, Julia Zielinski, Thomas Wiehe, Gavin Laird, John Marioni, Onuralp Soylemez, Fyodor Kondrashov, and Maria Leptin. “Structure and Evolutionary History of a Large Family of NLR Proteins in the Zebrafish.” Open Biology. Royal Society, The, 2016. https://doi.org/10.1098/rsob.160009. ieee: K. Howe et al., “Structure and evolutionary history of a large family of NLR proteins in the zebrafish,” Open Biology, vol. 6, no. 4. Royal Society, The, 2016. ista: Howe K, Schiffer P, Zielinski J, Wiehe T, Laird G, Marioni J, Soylemez O, Kondrashov F, Leptin M. 2016. Structure and evolutionary history of a large family of NLR proteins in the zebrafish. Open Biology. 6(4). mla: Howe, Kerstin, et al. “Structure and Evolutionary History of a Large Family of NLR Proteins in the Zebrafish.” Open Biology, vol. 6, no. 4, Royal Society, The, 2016, doi:10.1098/rsob.160009. short: K. Howe, P. Schiffer, J. Zielinski, T. Wiehe, G. Laird, J. Marioni, O. Soylemez, F. Kondrashov, M. Leptin, Open Biology 6 (2016). date_created: 2018-12-11T11:49:04Z date_published: 2016-01-01T00:00:00Z date_updated: 2021-01-12T08:21:32Z day: '01' doi: 10.1098/rsob.160009 extern: 1 intvolume: ' 6' issue: '4' month: '01' publication: Open Biology publication_status: published publisher: Royal Society, The publist_id: '6754' quality_controlled: 0 status: public title: Structure and evolutionary history of a large family of NLR proteins in the zebrafish tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 6 year: '2016' ... --- _id: '849' abstract: - lang: eng text: Understanding the principles that led to the current complexity of the genetic code is a central question in evolution. Expansion of the genetic code required the selection of new transfer RNAs (tRNAs) with specific recognition signals that allowed them to be matured, modified, aminoacylated, and processed by the ribosome without compromising the fidelity or efficiency of protein synthesis. We show that saturation of recognition signals blocks the emergence of new tRNA identities and that the rate of nucleotide substitutions in tRNAs is higher in species with fewer tRNA genes. We propose that the growth of the genetic code stalled because a limit was reached in the number of identity elements that can be effectively used in the tRNA structure. acknowledgement: |- We thank D. Söll, H. Grosjean, and L. Filonava for comments and suggestions. M.O. and P.D.D. thank the Barcelona Supercomputing Center for CPU/GPU time on MareNostrum/ MinoTauro. P.D.D. is a PEDECIBA (Programa de Desarrollo de las Ciencias Básicas) and an SNI (Sistema Nacional de Investigadores) (ANII, Uruguay) researcher. Funding: This work was supported in part by the Spanish Ministry of Economy and Competitiveness (grants BIO2012-32200, Sev-2012-0208, and BIO2012-32868 to L.R.d.P., F.A.K., and M.O., respectively) and by the Catalan Government (grants 2014-SGR-0771, 2014-SGR-0974, and 2014-SGR-0134 to L.R.d.P., F.A.K., and M.O., respectively). This work was also supported by the Howard Hughes Medical Institute International Early Career Scientist Program (55007424), by a European Research Council (ERC) Starting Grant (335980_EinME to F.K.), and by a grant from the ERC (ERC_SimDNA to M.O). A.G.T. and C.B. are funded by the Spanish Ministry of Economy and Competitiveness (FPDI-2013-17742 and BES-2013-064004, respectively). author: - first_name: Adélaïde full_name: Saint-Léger, Adélaïde last_name: Saint Léger - first_name: Carla full_name: Bello, Carla last_name: Bello - first_name: Pablo full_name: Dans, Pablo D last_name: Dans - first_name: Adrian full_name: Torres, Adrian G last_name: Torres - first_name: Eva full_name: Novoa, Eva M last_name: Novoa - first_name: Noelia full_name: Camacho, Noelia last_name: Camacho - first_name: Modesto full_name: Orozco, Modesto last_name: Orozco - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Lluís full_name: Ribas De Pouplana, Lluís last_name: Ribas De Pouplana citation: ama: Saint Léger A, Bello C, Dans P, et al. Saturation of recognition elements blocks evolution of new tRNA identities. Science advances. 2016;2(4):e1501860-e1501860. doi:10.1126/sciadv.1501860 apa: Saint Léger, A., Bello, C., Dans, P., Torres, A., Novoa, E., Camacho, N., … Ribas De Pouplana, L. (2016). Saturation of recognition elements blocks evolution of new tRNA identities. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.1501860 chicago: Saint Léger, Adélaïde, Carla Bello, Pablo Dans, Adrian Torres, Eva Novoa, Noelia Camacho, Modesto Orozco, Fyodor Kondrashov, and Lluís Ribas De Pouplana. “Saturation of Recognition Elements Blocks Evolution of New TRNA Identities.” Science Advances. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/sciadv.1501860. ieee: A. Saint Léger et al., “Saturation of recognition elements blocks evolution of new tRNA identities,” Science advances, vol. 2, no. 4. American Association for the Advancement of Science, pp. e1501860–e1501860, 2016. ista: Saint Léger A, Bello C, Dans P, Torres A, Novoa E, Camacho N, Orozco M, Kondrashov F, Ribas De Pouplana L. 2016. Saturation of recognition elements blocks evolution of new tRNA identities. Science advances. 2(4), e1501860–e1501860. mla: Saint Léger, Adélaïde, et al. “Saturation of Recognition Elements Blocks Evolution of New TRNA Identities.” Science Advances, vol. 2, no. 4, American Association for the Advancement of Science, 2016, pp. e1501860–e1501860, doi:10.1126/sciadv.1501860. short: A. Saint Léger, C. Bello, P. Dans, A. Torres, E. Novoa, N. Camacho, M. Orozco, F. Kondrashov, L. Ribas De Pouplana, Science Advances 2 (2016) e1501860–e1501860. date_created: 2018-12-11T11:48:50Z date_published: 2016-04-01T00:00:00Z date_updated: 2021-01-12T08:19:38Z day: '01' doi: 10.1126/sciadv.1501860 extern: 1 intvolume: ' 2' issue: '4' month: '04' page: e1501860 - e1501860 publication: Science advances publication_status: published publisher: American Association for the Advancement of Science publist_id: '6798' quality_controlled: 0 status: public title: Saturation of recognition elements blocks evolution of new tRNA identities tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article volume: 2 year: '2016' ... --- _id: '853' abstract: - lang: eng text: A comparative analysis of the metagenomes from two 30 000-year-old permafrost samples, one of lake-alluvial origin and the other from late Pleistocene Ice Complex sediments, revealed significant differences within microbial communities. The late Pleistocene Ice Complex sediments (which have been characterized by the absence of methane with lower values of redox potential and Fe2+ content) showed a low abundance of methanogenic archaea and enzymes from both the carbon and nitrogen cycles, but a higher abundance of enzymes associated with the sulfur cycle. The metagenomic and geochemical analyses described in the paper provide evidence that the formation of the sampled late Pleistocene Ice Complex sediments likely took place under much more aerobic conditions than lake-alluvial sediments. acknowledgement: This work was supported by grants from the Russian Scientific Fund (14-14-01115) to Elizaveta Rivkina; from the National Science Foundation (DEB-1442262) to Tatiana Vish- nivetskaya; and from the HHMI International Early Career Scientist Program (55007424), the EMBO Young Investigator Programme, MINECO (BFU2012-31329 and Sev-2012-0208), and the AGAUR program (2014 SGR 0974) to Fyodor Kondrashov. Support from the Russian Scientific Fund (14-14-01115) was allocated for sample collection, gDNA isolation, and analysis of metagenomic data. author: - first_name: Elizaveta full_name: Rivkina, Elizaveta last_name: Rivkina - first_name: Lada full_name: Petrovskaya, Lada E last_name: Petrovskaya - first_name: Tatiana full_name: Vishnivetskaya, Tatiana A last_name: Vishnivetskaya - first_name: Kirill full_name: Krivushin, Kirill V last_name: Krivushin - first_name: Lyubov full_name: Shmakova, Lyubov A last_name: Shmakova - first_name: Maria full_name: Tutukina, Maria last_name: Tutukina - first_name: Arthur full_name: Meyers, Arthur J last_name: Meyers - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Rivkina E, Petrovskaya L, Vishnivetskaya T, et al. Metagenomic analyses of the late Pleistocene permafrost - Additional tools for reconstruction of environmental conditions. Biogeosciences. 2016;13(7):2207-2219. doi:10.5194/bg-13-2207-2016 apa: Rivkina, E., Petrovskaya, L., Vishnivetskaya, T., Krivushin, K., Shmakova, L., Tutukina, M., … Kondrashov, F. (2016). Metagenomic analyses of the late Pleistocene permafrost - Additional tools for reconstruction of environmental conditions. Biogeosciences. European Geosciences Union. https://doi.org/10.5194/bg-13-2207-2016 chicago: Rivkina, Elizaveta, Lada Petrovskaya, Tatiana Vishnivetskaya, Kirill Krivushin, Lyubov Shmakova, Maria Tutukina, Arthur Meyers, and Fyodor Kondrashov. “Metagenomic Analyses of the Late Pleistocene Permafrost - Additional Tools for Reconstruction of Environmental Conditions.” Biogeosciences. European Geosciences Union, 2016. https://doi.org/10.5194/bg-13-2207-2016. ieee: E. Rivkina et al., “Metagenomic analyses of the late Pleistocene permafrost - Additional tools for reconstruction of environmental conditions,” Biogeosciences, vol. 13, no. 7. European Geosciences Union, pp. 2207–2219, 2016. ista: Rivkina E, Petrovskaya L, Vishnivetskaya T, Krivushin K, Shmakova L, Tutukina M, Meyers A, Kondrashov F. 2016. Metagenomic analyses of the late Pleistocene permafrost - Additional tools for reconstruction of environmental conditions. Biogeosciences. 13(7), 2207–2219. mla: Rivkina, Elizaveta, et al. “Metagenomic Analyses of the Late Pleistocene Permafrost - Additional Tools for Reconstruction of Environmental Conditions.” Biogeosciences, vol. 13, no. 7, European Geosciences Union, 2016, pp. 2207–19, doi:10.5194/bg-13-2207-2016. short: E. Rivkina, L. Petrovskaya, T. Vishnivetskaya, K. Krivushin, L. Shmakova, M. Tutukina, A. Meyers, F. Kondrashov, Biogeosciences 13 (2016) 2207–2219. date_created: 2018-12-11T11:48:51Z date_published: 2016-04-01T00:00:00Z date_updated: 2021-01-12T08:19:54Z day: '01' doi: 10.5194/bg-13-2207-2016 extern: 1 intvolume: ' 13' issue: '7' month: '04' page: 2207 - 2219 publication: Biogeosciences publication_status: published publisher: European Geosciences Union publist_id: '6793' quality_controlled: 0 status: public title: Metagenomic analyses of the late Pleistocene permafrost - Additional tools for reconstruction of environmental conditions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 13 year: '2016' ... --- _id: '848' abstract: - lang: eng text: The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution. author: - first_name: Dinara full_name: Usmanova, Dinara last_name: Usmanova - first_name: Luca full_name: Ferretti, Luca last_name: Ferretti - first_name: Inna full_name: Povolotskaya, Inna last_name: Povolotskaya - first_name: Peter full_name: Vlasov, Peter last_name: Vlasov - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. 2015;32(2):542-554. doi:10.1093/molbev/msu318 apa: Usmanova, D., Ferretti, L., Povolotskaya, I., Vlasov, P., & Kondrashov, F. (2015). A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msu318 chicago: Usmanova, Dinara, Luca Ferretti, Inna Povolotskaya, Peter Vlasov, and Fyodor Kondrashov. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” Molecular Biology and Evolution. Oxford University Press, 2015. https://doi.org/10.1093/molbev/msu318. ieee: D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, and F. Kondrashov, “A model of substitution trajectories in sequence space and long-term protein evolution,” Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press, pp. 542–554, 2015. ista: Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. 2015. A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. 32(2), 542–554. mla: Usmanova, Dinara, et al. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University Press, 2015, pp. 542–54, doi:10.1093/molbev/msu318. short: D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, F. Kondrashov, Molecular Biology and Evolution 32 (2015) 542–554. date_created: 2018-12-11T11:48:49Z date_published: 2015-02-01T00:00:00Z date_updated: 2021-01-12T08:19:33Z day: '01' doi: 10.1093/molbev/msu318 extern: '1' intvolume: ' 32' issue: '2' language: - iso: eng month: '02' oa_version: None page: 542 - 554 publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '6804' quality_controlled: '1' status: public title: A model of substitution trajectories in sequence space and long-term protein evolution type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2015' ... --- _id: '906' abstract: - lang: eng text: The origin and evolution of novel biochemical functions remains one of the key questions in molecular evolution. We study recently emerged methacrylate reductase function that is thought to have emerged in the last century and reported in Geobacter sulfurreducens strain AM-1. We report the sequence and study the evolution of the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme cytochrome (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex mechanism of biogenesis for chromoproteids of the methacrylate redox system. The homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres are also organized into an operon and their phylogenetic distribution suggested that these two genes tend to be horizontally transferred together. Specifically, the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any of the homologs found in other Geobacter genomes. The acquisition of methacrylate reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene transfer event. However, the new function of the products of mrd and mcc may have evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1. acknowledgement: 'Funding: The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, "Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)" and (BFU2012-31329), the European Union and the European Research Council under grant agreement 335980_EinME. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Our author Dr., Prof. Akimenko Vasilii K. (1942–2013) passed away during work on the article. Prof. Akimenko was a leading biochemist in IBPM RAS and active researcher until last days. A number of his work remains unfinished. We mourn premature care of Prof. Akimenko Vasilii. We thank Heinz Himmelbauer and the CRG Genomic Unit for the sequencing.' author: - first_name: Oksana full_name: Arkhipova, Oksana V last_name: Arkhipova - first_name: Margarita full_name: Meer, Margarita V last_name: Meer - first_name: Galina full_name: Mikoulinskaia, Galina V last_name: Mikoulinskaia - first_name: Marina full_name: Zakharova, Marina V last_name: Zakharova - first_name: Alexander full_name: Galushko, Alexander S last_name: Galushko - first_name: Vasilii full_name: Akimenko, Vasilii K last_name: Akimenko - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Arkhipova O, Meer M, Mikoulinskaia G, et al. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0125888 apa: Arkhipova, O., Meer, M., Mikoulinskaia, G., Zakharova, M., Galushko, A., Akimenko, V., & Kondrashov, F. (2015). Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0125888 chicago: Arkhipova, Oksana, Margarita Meer, Galina Mikoulinskaia, Marina Zakharova, Alexander Galushko, Vasilii Akimenko, and Fyodor Kondrashov. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0125888. ieee: O. Arkhipova et al., “Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015. ista: Arkhipova O, Meer M, Mikoulinskaia G, Zakharova M, Galushko A, Akimenko V, Kondrashov F. 2015. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 10(5). mla: Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0125888. short: O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko, F. Kondrashov, PLoS One 10 (2015). date_created: 2018-12-11T11:49:08Z date_published: 2015-05-11T00:00:00Z date_updated: 2021-01-12T08:21:48Z day: '11' doi: 10.1371/journal.pone.0125888 extern: 1 intvolume: ' 10' issue: '5' month: '05' publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '6742' quality_controlled: 0 status: public title: Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 10 year: '2015' ... --- _id: '866' abstract: - lang: eng text: Proteases play important roles in many biologic processes and are key mediators of cancer, inflammation, and thrombosis. However, comprehensive and quantitative techniques to define the substrate specificity profile of proteases are lacking. The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage display library based on a 73-amino acid fragment of VWF was constructed, and the ADAMTS13-dependent change in library complexity was evaluated over reaction time points, using high-throughput sequencing. Reaction rate constants (kcat/KM) were calculated for nearly every possible single amino acid substitution within this fragment. This massively parallel enzyme kinetics analysis detailed the specificity of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues while defining exosite binding domains. These data provided empirical evidence for the propensity for epistasis within VWF and showed strong correlation to conservation across orthologs, highlighting evolutionary selective pressures for VWF. acknowledgement: | We thank Isabel Wang and Vivian Cheung from the Life Sciences Institute, University of Michigan, for assistance with high- throughput sequencing experiments and valuable discussions. We also thank J. Evan Sadler (Washington University) and Sriram Krishnaswamy (Children’s Hospital of Philadelphia) for helpful discussions. We thank Jeff Weitz (McMaster University), Jim Fredenburgh (McMaster University), and Steve Weiss (University of Michigan) for critical review of the manuscript. C.A.K. was awarded the Judith Graham Pool Fellowship from National Hemophilia Foundation. This work was supported by the National Institutes of Health (R01 HL039693), the National Heart, Lung, and Blood Institute (P01- HL057346), Ministerio de Economía y Competitividad Grants BFU2012- 31329 and Sev-2012-0208, and European Research Council Starting Grant 335980_EinME. D.G. is an investigator of the Howard Hughes Medical In- stitute, and F.A.K. is a Howard Hughes Medical Institute International Early Career Scientist. author: - first_name: Colin full_name: Kretz, Colin A last_name: Kretz - first_name: Manhong full_name: Dai, Manhong last_name: Dai - first_name: Onuralp full_name: Soylemez, Onuralp last_name: Soylemez - first_name: Andrew full_name: Yee, Andrew last_name: Yee - first_name: Karl full_name: Desch, Karl C last_name: Desch - first_name: David full_name: Siemieniak, David R last_name: Siemieniak - first_name: Kärt full_name: Tomberg, Kärt last_name: Tomberg - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Fan full_name: Meng, Fan last_name: Meng - first_name: David full_name: Ginsburg, David B last_name: Ginsburg citation: ama: Kretz C, Dai M, Soylemez O, et al. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 2015;112(30):9328-9333. doi:10.1073/pnas.1511328112 apa: Kretz, C., Dai, M., Soylemez, O., Yee, A., Desch, K., Siemieniak, D., … Ginsburg, D. (2015). Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1511328112 chicago: Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511328112. ieee: C. Kretz et al., “Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13,” PNAS, vol. 112, no. 30. National Academy of Sciences, pp. 9328–9333, 2015. ista: Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333. mla: Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS, vol. 112, no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:10.1073/pnas.1511328112. short: C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg, F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333. date_created: 2018-12-11T11:48:55Z date_published: 2015-07-28T00:00:00Z date_updated: 2021-01-12T08:20:26Z day: '28' doi: 10.1073/pnas.1511328112 extern: 1 intvolume: ' 112' issue: '30' month: '07' page: 9328 - 9333 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '6783' quality_controlled: 0 status: public title: Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13 type: journal_article volume: 112 year: '2015' ... --- _id: '886' abstract: - lang: eng text: The factors that determine the tempo and mode of protein evolution continue to be a central question in molecular evolution. Traditionally, studies of protein evolution focused on the rates of amino acid substitutions. More recently, with the availability of sequence data and advanced experimental techniques, the focus of attention has shifted toward the study of evolutionary trajectories and the overall layout of protein fitness landscapes. In this review we describe the effect of epistasis on the topology of evolutionary pathways that are likely to be found in fitness landscapes and develop a simple theory to connect the number of maladapted genotypes to the topology of fitness landscapes with epistatic interactions. Finally, we review recent studies that have probed the extent of epistatic interactions and have begun to chart the fitness landscapes in protein sequence space. acknowledgement: 'This work has been supported by a grant from the HHMI International Early Career Scientist Program (#55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, Centro de Excelencia Severo Ochoa 2013–2017 (#Sev-2012-0208) and BES-2013-064004 funded by the European Regional Development Fund (ERDF), the European Union, and the European Research Council under grant agreement no 335980_EinME.' author: - first_name: Dmitry full_name: Kondrashov, Dmitry A last_name: Kondrashov - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kondrashov D, Kondrashov F. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 2015;31(1):24-33. doi:10.1016/j.tig.2014.09.009 apa: Kondrashov, D., & Kondrashov, F. (2015). Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2014.09.009 chicago: Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics. Elsevier, 2015. https://doi.org/10.1016/j.tig.2014.09.009. ieee: D. Kondrashov and F. Kondrashov, “Topological features of rugged fitness landscapes in sequence space,” Trends in Genetics, vol. 31, no. 1. Elsevier, pp. 24–33, 2015. ista: Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 31(1), 24–33. mla: Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics, vol. 31, no. 1, Elsevier, 2015, pp. 24–33, doi:10.1016/j.tig.2014.09.009. short: D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33. date_created: 2018-12-11T11:49:01Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T08:21:16Z day: '01' doi: 10.1016/j.tig.2014.09.009 extern: 1 intvolume: ' 31' issue: '1' month: '01' page: 24 - 33 publication: Trends in Genetics publication_status: published publisher: Elsevier publist_id: '6764' quality_controlled: 0 status: public title: Topological features of rugged fitness landscapes in sequence space type: journal_article volume: 31 year: '2015' ... --- _id: '852' abstract: - lang: eng text: 'Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on howlong the gene copies continue to experience an elevated rate of evolution remain scarce. Standard theory of gene duplications based on some level of genetic redundancy of gene copies predicts that the period of accelerated evolutionmust end relatively quickly. Using a maximum-likelihood approach we estimate preduplication, initial postduplication, and recent postduplication rates of evolution that occurred in themammalian lineage.Wefind that both gene copies experience a similar in magnitude acceleration in their rate of evolution. The copy located in the original genomic position typically returns to the preduplication rates of evolution in a short period of time. The burst of faster evolution of the copy that is located in a new genomic position typically lasts longer. Furthermore, the fast-evolving copies on average continue to evolve faster than the preduplication rates far longer than predicted by standard theory of gene duplications.We hypothesize that the prolonged elevated rates of evolution are determined by functional properties that were acquired during, or soon after, the gene duplication event. ' author: - first_name: Oriol full_name: Rosello, Oriol P last_name: Rosello - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Rosello O, Kondrashov F. Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. 2014;6(8):1949-1955. doi:10.1093/gbe/evu159 apa: Rosello, O., & Kondrashov, F. (2014). Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evu159 chicago: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication.” Genome Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/gbe/evu159. ieee: O. Rosello and F. Kondrashov, “Long-Term asymmetrical acceleration of protein evolution after gene duplication,” Genome Biology and Evolution, vol. 6, no. 8. Oxford University Press, pp. 1949–1955, 2014. ista: Rosello O, Kondrashov F. 2014. Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. 6(8), 1949–1955. mla: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication.” Genome Biology and Evolution, vol. 6, no. 8, Oxford University Press, 2014, pp. 1949–55, doi:10.1093/gbe/evu159. short: O. Rosello, F. Kondrashov, Genome Biology and Evolution 6 (2014) 1949–1955. date_created: 2018-12-11T11:48:51Z date_published: 2014-08-01T00:00:00Z date_updated: 2021-01-12T08:19:51Z day: '01' doi: 10.1093/gbe/evu159 extern: 1 intvolume: ' 6' issue: '8' month: '08' page: 1949 - 1955 publication: Genome Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '6797' quality_controlled: 0 status: public title: Long-Term asymmetrical acceleration of protein evolution after gene duplication tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 6 year: '2014' ... --- _id: '856' abstract: - lang: eng text: The emergence of new genes throughout evolution requires rewiring and extension of regulatory networks. However, the molecular details of how the transcriptional regulation of new gene copies evolves remain largely unexplored. Here we show how duplication of a transcription factor gene allowed the emergence of two independent regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous and could bind different motifs in its target promoters. After duplication, one paralogue evolved increased binding specificity so that it only binds one type of motif, whereas the other copy evolved a decreased activity so that it only activates promoters that contain multiple binding sites. Interestingly, only a few mutations in both the DNA-binding domains and in the promoter binding sites were required to gradually disentangle the two networks. These results reveal how duplication of a promiscuous transcription factor followed by concerted cis and trans mutations allows expansion of a regulatory network. acknowledgement: 'K.P. acknowledges financial support from TRIPLE I and a Belspo mobility grant from the Belgian Federal Science Policy Office co-funded by the Marie Curie Actions from the European Commission. Research in the lab of K.J.V. is supported by ERC Starting Grant 241426, HFSP programme grant RGP0050/2013, VIB, EMBO YIP programme, KU Leuven Programme Financing, FWO, and IWT. A.V. acknowledges RIKEN for the FPR grant. The work of F.A.K. was supported by a grant of the HHMI International Early Career Scientist Programme (grant #55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP programme, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (grant #Sev-2012-0208)’ and (grant #BES-2013-064004) funded by the European Regional Development Fund (ERDF), the European Union and the European Research Council (grant #335980_EinME). K.V. is supported by an FWO postdoctoral fellowship. Funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.' author: - first_name: Ksenia full_name: Pougach, Ksenia S last_name: Pougach - first_name: Arnout full_name: Voet, Arnout R last_name: Voet - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Karin full_name: Voordeckers, Karin last_name: Voordeckers - first_name: Joaquin full_name: Christiaens, Joaquin F last_name: Christiaens - first_name: Bianka full_name: Baying, Bianka last_name: Baying - first_name: Vladimı́R full_name: Bénès, Vladimı́r last_name: Bénès - first_name: Ryo full_name: Sakai, Ryo last_name: Sakai - first_name: Jan full_name: Aerts, Jan A last_name: Aerts - first_name: Bo full_name: Zhu, Bo last_name: Zhu - first_name: Patrick full_name: Van Dijck, Patrick last_name: Van Dijck - first_name: Kevin full_name: Verstrepen, Kevin J last_name: Verstrepen citation: ama: Pougach K, Voet A, Kondrashov F, et al. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. 2014;5. doi:10.1038/ncomms5868 apa: Pougach, K., Voet, A., Kondrashov, F., Voordeckers, K., Christiaens, J., Baying, B., … Verstrepen, K. (2014). Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms5868 chicago: Pougach, Ksenia, Arnout Voet, Fyodor Kondrashov, Karin Voordeckers, Joaquin Christiaens, Bianka Baying, Vladimı́R Bénès, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms5868. ieee: K. Pougach et al., “Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network,” Nature Communications, vol. 5. Nature Publishing Group, 2014. ista: Pougach K, Voet A, Kondrashov F, Voordeckers K, Christiaens J, Baying B, Bénès V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen K. 2014. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. 5. mla: Pougach, Ksenia, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature Communications, vol. 5, Nature Publishing Group, 2014, doi:10.1038/ncomms5868. short: K. Pougach, A. Voet, F. Kondrashov, K. Voordeckers, J. Christiaens, B. Baying, V. Bénès, R. Sakai, J. Aerts, B. Zhu, P. Van Dijck, K. Verstrepen, Nature Communications 5 (2014). date_created: 2018-12-11T11:48:52Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T08:20:01Z day: '01' doi: 10.1038/ncomms5868 extern: 1 intvolume: ' 5' month: '01' publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '6790' quality_controlled: 0 status: public title: Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 5 year: '2014' ... --- _id: '863' abstract: - lang: eng text: The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here we present the draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes, and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes. Our integrative analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis is supported by comparative analysis of multiple gene families, including the apparent absence of HOX genes, canonical microRNA machinery, and reduced immune complement in ctenophores. Although two distinct nervous systems are well recognized in ctenophores, many bilaterian neuron-specific genes and genes of 'classical' neurotransmitter pathways either are absent or, if present, are not expressed in neurons. Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals. acknowledgement: We thank Friday Harbor Laboratories for facilities during animal collection and Marine Genomics apprenticeships (L.L.M., B.J.S.); E. Dabe, G. Winters, J. Netherton, N. Churches and C. Bostwick for help with animal, tissue, in situ, RNA and DNA assays; and X.-X. Tan, F. Lu and T. Tyazelova for sequencing. We thank F. Nivens for videos and P. L. Williams for database support. This work was supported by NSF (NSF-0744649 and NSF CNS-0821622 to L.L.M.; NSF CHE-1111705 to J.V.S.), NIH (1R01GM097502, R01MH097062, R21RR025699 and 5R21DA030118 to L.L.M.; P30 DA018310 to J.V.S.; R01 AG029360 and 1S10RR027052 to E.I.R.), NASA NNX13AJ31G (to K.M.H., L.L.M. and K.M.K.), NSERC 458115 and 211598 (J.P.R.), University of Florida Opportunity Funds/McKnight Brain Research and Florida Biodiversity Institute (L.L.M.), Rostock Inc./A.V. Chikunov (E.I.R.), grant from Russian Federation Government 14.B25.31.0033 (Resolution No.220) (E.I.R.). F.A.K., I.S.P. and R.D. were supported by HHMI (55007424), EMBO and MINECO (BFU2012-31329 and Sev-2012-0208). Contributions of AU Marine Biology Program 117 and Molette laboratory 22. author: - first_name: Leonid full_name: Moroz, Leonid L last_name: Moroz - first_name: Kevin full_name: Kocot, Kevin M last_name: Kocot - first_name: Mathew full_name: Citarella, Mathew R last_name: Citarella - first_name: Sohn full_name: Dosung, Sohn last_name: Dosung - first_name: Tigran full_name: Norekian, Tigran P last_name: Norekian - first_name: Inna full_name: Povolotskaya, Inna last_name: Povolotskaya - first_name: Anastasia full_name: Grigorenko, Anastasia P last_name: Grigorenko - first_name: Christopher full_name: Dailey, Christopher A last_name: Dailey - first_name: Eugene full_name: Berezikov, Eugene last_name: Berezikov - first_name: Katherine full_name: Buckley, Katherine M last_name: Buckley - first_name: Andrey full_name: Ptitsyn, Andrey A last_name: Ptitsyn - first_name: Denis full_name: Reshetov, Denis A last_name: Reshetov - first_name: Krishanu full_name: Mukherjee, Krishanu last_name: Mukherjee - first_name: Tatiana full_name: Moroz, Tatiana P last_name: Moroz - first_name: Yelena full_name: Bobkova, Yelena V last_name: Bobkova - first_name: Fahong full_name: Yu, Fahong last_name: Yu - first_name: Vladimir full_name: Kapitonov, Vladimir V last_name: Kapitonov - first_name: Jerzy full_name: Jurka, Jerzy W last_name: Jurka - first_name: Yuriy full_name: Bobkov, Yuriy V last_name: Bobkov - first_name: Joshua full_name: Swore, Joshua J last_name: Swore - first_name: David full_name: Girardo, David O last_name: Girardo - first_name: Alexander full_name: Fodor, Alexander last_name: Fodor - first_name: Fedor full_name: Gusev, Fedor E last_name: Gusev - first_name: Rachel full_name: Sanford, Rachel S last_name: Sanford - first_name: Rebecca full_name: Bruders, Rebecca last_name: Bruders - first_name: Ellen full_name: Kittler, Ellen L last_name: Kittler - first_name: Claudia full_name: Mills, Claudia E last_name: Mills - first_name: Jonathan full_name: Rast, Jonathan P last_name: Rast - first_name: Romain full_name: Derelle, Romain last_name: Derelle - first_name: Victor full_name: Solovyev, Victor last_name: Solovyev - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Billie full_name: Swalla, Billie J last_name: Swalla - first_name: Jonathan full_name: Sweedler, Jonathan V last_name: Sweedler - first_name: Evgeny full_name: Rogaev, Evgeny I last_name: Rogaev - first_name: Kenneth full_name: Halanych, Kenneth M last_name: Halanych - first_name: Andrea full_name: Kohn, Andrea B last_name: Kohn citation: ama: Moroz L, Kocot K, Citarella M, et al. The ctenophore genome and the evolutionary origins of neural systems. Nature. 2014;510(7503):109-114. doi:10.1038/nature13400 apa: Moroz, L., Kocot, K., Citarella, M., Dosung, S., Norekian, T., Povolotskaya, I., … Kohn, A. (2014). The ctenophore genome and the evolutionary origins of neural systems. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13400 chicago: Moroz, Leonid, Kevin Kocot, Mathew Citarella, Sohn Dosung, Tigran Norekian, Inna Povolotskaya, Anastasia Grigorenko, et al. “The Ctenophore Genome and the Evolutionary Origins of Neural Systems.” Nature. Nature Publishing Group, 2014. https://doi.org/10.1038/nature13400. ieee: L. Moroz et al., “The ctenophore genome and the evolutionary origins of neural systems,” Nature, vol. 510, no. 7503. Nature Publishing Group, pp. 109–114, 2014. ista: Moroz L, Kocot K, Citarella M, Dosung S, Norekian T, Povolotskaya I, Grigorenko A, Dailey C, Berezikov E, Buckley K, Ptitsyn A, Reshetov D, Mukherjee K, Moroz T, Bobkova Y, Yu F, Kapitonov V, Jurka J, Bobkov Y, Swore J, Girardo D, Fodor A, Gusev F, Sanford R, Bruders R, Kittler E, Mills C, Rast J, Derelle R, Solovyev V, Kondrashov F, Swalla B, Sweedler J, Rogaev E, Halanych K, Kohn A. 2014. The ctenophore genome and the evolutionary origins of neural systems. Nature. 510(7503), 109–114. mla: Moroz, Leonid, et al. “The Ctenophore Genome and the Evolutionary Origins of Neural Systems.” Nature, vol. 510, no. 7503, Nature Publishing Group, 2014, pp. 109–14, doi:10.1038/nature13400. short: L. Moroz, K. Kocot, M. Citarella, S. Dosung, T. Norekian, I. Povolotskaya, A. Grigorenko, C. Dailey, E. Berezikov, K. Buckley, A. Ptitsyn, D. Reshetov, K. Mukherjee, T. Moroz, Y. Bobkova, F. Yu, V. Kapitonov, J. Jurka, Y. Bobkov, J. Swore, D. Girardo, A. Fodor, F. Gusev, R. Sanford, R. Bruders, E. Kittler, C. Mills, J. Rast, R. Derelle, V. Solovyev, F. Kondrashov, B. Swalla, J. Sweedler, E. Rogaev, K. Halanych, A. Kohn, Nature 510 (2014) 109–114. date_created: 2018-12-11T11:48:54Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T08:20:21Z day: '01' doi: 10.1038/nature13400 extern: 1 intvolume: ' 510' issue: '7503' license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '01' page: 109 - 114 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6785' quality_controlled: 0 status: public title: The ctenophore genome and the evolutionary origins of neural systems tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article volume: 510 year: '2014' ... --- _id: '865' abstract: - lang: eng text: Research on existing drugs often discovers novel mechanisms of their action and leads to the expansion of their therapeutic scope and subsequent remarketing. The Wnt signaling pathway is of the immediate therapeutic relevance, as it plays critical roles in cancer development and progression. However, drugs which disrupt this pathway are unavailable despite the high demand. Here we report an attempt to identify antagonists of the Wnt-FZD interaction among the library of the FDA-approved drugs. We performed an in silico screening which brought up several potential antagonists of the ligand-receptor interaction. 14 of these substances were tested using the TopFlash luciferase reporter assay and four of them identified as active and specific inhibitors of the Wnt3a-induced signaling. However, further analysis through GTP-binding and β-catenin stabilization assays showed that the compounds do not target the Wnt-FZD pair, but inhibit the signaling at downstream levels. We further describe the previously unknown inhibitory activity of an anti-leprosy drug clofazimine in the Wnt pathway and provide data demonstrating its efficiency in suppressing growth of Wnt-dependent triple-negative breast cancer cells. These data provide a basis for further investigations of the efficiency of clofazimine in treatment of Wnt-dependent cancers. author: - first_name: Alexey full_name: Koval, Alexey V last_name: Koval - first_name: Peter full_name: Vlasov, Peter K last_name: Vlasov - first_name: Polina full_name: Shichkova, Polina last_name: Shichkova - first_name: S full_name: Khunderyakova, S last_name: Khunderyakova - first_name: Yury full_name: Markov, Yury last_name: Markov - first_name: J full_name: Panchenko, J last_name: Panchenko - first_name: A full_name: Volodina, A last_name: Volodina - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Vladimir full_name: Katanaev, Vladimir L last_name: Katanaev citation: ama: Koval A, Vlasov P, Shichkova P, et al. Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochemical Pharmacology. 2014;87(4):571-578. doi:10.1016/j.bcp.2013.12.007 apa: Koval, A., Vlasov, P., Shichkova, P., Khunderyakova, S., Markov, Y., Panchenko, J., … Katanaev, V. (2014). Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochemical Pharmacology. Elsevier. https://doi.org/10.1016/j.bcp.2013.12.007 chicago: Koval, Alexey, Peter Vlasov, Polina Shichkova, S Khunderyakova, Yury Markov, J Panchenko, A Volodina, Fyodor Kondrashov, and Vladimir Katanaev. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” Biochemical Pharmacology. Elsevier, 2014. https://doi.org/10.1016/j.bcp.2013.12.007. ieee: A. Koval et al., “Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling,” Biochemical Pharmacology, vol. 87, no. 4. Elsevier, pp. 571–578, 2014. ista: Koval A, Vlasov P, Shichkova P, Khunderyakova S, Markov Y, Panchenko J, Volodina A, Kondrashov F, Katanaev V. 2014. Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochemical Pharmacology. 87(4), 571–578. mla: Koval, Alexey, et al. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” Biochemical Pharmacology, vol. 87, no. 4, Elsevier, 2014, pp. 571–78, doi:10.1016/j.bcp.2013.12.007. short: A. Koval, P. Vlasov, P. Shichkova, S. Khunderyakova, Y. Markov, J. Panchenko, A. Volodina, F. Kondrashov, V. Katanaev, Biochemical Pharmacology 87 (2014) 571–578. date_created: 2018-12-11T11:48:55Z date_published: 2014-02-15T00:00:00Z date_updated: 2021-01-12T08:20:24Z day: '15' doi: 10.1016/j.bcp.2013.12.007 extern: 1 intvolume: ' 87' issue: '4' month: '02' page: 571 - 578 publication: Biochemical Pharmacology publication_status: published publisher: Elsevier publist_id: '6782' quality_controlled: 0 status: public title: Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling type: journal_article volume: 87 year: '2014' ... --- _id: '845' abstract: - lang: eng text: Recombination between double-stranded DNA molecules is a key genetic process which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs during meiosis between genotypes with 98.0-99.9% sequence identity, because within-population nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable and it is unclear how CO can occur between genotypes with less than 90% sequence identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan basidiomycete mushroom, a frequently encountered decayer of woody substrates. We crossed two haploid individuals, from the United States and from Russia, and obtained genome sequences for their 17 offspring. The average genetic distance between the parents was 14%, making it possible to study CO at very high resolution. We found reduced levels of linkage disequilibrium between loci flanking the CO sites indicating that they are mostly confined to hotspots of recombination. Furthermore, CO events preferentially occurred in regions under stronger negative selection, in particular within exons that showed reduced levels of nucleotide diversity. Apparently, in hypervariable species CO must avoid regions of higher divergence between the recombining genomes due to limitations imposed by the mismatch repair system, with regions under strong negative selection providing the opportunity for recombination. These patterns are opposite to those observed in a number of less variable species indicating that population genomics of hypervariable species may reveal novel biological phenomena. acknowledgement: The authors are grateful to Georgii Bazykin for valuable discussion and to the DNA sequencing facility at Engelhardt Institute of Molecular Biology for Sanger sequencing. This study was supported by the Russian government grant No 11.G34.31.0008 and by Plan Nacional (BFU2012-31329), Howard Hughes Medical Institute International Early Career Scientist Award and EMBO Young Investigator Program, and core funds provided by the University of Michigan. author: - first_name: Vladimir full_name: Seplyarskiy, Vladimir B last_name: Seplyarskiy - first_name: Maria full_name: Logacheva, Maria D last_name: Logacheva - first_name: Aleksey full_name: Penin, Aleksey A last_name: Penin - first_name: Maria full_name: Baranová, Maria A last_name: Baranová - first_name: Evgeny full_name: Leushkin, Evgeny V last_name: Leushkin - first_name: Natalia full_name: Demidenko, Natalia V last_name: Demidenko - first_name: Anna full_name: Klepikova, Anna V last_name: Klepikova - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov - first_name: Timothy full_name: James, Timothy Y last_name: James citation: ama: Seplyarskiy V, Logacheva M, Penin A, et al. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. 2014;31(11):3016-3025. doi:10.1093/molbev/msu242 apa: Seplyarskiy, V., Logacheva, M., Penin, A., Baranová, M., Leushkin, E., Demidenko, N., … James, T. (2014). Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msu242 chicago: Seplyarskiy, Vladimir, Maria Logacheva, Aleksey Penin, Maria Baranová, Evgeny Leushkin, Natalia Demidenko, Anna Klepikova, Fyodor Kondrashov, Alexey Kondrashov, and Timothy James. “Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/msu242. ieee: V. Seplyarskiy et al., “Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity,” Molecular Biology and Evolution, vol. 31, no. 11. Oxford University Press, pp. 3016–3025, 2014. ista: Seplyarskiy V, Logacheva M, Penin A, Baranová M, Leushkin E, Demidenko N, Klepikova A, Kondrashov F, Kondrashov A, James T. 2014. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. 31(11), 3016–3025. mla: Seplyarskiy, Vladimir, et al. “Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution, vol. 31, no. 11, Oxford University Press, 2014, pp. 3016–25, doi:10.1093/molbev/msu242. short: V. Seplyarskiy, M. Logacheva, A. Penin, M. Baranová, E. Leushkin, N. Demidenko, A. Klepikova, F. Kondrashov, A. Kondrashov, T. James, Molecular Biology and Evolution 31 (2014) 3016–3025. date_created: 2018-12-11T11:48:48Z date_published: 2014-11-01T00:00:00Z date_updated: 2021-01-12T08:19:21Z day: '01' doi: 10.1093/molbev/msu242 extern: 1 intvolume: ' 31' issue: '11' month: '11' page: 3016 - 3025 publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '6801' quality_controlled: 0 status: public title: Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 31 year: '2014' ... --- _id: '892' abstract: - lang: eng text: The study of molecular evolution is important because it reveals how protein functions emerge and evolve. Recently, several types of studies indicated that substitutions in molecular evolution occur in a compensatory manner, whereby the occurrence of a substitution depends on the amino acid residues at other sites. However, a molecular or structural basis behind the compensation often remains obscure. Here, we review studies on the interface of structural biology and molecular evolution that revealed novel aspects of compensatory evolution. In many cases structural studies benefit from evolutionary data while structural data often add a functional dimension to the study of molecular evolution. acknowledgement: | The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)’ and (BFU2012-31329), the European Union and the European Research Council grant (335980_EinME), RFBR (13-04-00253a), MCB RAS (01201358029) and MES RK Grants. author: - first_name: Dmitry full_name: Ivankov, Dmitry N last_name: Ivankov - first_name: Alexei full_name: Finkelstein, Alexei V last_name: Finkelstein - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Ivankov D, Finkelstein A, Kondrashov F. A structural perspective of compensatory evolution. Current Opinion in Structural Biology. 2014;26(1):104-112. doi:10.1016/j.sbi.2014.05.004 apa: Ivankov, D., Finkelstein, A., & Kondrashov, F. (2014). A structural perspective of compensatory evolution. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2014.05.004 chicago: Ivankov, Dmitry, Alexei Finkelstein, and Fyodor Kondrashov. “A Structural Perspective of Compensatory Evolution.” Current Opinion in Structural Biology. Elsevier, 2014. https://doi.org/10.1016/j.sbi.2014.05.004. ieee: D. Ivankov, A. Finkelstein, and F. Kondrashov, “A structural perspective of compensatory evolution,” Current Opinion in Structural Biology, vol. 26, no. 1. Elsevier, pp. 104–112, 2014. ista: Ivankov D, Finkelstein A, Kondrashov F. 2014. A structural perspective of compensatory evolution. Current Opinion in Structural Biology. 26(1), 104–112. mla: Ivankov, Dmitry, et al. “A Structural Perspective of Compensatory Evolution.” Current Opinion in Structural Biology, vol. 26, no. 1, Elsevier, 2014, pp. 104–12, doi:10.1016/j.sbi.2014.05.004. short: D. Ivankov, A. Finkelstein, F. Kondrashov, Current Opinion in Structural Biology 26 (2014) 104–112. date_created: 2018-12-11T11:49:03Z date_published: 2014-06-01T00:00:00Z date_updated: 2021-01-12T08:21:21Z day: '01' doi: 10.1016/j.sbi.2014.05.004 extern: 1 intvolume: ' 26' issue: '1' month: '06' page: 104 - 112 publication: Current Opinion in Structural Biology publication_status: published publisher: Elsevier publist_id: '6756' quality_controlled: 0 status: public title: A structural perspective of compensatory evolution tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article volume: 26 year: '2014' ... --- _id: '899' abstract: - lang: eng text: Understanding fitness landscapes, a conceptual depiction of the genotype-to-phenotype relationship, is crucial to many areas of biology. Two aspects of fitness landscapes are the focus of contemporary studies of molecular evolution. First, the local shape of the fitness landscape defined by the contribution of individual alleles to fitness that is independent of all genetic interactions. Second, the global, multidimensional fitness landscape shape determined by how interactions between alleles at different loci change each other’s fitness impact, or epistasis. In explaining the high amino-acid usage (u), we focused on the global shape of the fitness landscape, ignoring the perturbations at individual sites. author: - first_name: Michael full_name: Breen, Michael S last_name: Breen - first_name: Carsten full_name: Kemena, Carsten last_name: Kemena - first_name: Peter full_name: Vlasov, Peter K last_name: Vlasov - first_name: Cédric full_name: Notredame, Cédric last_name: Notredame - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Breen et al. reply. Nature. 2013;497(7451):E2-E3. doi:10.1038/nature12220 apa: Breen, M., Kemena, C., Vlasov, P., Notredame, C., & Kondrashov, F. (2013). Breen et al. reply. Nature. Nature Publishing Group. https://doi.org/10.1038/nature12220 chicago: Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor Kondrashov. “Breen et Al. Reply.” Nature. Nature Publishing Group, 2013. https://doi.org/10.1038/nature12220. ieee: M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Breen et al. reply,” Nature, vol. 497, no. 7451. Nature Publishing Group, pp. E2–E3, 2013. ista: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2013. Breen et al. reply. Nature. 497(7451), E2–E3. mla: Breen, Michael, et al. “Breen et Al. Reply.” Nature, vol. 497, no. 7451, Nature Publishing Group, 2013, pp. E2–3, doi:10.1038/nature12220. short: M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 497 (2013) E2–E3. date_created: 2018-12-11T11:49:05Z date_published: 2013-05-30T00:00:00Z date_updated: 2021-01-12T08:21:40Z day: '30' doi: 10.1038/nature12220 extern: 1 intvolume: ' 497' issue: '7451' month: '05' page: E2 - E3 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6747' quality_controlled: 0 status: public title: Breen et al. reply type: journal_article volume: 497 year: '2013' ... --- _id: '894' abstract: - lang: eng text: 'Background: Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in many birds. Feral pigeons (Columba livia) show two major melanin-based colorations: a red coloration due to pheomelanic pigment and a black coloration due to eumelanic pigment. Furthermore, within each color type, feral pigeons display continuous variation in the amount of melanin pigment present in the feathers, with individuals varying from pure white to a full dark melanic color. Coloration is highly heritable and it has been suggested that it is under natural or sexual selection, or both. Our objective was to investigate whether MC1R allelic variants are associated with plumage color in feral pigeons. Findings. We sequenced 888 bp of the coding sequence of MC1R among pigeons varying both in the type, eumelanin or pheomelanin, and the amount of melanin in their feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution but none of them were associated with a plumage type. It remains possible that non-synonymous substitutions that influence coloration are present in the short MC1R fragment that we did not sequence but this seems unlikely because we analyzed the entire functionally important region of the gene. Conclusions: Our results show that color differences among feral pigeons are probably not attributable to amino acid variation at the MC1R locus. Therefore, variation in regulatory regions of MC1R or variation in other genes may be responsible for the color polymorphism of feral pigeons.' acknowledgement: Romain Derelle was supported by grant from Plan Nacional 004302 BFU2012-31329. Fyodor A Kondrashov was supported by grants HHMI (Howard Hughes Medical Institute) 003803 and EMBO 003691 EUI-EURYIP-2011-4320. author: - first_name: Romain full_name: Derelle, Romain last_name: Derelle - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Vladimir full_name: Arkhipov, Vladimir last_name: Arkhipov - first_name: Hélène full_name: Corbel, Hélène last_name: Corbel - first_name: Adrien full_name: Frantz, Adrien last_name: Frantz - first_name: Julien full_name: Gasparini, Julien last_name: Gasparini - first_name: Lisa full_name: Jacquin, Lisa last_name: Jacquin - first_name: Gwenaël full_name: Jacob, Gwenaël last_name: Jacob - first_name: Sophie full_name: Thibault, Sophie last_name: Thibault - first_name: Emmanuelle full_name: Baudry, Emmanuelle last_name: Baudry citation: ama: Derelle R, Kondrashov F, Arkhipov V, et al. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 2013;6(1). doi:10.1186/1756-0500-6-310 apa: Derelle, R., Kondrashov, F., Arkhipov, V., Corbel, H., Frantz, A., Gasparini, J., … Baudry, E. (2013). Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. BioMed Central. https://doi.org/10.1186/1756-0500-6-310 chicago: Derelle, Romain, Fyodor Kondrashov, Vladimir Arkhipov, Hélène Corbel, Adrien Frantz, Julien Gasparini, Lisa Jacquin, Gwenaël Jacob, Sophie Thibault, and Emmanuelle Baudry. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” BMC Research Notes. BioMed Central, 2013. https://doi.org/10.1186/1756-0500-6-310. ieee: R. Derelle et al., “Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R,” BMC Research Notes, vol. 6, no. 1. BioMed Central, 2013. ista: Derelle R, Kondrashov F, Arkhipov V, Corbel H, Frantz A, Gasparini J, Jacquin L, Jacob G, Thibault S, Baudry E. 2013. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 6(1). mla: Derelle, Romain, et al. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” BMC Research Notes, vol. 6, no. 1, BioMed Central, 2013, doi:10.1186/1756-0500-6-310. short: R. Derelle, F. Kondrashov, V. Arkhipov, H. Corbel, A. Frantz, J. Gasparini, L. Jacquin, G. Jacob, S. Thibault, E. Baudry, BMC Research Notes 6 (2013). date_created: 2018-12-11T11:49:04Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T08:21:25Z day: '01' doi: 10.1186/1756-0500-6-310 extern: '1' intvolume: ' 6' issue: '1' language: - iso: eng month: '01' oa_version: None publication: BMC Research Notes publication_status: published publisher: BioMed Central publist_id: '6752' status: public title: Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2013' ... --- _id: '905' abstract: - lang: eng text: A survey of avifauna was carried out in the Mys Shmidta area, north Chukotka, Russia from 8 June to 12 July 2011. A total of 90 species was recorded in the area, which together with literature data made a final list of 104 species. For several species this area is beyond the northern, north-eastern or north-western limits of their known distribution. We collected new data for 19 globally or locally threatened species. Tundra Swan Cygnus columbianus, Emperor Goose Anser canagica, American Golden Plover Pluvialis dominica, Western Sandpiper Calidris mauri, Semipalmated Sandpiper C. pusilla, Northern House Martin Delichon urbica and Barn Swallow Hirundo rustica were all confirmed to be breeding. Breeding of Brent Goose Branta bernicla nigricans, Spectacled Eider Somateria fischeri and Steller's Eider Polysticta stelleri was judged to be 'very likely'. There was no evidence for breeding of Ross's Gull Rhodostethia rosea despite several records. Two Eurasian Dotterels Eudromias morinellus were recorded displaying for the first time in the area, but the status of the species is unclear. The area is important for Snowy Owl Nyctea scandiaca, and as moulting grounds for Emperor Goose. Canada Goose Branta canadensis, Baikal Teal Anas formosa, Bar-tailed Godwit Limosa lapponica, Slaty-backed Gull Larus schistisagus, Thayer's Gull L. thayeri, Black-headed Gull L. ridibundus, White-tailed Eagle Haliaeetus albicilla, Steller's Sea Eagle H. pelagicus, Osprey Pandion haliaetus, Arctic Warbler Phylloscopus borealis and House Sparrow Passer domesticus are more likely to be rare vagrants or migrants. An observation of a Pine Siskin Carduelis pinus is the first record for Eurasia. acknowledgement: We thank Natalya Kveten and Oksana Makarova, heads of administrations of Mys Shmidta and Ryrkaypiy for hospitality and for help with organising our excursions. Warm thanks too to Pavel Tomkovich for useful comments on local birds and ornithological literature. We are very grateful to The David and Lucile Packard Foundation for the support to Birds Russia’s Spoon-billed Sandpiper conservation programme in 2011 and to Evgeny Syroechkovsky Jr, the leader of the Spoon-billed Sandpiper conservation team in Russia. author: - first_name: Vladimir full_name: Arkhipov, Vladimir Y last_name: Arkhipov - first_name: T full_name: Noah T last_name: Noah - first_name: Steffen full_name: Koschkar, Steffen last_name: Koschkar - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Arkhipov V, Noah T, Koschkar S, Kondrashov F. Birds of Mys Shmidta, north Chukotka, Russia. Forktail. 2013;(29):25-30. apa: Arkhipov, V., Noah, T., Koschkar, S., & Kondrashov, F. (2013). Birds of Mys Shmidta, north Chukotka, Russia. Forktail. Oriental Bird Club. chicago: Arkhipov, Vladimir, T Noah, Steffen Koschkar, and Fyodor Kondrashov. “Birds of Mys Shmidta, North Chukotka, Russia.” Forktail. Oriental Bird Club, 2013. ieee: V. Arkhipov, T. Noah, S. Koschkar, and F. Kondrashov, “Birds of Mys Shmidta, north Chukotka, Russia,” Forktail, no. 29. Oriental Bird Club, pp. 25–30, 2013. ista: Arkhipov V, Noah T, Koschkar S, Kondrashov F. 2013. Birds of Mys Shmidta, north Chukotka, Russia. Forktail. (29), 25–30. mla: Arkhipov, Vladimir, et al. “Birds of Mys Shmidta, North Chukotka, Russia.” Forktail, no. 29, Oriental Bird Club, 2013, pp. 25–30. short: V. Arkhipov, T. Noah, S. Koschkar, F. Kondrashov, Forktail (2013) 25–30. date_created: 2018-12-11T11:49:07Z date_published: 2013-09-01T00:00:00Z date_updated: 2021-01-12T08:21:48Z day: '01' extern: 1 issue: '29' main_file_link: - open_access: '1' url: http://orientalbirdclub.org/forktail29/ month: '09' oa: 1 page: 25 - 30 publication: Forktail publication_status: published publisher: Oriental Bird Club publist_id: '6741' quality_controlled: 0 status: public title: Birds of Mys Shmidta, north Chukotka, Russia type: journal_article year: '2013' ... --- _id: '846' abstract: - lang: eng text: Whether or not evolutionary change is inherently irreversible remains a controversial topic. Some examples of evolutionary irreversibility are known; however, this question has not been comprehensively addressed at the molecular level. Here, we use data from 221 human genes with known pathogenic mutations to estimate the rate of irreversibility in protein evolution. For these genes, we reconstruct ancestral amino acid sequences along the mammalian phylogeny and identify ancestral amino acid states that match known pathogenic mutations. Such cases represent inherent evolutionary irreversibility because, at the present moment, reversals to these ancestral amino acid states are impossible for the human lineage. We estimate that approximately 10% of all amino acid substitutions along the mammalian phylogeny are irreversible, such that a return to the ancestral amino acid state would lead to a pathogenic phenotype. For a subset of 51 genes with high rates of irreversibility, as much as 40% of all amino acid evolution was estimated to be irreversible. Because pathogenic phenotypes do not resemble ancestral phenotypes, the molecular nature of the high rate of irreversibility in proteins is best explained by evolution with a high prevalence of compensatory, epistatic interactions between amino acid sites. Under such mode of protein evolution, once an amino acid substitution is fixed, the probability of its reversal declines as the protein sequence accumulates changes that affect the phenotypic manifestation of the ancestral state. The prevalence of epistasis in evolution indicates that the observed high rate of irreversibility in protein evolution is an inherent property of protein structure and function. acknowledgement: This work was supported by Plan Nacional grant BFU2009-09271 from the Spanish Ministry of Science and Innovation and by FPU (Formación del Profesorado Universitario) program grant AP2008-01888 from the Spanish Ministry of Education to O.S. F.A.K. is a European Molecular Biology Organization Young Investigator and Howard Hughes Medical Institute International Early Career Scientist. author: - first_name: Onuralp full_name: Soylemez, Onuralp last_name: Soylemez - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Soylemez O, Kondrashov F. Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. 2012;4(12):1213-1222. doi:10.1093/gbe/evs096 apa: Soylemez, O., & Kondrashov, F. (2012). Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evs096 chicago: Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility in Protein Evolution.” Genome Biology and Evolution. Oxford University Press, 2012. https://doi.org/10.1093/gbe/evs096. ieee: O. Soylemez and F. Kondrashov, “Estimating the rate of irreversibility in protein evolution,” Genome Biology and Evolution, vol. 4, no. 12. Oxford University Press, pp. 1213–1222, 2012. ista: Soylemez O, Kondrashov F. 2012. Estimating the rate of irreversibility in protein evolution. Genome Biology and Evolution. 4(12), 1213–1222. mla: Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility in Protein Evolution.” Genome Biology and Evolution, vol. 4, no. 12, Oxford University Press, 2012, pp. 1213–22, doi:10.1093/gbe/evs096. short: O. Soylemez, F. Kondrashov, Genome Biology and Evolution 4 (2012) 1213–1222. date_created: 2018-12-11T11:48:49Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T08:19:25Z day: '01' doi: 10.1093/gbe/evs096 extern: 1 intvolume: ' 4' issue: '12' month: '01' page: 1213 - 1222 publication: Genome Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '6802' quality_controlled: 0 status: public title: Estimating the rate of irreversibility in protein evolution tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article volume: 4 year: '2012' ... --- _id: '858' abstract: - lang: eng text: 'ackground: The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of stop codons in bacterial genomes.Results: We show that in bacteria stop codons evolve slower than synonymous sites, suggesting the action of weak negative selection. However, the frequency of stop codons relative to genomic nucleotide content indicated that this selection regime is not straightforward. The frequency of TAA and TGA stop codons is GC-content dependent, with TAA decreasing and TGA increasing with GC-content, while TAG frequency is independent of GC-content. Applying a formal, analytical model to these data we found that the relationship between stop codon frequencies and nucleotide content cannot be explained by mutational biases or selection on nucleotide content. However, with weak nucleotide content-dependent selection on TAG, -0.5 < Nes < 1.5, the model fits all of the data and recapitulates the relationship between TAG and nucleotide content. For biologically plausible rates of mutations we show that, in bacteria, TAG stop codon is universally associated with lower fitness, with TAA being the optimal for G-content < 16% while for G-content > 16% TGA has a higher fitness than TAG.Conclusions: Our data indicate that TAG codon is universally suboptimal in the bacterial lineage, such that TAA is likely to be the preferred stop codon for low GC content while the TGA is the preferred stop codon for high GC content. The optimization of stop codon usage may therefore be useful in genome engineering or gene expression optimization applications.Reviewers: This article was reviewed by Michail Gelfand, Arcady Mushegian and Shamil Sunyaev. For the full reviews, please go to the Reviewers'' Comments section.' acknowledgement: | We thank Elena Alkalaeva and Peter Kolosov for insightful discussion and Brian Charlesworth for a critical reading of our manuscript. The work has been supported by a Plan Nacional grant from the Spanish Ministry of Science and Innovation, EMBO Young Investigator and Howard Hughes Medical Institute International Early Career Scientist awards. author: - first_name: Inna full_name: Povolotskaya, Inna last_name: Povolotskaya - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Alice full_name: Ledda, Alice last_name: Ledda - first_name: Peter full_name: Vlasov, Peter K last_name: Vlasov citation: ama: Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. Stop codons in bacteria are not selectively equivalent. Biology Direct. 2012;7. doi:10.1186/1745-6150-7-30 apa: Povolotskaya, I., Kondrashov, F., Ledda, A., & Vlasov, P. (2012). Stop codons in bacteria are not selectively equivalent. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-7-30 chicago: Povolotskaya, Inna, Fyodor Kondrashov, Alice Ledda, and Peter Vlasov. “Stop Codons in Bacteria Are Not Selectively Equivalent.” Biology Direct. BioMed Central, 2012. https://doi.org/10.1186/1745-6150-7-30. ieee: I. Povolotskaya, F. Kondrashov, A. Ledda, and P. Vlasov, “Stop codons in bacteria are not selectively equivalent,” Biology Direct, vol. 7. BioMed Central, 2012. ista: Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. 2012. Stop codons in bacteria are not selectively equivalent. Biology Direct. 7. mla: Povolotskaya, Inna, et al. “Stop Codons in Bacteria Are Not Selectively Equivalent.” Biology Direct, vol. 7, BioMed Central, 2012, doi:10.1186/1745-6150-7-30. short: I. Povolotskaya, F. Kondrashov, A. Ledda, P. Vlasov, Biology Direct 7 (2012). date_created: 2018-12-11T11:48:52Z date_published: 2012-09-01T00:00:00Z date_updated: 2021-01-12T08:20:08Z day: '01' doi: 10.1186/1745-6150-7-30 extern: 1 intvolume: ' 7' month: '09' publication: Biology Direct publication_status: published publisher: BioMed Central publist_id: '6792' quality_controlled: 0 status: public title: Stop codons in bacteria are not selectively equivalent tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 7 year: '2012' ... --- _id: '900' abstract: - lang: eng text: 'The main forces directing long-term molecular evolution remain obscure. A sizable fraction of amino-acid substitutions seem to be fixed by positive selection, but it is unclear to what degree long-term protein evolution is constrained by epistasis, that is, instances when substitutions that are accepted in one genotype are deleterious in another. Here we obtain a quantitative estimate of the prevalence of epistasis in long-term protein evolution by relating data on amino-acid usage in 14 organelle proteins and 2 nuclear-encoded proteins to their rates of short-term evolution. We studied multiple alignments of at least 1,000 orthologues for each of these 16 proteins from species from a diverse phylogenetic background and found that an average site contained approximately eight different amino acids. Thus, without epistasis an average site should accept two-fifths of all possible amino acids, and the average rate of amino-acid substitutions should therefore be about three-fifths lower than the rate of neutral evolution. However, we found that the measured rate of amino-acid substitution in recent evolution is 20 times lower than the rate of neutral evolution and an order of magnitude lower than that expected in the absence of epistasis. These data indicate that epistasis is pervasive throughout protein evolution: about 90 per cent of all amino-acid substitutions have a neutral or beneficial impact only in the genetic backgrounds in which they occur, and must therefore be deleterious in a different background of other species. Our findings show that most amino-acid substitutions have different fitness effects in different species and that epistasis provides the primary conceptual framework to describe the tempo and mode of long-term protein evolution.' acknowledgement: | The work was supported by Plan Nacional grants from the Spanish Ministry of Science and Innovation, to F.A.K. and C.N. C.K. was supported by the European Union FP7 project Quantomics (KBBE2A222664). F.A.K. is a European Molecular Biology Organization Young Investigator and Howard Hughes Medical Institute International Early Career Scientist. We thank B. Lehner and T. Warnecke for input and a critical reading of the manuscript. author: - first_name: Michael full_name: Breen, Michael S last_name: Breen - first_name: Carsten full_name: Kemena, Carsten last_name: Kemena - first_name: Peter full_name: Vlasov, Peter K last_name: Vlasov - first_name: Cédric full_name: Notredame, Cédric last_name: Notredame - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Epistasis as the primary factor in molecular evolution. Nature. 2012;490(7421):535-538. doi:10.1038/nature11510 apa: Breen, M., Kemena, C., Vlasov, P., Notredame, C., & Kondrashov, F. (2012). Epistasis as the primary factor in molecular evolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11510 chicago: Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor Kondrashov. “Epistasis as the Primary Factor in Molecular Evolution.” Nature. Nature Publishing Group, 2012. https://doi.org/10.1038/nature11510. ieee: M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Epistasis as the primary factor in molecular evolution,” Nature, vol. 490, no. 7421. Nature Publishing Group, pp. 535–538, 2012. ista: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2012. Epistasis as the primary factor in molecular evolution. Nature. 490(7421), 535–538. mla: Breen, Michael, et al. “Epistasis as the Primary Factor in Molecular Evolution.” Nature, vol. 490, no. 7421, Nature Publishing Group, 2012, pp. 535–38, doi:10.1038/nature11510. short: M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 490 (2012) 535–538. date_created: 2018-12-11T11:49:06Z date_published: 2012-10-25T00:00:00Z date_updated: 2021-01-12T08:21:45Z day: '25' doi: 10.1038/nature11510 extern: 1 intvolume: ' 490' issue: '7421' month: '10' page: 535 - 538 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6748' quality_controlled: 0 status: public title: Epistasis as the primary factor in molecular evolution type: journal_article volume: 490 year: '2012' ... --- _id: '887' abstract: - lang: eng text: A subject of extensive study in evolutionary theory has been the issue of how neutral, redundant copies can be maintained in the genome for long periods of time. Concurrently, examples of adaptive gene duplications to various environmental conditions in different species have been described. At this point, it is too early to tell whether or not a substantial fraction of gene copies have initially achieved fixation by positive selection for increased dosage. Nevertheless, enough examples have accumulated in the literature that such a possibility should be considered. Here, I review the recent examples of adaptive gene duplications and make an attempt to draw generalizations on what types of genes may be particularly prone to be selected for under certain environmental conditions. The identification of copy-number variation in ecological field studies of species adapting to stressful or novel environmental conditions may improve our understanding of gene duplications as a mechanism of adaptation and its relevance to the long-term persistence of gene duplications. acknowledgement: The work was supported by a Plan Nacional grant no. BFU2009-09271 from the Spanish Ministry of Science and Innovation. The author is a European Molecular Biology Organization Young Investigator and Howard Hughes Medical Institute International Early Career Scientist. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kondrashov F. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society of London Series B Biological Sciences. 2012;279(1749):5048-5057. doi:10.1098/rspb.2012.1108 apa: Kondrashov, F. (2012). Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2012.1108 chicago: Kondrashov, Fyodor. “Gene Duplication as a Mechanism of Genomic Adaptation to a Changing Environment.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2012. https://doi.org/10.1098/rspb.2012.1108. ieee: F. Kondrashov, “Gene duplication as a mechanism of genomic adaptation to a changing environment,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 279, no. 1749. Royal Society, The, pp. 5048–5057, 2012. ista: Kondrashov F. 2012. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society of London Series B Biological Sciences. 279(1749), 5048–5057. mla: Kondrashov, Fyodor. “Gene Duplication as a Mechanism of Genomic Adaptation to a Changing Environment.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 279, no. 1749, Royal Society, The, 2012, pp. 5048–57, doi:10.1098/rspb.2012.1108. short: F. Kondrashov, Proceedings of the Royal Society of London Series B Biological Sciences 279 (2012) 5048–5057. date_created: 2018-12-11T11:49:01Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T08:21:16Z day: '01' doi: 10.1098/rspb.2012.1108 extern: 1 intvolume: ' 279' issue: '1749' month: '01' page: 5048 - 5057 publication: Proceedings of the Royal Society of London Series B Biological Sciences publication_status: published publisher: Royal Society, The publist_id: '6765' quality_controlled: 0 status: public title: Gene duplication as a mechanism of genomic adaptation to a changing environment tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 279 year: '2012' ... --- _id: '890' abstract: - lang: eng text: Recent discovery of the Large-billed Reed Warbler (Acrocephalus orinus) in museums and in the wild significantly expanded our knowledge of its morphological traits and genetic variability, and revealed new data on geographical distribution of the breeding grounds, migration routes and wintering locations of this species. It is now certain that A. orinus is breeding in Central Asia; however, the precise area of distribution remains unclear. The difficulty in the further study of this species lies in the small number of known specimens, with only 13 currently available in museums, and in the relative uncertainty of the breeding area and habitat of this species. Following morphological and genetic analyses from Svensson, et al, we describe 14 new A. orinus specimens from collections of Zoological Museums of the former USSR from the territory of Central Asian states. All of these specimens were erroneously labeled as Blyth's Reed Warbler (A. dumetorum), which is thought to be a breeding species in these areas. The 14 new A. orinus specimens were collected during breeding season while most of the 85 A. dumetorum specimens from the same area were collected during the migration period. Our data indicate that the Central Asian territory previously attributed as breeding grounds of A. dumetorum is likely to constitute the breeding territory of A. orinus. This rare case of a re-description of the breeding territory of a lost species emphasizes the importance of maintenance of museum collections around the world. If the present data on the breeding grounds of A. orinus are confirmed with field observations and collections, the literature on the biology of A. dumetorum from the southern part of its range may have to be reconsidered. acknowledgement: | The work was supported by the Plan Nacional grant number BFU2009-09271 from the Spanish Ministry of Science and Innovation. We extend our thanks to A.M. Peklo and I.V. Fadeev for granting us access to ornithological collections, to V.S. Shishkin, M.V. Kalyakin, R.D. Kashkarov, O.V. Belyalov and V.M. Loskot for valuable insights and to L. Svensson for extensive feedback on the manuscript. We thank E.I. Rogaev for access to ancient DNA facility. author: - first_name: Evgeniy full_name: Koblik, Evgeniy A last_name: Koblik - first_name: Yaroslav full_name: Red'Kin, Yaroslav A last_name: Red'Kin - first_name: Margarita full_name: Meer, Margarita S last_name: Meer - first_name: Romain full_name: Derelle, Romain last_name: Derelle - first_name: Sofia full_name: Golenkina, Sofia A last_name: Golenkina - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Vladimir full_name: Arkhipov, Vladimir Y last_name: Arkhipov citation: ama: 'Koblik E, Red’Kin Y, Meer M, et al. Acrocephalus orinus: A case of Mistaken identity. PLoS One. 2011;6(4). doi:10.1371/journal.pone.0017716' apa: 'Koblik, E., Red’Kin, Y., Meer, M., Derelle, R., Golenkina, S., Kondrashov, F., & Arkhipov, V. (2011). Acrocephalus orinus: A case of Mistaken identity. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0017716' chicago: 'Koblik, Evgeniy, Yaroslav Red’Kin, Margarita Meer, Romain Derelle, Sofia Golenkina, Fyodor Kondrashov, and Vladimir Arkhipov. “Acrocephalus Orinus: A Case of Mistaken Identity.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0017716.' ieee: 'E. Koblik et al., “Acrocephalus orinus: A case of Mistaken identity,” PLoS One, vol. 6, no. 4. Public Library of Science, 2011.' ista: 'Koblik E, Red’Kin Y, Meer M, Derelle R, Golenkina S, Kondrashov F, Arkhipov V. 2011. Acrocephalus orinus: A case of Mistaken identity. PLoS One. 6(4).' mla: 'Koblik, Evgeniy, et al. “Acrocephalus Orinus: A Case of Mistaken Identity.” PLoS One, vol. 6, no. 4, Public Library of Science, 2011, doi:10.1371/journal.pone.0017716.' short: E. Koblik, Y. Red’Kin, M. Meer, R. Derelle, S. Golenkina, F. Kondrashov, V. Arkhipov, PLoS One 6 (2011). date_created: 2018-12-11T11:49:02Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T08:21:18Z day: '01' doi: 10.1371/journal.pone.0017716 extern: 1 intvolume: ' 6' issue: '4' month: '01' publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '6760' quality_controlled: 0 status: public title: 'Acrocephalus orinus: A case of Mistaken identity' type: journal_article volume: 6 year: '2011' ... --- _id: '881' author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: 'Kondrashov F. Gene Dosage and Duplication. In: Evolution after Gene Duplication. Wiley-Blackwell; 2011:57-76. doi:10.1002/9780470619902.ch4' apa: Kondrashov, F. (2011). Gene Dosage and Duplication. In Evolution after Gene Duplication (pp. 57–76). Wiley-Blackwell. https://doi.org/10.1002/9780470619902.ch4 chicago: Kondrashov, Fyodor. “Gene Dosage and Duplication.” In Evolution after Gene Duplication, 57–76. Wiley-Blackwell, 2011. https://doi.org/10.1002/9780470619902.ch4. ieee: F. Kondrashov, “Gene Dosage and Duplication,” in Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76. ista: 'Kondrashov F. 2011.Gene Dosage and Duplication. In: Evolution after Gene Duplication. , 57–76.' mla: Kondrashov, Fyodor. “Gene Dosage and Duplication.” Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76, doi:10.1002/9780470619902.ch4. short: F. Kondrashov, in:, Evolution after Gene Duplication, Wiley-Blackwell, 2011, pp. 57–76. date_created: 2018-12-11T11:49:00Z date_published: 2011-03-14T00:00:00Z date_updated: 2021-01-12T08:21:08Z day: '14' doi: 10.1002/9780470619902.ch4 extern: 1 month: '03' page: 57 - 76 publication: Evolution after Gene Duplication publication_status: published publisher: Wiley-Blackwell publist_id: '6766' quality_controlled: 0 status: public title: Gene Dosage and Duplication type: book_chapter year: '2011' ... --- _id: '891' abstract: - lang: eng text: Gene duplications and their subsequent divergence play an important part in the evolution of novel gene functions. Several models for the emergence, maintenance and evolution of gene copies have been proposed. However, a clear consensus on how gene duplications are fixed and maintained in genomes is lacking. Here, we present a comprehensive classification of the models that are relevant to all stages of the evolution of gene duplications. Each model predicts a unique combination of evolutionary dynamics and functional properties. Setting out these predictions is an important step towards identifying the main mechanisms that are involved in the evolution of gene duplications. acknowledgement: | We thank M. Lynch for insightful comments on the manuscript. author: - first_name: Hideki full_name: Innan, Hideki last_name: Innan - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: 'Innan H, Kondrashov F. The evolution of gene duplications: Classifying and distinguishing between models. Nature Reviews Genetics. 2010;11(2):97-108. doi:10.1038/nrg2689' apa: 'Innan, H., & Kondrashov, F. (2010). The evolution of gene duplications: Classifying and distinguishing between models. Nature Reviews Genetics. Nature Publishing Group. https://doi.org/10.1038/nrg2689' chicago: 'Innan, Hideki, and Fyodor Kondrashov. “The Evolution of Gene Duplications: Classifying and Distinguishing between Models.” Nature Reviews Genetics. Nature Publishing Group, 2010. https://doi.org/10.1038/nrg2689.' ieee: 'H. Innan and F. Kondrashov, “The evolution of gene duplications: Classifying and distinguishing between models,” Nature Reviews Genetics, vol. 11, no. 2. Nature Publishing Group, pp. 97–108, 2010.' ista: 'Innan H, Kondrashov F. 2010. The evolution of gene duplications: Classifying and distinguishing between models. Nature Reviews Genetics. 11(2), 97–108.' mla: 'Innan, Hideki, and Fyodor Kondrashov. “The Evolution of Gene Duplications: Classifying and Distinguishing between Models.” Nature Reviews Genetics, vol. 11, no. 2, Nature Publishing Group, 2010, pp. 97–108, doi:10.1038/nrg2689.' short: H. Innan, F. Kondrashov, Nature Reviews Genetics 11 (2010) 97–108. date_created: 2018-12-11T11:49:03Z date_published: 2010-02-01T00:00:00Z date_updated: 2021-01-12T08:21:19Z day: '01' doi: 10.1038/nrg2689 extern: 1 intvolume: ' 11' issue: '2' month: '02' page: 97 - 108 publication: Nature Reviews Genetics publication_status: published publisher: Nature Publishing Group publist_id: '6755' quality_controlled: 0 status: public title: 'The evolution of gene duplications: Classifying and distinguishing between models' type: journal_article volume: 11 year: '2010' ... --- _id: '901' abstract: - lang: eng text: 'Background: Surveying deleterious variation in human populations is crucial for our understanding, diagnosis and potential treatment of human genetic pathologies. A number of recent genome-wide analyses focused on the prevalence of segregating deleterious alleles in the nuclear genome. However, such studies have not been conducted for the mitochondrial genome.Results: We present a systematic survey of polymorphisms in the human mitochondrial genome, including those predicted to be deleterious and those that correspond to known pathogenic mutations. Analyzing 4458 completely sequenced mitochondrial genomes we characterize the genetic diversity of different types of single nucleotide polymorphisms (SNPs) in African (L haplotypes) and non-African (M and N haplotypes) populations. We find that the overall level of polymorphism is higher in the mitochondrial compared to the nuclear genome, although the mitochondrial genome appears to be under stronger selection as indicated by proportionally fewer nonsynonymous than synonymous substitutions. The African mitochondrial genomes show higher heterozygosity, a greater number of polymorphic sites and higher frequencies of polymorphisms for synonymous, benign and damaging polymorphism than non-African genomes. However, African genomes carry significantly fewer SNPs that have been previously characterized as pathogenic compared to non-African genomes.Conclusions: Finding SNPs classified as pathogenic to be the only category of polymorphisms that are more abundant in non-African genomes is best explained by a systematic ascertainment bias that favours the discovery of pathogenic polymorphisms segregating in non-African populations. This further suggests that, contrary to the common disease-common variant hypothesis, pathogenic mutations are largely population-specific and different SNPs may be associated with the same disease in different populations. Therefore, to obtain a comprehensive picture of the deleterious variability in the human population, as well as to improve the diagnostics of individuals carrying African mitochondrial haplotypes, it is necessary to survey different populations independently.Reviewers: This article was reviewed by Dr Mikhail Gelfand, Dr Vasily Ramensky (nominated by Dr Eugene Koonin) and Dr David Rand (nominated by Dr Laurence Hurst).' acknowledgement: We thank Ivan Adzhubei and Shamil Sunyaev for extensive assistance with PolyPhen 2 and insightful discussion. We thank the Spanish Ministry of Science and Innovation, Plan Nacional Program grant BFU2009-09271 for funding. author: - first_name: Michael full_name: Breen, Michael S last_name: Breen - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Breen M, Kondrashov F. Mitochondrial pathogenic mutations are population-specific. Biology Direct. 2010;5. doi:10.1186/1745-6150-5-68 apa: Breen, M., & Kondrashov, F. (2010). Mitochondrial pathogenic mutations are population-specific. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-5-68 chicago: Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations Are Population-Specific.” Biology Direct. BioMed Central, 2010. https://doi.org/10.1186/1745-6150-5-68. ieee: M. Breen and F. Kondrashov, “Mitochondrial pathogenic mutations are population-specific,” Biology Direct, vol. 5. BioMed Central, 2010. ista: Breen M, Kondrashov F. 2010. Mitochondrial pathogenic mutations are population-specific. Biology Direct. 5. mla: Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations Are Population-Specific.” Biology Direct, vol. 5, BioMed Central, 2010, doi:10.1186/1745-6150-5-68. short: M. Breen, F. Kondrashov, Biology Direct 5 (2010). date_created: 2018-12-11T11:49:06Z date_published: 2010-12-31T00:00:00Z date_updated: 2021-01-12T08:21:46Z day: '31' doi: 10.1186/1745-6150-5-68 extern: 1 intvolume: ' 5' month: '12' publication: Biology Direct publication_status: published publisher: BioMed Central publist_id: '6749' quality_controlled: 0 status: public title: Mitochondrial pathogenic mutations are population-specific tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 5 year: '2010' ... --- _id: '857' abstract: - lang: eng text: 'The need to maintain the structural and functional integrity of an evolving protein severely restricts the repertoire of acceptable amino-acid substitutions. However, it is not known whether these restrictions impose a global limit on how far homologous protein sequences can diverge from each other. Here we explore the limits of protein evolution using sequence divergence data. We formulate a computational approach to study the rate of divergence of distant protein sequences and measure this rate for ancient proteins, those that were present in the last universal common ancestor. We show that ancient proteins are still diverging from each other, indicating an ongoing expansion of the protein sequence universe. The slow rate of this divergence is imposed by the sparseness of functional protein sequences in sequence space and the ruggedness of the protein fitness landscape: 98 per cent of sites cannot accept an amino-acid substitution at any given moment but a vast majority of all sites may eventually be permitted to evolve when other, compensatory, changes occur. Thus, 3.5 × 10 9 yr has not been enough to reach the limit of divergent evolution of proteins, and for most proteins the limit of sequence similarity imposed by common function may not exceed that of random sequences.' acknowledgement: | We thank E. Koonin, Y. Wolf, A. Lobkovsky, D. Petrov, D. Ivankov, J. Sharpe, B. Lehner, Y. Jaeger, P. Vlasov, M. Ptitsyn and M. Roytberg for discussions and A. Kondrashov for extensive feedback on our manuscript. We thank D. Tawfik for inspiring us to start the investigation of the functional limits in sequence space. author: - first_name: Inna full_name: Povolotskaya, Inna last_name: Povolotskaya - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Povolotskaya I, Kondrashov F. Sequence space and the ongoing expansion of the protein universe. Nature. 2010;465(7300):922-926. doi:10.1038/nature09105 apa: Povolotskaya, I., & Kondrashov, F. (2010). Sequence space and the ongoing expansion of the protein universe. Nature. Nature Publishing Group. https://doi.org/10.1038/nature09105 chicago: Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing Expansion of the Protein Universe.” Nature. Nature Publishing Group, 2010. https://doi.org/10.1038/nature09105. ieee: I. Povolotskaya and F. Kondrashov, “Sequence space and the ongoing expansion of the protein universe,” Nature, vol. 465, no. 7300. Nature Publishing Group, pp. 922–926, 2010. ista: Povolotskaya I, Kondrashov F. 2010. Sequence space and the ongoing expansion of the protein universe. Nature. 465(7300), 922–926. mla: Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing Expansion of the Protein Universe.” Nature, vol. 465, no. 7300, Nature Publishing Group, 2010, pp. 922–26, doi:10.1038/nature09105. short: I. Povolotskaya, F. Kondrashov, Nature 465 (2010) 922–926. date_created: 2018-12-11T11:48:52Z date_published: 2010-06-17T00:00:00Z date_updated: 2021-01-12T08:20:05Z day: '17' doi: 10.1038/nature09105 extern: 1 intvolume: ' 465' issue: '7300' month: '06' page: 922 - 926 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6791' quality_controlled: 0 status: public title: Sequence space and the ongoing expansion of the protein universe type: journal_article volume: 465 year: '2010' ... --- _id: '862' abstract: - lang: eng text: A long-standing controversy in evolutionary biology is whether or not evolving lineages can cross valleys on the fitness landscape that correspond to low-fitness genotypes, which can eventually enable them to reach isolated fitness peaks1-9. Here we study the fitness landscapes traversed by switches between different AU and GC Watson-Crick nucleotide pairs at complementary sites of mitochondrial transfer RNA stem regions in 83 mammalian species. We find that such Watson-Crick switches occur 30-40 times more slowly than pairs of neutral substitutions, and that alleles corresponding to GU and AC non-Watson-Crick intermediate states segregate within human populations at low frequencies, similar to those of non-synonymous alleles. Substitutions leading to a Watson-Crick switch are strongly correlated, especially in mitochondrial tRNAs encoded on the GT-nucleotide-rich strand of the mitochondrial genome. Using these data we estimate that a typical Watson-Crick switch involves crossing a fitness valley of a depth of about 10-3 or even about 10-2, with AC intermediates being slightly more deleterious than GU intermediates. This compensatory evolution must proceed through rare intermediate variants that never reach fixation. The ubiquitous nature of compensatory evolution in mammalian mitochondrial tRNAs and other molecules implies that simultaneous fixation of two alleles that are individually deleterious may be a common phenomenon at the molecular level. acknowledgement: We thank H. Innan, M. Laessig, R. Guigo, I. Povolotskaya, D. Ivankov and M. Breen for thoughtful discussions and critical reading of the manuscript. author: - first_name: Margarita full_name: Meer, Margarita V last_name: Meer - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov - first_name: Yael full_name: Artzy-Randrup, Yael last_name: Artzy Randrup - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Meer M, Kondrashov A, Artzy Randrup Y, Kondrashov F. Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature. 2010;464(7286):279-282. doi:10.1038/nature08691 apa: Meer, M., Kondrashov, A., Artzy Randrup, Y., & Kondrashov, F. (2010). Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature. Nature Publishing Group. https://doi.org/10.1038/nature08691 chicago: Meer, Margarita, Alexey Kondrashov, Yael Artzy Randrup, and Fyodor Kondrashov. “Compensatory Evolution in Mitochondrial TRNAs Navigates Valleys of Low Fitness.” Nature. Nature Publishing Group, 2010. https://doi.org/10.1038/nature08691. ieee: M. Meer, A. Kondrashov, Y. Artzy Randrup, and F. Kondrashov, “Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness,” Nature, vol. 464, no. 7286. Nature Publishing Group, pp. 279–282, 2010. ista: Meer M, Kondrashov A, Artzy Randrup Y, Kondrashov F. 2010. Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature. 464(7286), 279–282. mla: Meer, Margarita, et al. “Compensatory Evolution in Mitochondrial TRNAs Navigates Valleys of Low Fitness.” Nature, vol. 464, no. 7286, Nature Publishing Group, 2010, pp. 279–82, doi:10.1038/nature08691. short: M. Meer, A. Kondrashov, Y. Artzy Randrup, F. Kondrashov, Nature 464 (2010) 279–282. date_created: 2018-12-11T11:48:54Z date_published: 2010-03-11T00:00:00Z date_updated: 2021-01-12T08:20:20Z day: '11' doi: 10.1038/nature08691 extern: 1 intvolume: ' 464' issue: '7286' month: '03' page: 279 - 282 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6784' quality_controlled: 0 status: public title: Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness type: journal_article volume: 464 year: '2010' ... --- _id: '872' abstract: - lang: eng text: The rate of spontaneous mutation in natural populations is a fundamental parameter for many evolutionary phenomena. Because the rate of mutation is generally low, most of what is currently known about mutation has been obtained through indirect, complex and imprecise methodological approaches. However, in the past few years genome-wide sequencing of closely related individuals has made it possible to estimate the rates of mutation directly at the level of the DNA, avoiding most of the problems associated with using indirect methods. Here, we review the methods used in the past with an emphasis on next generation sequencing, which may soon make the accurate measurement of spontaneous mutation rates a matter of routine. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov citation: ama: Kondrashov F, Kondrashov A. Measurements of spontaneous rates of mutations in the recent past and the near future. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2010;365(1544):1169-1176. doi:10.1098/rstb.2009.0286 apa: Kondrashov, F., & Kondrashov, A. (2010). Measurements of spontaneous rates of mutations in the recent past and the near future. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The. https://doi.org/10.1098/rstb.2009.0286 chicago: Kondrashov, Fyodor, and Alexey Kondrashov. “Measurements of Spontaneous Rates of Mutations in the Recent Past and the near Future.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The, 2010. https://doi.org/10.1098/rstb.2009.0286. ieee: F. Kondrashov and A. Kondrashov, “Measurements of spontaneous rates of mutations in the recent past and the near future,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544. Royal Society, The, pp. 1169–1176, 2010. ista: Kondrashov F, Kondrashov A. 2010. Measurements of spontaneous rates of mutations in the recent past and the near future. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544), 1169–1176. mla: Kondrashov, Fyodor, and Alexey Kondrashov. “Measurements of Spontaneous Rates of Mutations in the Recent Past and the near Future.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544, Royal Society, The, 2010, pp. 1169–76, doi:10.1098/rstb.2009.0286. short: F. Kondrashov, A. Kondrashov, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1169–1176. date_created: 2018-12-11T11:48:57Z date_published: 2010-04-27T00:00:00Z date_updated: 2021-01-12T08:20:43Z day: '27' doi: 10.1098/rstb.2009.0286 extern: 1 intvolume: ' 365' issue: '1544' month: '04' page: 1169 - 1176 publication: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences publication_status: published publisher: Royal Society, The publist_id: '6772' quality_controlled: 0 status: public title: Measurements of spontaneous rates of mutations in the recent past and the near future type: journal_article volume: 365 year: '2010' ... --- _id: '884' abstract: - lang: eng text: 'Background: Divergence of two independently evolving sequences that originated from a common ancestor can be described by two parameters, the asymptotic level of divergence E and the rate r at which this level of divergence is approached. Constant negative selection impedes allele replacements and, therefore, is routinely assumed to decelerate sequence divergence. However, its impact on E and on r has not been formally investigated.Results: Strong selection that favors only one allele can make E arbitrarily small and r arbitrarily large. In contrast, in the case of 4 possible alleles and equal mutation rates, the lowest value of r, attained when two alleles confer equal fitnesses and the other two are strongly deleterious, is only two times lower than its value under selective neutrality.Conclusions: Constant selection can strongly constrain the level of sequence divergence, but cannot reduce substantially the rate at which this level is approached. In particular, under any constant selection the divergence of sequences that accumulated one substitution per neutral site since their origin from the common ancestor must already constitute at least one half of the asymptotic divergence at sites under such selection.Reviewers: This article was reviewed by Drs. Nicolas Galtier, Sergei Maslov, and Nick Grishin.' author: - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov - first_name: Inna full_name: Povolotskaya, Inna last_name: Povolotskaya - first_name: Dmitry full_name: Ivankov, Dmitry N last_name: Ivankov - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. Rate of sequence divergence under constant selection. Biology Direct. 2010;5. doi:10.1186/1745-6150-5-5 apa: Kondrashov, A., Povolotskaya, I., Ivankov, D., & Kondrashov, F. (2010). Rate of sequence divergence under constant selection. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-5-5 chicago: Kondrashov, Alexey, Inna Povolotskaya, Dmitry Ivankov, and Fyodor Kondrashov. “Rate of Sequence Divergence under Constant Selection.” Biology Direct. BioMed Central, 2010. https://doi.org/10.1186/1745-6150-5-5. ieee: A. Kondrashov, I. Povolotskaya, D. Ivankov, and F. Kondrashov, “Rate of sequence divergence under constant selection,” Biology Direct, vol. 5. BioMed Central, 2010. ista: Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. 2010. Rate of sequence divergence under constant selection. Biology Direct. 5. mla: Kondrashov, Alexey, et al. “Rate of Sequence Divergence under Constant Selection.” Biology Direct, vol. 5, BioMed Central, 2010, doi:10.1186/1745-6150-5-5. short: A. Kondrashov, I. Povolotskaya, D. Ivankov, F. Kondrashov, Biology Direct 5 (2010). date_created: 2018-12-11T11:49:00Z date_published: 2010-01-21T00:00:00Z date_updated: 2021-01-12T08:21:15Z day: '21' doi: 10.1186/1745-6150-5-5 extern: 1 intvolume: ' 5' month: '01' publication: Biology Direct publication_status: published publisher: BioMed Central publist_id: '6762' quality_controlled: 0 status: public title: Rate of sequence divergence under constant selection tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 5 year: '2010' ... --- _id: '908' abstract: - lang: eng text: Although some data link archaeal and eukaryotic translation, the overall mechanism of protein synthesis in archaea remains largely obscure. Both archaeal (aRF1) and eukaryotic (eRF1) single release factors recognize all three stop codons. The archaeal genus Methanosarcinaceae contains two aRF1 homologs, and also uses the UAG stop to encode the 22nd amino acid, pyrrolysine. Here we provide an analysis of the last stage of archaeal translation in pyrrolysine-utilizing species. We demonstrated that only one of two Methanosarcina barkeri aRF1 homologs possesses activity and recognizes all three stop codons. The second aRF1 homolog may have another unknown function. The mechanism of pyrrolysine incorporation in the Methanosarcinaceae is discussed. acknowledgement: We are grateful to Andrey Poltaraus and his colleagues for sequencing a/eRF1 genes. We thank Tatyana Pestova and Chris Hellen for the gift of plasmids encoding initiation factors eIF1, eIF1A, eIF4A, eIF4B, eIF4G, eIF5, eIF5B, and Anna Yaremchuk and Michael Tukalo for M. jannaschii aRF1. This work was supported by grants from the Presidium of the (Program Molecular and Cell Biology), the Russian Foundation for Basic Research (08-04-01091-а to E.A. and 08-04-00375a to L.F.), the National Institute for General Medical Sciences (to D.S.), the National Science Foundation (to D.S.) and the Office of Basic Energy Sciences, DOE (to D.S.). author: - first_name: Elena full_name: Alkalaeva, Elena Z last_name: Alkalaeva - first_name: Boris full_name: Eliseev, Boris D last_name: Eliseev - first_name: Alexandre full_name: Ambrogelly, Alexandre last_name: Ambrogelly - first_name: Peter full_name: Vlasov, Peter K last_name: Vlasov - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Sarath full_name: Gundllapalli, Sarath B last_name: Gundllapalli - first_name: Ludmila full_name: Frolova, Ludmila Y last_name: Frolova - first_name: Dieter full_name: Söll, Dieter G last_name: Söll - first_name: Lev full_name: Kisselev, Lev L last_name: Kisselev citation: ama: Alkalaeva E, Eliseev B, Ambrogelly A, et al. Translation termination in pyrrolysine-utilizing archaea. FEBS Letters. 2009;583(21):3455-3460. doi:10.1016/j.febslet.2009.09.044 apa: Alkalaeva, E., Eliseev, B., Ambrogelly, A., Vlasov, P., Kondrashov, F., Gundllapalli, S., … Kisselev, L. (2009). Translation termination in pyrrolysine-utilizing archaea. FEBS Letters. Elsevier. https://doi.org/10.1016/j.febslet.2009.09.044 chicago: Alkalaeva, Elena, Boris Eliseev, Alexandre Ambrogelly, Peter Vlasov, Fyodor Kondrashov, Sarath Gundllapalli, Ludmila Frolova, Dieter Söll, and Lev Kisselev. “Translation Termination in Pyrrolysine-Utilizing Archaea.” FEBS Letters. Elsevier, 2009. https://doi.org/10.1016/j.febslet.2009.09.044. ieee: E. Alkalaeva et al., “Translation termination in pyrrolysine-utilizing archaea,” FEBS Letters, vol. 583, no. 21. Elsevier, pp. 3455–3460, 2009. ista: Alkalaeva E, Eliseev B, Ambrogelly A, Vlasov P, Kondrashov F, Gundllapalli S, Frolova L, Söll D, Kisselev L. 2009. Translation termination in pyrrolysine-utilizing archaea. FEBS Letters. 583(21), 3455–3460. mla: Alkalaeva, Elena, et al. “Translation Termination in Pyrrolysine-Utilizing Archaea.” FEBS Letters, vol. 583, no. 21, Elsevier, 2009, pp. 3455–60, doi:10.1016/j.febslet.2009.09.044. short: E. Alkalaeva, B. Eliseev, A. Ambrogelly, P. Vlasov, F. Kondrashov, S. Gundllapalli, L. Frolova, D. Söll, L. Kisselev, FEBS Letters 583 (2009) 3455–3460. date_created: 2018-12-11T11:49:08Z date_published: 2009-11-03T00:00:00Z date_updated: 2021-01-12T08:21:49Z day: '03' doi: 10.1016/j.febslet.2009.09.044 extern: 1 intvolume: ' 583' issue: '21' month: '11' page: 3455 - 3460 publication: FEBS Letters publication_status: published publisher: Elsevier publist_id: '6740' quality_controlled: 0 status: public title: Translation termination in pyrrolysine-utilizing archaea type: journal_article volume: 583 year: '2009' ... --- _id: '844' abstract: - lang: eng text: Mutation rate varies greatly between nucleotide sites of the human genome and depends both on the global genomic location and the local sequence context of a site. In particular, CpG context elevates the mutation rate by an order of magnitude. Mutations also vary widely in their effect on the molecular function, phenotype, and fitness. Independence of the probability of occurrence of a new mutation's effect has been a fundamental premise in genetics. However, highly mutable contexts may be preserved by negative selection at important sites but destroyed by mutation at sites under no selection. Thus, there may be a positive correlation between the rate of mutations at a nucleotide site and the magnitude of their effect on fitness. We studied the impact of CpG context on the rate of human-chimpanzee divergence and on intrahuman nucleotide diversity at non-synonymous coding sites. We compared nucleotides that occupy identical positions within codons of identical amino acids and only differ by being within versus outside CpG context. Nucleotides within CpG context are under a stronger negative selection, as revealed by their lower, proportionally to the mutation rate, rate of evolution and nucleotide diversity. In particular, the probability of fixation of a non-synonymous transition at a CpG site is two times lower than at a CpG site. Thus, sites with different mutation rates are not necessarily selectively equivalent. This suggests that the mutation rate may complement sequence conservation as a characteristic predictive of functional importance of nucleotide sites. acknowledgement: This work was supported in part by NIH grants R01 GM078598 and U54 LM008748. author: - first_name: Steffen full_name: Schmidt, Steffen last_name: Schmidt - first_name: Anna full_name: Gerasimova, Anna last_name: Gerasimova - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Ivan full_name: Adzuhbei, Ivan A last_name: Adzuhbei - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov - first_name: Shamil full_name: Sunyaev, Shamil R last_name: Sunyaev citation: ama: Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S. Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genetics. 2008;4(11). doi:10.1371/journal.pgen.1000281 apa: Schmidt, S., Gerasimova, A., Kondrashov, F., Adzuhbei, I., Kondrashov, A., & Sunyaev, S. (2008). Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1000281 chicago: Schmidt, Steffen, Anna Gerasimova, Fyodor Kondrashov, Ivan Adzuhbei, Alexey Kondrashov, and Shamil Sunyaev. “Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection.” PLoS Genetics. Public Library of Science, 2008. https://doi.org/10.1371/journal.pgen.1000281. ieee: S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, and S. Sunyaev, “Hypermutable non-synonymous sites are under stronger negative selection,” PLoS Genetics, vol. 4, no. 11. Public Library of Science, 2008. ista: Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S. 2008. Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genetics. 4(11). mla: Schmidt, Steffen, et al. “Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection.” PLoS Genetics, vol. 4, no. 11, Public Library of Science, 2008, doi:10.1371/journal.pgen.1000281. short: S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, S. Sunyaev, PLoS Genetics 4 (2008). date_created: 2018-12-11T11:48:48Z date_published: 2008-11-01T00:00:00Z date_updated: 2021-01-12T08:19:16Z day: '01' doi: 10.1371/journal.pgen.1000281 extern: 1 intvolume: ' 4' issue: '11' month: '11' publication: PLoS Genetics publication_status: published publisher: Public Library of Science publist_id: '6800' quality_controlled: 0 status: public title: Hypermutable non-synonymous sites are under stronger negative selection tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 4 year: '2008' ... --- _id: '895' abstract: - lang: eng text: Background. The arginine vasopressin V1a receptor (V1aR) modulates social cognition and behavior in a wide variety of species. Variation in a repetitive microsatellite element in the 5′ flanking region of the V1aR gene (AVPR1A) in rodents has been associated with variation in brain V1aR expression and in social behavior. In humans, the 5′ flanking region of AVPR1A contains a tandem duplication of two ∼350 bp, microsatellite-containing elements located approximately 3.5 kb upstream of the transcription start site. The first block, referred to as DupA, contains a polymorphic (GT) 25microsatellite; the second block, DupB, has a complex (CT) 4-(TT)-(CT)8-(GT)24polymorphic motif, known as RS3. Polymorphisms in RS3 have been associated with variation in sociobehavioral traits in humans, including autism spectrum disorders. Thus, evolution of these regions may have contributed to variation in social behavior in primates. We examined the structure of these regions in six ape, six monkey, and one prosimian species. Results. Both tandem repeat blocks are present upstream of the AVPR1A coding region in five of the ape species we investigated, while monkeys have only one copy of this region. As in humans, the microsatellites within DupA and DupB are polymorphic in many primate species. Furthermore, both single (lacking DupB) and duplicated alleles (containing both DupA and DupB) are present in chimpanzee (Pan troglodytes) populations with allele frequencies of 0.795 and 0.205 for the single and duplicated alleles, respectively, based on the analysis of 47 wild-caught individuals. Finally, a phylogenetic reconstruction suggests two alternate evolutionary histories for this locus. Conclusion. There is no obvious relationship between the presence of the RS3 duplication and social organization in primates. However, polymorphisms identified in some species may be useful in future genetic association studies. In particular, the presence of both single and duplicated alleles in chimpanzees provides a unique opportunity to assess the functional role of this duplication in contributing to variation in social behavior in primates. While our initial studies show no signs of directional selection on this locus in chimps, pharmacological and genetic association studies support a potential role for this region in influencing V1aR expression and social behavior. acknowledgement: | We thank the caretakers at Zoo Atlanta and Yerkes National Primate Center for help with procuring specimens. Additional DNA samples were supplied by Bill Hopkins, Emory University (chimpanzee), Allyson Bennet, Wake Forest University (chimpanzee, rhesus macaque, bonnet macaque), Mar Sanchez, Emory University (rhesus macaque), and Anne Yoder, Duke University (galago). Susan Lambeth, M.D. Anderson Cancer Center, and Katie Chace, Yerkes National Primate Center, helped provide records regarding the origins of wild born chimps at these centers. We would like to thank Dr Lisa McGraw and two anonymous reviewers for their com- ments on this manuscript. This work was supported by NSF IBN-9876754, NIH RR00165, NIMH56897 (LJY), MH64692 (LJY) and a Howard Hughes Predoctoral Fellowship (ZRD). author: - first_name: Zoe full_name: Donaldson, Zoe R last_name: Donaldson - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Andrea full_name: Putnam, Andrea S last_name: Putnam - first_name: Yaohui full_name: Bai, Yaohui last_name: Bai - first_name: Tara full_name: Stoinski, Tara S last_name: Stoinski - first_name: Elizabeth full_name: Hammock, Elizabeth A last_name: Hammock - first_name: Larry full_name: Young, Larry last_name: Young citation: ama: Donaldson Z, Kondrashov F, Putnam A, et al. Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. BMC Evolutionary Biology. 2008;8(1). doi:10.1186/1471-2148-8-180 apa: Donaldson, Z., Kondrashov, F., Putnam, A., Bai, Y., Stoinski, T., Hammock, E., & Young, L. (2008). Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-8-180 chicago: Donaldson, Zoe, Fyodor Kondrashov, Andrea Putnam, Yaohui Bai, Tara Stoinski, Elizabeth Hammock, and Larry Young. “Evolution of a Behavior-Linked Microsatellite-Containing Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” BMC Evolutionary Biology. BioMed Central, 2008. https://doi.org/10.1186/1471-2148-8-180. ieee: Z. Donaldson et al., “Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene,” BMC Evolutionary Biology, vol. 8, no. 1. BioMed Central, 2008. ista: Donaldson Z, Kondrashov F, Putnam A, Bai Y, Stoinski T, Hammock E, Young L. 2008. Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. BMC Evolutionary Biology. 8(1). mla: Donaldson, Zoe, et al. “Evolution of a Behavior-Linked Microsatellite-Containing Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” BMC Evolutionary Biology, vol. 8, no. 1, BioMed Central, 2008, doi:10.1186/1471-2148-8-180. short: Z. Donaldson, F. Kondrashov, A. Putnam, Y. Bai, T. Stoinski, E. Hammock, L. Young, BMC Evolutionary Biology 8 (2008). date_created: 2018-12-11T11:49:04Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T08:21:29Z day: '01' doi: 10.1186/1471-2148-8-180 extern: 1 intvolume: ' 8' issue: '1' month: '01' publication: BMC Evolutionary Biology publication_status: published publisher: BioMed Central publist_id: '6753' quality_controlled: 0 status: public title: Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 8 year: '2008' ... --- _id: '907' abstract: - lang: eng text: The most common form of protein-coding gene overlap in eukaryotes is a simple nested structure, whereby one gene is embedded in an intron of another. Analysis of nested protein-coding genes in vertebrates, fruit flies and nematodes revealed substantially higher rates of evolutionary gains than losses. The accumulation of nested gene structures could not be attributed to any obvious functional relationships between the genes involved and represents an increase of the organizational complexity of animal genomes via a neutral process. author: - first_name: Raquel full_name: Assis, Raquel last_name: Assis - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov - first_name: Eugene full_name: Koonin, Eugene V last_name: Koonin - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Assis R, Kondrashov A, Koonin E, Kondrashov F. Nested genes and increasing organizational complexity of metazoan genomes. Trends in Genetics. 2008;24(10):475-478. doi:10.1016/j.tig.2008.08.003 apa: Assis, R., Kondrashov, A., Koonin, E., & Kondrashov, F. (2008). Nested genes and increasing organizational complexity of metazoan genomes. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2008.08.003 chicago: Assis, Raquel, Alexey Kondrashov, Eugene Koonin, and Fyodor Kondrashov. “Nested Genes and Increasing Organizational Complexity of Metazoan Genomes.” Trends in Genetics. Elsevier, 2008. https://doi.org/10.1016/j.tig.2008.08.003. ieee: R. Assis, A. Kondrashov, E. Koonin, and F. Kondrashov, “Nested genes and increasing organizational complexity of metazoan genomes,” Trends in Genetics, vol. 24, no. 10. Elsevier, pp. 475–478, 2008. ista: Assis R, Kondrashov A, Koonin E, Kondrashov F. 2008. Nested genes and increasing organizational complexity of metazoan genomes. Trends in Genetics. 24(10), 475–478. mla: Assis, Raquel, et al. “Nested Genes and Increasing Organizational Complexity of Metazoan Genomes.” Trends in Genetics, vol. 24, no. 10, Elsevier, 2008, pp. 475–78, doi:10.1016/j.tig.2008.08.003. short: R. Assis, A. Kondrashov, E. Koonin, F. Kondrashov, Trends in Genetics 24 (2008) 475–478. date_created: 2018-12-11T11:49:08Z date_published: 2008-10-01T00:00:00Z date_updated: 2021-01-12T08:21:49Z day: '01' doi: 10.1016/j.tig.2008.08.003 extern: 1 intvolume: ' 24' issue: '10' month: '10' page: 475 - 478 publication: Trends in Genetics publication_status: published publisher: Elsevier publist_id: '6743' quality_controlled: 0 status: public title: Nested genes and increasing organizational complexity of metazoan genomes type: journal_article volume: 24 year: '2008' ... --- _id: '860' abstract: - lang: eng text: We identified a mutation in the CRYGD gene (P23S) of the γ-crystallin gene cluster that is associated with a polymorphic congenital cataract that occurs with frequency of ∼0.3% in a human population. To gain insight into the molecular mechanism of the pathogenesis of γ-crystallin isoforms, we undertook an evolutionary analysis of the available mammalian and newly obtained primate sequences of the γ-crystallin genes. The cataract-associated serine at site 23 corresponds to the ancestral state, since it was found in CRYGD of a lower primate and all the surveyed nonprimate mammals. Crystallin proteins include two structurally similar domains, and substitutions in mammalian CRYGD protein at site 23 of the first domain were always associated with substitutions in the structurally reciprocal sites 109 and 136 of the second domain. These data suggest that the cataractogenic effect of serine at site 23 in the N-terminal domain of CRYGD may be compensated indirectly by amino acid changes in a distal domain. We also found that gene conversion was a factor in the evolution of the γ-crystallin gene cluster throughout different mammalian clades. The high rate of gene conversion observed between the functional CRYGD gene and two primate γ-crystallin pseudogenes (CRYGEP1 and CRYGFP1) coupled with a surprising finding of apparent negative selection in primate pseudogenes suggest a deleterious impact of recently derived pseudogenes involved in gene conversion in the γ-crystallin gene cluster. acknowledgement: This study was supported by the Biodiversity and Dynamics of Gene Pools program of the Presidium of the Russian Academy of Sciences (support to E.I.R.). E.I.R. is also supported in part by the National Institute of Diabetes and Digestive and Kidney Diseases and National Institute of Neurological Disorders and Stroke (National Institutes of Health), and F.A.K. is supported by a National Science Foundation graduate research fellowship. author: - first_name: Olga full_name: Plotnikova, Olga V last_name: Plotnikova - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Peter full_name: Vlasov, Peter K last_name: Vlasov - first_name: Anastasia full_name: Grigorenko, Anastasia P last_name: Grigorenko - first_name: Evgeny full_name: Ginter, Evgeny K last_name: Ginter - first_name: Evgeny full_name: Rogaev, Evgeny I last_name: Rogaev citation: ama: Plotnikova O, Kondrashov F, Vlasov P, Grigorenko A, Ginter E, Rogaev E. Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state. American Journal of Human Genetics. 2007;81(1):32-43. doi:10.1086/518616 apa: Plotnikova, O., Kondrashov, F., Vlasov, P., Grigorenko, A., Ginter, E., & Rogaev, E. (2007). Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state. American Journal of Human Genetics. Cell Press. https://doi.org/10.1086/518616 chicago: Plotnikova, Olga, Fyodor Kondrashov, Peter Vlasov, Anastasia Grigorenko, Evgeny Ginter, and Evgeny Rogaev. “Conversion and Compensatory Evolution of the γ-Crystallin Genes and Identification of a Cataractogenic Mutation That Reverses the Sequence of the Human CRYGD Gene to an Ancestral State.” American Journal of Human Genetics. Cell Press, 2007. https://doi.org/10.1086/518616. ieee: O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, and E. Rogaev, “Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state,” American Journal of Human Genetics, vol. 81, no. 1. Cell Press, pp. 32–43, 2007. ista: Plotnikova O, Kondrashov F, Vlasov P, Grigorenko A, Ginter E, Rogaev E. 2007. Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state. American Journal of Human Genetics. 81(1), 32–43. mla: Plotnikova, Olga, et al. “Conversion and Compensatory Evolution of the γ-Crystallin Genes and Identification of a Cataractogenic Mutation That Reverses the Sequence of the Human CRYGD Gene to an Ancestral State.” American Journal of Human Genetics, vol. 81, no. 1, Cell Press, 2007, pp. 32–43, doi:10.1086/518616. short: O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, E. Rogaev, American Journal of Human Genetics 81 (2007) 32–43. date_created: 2018-12-11T11:48:53Z date_published: 2007-07-01T00:00:00Z date_updated: 2021-01-12T08:20:14Z day: '01' doi: 10.1086/518616 extern: 1 intvolume: ' 81' issue: '1' month: '07' page: 32 - 43 publication: American Journal of Human Genetics publication_status: published publisher: Cell Press publist_id: '6788' quality_controlled: 0 status: public title: Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state type: journal_article volume: 81 year: '2007' ... --- _id: '879' abstract: - lang: eng text: Having an extra copy of a gene is thought to provide some functional redundancy, which results in a higher rate of evolution in duplicated genes. In this article, we estimate the impact of gene duplication on the selection of tuf paralogs, and we find that in the absence of gene conversion, tuf paralogs have evolved significantly slower than when gene conversion has been a factor in their evolution. Thus, tuf gene copies evolve under a selective pressure that ensures their functional uniformity, and gene conversion reduces selection against amino acid substitutions that affect the function of the encoded protein, EF-Tu. acknowledgement: We thank Peter Andolfatto, Doris Bachtrog, Robert Cutler, Hideki Innan, Eugene Koonin, Alexey Kondrashov and Martin Lercher for comments on the manuscript and for discussions on the interplay between gene conversion and selection. This work was supported by a National Science Foundation Graduate Research Fellowship (F.A.K.) and a Molecular and Cellular Biology RAS (Program No 10) grant (P.K.V.). author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Tatiana full_name: Gurbich, Tatiana A last_name: Gurbich - first_name: Peter full_name: Vlasov, Peter K last_name: Vlasov citation: ama: Kondrashov F, Gurbich T, Vlasov P. Selection for functional uniformity of tuf duplicates in γ-proteobacteria. Trends in Genetics. 2007;23(5):215-218. doi:10.1016/j.tig.2007.03.002 apa: Kondrashov, F., Gurbich, T., & Vlasov, P. (2007). Selection for functional uniformity of tuf duplicates in γ-proteobacteria. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2007.03.002 chicago: Kondrashov, Fyodor, Tatiana Gurbich, and Peter Vlasov. “Selection for Functional Uniformity of Tuf Duplicates in γ-Proteobacteria.” Trends in Genetics. Elsevier, 2007. https://doi.org/10.1016/j.tig.2007.03.002. ieee: F. Kondrashov, T. Gurbich, and P. Vlasov, “Selection for functional uniformity of tuf duplicates in γ-proteobacteria,” Trends in Genetics, vol. 23, no. 5. Elsevier, pp. 215–218, 2007. ista: Kondrashov F, Gurbich T, Vlasov P. 2007. Selection for functional uniformity of tuf duplicates in γ-proteobacteria. Trends in Genetics. 23(5), 215–218. mla: Kondrashov, Fyodor, et al. “Selection for Functional Uniformity of Tuf Duplicates in γ-Proteobacteria.” Trends in Genetics, vol. 23, no. 5, Elsevier, 2007, pp. 215–18, doi:10.1016/j.tig.2007.03.002. short: F. Kondrashov, T. Gurbich, P. Vlasov, Trends in Genetics 23 (2007) 215–218. date_created: 2018-12-11T11:48:59Z date_published: 2007-05-01T00:00:00Z date_updated: 2021-01-12T08:21:04Z day: '01' doi: 10.1016/j.tig.2007.03.002 extern: 1 intvolume: ' 23' issue: '5' month: '05' page: 215 - 218 publication: Trends in Genetics publication_status: published publisher: Elsevier publist_id: '6771' quality_controlled: 0 status: public title: Selection for functional uniformity of tuf duplicates in γ-proteobacteria type: journal_article volume: 23 year: '2007' ... --- _id: '904' abstract: - lang: eng text: 'Background: Independently evolving lineages mostly accumulate different changes, which leads to their gradual divergence. However, parallel accumulation of identical changes is also common, especially in traits with only a small number of possible states. Results: We characterize parallelism in evolution of coding sequences in three four-species sets of genomes of mammals, Drosophila, and yeasts. Each such set contains two independent evolutionary paths, which we call paths I and II. An amino acid replacement which occurred along path I also occurs along path II with the probability 50-8211;80% of that expected under selective neutrality. Thus, the per site rate of parallel evolution of proteins is several times higher than their average rate of evolution, but still lower than the rate of evolution of neutral sequences. This deficit may be caused by changes in the fitness landscape, leading to a replacement being possible along path I but not along path II. However, constant, weak selection assumed by the nearly neutral model of evolution appears to be a more likely explanation. Then, the average coefficient of selection associated with an amino acid replacement, in the units of the effective population size, must exceed ∼0.4, and the fraction of effectively neutral replacements must be below ∼30%. At a majority of evolvable amino acid sites, only a relatively small number of different amino acids is permitted. Conclusion: High, but below-neutral, rates of parallel amino acid replacements suggest that a majority of amino acid replacements that occur in evolution are subject to weak, but non-trivial, selection, as predicted by Ohta''s nearly-neutral theory.' acknowledgement: G.A.B. gratefully acknowledges fellowships from the Pew Charitable Trusts award 2000-002558 and the Burroughs Wellcome Fund award 1001782, both to Princeton University. F.A.K. is a National Science Foundation Graduate Fellow. M.B.'s work is partially supported by the NSERC Discovery grant. I.D. and A.P. were partially supported by grant HL066681 (L.A.P., I.D. and S.M.), Berkeley-PGA, under the Programs for Genomic Applications, funded by National Heart, Lung, & Blood Institute and Department of Energy Contract DE-AC02-05CH11231, University of California. This work was partially supported through the Molecular and Cellular Biology Program of the Russian Academy of Sciences. author: - first_name: Georgii full_name: Bazykin, Georgii A last_name: Bazykin - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Michael full_name: Brudno, Michael last_name: Brudno - first_name: Alexander full_name: Poliakov, Alexander V last_name: Poliakov - first_name: Inna full_name: Dubchak, Inna L last_name: Dubchak - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov citation: ama: Bazykin G, Kondrashov F, Brudno M, Poliakov A, Dubchak I, Kondrashov A. Extensive parallelism in protein evolution. Biology Direct. 2007;2. doi:10.1186/1745-6150-2-20 apa: Bazykin, G., Kondrashov, F., Brudno, M., Poliakov, A., Dubchak, I., & Kondrashov, A. (2007). Extensive parallelism in protein evolution. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-2-20 chicago: Bazykin, Georgii, Fyodor Kondrashov, Michael Brudno, Alexander Poliakov, Inna Dubchak, and Alexey Kondrashov. “Extensive Parallelism in Protein Evolution.” Biology Direct. BioMed Central, 2007. https://doi.org/10.1186/1745-6150-2-20. ieee: G. Bazykin, F. Kondrashov, M. Brudno, A. Poliakov, I. Dubchak, and A. Kondrashov, “Extensive parallelism in protein evolution,” Biology Direct, vol. 2. BioMed Central, 2007. ista: Bazykin G, Kondrashov F, Brudno M, Poliakov A, Dubchak I, Kondrashov A. 2007. Extensive parallelism in protein evolution. Biology Direct. 2. mla: Bazykin, Georgii, et al. “Extensive Parallelism in Protein Evolution.” Biology Direct, vol. 2, BioMed Central, 2007, doi:10.1186/1745-6150-2-20. short: G. Bazykin, F. Kondrashov, M. Brudno, A. Poliakov, I. Dubchak, A. Kondrashov, Biology Direct 2 (2007). date_created: 2018-12-11T11:49:07Z date_published: 2007-08-16T00:00:00Z date_updated: 2021-01-12T08:21:47Z day: '16' doi: 10.1186/1745-6150-2-20 extern: 1 intvolume: ' 2' month: '08' publication: Biology Direct publication_status: published publisher: BioMed Central publist_id: '6745' quality_controlled: 0 status: public title: Extensive parallelism in protein evolution tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 2 year: '2007' ... --- _id: '861' abstract: - lang: eng text: 'Background: Mitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and structural evolution and medical studies have been directed towards understanding the basis of human disease. However, an up to date, manually curated database of mitochondrially encoded tRNAs from higher animals is currently not available. Description: We obtained the complete mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated all of the tRNAs based on a multiple alignment of each tRNA gene and secondary structure prediction made independently for each tRNA. The mitochondrial (mt) tRNA sequences and the secondary structure based multiple alignments are freely available as Supplemental Information online. Conclusion: We compiled a manually curated database of mitochondrially encoded tRNAs from tetrapods with completely sequenced genomes. In the course of our work, we reannotated more than 10% of all tetrapod mt-tRNAs and subsequently predicted the secondary structures of 6060 mitochondrial tRNAs. This carefully constructed database can be utilized to enhance our knowledge in several different fields including the evolution of mt-tRNA secondary structure and prediction of pathogenic mt-tRNA mutations. In addition, researchers reporting novel mitochondrial genome sequences should check their tRNA gene annotations against our database to ensure a higher level of fidelity of their annotation.' acknowledgement: KYuP and LAM were supported by the Molecular and Cellular Biology Program of the Russian Academy of Science. KYuP was supported by the Russian Fund of Basic Research (grant 04-04-49623). LAM was partially supported by grants from the Howard Hughes Medical Institute (55005610), INTAS (05-1000008-8028). FAK is a National Science Foundation Graduate Research Fellow. author: - first_name: Konstantin full_name: Popadin, Konstantin Yu last_name: Popadin - first_name: Leila full_name: Mamirova, Leila A last_name: Mamirova - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Popadin K, Mamirova L, Kondrashov F. A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics. 2007;8. doi:10.1186/1471-2105-8-441 apa: Popadin, K., Mamirova, L., & Kondrashov, F. (2007). A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics. BioMed Central. https://doi.org/10.1186/1471-2105-8-441 chicago: Popadin, Konstantin, Leila Mamirova, and Fyodor Kondrashov. “A Manually Curated Database of Tetrapod Mitochondrially Encoded TRNA Sequences and Secondary Structures.” BMC Bioinformatics. BioMed Central, 2007. https://doi.org/10.1186/1471-2105-8-441. ieee: K. Popadin, L. Mamirova, and F. Kondrashov, “A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures,” BMC Bioinformatics, vol. 8. BioMed Central, 2007. ista: Popadin K, Mamirova L, Kondrashov F. 2007. A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics. 8. mla: Popadin, Konstantin, et al. “A Manually Curated Database of Tetrapod Mitochondrially Encoded TRNA Sequences and Secondary Structures.” BMC Bioinformatics, vol. 8, BioMed Central, 2007, doi:10.1186/1471-2105-8-441. short: K. Popadin, L. Mamirova, F. Kondrashov, BMC Bioinformatics 8 (2007). date_created: 2018-12-11T11:48:54Z date_published: 2007-11-14T00:00:00Z date_updated: 2021-01-12T08:20:18Z day: '14' doi: 10.1186/1471-2105-8-441 extern: 1 intvolume: ' 8' month: '11' publication: BMC Bioinformatics publication_status: published publisher: BioMed Central publist_id: '6789' quality_controlled: 0 status: public title: A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 8 year: '2007' ... --- _id: '854' abstract: - lang: eng text: Phylogenetic relationships between the extinct woolly mammoth (Mammuthus primigenius), and the Asian (Elephas maximus) and African savanna (Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch - the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as ∼1,600-1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests that M. primigenius and E. maximus are sister species that diverged soon after their common ancestor split from the L. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population of M. primigenius throughout the late Pleistocene. acknowledgement: |- FAK is supported by the NSF Graduate Research Fellowship. We thank the Natural History Museum, North-Eastern Research Center, Far Eastern Branch of the Russian Academy of Sciences for photographic material ofM. primigenius leg, V. A. Nikishina for artwork and technical support, Y.B. Yurov, G. Dvoryanchikov, N. Riazanskaya and T. Kolesnikova for technical support, K. Mehren and C. Gray for elephant specimens, and V. Y. Solovyev for help with artwork of animal images. author: - first_name: Evgeny full_name: Rogaev, Evgeny I last_name: Rogaev - first_name: Yuri full_name: Moliaka, Yuri K last_name: Moliaka - first_name: Boris full_name: Malyarchuk, Boris A last_name: Malyarchuk - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Miroslava full_name: Derenko, Miroslava V last_name: Derenko - first_name: Ilya full_name: Chumakov, Ilya M last_name: Chumakov - first_name: Anastasia full_name: Grigorenko, Anastasia P last_name: Grigorenko citation: ama: Rogaev E, Moliaka Y, Malyarchuk B, et al. Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius. PLoS Biology. 2006;4(3):0403-0410. doi:10.1371/journal.pbio.0040073 apa: Rogaev, E., Moliaka, Y., Malyarchuk, B., Kondrashov, F., Derenko, M., Chumakov, I., & Grigorenko, A. (2006). Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.0040073 chicago: Rogaev, Evgeny, Yuri Moliaka, Boris Malyarchuk, Fyodor Kondrashov, Miroslava Derenko, Ilya Chumakov, and Anastasia Grigorenko. “Complete Mitochondrial Genome and Phylogeny of Pleistocene Mammoth Mammuthus Primigenius.” PLoS Biology. Public Library of Science, 2006. https://doi.org/10.1371/journal.pbio.0040073. ieee: E. Rogaev et al., “Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius,” PLoS Biology, vol. 4, no. 3. Public Library of Science, pp. 0403–0410, 2006. ista: Rogaev E, Moliaka Y, Malyarchuk B, Kondrashov F, Derenko M, Chumakov I, Grigorenko A. 2006. Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius. PLoS Biology. 4(3), 0403–0410. mla: Rogaev, Evgeny, et al. “Complete Mitochondrial Genome and Phylogeny of Pleistocene Mammoth Mammuthus Primigenius.” PLoS Biology, vol. 4, no. 3, Public Library of Science, 2006, pp. 0403–10, doi:10.1371/journal.pbio.0040073. short: E. Rogaev, Y. Moliaka, B. Malyarchuk, F. Kondrashov, M. Derenko, I. Chumakov, A. Grigorenko, PLoS Biology 4 (2006) 0403–0410. date_created: 2018-12-11T11:48:51Z date_published: 2006-03-01T00:00:00Z date_updated: 2021-01-12T08:19:58Z day: '01' doi: 10.1371/journal.pbio.0040073 extern: 1 intvolume: ' 4' issue: '3' month: '03' page: 0403 - 0410 publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '6794' quality_controlled: 0 status: public title: Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius type: journal_article volume: 4 year: '2006' ... --- _id: '868' abstract: - lang: eng text: 'Background: The glyoxylate cycle is thought to be present in bacteria, protists, plants, fungi, and nematodes, but not in other Metazoa. However, activity of the glyoxylate cycle enzymes, malate synthase (MS) and isocitrate lyase (ICL), in animal tissues has been reported. In order to clarify the status of the MS and ICL genes in animals and get an insight into their evolution, we undertook a comparative-genomic study. Results: Using sequence similarity searches, we identified MS genes in arthropods, echinoderms, and vertebrates, including platypus and opossum, but not in the numerous sequenced genomes of placental mammals. The regions of the placental mammals'' genomes expected to code for malate synthase, as determined by comparison of the gene orders in vertebrate genomes, show clear similarity to the opossum MS sequence but contain stop codons, indicating that the MS gene became a pseudogene in placental mammals. By contrast, the ICL gene is undetectable in animals other than the nematodes that possess a bifunctional, fused ICL-MS gene. Examination of phylogenetic trees of MS and ICL suggests multiple horizontal gene transfer events that probably went in both directions between several bacterial and eukaryotic lineages. The strongest evidence was obtained for the acquisition of the bifunctional ICL-MS gene from an as yet unknown bacterial source with the corresponding operonic organization by the common ancestor of the nematodes. Conclusion: The distribution of the MS and ICL genes in animals suggests that either they encode alternative enzymes of the glyoxylate cycle that are not orthologous to the known MS and ICL or the animal MS acquired a new function that remains to be characterized. Regardless of the ultimate solution to this conundrum, the genes for the glyoxylate cycle enzymes present a remarkable variety of evolutionary events including unusual horizontal gene transfer from bacteria to animals.' acknowledgement: The authors thank Alexey Kondrashov for suggesting the possibility of non- orthologous gene displacement in glyoxylate cycle specific enzymes and for critical reading of this manuscript. FAK is a National Science Foundation Graduate Fellow. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Eugene full_name: Koonin, Eugene V last_name: Koonin - first_name: Igor full_name: Morgunov, Igor G last_name: Morgunov - first_name: Tatiana full_name: Finogenova, Tatiana V last_name: Finogenova - first_name: Marie full_name: Kondrashova, Marie N last_name: Kondrashova citation: ama: Kondrashov F, Koonin E, Morgunov I, Finogenova T, Kondrashova M. Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation. Biology Direct. 2006;1. doi:10.1186/1745-6150-1-31 apa: Kondrashov, F., Koonin, E., Morgunov, I., Finogenova, T., & Kondrashova, M. (2006). Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-1-31 chicago: Kondrashov, Fyodor, Eugene Koonin, Igor Morgunov, Tatiana Finogenova, and Marie Kondrashova. “Evolution of Glyoxylate Cycle Enzymes in Metazoa Evidence of Multiple Horizontal Transfer Events and Pseudogene Formation.” Biology Direct. BioMed Central, 2006. https://doi.org/10.1186/1745-6150-1-31. ieee: F. Kondrashov, E. Koonin, I. Morgunov, T. Finogenova, and M. Kondrashova, “Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation,” Biology Direct, vol. 1. BioMed Central, 2006. ista: Kondrashov F, Koonin E, Morgunov I, Finogenova T, Kondrashova M. 2006. Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation. Biology Direct. 1. mla: Kondrashov, Fyodor, et al. “Evolution of Glyoxylate Cycle Enzymes in Metazoa Evidence of Multiple Horizontal Transfer Events and Pseudogene Formation.” Biology Direct, vol. 1, BioMed Central, 2006, doi:10.1186/1745-6150-1-31. short: F. Kondrashov, E. Koonin, I. Morgunov, T. Finogenova, M. Kondrashova, Biology Direct 1 (2006). date_created: 2018-12-11T11:48:56Z date_published: 2006-10-23T00:00:00Z date_updated: 2021-01-12T08:20:31Z day: '23' doi: 10.1186/1745-6150-1-31 extern: 1 intvolume: ' 1' month: '10' publication: Biology Direct publication_status: published publisher: BioMed Central publist_id: '6778' quality_controlled: 0 status: public title: Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 1 year: '2006' ... --- _id: '873' abstract: - lang: eng text: New genes commonly appear through complete or partial duplications of pre-existing genes. Duplications of long DNA segments are constantly produced by rare mutations, may become fixed in a population by selection or random drift, and are subject to divergent evolution of the paralogous sequences after fixation, although gene conversion can impede this process. New data shed some light on each of these processes. Mutations which involve duplications can occur through at least two different mechanisms, backward strand slippage during DNA replication and unequal crossing-over. The background rate of duplication of a complete gene in humans is 10-9-10-10 per generation, although many genes located within hot-spots of large-scale mutation are duplicated much more often. Many gene duplications affect fitness strongly, and are responsible, through gene dosage effects, for a number of genetic diseases. However, high levels of intrapopulation polymorphism caused by presence or absence of long, gene-containing DNA segments imply that some duplications are not under strong selection. The polymorphism to fixation ratios appear to be approximately the same for gene duplications and for presumably selectively neutral nucleotide substitutions, which, according to the McDonald-Kreitman test, is consistent with selective neutrality of duplications. However, this pattern can also be due to negative selection against most of segregating duplications and positive selection for at least some duplications which become fixed. Patterns in post-fixation evolution of duplicated genes do not easily reveal the causes of fixations. Many gene duplications which became fixed recently in a variety of organisms were positively selected because the increased expression of the corresponding genes was beneficial. The effects of gene dosage provide a unified framework for studying all phases of the life history of a gene duplication. Application of well-known methods of evolutionary genetics to accumulating data on new, polymorphic, and fixed duplication will enhance our understanding of the role of natural selection in the evolution by gene duplication. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov citation: ama: Kondrashov F, Kondrashov A. Role of selection in fixation of gene duplications. Journal of Theoretical Biology. 2006;239(2):141-151. doi:10.1016/j.jtbi.2005.08.033 apa: Kondrashov, F., & Kondrashov, A. (2006). Role of selection in fixation of gene duplications. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2005.08.033 chicago: Kondrashov, Fyodor, and Alexey Kondrashov. “Role of Selection in Fixation of Gene Duplications.” Journal of Theoretical Biology. Elsevier, 2006. https://doi.org/10.1016/j.jtbi.2005.08.033. ieee: F. Kondrashov and A. Kondrashov, “Role of selection in fixation of gene duplications,” Journal of Theoretical Biology, vol. 239, no. 2. Elsevier, pp. 141–151, 2006. ista: Kondrashov F, Kondrashov A. 2006. Role of selection in fixation of gene duplications. Journal of Theoretical Biology. 239(2), 141–151. mla: Kondrashov, Fyodor, and Alexey Kondrashov. “Role of Selection in Fixation of Gene Duplications.” Journal of Theoretical Biology, vol. 239, no. 2, Elsevier, 2006, pp. 141–51, doi:10.1016/j.jtbi.2005.08.033. short: F. Kondrashov, A. Kondrashov, Journal of Theoretical Biology 239 (2006) 141–151. date_created: 2018-12-11T11:48:57Z date_published: 2006-03-21T00:00:00Z date_updated: 2021-01-12T08:20:47Z day: '21' doi: 10.1016/j.jtbi.2005.08.033 extern: 1 intvolume: ' 239' issue: '2' month: '03' page: 141 - 151 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '6773' quality_controlled: 0 status: public title: Role of selection in fixation of gene duplications type: journal_article volume: 239 year: '2006' ... --- _id: '869' abstract: - lang: eng text: The impact of synonymous nucleotide substitutions on fitness in mammals remains controversial. Despite some indications of selective constraint, synonymous sites are often assumed to be neutral, and the rate of their evolution is used as a proxy for mutation rate. We subdivide all sites into four classes in terms of the mutable CpG context, nonCpG, postC, preG, and postCpreG, and compare four-fold synonymous sites and intron sites residing outside transposable elements. The distribution of the rate of evolution across all synonymous sites is trimodal. Rate of evolution at nonCpG synonymous sites, not preceded by C and not followed by G, is ∼10% below that at such intron sites. In contrast, rate of evolution at postCpreG synonymous sites is ∼30% above that at such intron sites. Finally, synonymous and intron postC and preG sites evolve at similar rates. The relationship between the levels of polymorphism at the corresponding synonymous and intron sites is very similar to that between their rates of evolution. Within every class, synonymous sites are occupied by G or C much more often than intron sites, whose nucleotide composition is consistent with neutral mutation-drift equilibrium. These patterns suggest that synonymous sites are under weak selection in favor of G and C, with the average coefficient s∼0.25/Ne∼10-5, where Ne is the effective population size. Such selection decelerates evolution and reduces variability at sites with symmetric mutation, but has the opposite effects at sites where the favored nucleotides are more mutable. The amino-acid composition of proteins dictates that many synonymous sites are CpGprone, which causes them, on average, to evolve faster and to be more polymorphic than intron sites. An average genotype carries ∼107 suboptimal nucleotides at synonymous sites, implying synergistic epistasis in selection against them. acknowledgement: This research was supported in part by the Intramural Research Program of the NIH, National Library of Medicine. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Aleksey full_name: Ogurtsov, Aleksey Yu last_name: Ogurtsov - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov citation: ama: Kondrashov F, Ogurtsov A, Kondrashov A. Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. Journal of Theoretical Biology. 2006;240(4):616-626. doi:10.1016/j.jtbi.2005.10.020 apa: Kondrashov, F., Ogurtsov, A., & Kondrashov, A. (2006). Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2005.10.020 chicago: Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Selection in Favor of Nucleotides G and C Diversifies Evolution Rates and Levels of Polymorphism at Mammalian Synonymous Sites.” Journal of Theoretical Biology. Elsevier, 2006. https://doi.org/10.1016/j.jtbi.2005.10.020. ieee: F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites,” Journal of Theoretical Biology, vol. 240, no. 4. Elsevier, pp. 616–626, 2006. ista: Kondrashov F, Ogurtsov A, Kondrashov A. 2006. Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. Journal of Theoretical Biology. 240(4), 616–626. mla: Kondrashov, Fyodor, et al. “Selection in Favor of Nucleotides G and C Diversifies Evolution Rates and Levels of Polymorphism at Mammalian Synonymous Sites.” Journal of Theoretical Biology, vol. 240, no. 4, Elsevier, 2006, pp. 616–26, doi:10.1016/j.jtbi.2005.10.020. short: F. Kondrashov, A. Ogurtsov, A. Kondrashov, Journal of Theoretical Biology 240 (2006) 616–626. date_created: 2018-12-11T11:48:56Z date_published: 2006-06-21T00:00:00Z date_updated: 2021-01-12T08:20:33Z day: '21' doi: 10.1016/j.jtbi.2005.10.020 extern: 1 intvolume: ' 240' issue: '4' month: '06' page: 616 - 626 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '6779' quality_controlled: 0 status: public title: Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites type: journal_article volume: 240 year: '2006' ... --- _id: '903' abstract: - lang: eng text: 'Background: Carcinogenesis typically involves multiple somatic mutations in caretaker (DNA repair) and gatekeeper (tumor suppressors and oncogenes) genes. Analysis of mutation spectra of the tumor suppressor that is most commonly mutated in human cancers, p53, unexpectedly suggested that somatic evolution of the p53 gene during tumorigenesis is dominated by positive selection for gain of function. This conclusion is supported by accumulating experimental evidence of evolution of new functions of p53 in tumors. These findings prompted a genome-wide analysis of possible positive selection during tumor evolution. Methods: A comprehensive analysis of probable somatic mutations in the sequences of Expressed Sequence Tags (ESTs) from malignant tumors and normal tissues was performed in order to access the prevalence of positive selection in cancer evolution. For each EST, the numbers of synonymous and non-synonymous substitutions were calculated. In order to identify genes with a signature of positive selection in cancers, these numbers were compared to: i) expected numbers and ii) the numbers for the respective genes in the ESTs from normal tissues. Results: We identified 112 genes with a signature of positive selection in cancers, i.e., a significantly elevated ratio of non-synonymous to synonymous substitutions, in tumors as compared to 37 such genes in an approximately equal-sized EST collection from normal tissues. A substantial fraction of the tumor-specific positive-selection candidates have experimentally demonstrated or strongly predicted links to cancer. Conclusion: The results of EST analysis should be interpreted with extreme caution given the noise introduced by sequencing errors and undetected polymorphisms. Furthermore, an inherent limitation of EST analysis is that multiple mutations amenable to statistical analysis can be detected only in relatively highly expressed genes. Nevertheless, the present results suggest that positive selection might affect a substantial number of genes during tumorigenic somatic evolution.' acknowledgement: This work was supported by the Intramural Research Program of the National Library of Medicine at the National Institutes of Health/DHHS. FAK is an NSF Graduate Fellow. We thank Yuri Pavlov for helpful discussions. author: - first_name: Vladimir full_name: Babenko, Vladimir N last_name: Babenko - first_name: Malay full_name: Basu, Malay K last_name: Basu - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Igor full_name: Rogozin, Igor B last_name: Rogozin - first_name: Eugene full_name: Koonin, Eugene V last_name: Koonin citation: ama: Babenko V, Basu M, Kondrashov F, Rogozin I, Koonin E. Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis. BMC Cancer. 2006;6. doi:10.1186/1471-2407-6-36 apa: Babenko, V., Basu, M., Kondrashov, F., Rogozin, I., & Koonin, E. (2006). Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis. BMC Cancer. BioMed Central. https://doi.org/10.1186/1471-2407-6-36 chicago: Babenko, Vladimir, Malay Basu, Fyodor Kondrashov, Igor Rogozin, and Eugene Koonin. “Signs of Positive Selection of Somatic Mutations in Human Cancers Detected by EST Sequence Analysis.” BMC Cancer. BioMed Central, 2006. https://doi.org/10.1186/1471-2407-6-36. ieee: V. Babenko, M. Basu, F. Kondrashov, I. Rogozin, and E. Koonin, “Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis,” BMC Cancer, vol. 6. BioMed Central, 2006. ista: Babenko V, Basu M, Kondrashov F, Rogozin I, Koonin E. 2006. Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis. BMC Cancer. 6. mla: Babenko, Vladimir, et al. “Signs of Positive Selection of Somatic Mutations in Human Cancers Detected by EST Sequence Analysis.” BMC Cancer, vol. 6, BioMed Central, 2006, doi:10.1186/1471-2407-6-36. short: V. Babenko, M. Basu, F. Kondrashov, I. Rogozin, E. Koonin, BMC Cancer 6 (2006). date_created: 2018-12-11T11:49:07Z date_published: 2006-02-09T00:00:00Z date_updated: 2021-01-12T08:21:47Z day: '09' doi: 10.1186/1471-2407-6-36 extern: 1 intvolume: ' 6' month: '02' publication: BMC Cancer publication_status: published publisher: BioMed Central publist_id: '6744' quality_controlled: 0 status: public title: Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 6 year: '2006' ... --- _id: '843' abstract: - lang: eng text: The impact of an amino acid replacement on the organism's fitness can vary from lethal to selectively neutral and even, in rare cases, beneficial. Substantial data are available on either pathogenic or acceptable replacements. However, the whole distribution of coefficients of selection against individual replacements is not known for any organism. To ascertain this distribution for human proteins, we combined data on pathogenic missense mutations, on human non-synonymous SNPs and on human-chimpanzee divergence of orthologous proteins. Fractions of amino acid replacements which reduce fitness by >10-2, 10-2-10-4, 10-4-10-5 and <10-5 are 25, 49, 14 and 12%, respectively. On average, the strength of selection against a replacement is substantially higher when chemically dissimilar amino acids are involved, and the Grantham's index of a replacement explains 35% of variance in the average logarithm of selection coefficients associated with different replacements. Still, the impact of a replacement depends on its context within the protein more than on its own nature. Reciprocal replacements are often associated with rather different selection coefficients, in particular, replacements of non-polar amino acids with polar ones are typically much more deleterious than replacements in the opposite direction. However, differences between evolutionary fluxes of reciprocal replacements are only weakly correlated with the differences between the corresponding selection coefficients. author: - first_name: Lev full_name: Yampolsky, Lev Y last_name: Yampolsky - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov citation: ama: Yampolsky L, Kondrashov F, Kondrashov A. Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. 2005;14(21):3191-3201. doi:10.1093/hmg/ddi350 apa: Yampolsky, L., Kondrashov, F., & Kondrashov, A. (2005). Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/ddi350 chicago: Yampolsky, Lev, Fyodor Kondrashov, and Alexey Kondrashov. “Distribution of the Strength of Selection against Amino Acid Replacements in Human Proteins.” Human Molecular Genetics. Oxford University Press, 2005. https://doi.org/10.1093/hmg/ddi350. ieee: L. Yampolsky, F. Kondrashov, and A. Kondrashov, “Distribution of the strength of selection against amino acid replacements in human proteins,” Human Molecular Genetics, vol. 14, no. 21. Oxford University Press, pp. 3191–3201, 2005. ista: Yampolsky L, Kondrashov F, Kondrashov A. 2005. Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. 14(21), 3191–3201. mla: Yampolsky, Lev, et al. “Distribution of the Strength of Selection against Amino Acid Replacements in Human Proteins.” Human Molecular Genetics, vol. 14, no. 21, Oxford University Press, 2005, pp. 3191–201, doi:10.1093/hmg/ddi350. short: L. Yampolsky, F. Kondrashov, A. Kondrashov, Human Molecular Genetics 14 (2005) 3191–3201. date_created: 2018-12-11T11:48:48Z date_published: 2005-11-01T00:00:00Z date_updated: 2021-01-12T08:19:13Z day: '01' doi: 10.1093/hmg/ddi350 extern: 1 intvolume: ' 14' issue: '21' month: '11' page: 3191 - 3201 publication: Human Molecular Genetics publication_status: published publisher: Oxford University Press publist_id: '6807' quality_controlled: 0 status: public title: Distribution of the strength of selection against amino acid replacements in human proteins type: journal_article volume: 14 year: '2005' ... --- _id: '877' abstract: - lang: eng text: "Sequence analysis of protein and mitochondrially encoded tRNA genes shows that substitutions\r\nproducing pathogenic effects in humans are often found in normal, healthy individuals from other species.\r\nAnalysis of stability of protein and tRNA structures shows that the disease-causing effects of pathogenic\r\nmutations can be neutralized by other, compensatory substitutions that restore the structural stability of the\r\nmolecule. Further study of such substitutions will, hopefully, lead to new methods for curing genetic dis-\r\neases that may be based on the correction of molecule stability as a whole instead of reversing an individual\r\npathogenic mutation." article_processing_charge: No article_type: original author: - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kondrashov F. The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. Biofizika. 2005;50(3):389-395. apa: Kondrashov, F. (2005). The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. Biofizika. Pleiades Publishing. chicago: Kondrashov, Fyodor. “The Analysis of Monomer Sequences in Protein and TRNA and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution.” Biofizika. Pleiades Publishing, 2005. ieee: F. Kondrashov, “The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution,” Biofizika, vol. 50, no. 3. Pleiades Publishing, pp. 389–395, 2005. ista: Kondrashov F. 2005. The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. Biofizika. 50(3), 389–395. mla: Kondrashov, Fyodor. “The Analysis of Monomer Sequences in Protein and TRNA and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution.” Biofizika, vol. 50, no. 3, Pleiades Publishing, 2005, pp. 389–95. short: F. Kondrashov, Biofizika 50 (2005) 389–395. date_created: 2018-12-11T11:48:58Z date_published: 2005-05-01T00:00:00Z date_updated: 2021-01-12T08:21:01Z day: '01' extern: '1' external_id: pmid: - '15977826' intvolume: ' 50' issue: '3' language: - iso: eng main_file_link: - url: http://pleiades.online/abstract/biophys/5/biophys0349_abstract.pdf month: '05' oa_version: None page: 389 - 395 pmid: 1 publication: Biofizika publication_status: published publisher: Pleiades Publishing publist_id: '6769' quality_controlled: '1' status: public title: The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2005' ... --- _id: '878' abstract: - lang: eng text: | Negative trade-offs are thought to be a pervasive phenomenon and to inhibit evolution at all levels. New evidence shows that at the molecular level, there may be no trade-offs preventing the emergence of an enzyme with multiple functions. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kondrashov F. In search of the limits of evolution. Nature Genetics. 2005;37(1):9-10. doi:10.1038/ng0105-9 apa: Kondrashov, F. (2005). In search of the limits of evolution. Nature Genetics. Nature Publishing Group. https://doi.org/10.1038/ng0105-9 chicago: Kondrashov, Fyodor. “In Search of the Limits of Evolution.” Nature Genetics. Nature Publishing Group, 2005. https://doi.org/10.1038/ng0105-9. ieee: F. Kondrashov, “In search of the limits of evolution,” Nature Genetics, vol. 37, no. 1. Nature Publishing Group, pp. 9–10, 2005. ista: Kondrashov F. 2005. In search of the limits of evolution. Nature Genetics. 37(1), 9–10. mla: Kondrashov, Fyodor. “In Search of the Limits of Evolution.” Nature Genetics, vol. 37, no. 1, Nature Publishing Group, 2005, pp. 9–10, doi:10.1038/ng0105-9. short: F. Kondrashov, Nature Genetics 37 (2005) 9–10. date_created: 2018-12-11T11:48:59Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T08:21:02Z day: '01' doi: 10.1038/ng0105-9 extern: 1 intvolume: ' 37' issue: '1' month: '01' page: 9 - 10 publication: Nature Genetics publication_status: published publisher: Nature Publishing Group publist_id: '6770' quality_controlled: 0 status: public title: In search of the limits of evolution type: journal_article volume: 37 year: '2005' ... --- _id: '882' abstract: - lang: eng text: Some mutations in human mitochondrial tRNAs are severely pathogenic. The available computational methods have a poor record of predicting the impact of a tRNA mutation on the phenotype and fitness. Here patterns of evolution at tRNA sites that harbor pathogenic mutations and at sites that harbor phenotypically cryptic polymorphisms were compared. Mutations that are pathogenic to humans occupy more conservative sites, are only rarely fixed in closely related species, and, when located in stem structures, often disrupt Watson-Crick pairing and display signs of compensatory evolution. These observations make it possible to classify ∼90% of all known pathogenic mutations as deleterious together with only ∼30% of polymorphisms. These polymorphisms segregate at frequencies that are more than two times lower than frequencies of polymorphisms classified as benign, indicating that at least ∼30% of known polymorphisms in mitochondrial tRNAs affect fitness negatively. acknowledgement: | The author thanks P. Andolfatto, D. Bachtrog, N. Esipova, S. Makeev, A. Kondrashov, V. Ramensky, V. Tumanyan and P. Vlasov for a critical reading of the manuscript. The author is an NSF Graduate Research Fellow. This work was supported by a Contract of the Russian Ministry of Science and Education (02.434.11.1008) and a grant on Molecular and Cellular Biology from RAS. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kondrashov F. Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. Human Molecular Genetics. 2005;14(16):2415-2419. doi:10.1093/hmg/ddi243 apa: Kondrashov, F. (2005). Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. Human Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/ddi243 chicago: Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially Encoded Human TRNAs.” Human Molecular Genetics. Oxford University Press, 2005. https://doi.org/10.1093/hmg/ddi243. ieee: F. Kondrashov, “Prediction of pathogenic mutations in mitochondrially encoded human tRNAs,” Human Molecular Genetics, vol. 14, no. 16. Oxford University Press, pp. 2415–2419, 2005. ista: Kondrashov F. 2005. Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. Human Molecular Genetics. 14(16), 2415–2419. mla: Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially Encoded Human TRNAs.” Human Molecular Genetics, vol. 14, no. 16, Oxford University Press, 2005, pp. 2415–19, doi:10.1093/hmg/ddi243. short: F. Kondrashov, Human Molecular Genetics 14 (2005) 2415–2419. date_created: 2018-12-11T11:49:00Z date_published: 2005-08-15T00:00:00Z date_updated: 2021-01-12T08:21:10Z day: '15' doi: 10.1093/hmg/ddi243 extern: 1 intvolume: ' 14' issue: '16' month: '08' page: 2415 - 2419 publication: Human Molecular Genetics publication_status: published publisher: Oxford University Press publist_id: '6767' quality_controlled: 0 status: public title: Prediction of pathogenic mutations in mitochondrially encoded human tRNAs type: journal_article volume: 14 year: '2005' ... --- _id: '880' abstract: - lang: eng text: Here, I describe a case of loss of the D-arm by mitochondrial cysteine tRNA in the nine-banded armadillo (Dasypus novemcinctus) convergent with mt tRNASer(AGY). Such evolution sheds light on the relationship between structure and function of tRNA molecules and its impact on the patterns of molecular evolution. article_processing_charge: No author: - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kondrashov F. The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. Biofizika. 2005;50(3):396-403. apa: Kondrashov, F. (2005). The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. Biofizika. Pleiades Publishing. chicago: Kondrashov, Fyodor. “The Convergent Evolution of the Secondary Structure of Mitochondrial Cysteine TRNA in the Nine-Banded Armadillo Dasypus Novemcinctus.” Biofizika. Pleiades Publishing, 2005. ieee: F. Kondrashov, “The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus,” Biofizika, vol. 50, no. 3. Pleiades Publishing, pp. 396–403, 2005. ista: Kondrashov F. 2005. The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. Biofizika. 50(3), 396–403. mla: Kondrashov, Fyodor. “The Convergent Evolution of the Secondary Structure of Mitochondrial Cysteine TRNA in the Nine-Banded Armadillo Dasypus Novemcinctus.” Biofizika, vol. 50, no. 3, Pleiades Publishing, 2005, pp. 396–403. short: F. Kondrashov, Biofizika 50 (2005) 396–403. date_created: 2018-12-11T11:48:59Z date_published: 2005-05-01T00:00:00Z date_updated: 2021-01-12T08:21:07Z day: '01' extern: '1' external_id: pmid: - '15977827' intvolume: ' 50' issue: '3' language: - iso: eng main_file_link: - url: http://pleiades.online/abstract/biophys/5/biophys0356_abstract.pdf month: '05' oa_version: None page: 396 - 403 pmid: 1 publication: Biofizika publication_status: published publisher: Pleiades Publishing publist_id: '6768' quality_controlled: '1' status: public title: The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2005' ... --- _id: '893' abstract: - lang: eng text: Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. For example, proteins from organisms with (G+C)-rich (or (A+T)-rich) genomes contain more (or fewer) amino acids encoded by (G+C)-rich codons. However, no universal trends in ongoing changes of amino acid frequencies have been reported. We compared sets of orthologous proteins encoded by triplets of closely related genomes from 15 taxa representing all three domains of life (Bacteria, Archaea and Eukaryota), and used phylogenies to polarize amino acid substitutions. Cys, Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly are consistently lost. The same nine amino acids are currently accrued or lost in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms. All amino acids with declining frequencies are thought to be among the first incorporated into the genetic code; conversely, all amino acids with increasing frequencies, except Ser, were probably recruited late. Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago, apparently continues to this day. acknowledgement: S.S. and I.A.A. were supported by the Genome Canada Foundation. author: - first_name: Ingo full_name: Jordan, Ingo K last_name: Jordan - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Ivan full_name: Adzhubeǐ, Ivan A last_name: Adzhubeǐ - first_name: Yuri full_name: Wolf, Yuri I last_name: Wolf - first_name: Eugene full_name: Koonin, Eugene V last_name: Koonin - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov - first_name: Shamil full_name: Sunyaev, Shamil R last_name: Sunyaev citation: ama: Jordan I, Kondrashov F, Adzhubeǐ I, et al. A universal trend of amino acid gain and loss in protein evolution. Nature. 2005;433(7026):633-638. doi:10.1038/nature03306 apa: Jordan, I., Kondrashov, F., Adzhubeǐ, I., Wolf, Y., Koonin, E., Kondrashov, A., & Sunyaev, S. (2005). A universal trend of amino acid gain and loss in protein evolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature03306 chicago: Jordan, Ingo, Fyodor Kondrashov, Ivan Adzhubeǐ, Yuri Wolf, Eugene Koonin, Alexey Kondrashov, and Shamil Sunyaev. “A Universal Trend of Amino Acid Gain and Loss in Protein Evolution.” Nature. Nature Publishing Group, 2005. https://doi.org/10.1038/nature03306. ieee: I. Jordan et al., “A universal trend of amino acid gain and loss in protein evolution,” Nature, vol. 433, no. 7026. Nature Publishing Group, pp. 633–638, 2005. ista: Jordan I, Kondrashov F, Adzhubeǐ I, Wolf Y, Koonin E, Kondrashov A, Sunyaev S. 2005. A universal trend of amino acid gain and loss in protein evolution. Nature. 433(7026), 633–638. mla: Jordan, Ingo, et al. “A Universal Trend of Amino Acid Gain and Loss in Protein Evolution.” Nature, vol. 433, no. 7026, Nature Publishing Group, 2005, pp. 633–38, doi:10.1038/nature03306. short: I. Jordan, F. Kondrashov, I. Adzhubeǐ, Y. Wolf, E. Koonin, A. Kondrashov, S. Sunyaev, Nature 433 (2005) 633–638. date_created: 2018-12-11T11:49:03Z date_published: 2005-02-10T00:00:00Z date_updated: 2021-01-12T08:21:23Z day: '10' doi: 10.1038/nature03306 extern: 1 intvolume: ' 433' issue: '7026' month: '02' page: 633 - 638 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6757' quality_controlled: 0 status: public title: A universal trend of amino acid gain and loss in protein evolution type: journal_article volume: 433 year: '2005' ... --- _id: '864' abstract: - lang: eng text: 'We present a method for prediction of functional sites in a set of aligned protein sequences. The method selects sites which are both well conserved and clustered together in space, as inferred from the 3D structures of proteins included in the alignment. We tested the method using 86 alignments from the NCBI CDD database, where the sites of experimentally determined ligand and/or macromolecular interactions are annotated. In agreement with earlier investigations, we found that functional site predictions are most successful when overall background sequence conservation is low, such that sites under evolutionary constraint become apparent. In addition, we found that averaging of conservation values across spatially clustered sites improves predictions under certain conditions: that is, when overall conservation is relatively high and when the site in question involves a large macromolecular binding interface. Under these conditions it is better to look for clusters of conserved sites than to look for particular conserved sites.' acknowledgement: We thank John Spouge, Ben Shoemaker, and Michael Galperin forhelpful suggestions, and the NIH Intramural Research Program forsupport. author: - first_name: Anna full_name: Panchenko, Anna R last_name: Panchenko - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Stephen full_name: Bryant, Stephen H last_name: Bryant citation: ama: Panchenko A, Kondrashov F, Bryant S. Prediction of functional sites by analysis of sequence and structure conservation. Protein Science. 2004;13(4):884-892. doi:10.1110/ps.03465504 apa: Panchenko, A., Kondrashov, F., & Bryant, S. (2004). Prediction of functional sites by analysis of sequence and structure conservation. Protein Science. Wiley-Blackwell. https://doi.org/10.1110/ps.03465504 chicago: Panchenko, Anna, Fyodor Kondrashov, and Stephen Bryant. “Prediction of Functional Sites by Analysis of Sequence and Structure Conservation.” Protein Science. Wiley-Blackwell, 2004. https://doi.org/10.1110/ps.03465504. ieee: A. Panchenko, F. Kondrashov, and S. Bryant, “Prediction of functional sites by analysis of sequence and structure conservation,” Protein Science, vol. 13, no. 4. Wiley-Blackwell, pp. 884–892, 2004. ista: Panchenko A, Kondrashov F, Bryant S. 2004. Prediction of functional sites by analysis of sequence and structure conservation. Protein Science. 13(4), 884–892. mla: Panchenko, Anna, et al. “Prediction of Functional Sites by Analysis of Sequence and Structure Conservation.” Protein Science, vol. 13, no. 4, Wiley-Blackwell, 2004, pp. 884–92, doi:10.1110/ps.03465504. short: A. Panchenko, F. Kondrashov, S. Bryant, Protein Science 13 (2004) 884–892. date_created: 2018-12-11T11:48:55Z date_published: 2004-04-01T00:00:00Z date_updated: 2021-01-12T08:20:22Z day: '01' doi: 10.1110/ps.03465504 extern: 1 intvolume: ' 13' issue: '4' month: '04' page: 884 - 892 publication: Protein Science publication_status: published publisher: Wiley-Blackwell publist_id: '6786' quality_controlled: 0 status: public title: Prediction of functional sites by analysis of sequence and structure conservation type: journal_article volume: 13 year: '2004' ... --- _id: '870' abstract: - lang: eng text: Only a fraction of eukaryotic genes affect the phenotype drastically. We compared 18 parameters in 1273 human morbid genes, known to cause diseases, and in the remaining 16 580 unambiguous human genes. Morbid genes evolve more slowly, have wider phylogenetic distributions, are more similar to essential genes of Drosophila melanogaster, code for longer proteins containing more alanine and glycine and less histidine, lysine and methionine, possess larger numbers of longer introns with more accurate splicing signals and have higher and broader expressions. These differences make it possible to classify as non-morbid 34% of human genes with unknown morbidity, when only 5% of known morbid genes are incorrectly classified as non-morbid. This classification can help to identify disease-causing genes among multiple candidates. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Aleksey full_name: Ogurtsov, Aleksey Yu last_name: Ogurtsov - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov citation: ama: Kondrashov F, Ogurtsov A, Kondrashov A. Bioinformatical assay of human gene morbidity. Nucleic Acids Research. 2004;32(5):1731-1737. doi:10.1093/nar/gkh330 apa: Kondrashov, F., Ogurtsov, A., & Kondrashov, A. (2004). Bioinformatical assay of human gene morbidity. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkh330 chicago: Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Bioinformatical Assay of Human Gene Morbidity.” Nucleic Acids Research. Oxford University Press, 2004. https://doi.org/10.1093/nar/gkh330. ieee: F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Bioinformatical assay of human gene morbidity,” Nucleic Acids Research, vol. 32, no. 5. Oxford University Press, pp. 1731–1737, 2004. ista: Kondrashov F, Ogurtsov A, Kondrashov A. 2004. Bioinformatical assay of human gene morbidity. Nucleic Acids Research. 32(5), 1731–1737. mla: Kondrashov, Fyodor, et al. “Bioinformatical Assay of Human Gene Morbidity.” Nucleic Acids Research, vol. 32, no. 5, Oxford University Press, 2004, pp. 1731–37, doi:10.1093/nar/gkh330. short: F. Kondrashov, A. Ogurtsov, A. Kondrashov, Nucleic Acids Research 32 (2004) 1731–1737. date_created: 2018-12-11T11:48:56Z date_published: 2004-01-01T00:00:00Z date_updated: 2021-01-12T08:20:37Z day: '01' doi: 10.1093/nar/gkh330 extern: 1 intvolume: ' 32' issue: '5' month: '01' page: 1731 - 1737 publication: Nucleic Acids Research publication_status: published publisher: Oxford University Press publist_id: '6780' quality_controlled: 0 status: public title: Bioinformatical assay of human gene morbidity type: journal_article volume: 32 year: '2004' ... --- _id: '875' abstract: - lang: eng text: The dominance of wild-type alleles and the concomitant recessivity of deleterious mutant alleles might have evolved by natural selection or could be a by-product of the molecular and physiological mechanisms of gene action. We compared the properties of human haplosufficient genes, whose wild-type alleles are dominant over loss-of-function alleles, with haploinsufficient (recessive wild-type) genes, which produce an abnormal phenotype when heterozygous for a loss-of-function allele. The fraction of haplosufficient genes is the highest among the genes that encode enzymes, which is best compatible with the physiological theory. Haploinsufficient genes, on average, have more paralogs than haplosufficient genes, supporting the idea that gene dosage could be important for the initial fixation of duplications. Thus, haplo(in)sufficiency of a gene and its propensity for duplication might have a common evolutionary basis. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Eugene full_name: Koonin, Eugene V last_name: Koonin citation: ama: Kondrashov F, Koonin E. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics. 2004;20(7):287-291. doi:10.1016/j.tig.2004.05.001 apa: Kondrashov, F., & Koonin, E. (2004). A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2004.05.001 chicago: Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.” Trends in Genetics. Elsevier, 2004. https://doi.org/10.1016/j.tig.2004.05.001. ieee: F. Kondrashov and E. Koonin, “A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications,” Trends in Genetics, vol. 20, no. 7. Elsevier, pp. 287–291, 2004. ista: Kondrashov F, Koonin E. 2004. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics. 20(7), 287–291. mla: Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.” Trends in Genetics, vol. 20, no. 7, Elsevier, 2004, pp. 287–91, doi:10.1016/j.tig.2004.05.001. short: F. Kondrashov, E. Koonin, Trends in Genetics 20 (2004) 287–291. date_created: 2018-12-11T11:48:58Z date_published: 2004-07-01T00:00:00Z date_updated: 2021-01-12T08:20:54Z day: '01' doi: 10.1016/j.tig.2004.05.001 extern: 1 intvolume: ' 20' issue: '7' month: '07' page: 287 - 291 publication: Trends in Genetics publication_status: published publisher: Elsevier publist_id: '6775' quality_controlled: 0 status: public title: A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications type: journal_article volume: 20 year: '2004' ... --- _id: '889' abstract: - lang: eng text: 'The function of protein and RNA molecules depends on complex epistatic interactions between sites. Therefore, the deleterious effect of a mutation can be suppressed by a compensatory second-site substitution. In relating a list of 86 pathogenic mutations in human IRNAs encoded by mitochondrial genes to the sequences of their mammalian orthologs, we noted that 52 pathogenic mutations were present in normal tRNAs of one or several nonhuman mammals. We found at least five mechanisms of compensation for 32 pathogenic mutations that destroyed a Watson-Crick pair in one of the four tRNA stems: restoration of the affected Watson-Crick interaction (25 cases), strengthening of another pair (4 cases), creation of a new pair (8 cases), changes of multiple interactions in the affected stem (11 cases) and changes involving the interaction between the loop and stem structures (3 cases). A pathogenic mutation and its compensating substitution are fixed in a lineage in rapid succession, and often a compensatory interaction evolves convergently in different clades. At least 10%, and perhaps as many as 50%, of all nucleotide substitutions in evolving mammalian (RNAs participate in such interactions, indicating that the evolution of tRNAs proceeds along highly epistatic fitness ridges.' acknowledgement: We thank J. Gillespie, M. Hahn, L. Horth, A. Kondrashov, A. Kopp, S. Nuzhdin, M. Turelli and D. Weinreich for their contributions. The authors were supported by a grant from the US National Institutes of Health to S. Nuzhdin, and A.D.K. is a Howard Hughes author: - first_name: Andrew full_name: Kern, Andrew D last_name: Kern - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kern A, Kondrashov F. Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. Nature Genetics. 2004;36(11):1207-1212. doi:10.1038/ng1451 apa: Kern, A., & Kondrashov, F. (2004). Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. Nature Genetics. Nature Publishing Group. https://doi.org/10.1038/ng1451 chicago: Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics. Nature Publishing Group, 2004. https://doi.org/10.1038/ng1451. ieee: A. Kern and F. Kondrashov, “Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs,” Nature Genetics, vol. 36, no. 11. Nature Publishing Group, pp. 1207–1212, 2004. ista: Kern A, Kondrashov F. 2004. Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. Nature Genetics. 36(11), 1207–1212. mla: Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics, vol. 36, no. 11, Nature Publishing Group, 2004, pp. 1207–12, doi:10.1038/ng1451. short: A. Kern, F. Kondrashov, Nature Genetics 36 (2004) 1207–1212. date_created: 2018-12-11T11:49:02Z date_published: 2004-11-01T00:00:00Z date_updated: 2021-01-12T08:21:17Z day: '01' doi: 10.1038/ng1451 extern: 1 intvolume: ' 36' issue: '11' month: '11' page: 1207 - 1212 publication: Nature Genetics publication_status: published publisher: Nature Publishing Group publist_id: '6759' quality_controlled: 0 status: public title: Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs type: journal_article volume: 36 year: '2004' ... --- _id: '898' abstract: - lang: eng text: New alleles become fixed owing to random drift of nearly neutral mutations or to positive selection of substantially advantageous mutations. After decades of debate, the fraction of fixations driven by selection remains uncertain. Within 9,390 genes, we analysed 28,196 codons at which rat and mouse differ from each other at two nucleotide sites and 1,982 codons with three differences. At codons where rat-mouse divergence involved two non-synonymous substitutions, both of them occurred in the same lineage, either rat or mouse, in 64% of cases; however, independent substitutions would occur in the same lineage with a probability of only 50%. All three non-synonymous substitutions occurred in the same lineage for 46% of codons, instead of the 25% expected. Furthermore, comparison of 12 pairs of prokaryotic genomes also shows clumping of multiple non-synonymous substitutions in the same lineage. This pattern cannot be explained by correlated mutation or episodes of relaxed negative selection, but instead indicates that positive selection acts at many sites of rapid, successive amino acid replacement. acknowledgement: We thank N. Bierne for a number of suggestions. G.A.B. was supported by a BWF graduate fellowship. S.S. was supported by Genome Canada Foundation. author: - first_name: Georgii full_name: Bazykin, Georgii A last_name: Bazykin - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Aleksey full_name: Ogurtsov, Aleksey Yu last_name: Ogurtsov - first_name: Shamil full_name: Sunyaev, Shamil R last_name: Sunyaev - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov citation: ama: Bazykin G, Kondrashov F, Ogurtsov A, Sunyaev S, Kondrashov A. Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature. 2004;429(6991):558-562. doi:10.1038/nature02601 apa: Bazykin, G., Kondrashov, F., Ogurtsov, A., Sunyaev, S., & Kondrashov, A. (2004). Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature. Nature Publishing Group. https://doi.org/10.1038/nature02601 chicago: Bazykin, Georgii, Fyodor Kondrashov, Aleksey Ogurtsov, Shamil Sunyaev, and Alexey Kondrashov. “Positive Selection at Sites of Multiple Amino Acid Replacements since Rat-Mouse Divergence.” Nature. Nature Publishing Group, 2004. https://doi.org/10.1038/nature02601. ieee: G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, and A. Kondrashov, “Positive selection at sites of multiple amino acid replacements since rat-mouse divergence,” Nature, vol. 429, no. 6991. Nature Publishing Group, pp. 558–562, 2004. ista: Bazykin G, Kondrashov F, Ogurtsov A, Sunyaev S, Kondrashov A. 2004. Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature. 429(6991), 558–562. mla: Bazykin, Georgii, et al. “Positive Selection at Sites of Multiple Amino Acid Replacements since Rat-Mouse Divergence.” Nature, vol. 429, no. 6991, Nature Publishing Group, 2004, pp. 558–62, doi:10.1038/nature02601. short: G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, A. Kondrashov, Nature 429 (2004) 558–562. date_created: 2018-12-11T11:49:05Z date_published: 2004-06-03T00:00:00Z date_updated: 2021-01-12T08:21:37Z day: '03' doi: 10.1038/nature02601 extern: 1 intvolume: ' 429' issue: '6991' month: '06' page: 558 - 562 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6746' quality_controlled: 0 status: public title: Positive selection at sites of multiple amino acid replacements since rat-mouse divergence type: journal_article volume: 429 year: '2004' ... --- _id: '902' abstract: - lang: eng text: 'We compare the functional spectrum of protein evolution in two separate animal lineages with respect to two hypotheses: (1) rates of divergence are distributed similarly among functional classes within both lineages, indicating that selective pressure on the proteome is largely independent of organismic-level biological requirements; and (2) rates of divergence are distributed differently among functional classes within each lineage, indicating species-specific selective regimes impact genome-wide substitutional patterns. Integrating comparative genome sequence with data from tissue-specific expressed-sequence-tag (EST) libraries and detailed database annotations, we find a functional genomic signature of rapid evolution and selective constraint shared between mammalian and nematode lineages despite their extensive morphological and ecological differences and distant common ancestry. In both phyla, we find evidence of accelerated evolution among components of molecular systems involved in coevolutionary change. In mammals, lineage-specific fast evolving genes include those involved in reproduction, immunity, and possibly, maternal-fetal conflict. Likelihood ratio tests provide evidence for positive selection in these rapidly evolving functional categories in mammals. In contrast, slowly evolving genes, in terms of amino acid or insertion/deletion (indel) change, in both phyla are involved in core molecular processes such as transcription, translation, and protein transport. Thus, strong purifying selection appears to act on the same core cellular processes in both mammalian and nematode lineages, whereas positive and/or relaxed selection acts on different biological processes in each lineage.' acknowledgement: |- We thank all members of the Hartl lab for their friendly support and Guillaume Achaz for valuable comments. We also thank the Sanger Institute and the Genome Sequencing Center at Wash- ington University, St. Louis and Lincoln Stein for providing un- finished C. briggsae sequence. Special thanks to the Bauer Center for Genomics Research at Harvard University and Gordon Kindl- mann at the University of Utah Scientific Computing and Imag- ing Institute for computational resources. R.J.K. is financially supported by a postdoctoral fellowship from the Natural Sciences and Engineering Research Council of Canada. The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 USC section 1734 solely to indicate this fact. author: - first_name: Cristian full_name: Castillo-Davis, Cristian I last_name: Castillo Davis - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Daniel full_name: Hartl, Daniel L last_name: Hartl - first_name: Rob full_name: Kulathinal, Rob J last_name: Kulathinal citation: ama: 'Castillo Davis C, Kondrashov F, Hartl D, Kulathinal R. The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. Genome Research. 2004;14(5):802-811. doi:10.1101/gr.2195604' apa: 'Castillo Davis, C., Kondrashov, F., Hartl, D., & Kulathinal, R. (2004). The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. Genome Research. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gr.2195604' chicago: 'Castillo Davis, Cristian, Fyodor Kondrashov, Daniel Hartl, and Rob Kulathinal. “The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint.” Genome Research. Cold Spring Harbor Laboratory Press, 2004. https://doi.org/10.1101/gr.2195604.' ieee: 'C. Castillo Davis, F. Kondrashov, D. Hartl, and R. Kulathinal, “The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint,” Genome Research, vol. 14, no. 5. Cold Spring Harbor Laboratory Press, pp. 802–811, 2004.' ista: 'Castillo Davis C, Kondrashov F, Hartl D, Kulathinal R. 2004. The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. Genome Research. 14(5), 802–811.' mla: 'Castillo Davis, Cristian, et al. “The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint.” Genome Research, vol. 14, no. 5, Cold Spring Harbor Laboratory Press, 2004, pp. 802–11, doi:10.1101/gr.2195604.' short: C. Castillo Davis, F. Kondrashov, D. Hartl, R. Kulathinal, Genome Research 14 (2004) 802–811. date_created: 2018-12-11T11:49:06Z date_published: 2004-05-01T00:00:00Z date_updated: 2021-01-12T08:21:47Z day: '01' doi: 10.1101/gr.2195604 extern: 1 intvolume: ' 14' issue: '5' month: '05' page: 802 - 811 publication: Genome Research publication_status: published publisher: Cold Spring Harbor Laboratory Press publist_id: '6750' quality_controlled: 0 status: public title: 'The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint' type: journal_article volume: 14 year: '2004' ... --- _id: '847' abstract: - lang: eng text: The accumulation of genome-wide information on single nucleotide polymorphisms in humans provides an unprecedented opportunity to detect the evolutionary forces responsible for heterogeneity of the level of genetic variability across loci. Previous studies have shown that history of recombination events has produced long haplotype blocks in the human genome, which contribute to this heterogeneity. Other factors, however, such as natural selection or the heterogeneity of mutation rates across loci, may also lead to heterogeneity of genetic variability. We compared synonymous and non-synonymous variability within human genes with their divergence from murine orthologs. We separately analyzed the non-synonymous variants predicted to damage protein structure or function and the variants predicted to be functionally benign. The predictions were based on comparative sequence analysis and, in some cases, on the analysis of protein structure. A strong correlation between non-synonymous, benign variability and non-synonymous human-mouse divergence suggests that selection played an important role in shaping the pattern of variability in coding regions of human genes. However, the lack of correlation between deleterious variability and evolutionary divergence shows that a substantial proportion of the observed non-synonymous single-nucleotide polymorphisms reduces fitness and never reaches fixation. Evolutionary and medical implications of the impact of selection on human polymorphisms are discussed. acknowledgement: We are grateful to Alexey Kondrashov and Alison Wellman for the careful reading of the manuscript and providing us with their valuable comments. author: - first_name: Shamil full_name: Sunyaev, Shamil R last_name: Sunyaev - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Peer full_name: Bork, Peer last_name: Bork - first_name: Vasily full_name: Ramensky, Vasily last_name: Ramensky citation: ama: Sunyaev S, Kondrashov F, Bork P, Ramensky V. Impact of selection, mutation rate and genetic drift on human genetic variation. Human Molecular Genetics. 2003;12(24):3325-3330. doi:10.1093/hmg/ddg359 apa: Sunyaev, S., Kondrashov, F., Bork, P., & Ramensky, V. (2003). Impact of selection, mutation rate and genetic drift on human genetic variation. Human Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/ddg359 chicago: Sunyaev, Shamil, Fyodor Kondrashov, Peer Bork, and Vasily Ramensky. “Impact of Selection, Mutation Rate and Genetic Drift on Human Genetic Variation.” Human Molecular Genetics. Oxford University Press, 2003. https://doi.org/10.1093/hmg/ddg359. ieee: S. Sunyaev, F. Kondrashov, P. Bork, and V. Ramensky, “Impact of selection, mutation rate and genetic drift on human genetic variation,” Human Molecular Genetics, vol. 12, no. 24. Oxford University Press, pp. 3325–3330, 2003. ista: Sunyaev S, Kondrashov F, Bork P, Ramensky V. 2003. Impact of selection, mutation rate and genetic drift on human genetic variation. Human Molecular Genetics. 12(24), 3325–3330. mla: Sunyaev, Shamil, et al. “Impact of Selection, Mutation Rate and Genetic Drift on Human Genetic Variation.” Human Molecular Genetics, vol. 12, no. 24, Oxford University Press, 2003, pp. 3325–30, doi:10.1093/hmg/ddg359. short: S. Sunyaev, F. Kondrashov, P. Bork, V. Ramensky, Human Molecular Genetics 12 (2003) 3325–3330. date_created: 2018-12-11T11:48:49Z date_published: 2003-12-15T00:00:00Z date_updated: 2021-01-12T08:19:29Z day: '15' doi: 10.1093/hmg/ddg359 extern: 1 intvolume: ' 12' issue: '24' month: '12' page: 3325 - 3330 publication: Human Molecular Genetics publication_status: published publisher: Oxford University Press publist_id: '6803' quality_controlled: 0 status: public title: Impact of selection, mutation rate and genetic drift on human genetic variation type: journal_article volume: 12 year: '2003' ... --- _id: '876' abstract: - lang: eng text: Alternative splicing is thought to be a major source of functional diversity in animal proteins. We analyzed the evolutionary conservation of proteins encoded by alternatively spliced genes and predicted the ancestral state for 73 cases of alternative splicing (25 insertions and 48 deletions). The amino acid sequences of most of the inserts in proteins produced by alternative splicing are as conserved as the surrounding sequences. Thus, alternative splicing often creates novel isoforms by the insertion of new, functional protein sequences that probably originated from noncoding sequences of introns. acknowledgement: We thank Peer Bork, Mikhail Gelfand, Alexey Kondrashov, David Lipman and Shamil Sunyaev for critical reading of the manuscript and useful suggestions and the Koonin group members for helpful discussions. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Eugene full_name: Koonin, Eugene V last_name: Koonin citation: ama: 'Kondrashov F, Koonin E. Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences. Trends in Genetics. 2003;19(3):115-119. doi:10.1016/S0168-9525(02)00029-X' apa: 'Kondrashov, F., & Koonin, E. (2003). Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences. Trends in Genetics. Elsevier. https://doi.org/10.1016/S0168-9525(02)00029-X' chicago: 'Kondrashov, Fyodor, and Eugene Koonin. “Evolution of Alternative Splicing: Deletions, Insertions and Origin of Functional Parts of Proteins from Intron Sequences.” Trends in Genetics. Elsevier, 2003. https://doi.org/10.1016/S0168-9525(02)00029-X.' ieee: 'F. Kondrashov and E. Koonin, “Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences,” Trends in Genetics, vol. 19, no. 3. Elsevier, pp. 115–119, 2003.' ista: 'Kondrashov F, Koonin E. 2003. Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences. Trends in Genetics. 19(3), 115–119.' mla: 'Kondrashov, Fyodor, and Eugene Koonin. “Evolution of Alternative Splicing: Deletions, Insertions and Origin of Functional Parts of Proteins from Intron Sequences.” Trends in Genetics, vol. 19, no. 3, Elsevier, 2003, pp. 115–19, doi:10.1016/S0168-9525(02)00029-X.' short: F. Kondrashov, E. Koonin, Trends in Genetics 19 (2003) 115–119. date_created: 2018-12-11T11:48:58Z date_published: 2003-01-01T00:00:00Z date_updated: 2021-01-12T08:20:58Z day: '01' doi: 10.1016/S0168-9525(02)00029-X extern: 1 intvolume: ' 19' issue: '3' month: '01' page: 115 - 119 publication: Trends in Genetics publication_status: published publisher: Elsevier publist_id: '6776' quality_controlled: 0 status: public title: 'Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences' type: journal_article volume: 19 year: '2003' ... --- _id: '885' abstract: - lang: eng text: We study fitness landscape in the space of protein sequences by relating sets of human pathogenic missense mutations in 32 proteins to amino acid substitutions that occurred in the course of evolution of these proteins. On average, ≈10% of deviations of a nonhuman protein from its human ortholog are compensated pathogenic deviations (CPDs), i.e., are caused by an amino acid substitution that, at this site, would be pathogenic to humans. Normal functioning of a CPD-containing protein must be caused by other, compensatory deviations of the nonhuman species from humans. Together, a CPD and the corresponding compensatory deviation form a Dobzhansky-Muller incompatibility that can be visualized as the corner on a fitness ridge. Thus, proteins evolve along fitness ridges which contain only ≈10 steps between sucessive corners. The fraction of CPDs among all deviations of a protein from its human ortholog does not increase with the evolutionary distance between the proteins, indicating that subtitutions that carry evolving proteins around these corners occur in rapid succession, driven by positive selection. Data on fitness of interspecies hybrids suggest that the compensatory change that makes a CPD fit usually occurs within the same protein. Data on protein structures and on cooccurrence of amino acids at different sites of multiple orthologous proteins often make it possible to provisionally identify the substitution that compensates a partiCUlar CPD. article_processing_charge: No article_type: original author: - first_name: Alexey full_name: Kondrashov, Alexey last_name: Kondrashov - first_name: Shamil full_name: Sunyaev, Shamil last_name: Sunyaev - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kondrashov A, Sunyaev S, Kondrashov F. Dobzhansky-Muller incompatibilities in protein evolution. PNAS. 2002;99(23):14878-14883. doi:10.1073/pnas.232565499 apa: Kondrashov, A., Sunyaev, S., & Kondrashov, F. (2002). Dobzhansky-Muller incompatibilities in protein evolution. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.232565499 chicago: Kondrashov, Alexey, Shamil Sunyaev, and Fyodor Kondrashov. “Dobzhansky-Muller Incompatibilities in Protein Evolution.” PNAS. National Academy of Sciences, 2002. https://doi.org/10.1073/pnas.232565499. ieee: A. Kondrashov, S. Sunyaev, and F. Kondrashov, “Dobzhansky-Muller incompatibilities in protein evolution,” PNAS, vol. 99, no. 23. National Academy of Sciences, pp. 14878–14883, 2002. ista: Kondrashov A, Sunyaev S, Kondrashov F. 2002. Dobzhansky-Muller incompatibilities in protein evolution. PNAS. 99(23), 14878–14883. mla: Kondrashov, Alexey, et al. “Dobzhansky-Muller Incompatibilities in Protein Evolution.” PNAS, vol. 99, no. 23, National Academy of Sciences, 2002, pp. 14878–83, doi:10.1073/pnas.232565499. short: A. Kondrashov, S. Sunyaev, F. Kondrashov, PNAS 99 (2002) 14878–14883. date_created: 2018-12-11T11:49:01Z date_published: 2002-11-12T00:00:00Z date_updated: 2023-07-26T09:48:37Z day: '12' doi: 10.1073/pnas.232565499 extern: '1' external_id: pmid: - '12403824' intvolume: ' 99' issue: '23' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC137512/ month: '11' oa: 1 oa_version: Published Version page: 14878 - 14883 pmid: 1 publication: PNAS publication_identifier: issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences publist_id: '6763' quality_controlled: '1' scopus_import: '1' status: public title: Dobzhansky-Muller incompatibilities in protein evolution type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 99 year: '2002' ... --- _id: '897' abstract: - lang: eng text: "Transcription is a slow and expensive process: in eukaryotes, approximately 20 nucleotides can be transcribed per second at the expense of at least two ATP molecules per nucleotide. Thus, at least for highly expressed genes, transcription of long introns, which are particularly common in mammals, is costly. Using data on the expression of genes that encode proteins in Caenorhabditis elegans and Homo sapiens, we show that introns in highly expressed genes are substantially shorter than those in genes that are expressed at low levels. This difference is greater in humans, such that introns are, on average, 14 times shorter in highly expressed genes than in genes with low expression, whereas in C. Elegans the difference in intron length is only twofold. In contrast, the density of introns in a gene does not strongly depend on the level of gene expression. Thus, natural selection appears to favor short introns in highly expressed genes to minimize the cost of transcription and other molecular processes, such as splicing.\r\n" acknowledgement: We are grateful to A. Kondrashov, I. Rogozin and A. Feldman for reading the manuscript and P. Bouman, J. Cherry, J. Blumensteil and T. Kim for discussion. article_processing_charge: No article_type: original author: - first_name: Cristian full_name: Castillo Davis, Cristian last_name: Castillo Davis - first_name: Sergei full_name: Mekhedov, Sergei last_name: Mekhedov - first_name: Daniel full_name: Hartl, Daniel last_name: Hartl - first_name: Eugene full_name: Koonin, Eugene last_name: Koonin - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Castillo Davis C, Mekhedov S, Hartl D, Koonin E, Kondrashov F. Selection for short introns in highly expressed genes. Nature Genetics. 2002;31(4):415-418. doi:10.1038/ng940 apa: Castillo Davis, C., Mekhedov, S., Hartl, D., Koonin, E., & Kondrashov, F. (2002). Selection for short introns in highly expressed genes. Nature Genetics. Nature Publishing Group. https://doi.org/10.1038/ng940 chicago: Castillo Davis, Cristian, Sergei Mekhedov, Daniel Hartl, Eugene Koonin, and Fyodor Kondrashov. “Selection for Short Introns in Highly Expressed Genes.” Nature Genetics. Nature Publishing Group, 2002. https://doi.org/10.1038/ng940. ieee: C. Castillo Davis, S. Mekhedov, D. Hartl, E. Koonin, and F. Kondrashov, “Selection for short introns in highly expressed genes,” Nature Genetics, vol. 31, no. 4. Nature Publishing Group, pp. 415–418, 2002. ista: Castillo Davis C, Mekhedov S, Hartl D, Koonin E, Kondrashov F. 2002. Selection for short introns in highly expressed genes. Nature Genetics. 31(4), 415–418. mla: Castillo Davis, Cristian, et al. “Selection for Short Introns in Highly Expressed Genes.” Nature Genetics, vol. 31, no. 4, Nature Publishing Group, 2002, pp. 415–18, doi:10.1038/ng940. short: C. Castillo Davis, S. Mekhedov, D. Hartl, E. Koonin, F. Kondrashov, Nature Genetics 31 (2002) 415–418. date_created: 2018-12-11T11:49:05Z date_published: 2002-08-01T00:00:00Z date_updated: 2023-07-26T09:45:30Z day: '01' doi: 10.1038/ng940 extern: '1' external_id: pmid: - '12134150' intvolume: ' 31' issue: '4' language: - iso: eng month: '08' oa_version: None page: 415 - 418 pmid: 1 publication: Nature Genetics publication_status: published publisher: Nature Publishing Group publist_id: '6751' quality_controlled: '1' scopus_import: '1' status: public title: Selection for short introns in highly expressed genes type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 31 year: '2002' ... --- _id: '871' abstract: - lang: eng text: 'BACKGROUND: Gene duplications have a major role in the evolution of new biological functions. Theoretical studies often assume that a duplication per se is selectively neutral and that, following a duplication, one of the gene copies is freed from purifying (stabilizing) selection, which creates the potential for evolution of a new function. RESULTS: In search of systematic evidence of accelerated evolution after duplication, we used data from 26 bacterial, six archaeal, and seven eukaryotic genomes to compare the mode and strength of selection acting on recently duplicated genes (paralogs) and on similarly diverged, unduplicated orthologous genes in different species. We find that the ratio of nonsynonymous to synonymous substitutions (Kn/Ks) in most paralogous pairs is <<1 and that paralogs typically evolve at similar rates, without significant asymmetry, indicating that both paralogs produced by a duplication are subject to purifying selection. This selection is, however, substantially weaker than the purifying selection affecting unduplicated orthologs that have diverged to the same extent as the analyzed paralogs. Most of the recently duplicated genes appear to be involved in various forms of environmental response; in particular, many of them encode membrane and secreted proteins. CONCLUSIONS: The results of this analysis indicate that recently duplicated paralogs evolve faster than orthologs with the same level of divergence and similar functions, but apparently do not experience a phase of neutral evolution. We hypothesize that gene duplications that persist in an evolving lineage are beneficial from the time of their origin, due primarily to a protein dosage effect in response to variable environmental conditions; duplications are likely to give rise to new functions at a later phase of their evolution once a higher level of divergence is reached.' acknowledgement: We are grateful to A.S. Kondrashov for numerous helpful suggestions, to I. King Jordan, M.A. Roytberg, J.L. Spouge and D.A. Kondrashov for useful discussions and to A.S. Kondrashov, I. King Jordan and D.J. Lipman for critical reading of the manuscript. article_processing_charge: No article_type: original author: - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Igor full_name: Rogozin, Igor last_name: Rogozin - first_name: Yuri full_name: Wolf, Yuri last_name: Wolf - first_name: Eugene full_name: Koonin, Eugene last_name: Koonin citation: ama: Kondrashov F, Rogozin I, Wolf Y, Koonin E. Selection in the evolution of gene duplications . Genome Biology. 2002;3(2). doi:10.1186/gb-2002-3-2-research0008 apa: Kondrashov, F., Rogozin, I., Wolf, Y., & Koonin, E. (2002). Selection in the evolution of gene duplications . Genome Biology. BioMed Central. https://doi.org/10.1186/gb-2002-3-2-research0008 chicago: Kondrashov, Fyodor, Igor Rogozin, Yuri Wolf, and Eugene Koonin. “Selection in the Evolution of Gene Duplications .” Genome Biology. BioMed Central, 2002. https://doi.org/10.1186/gb-2002-3-2-research0008. ieee: F. Kondrashov, I. Rogozin, Y. Wolf, and E. Koonin, “Selection in the evolution of gene duplications ,” Genome Biology, vol. 3, no. 2. BioMed Central, 2002. ista: Kondrashov F, Rogozin I, Wolf Y, Koonin E. 2002. Selection in the evolution of gene duplications . Genome Biology. 3(2). mla: Kondrashov, Fyodor, et al. “Selection in the Evolution of Gene Duplications .” Genome Biology, vol. 3, no. 2, BioMed Central, 2002, doi:10.1186/gb-2002-3-2-research0008. short: F. Kondrashov, I. Rogozin, Y. Wolf, E. Koonin, Genome Biology 3 (2002). date_created: 2018-12-11T11:48:57Z date_published: 2002-01-01T00:00:00Z date_updated: 2023-07-26T11:48:27Z day: '01' doi: 10.1186/gb-2002-3-2-research0008 extern: '1' external_id: pmid: - '11864370' intvolume: ' 3' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC65685/ month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Genome Biology publication_identifier: issn: - 1465-6906 publication_status: published publisher: BioMed Central publist_id: '6781' quality_controlled: '1' scopus_import: '1' status: public title: 'Selection in the evolution of gene duplications ' type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 3 year: '2002' ... --- _id: '859' abstract: - lang: eng text: The polymeric ubiquitin (poly-u) genes are composed of tandem 228-bp repeats with no spacer sequences between individual monomer units. Ubiquitin is one of the most conserved proteins known to date, and the individual units within a number of poly-u genes are significantly more similar to each other than would be expected if each unit evolved independently. It has been proposed that the rather striking similarity among poly-u monomers in some lineages is caused by a series of homogenization events. Here we report the sequences of the polyubiquitin-C (Ubc) genes in two mouse strains. Analysis of these sequences, as well as those of the previously reported Chinese hamster and rat poly-u genes, supports the assertion that the homogenization of the ubiquitin-C gene in rodents is due to unequal crossing-over events. The sequence divergence of noncoding DNA was used to estimate the frequency of unequal crossing-over events (6.3 x 10-5 events per generation) in the Ubc gene, as well as to provide evidence of apparent selection in the poly-u gene. acknowledgement: We are thankful to J.A. Southerland and P.L. Jiang for technical assistance in DNA sequencing, as well as to Y.I. Pavlov for helpful discussions. This work was supported by public Health Service Research Grant AI45135 from the Institute of Allergy and Infectious Diseases, National Institutes of Health. article_processing_charge: No article_type: original author: - first_name: Andrey full_name: Perelygin, Andrey last_name: Perelygin - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Igor full_name: Rogozin, Igor last_name: Rogozin - first_name: Margo full_name: Brinton, Margo last_name: Brinton citation: ama: Perelygin A, Kondrashov F, Rogozin I, Brinton M. Evolution of the mouse polyubiquitin C gene. Journal of Molecular Evolution. 2002;55(2):202-210. doi:10.1007/s00239-002-2318-0 apa: Perelygin, A., Kondrashov, F., Rogozin, I., & Brinton, M. (2002). Evolution of the mouse polyubiquitin C gene. Journal of Molecular Evolution. Springer. https://doi.org/10.1007/s00239-002-2318-0 chicago: Perelygin, Andrey, Fyodor Kondrashov, Igor Rogozin, and Margo Brinton. “Evolution of the Mouse Polyubiquitin C Gene.” Journal of Molecular Evolution. Springer, 2002. https://doi.org/10.1007/s00239-002-2318-0. ieee: A. Perelygin, F. Kondrashov, I. Rogozin, and M. Brinton, “Evolution of the mouse polyubiquitin C gene,” Journal of Molecular Evolution, vol. 55, no. 2. Springer, pp. 202–210, 2002. ista: Perelygin A, Kondrashov F, Rogozin I, Brinton M. 2002. Evolution of the mouse polyubiquitin C gene. Journal of Molecular Evolution. 55(2), 202–210. mla: Perelygin, Andrey, et al. “Evolution of the Mouse Polyubiquitin C Gene.” Journal of Molecular Evolution, vol. 55, no. 2, Springer, 2002, pp. 202–10, doi:10.1007/s00239-002-2318-0. short: A. Perelygin, F. Kondrashov, I. Rogozin, M. Brinton, Journal of Molecular Evolution 55 (2002) 202–210. date_created: 2018-12-11T11:48:53Z date_published: 2002-01-01T00:00:00Z date_updated: 2023-07-26T12:01:34Z day: '01' doi: 10.1007/s00239-002-2318-0 extern: '1' external_id: pmid: - '12107596' intvolume: ' 55' issue: '2' language: - iso: eng month: '01' oa_version: None page: 202 - 210 pmid: 1 publication: Journal of Molecular Evolution publication_identifier: issn: - 0022-2844 publication_status: published publisher: Springer publist_id: '6787' quality_controlled: '1' scopus_import: '1' status: public title: Evolution of the mouse polyubiquitin C gene type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 55 year: '2002' ... --- _id: '888' abstract: - lang: eng text: 'BACKGROUND: Detection of changes in a protein''s evolutionary rate may reveal cases of change in that protein''s function. We developed and implemented a simple relative rates test in an attempt to assess the rate constancy of protein evolution and to detect cases of functional diversification between orthologous proteins. The test was performed on clusters of orthologous protein sequences from complete bacterial genomes (Chlamydia trachomatis, C. muridarum and Chlamydophila pneumoniae), complete archaeal genomes (Pyrococcus horikoshii, P. abyssi and P. furiosus) and partially sequenced mammalian genomes (human, mouse and rat). RESULTS: Amino-acid sequence evolution rates are significantly correlated on different branches of phylogenetic trees representing the great majority of analyzed orthologous protein sets from all three domains of life. However, approximately 1% of the proteins from each group of species deviates from this pattern and instead shows variation that is consistent with an acceleration of the rate of amino-acid substitution, which may be due to functional diversification. Most of the putative functionally diversified proteins from all three species groups are predicted to function at the periphery of the cells and mediate their interaction with the environment. CONCLUSIONS: Relative rates of protein evolution are remarkably constant for the three species groups analyzed here. Deviations from this rate constancy are probably due to changes in selective constraints associated with diversification between orthologs. Functional diversification between orthologs is thought to be a relatively rare event. However, the resolution afforded by the test designed specifically for genomic-scale datasets allowed us to identify numerous cases of possible functional diversification between orthologous proteins.' acknowledgement: We thank Alexey Kondrashov for many helpful discussions and constructive criticisms, Charles DeLisi, David Landsman, Detlef Leipe, Wojciech Makalowski and Itai Yanai for critical reading of the manuscript and constructive comments and L. Aravind for advice on protein function prediction. The release of the unpublished P. furiosus genome sequence by the Utah Genome Center at the University of Utah is acknowledged and appreciated. article_number: research0053.1 article_processing_charge: No article_type: original author: - first_name: Ingo full_name: Jordan, Ingo last_name: Jordan - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Igor full_name: Rogozin, Igor last_name: Rogozin - first_name: Roman full_name: Tatusov, Roman last_name: Tatusov - first_name: Yuri full_name: Wolf, Yuri last_name: Wolf - first_name: Eugene full_name: Koonin, Eugene last_name: Koonin citation: ama: Jordan I, Kondrashov F, Rogozin I, Tatusov R, Wolf Y, Koonin E. Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins . Genome Biology. 2001;2(12). doi:10.1186/gb-2001-2-12-research0053 apa: Jordan, I., Kondrashov, F., Rogozin, I., Tatusov, R., Wolf, Y., & Koonin, E. (2001). Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins . Genome Biology. BioMed Central. https://doi.org/10.1186/gb-2001-2-12-research0053 chicago: Jordan, Ingo, Fyodor Kondrashov, Igor Rogozin, Roman Tatusov, Yuri Wolf, and Eugene Koonin. “Constant Relative Rate of Protein Evolution and Detection of Functional Diversification among Bacterial, Archaeal and Eukaryotic Proteins .” Genome Biology. BioMed Central, 2001. https://doi.org/10.1186/gb-2001-2-12-research0053. ieee: I. Jordan, F. Kondrashov, I. Rogozin, R. Tatusov, Y. Wolf, and E. Koonin, “Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins ,” Genome Biology, vol. 2, no. 12. BioMed Central, 2001. ista: Jordan I, Kondrashov F, Rogozin I, Tatusov R, Wolf Y, Koonin E. 2001. Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins . Genome Biology. 2(12), research0053.1. mla: Jordan, Ingo, et al. “Constant Relative Rate of Protein Evolution and Detection of Functional Diversification among Bacterial, Archaeal and Eukaryotic Proteins .” Genome Biology, vol. 2, no. 12, research0053.1, BioMed Central, 2001, doi:10.1186/gb-2001-2-12-research0053. short: I. Jordan, F. Kondrashov, I. Rogozin, R. Tatusov, Y. Wolf, E. Koonin, Genome Biology 2 (2001). date_created: 2018-12-11T11:49:02Z date_published: 2001-01-01T00:00:00Z date_updated: 2023-05-31T12:15:37Z day: '01' doi: 10.1186/gb-2001-2-12-research0053 extern: '1' external_id: pmid: - '11790256' intvolume: ' 2' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC64838/ month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Genome Biology publication_identifier: issn: - 1465-6906 publication_status: published publisher: BioMed Central publist_id: '6758' quality_controlled: '1' scopus_import: '1' status: public title: 'Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins ' type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 2 year: '2001' ... --- _id: '855' abstract: - lang: eng text: 'Motivation: The context of the start codon (typically, AUG) and the features of the 5′ Untranslated Regions (5′ UTRs) are important for understanding translation regulation in eukaryotic mRNAs and for accurate prediction of the coding region in genomic and cDNA sequences. The presence of AUG triplets in 5′ UTRs (upstream AUGs) might effect the initiation rate and, in the context of gene prediction, could reduce the accuracy of the identification of the authentic start. To reveal potential connections between the presence of upstream AUGs and other features of 5′ UTRs, such as their length and the start codon context, we undertook a systematic analysis of the available eukaryotic 5′ UTR sequences. Results: We show that a large fraction of 5′ UTRs in the available cDNA sequences, 15-53% depending on the organism, contain upstream ATGs. A negative correlation was observed between the information content of the translation start signal and the length of the 5′ UTR. Similarly, a negative correlation exists between the ''strength'' of the start context and the number of upstream ATGs. Typically, cDNAs containing long 5′ UTRs with multiple upstream ATGs have a ''weak'' start context, and in contrast, cDNAs containing short 5′ UTRs without ATGs have ''strong'' starts. These counter-intuitive results may be interpreted in terms of upstream AUGs having an important role in the regulation of translation efficiency by ensuring low basal translation level via double negative control and creating the potential for additional regulatory mechanisms. One of such mechanisms, supported by experimental studies of some mRNAs, includes removal of the AUG-containing portion of the 5′ UTR by alternative splicing.' acknowledgement: This work has been partially supported by EU 'TRADAT' project and by CNR Genetic Engineering (Italy), the RFBR grant for support of scientific schools (00-15-97968) and SD RAS grant for young scientists (AVK). The authors wish to thank J.Lyons-Weiler for helpful comments and A. Sorokin for help with the ATG_EVALUATOR program. article_processing_charge: No article_type: original author: - first_name: Igor full_name: Rogozin, Igor last_name: Rogozin - first_name: Alex full_name: Kochetov, Alex last_name: Kochetov - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Eugene full_name: Koonin, Eugene last_name: Koonin - first_name: Luciano full_name: Milanesi, Luciano last_name: Milanesi citation: ama: Rogozin I, Kochetov A, Kondrashov F, Koonin E, Milanesi L. Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ’weak’context of the start codon. Bioinformatics. 2001;17(10):890-900. doi:10.1093/bioinformatics/17.10.890 apa: Rogozin, I., Kochetov, A., Kondrashov, F., Koonin, E., & Milanesi, L. (2001). Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ’weak’context of the start codon. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/17.10.890 chicago: Rogozin, Igor, Alex Kochetov, Fyodor Kondrashov, Eugene Koonin, and Luciano Milanesi. “Presence of ATG Triplets in 5′ Untranslated Regions of Eukaryotic CDNAs Correlates with a ’weak’context of the Start Codon.” Bioinformatics. Oxford University Press, 2001. https://doi.org/10.1093/bioinformatics/17.10.890. ieee: I. Rogozin, A. Kochetov, F. Kondrashov, E. Koonin, and L. Milanesi, “Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ’weak’context of the start codon,” Bioinformatics, vol. 17, no. 10. Oxford University Press, pp. 890–900, 2001. ista: Rogozin I, Kochetov A, Kondrashov F, Koonin E, Milanesi L. 2001. Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ’weak’context of the start codon. Bioinformatics. 17(10), 890–900. mla: Rogozin, Igor, et al. “Presence of ATG Triplets in 5′ Untranslated Regions of Eukaryotic CDNAs Correlates with a ’weak’context of the Start Codon.” Bioinformatics, vol. 17, no. 10, Oxford University Press, 2001, pp. 890–900, doi:10.1093/bioinformatics/17.10.890. short: I. Rogozin, A. Kochetov, F. Kondrashov, E. Koonin, L. Milanesi, Bioinformatics 17 (2001) 890–900. date_created: 2018-12-11T11:48:52Z date_published: 2001-10-01T00:00:00Z date_updated: 2023-06-02T09:08:25Z day: '01' doi: 10.1093/bioinformatics/17.10.890 extern: '1' external_id: pmid: - '11673233' intvolume: ' 17' issue: '10' language: - iso: eng month: '10' oa_version: None page: 890 - 900 pmid: 1 publication: Bioinformatics publication_identifier: issn: - 1367-4803 publication_status: published publisher: Oxford University Press publist_id: '6795' quality_controlled: '1' scopus_import: '1' status: public title: Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a 'weak'context of the start codon type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 17 year: '2001' ... --- _id: '874' abstract: - lang: eng text: Sex is thought to facilitate accumulation of initially rare beneficial mutations by allowing simultaneous allele replacements at many loci. However, this advantage of sex depends on a restrictive assumption that the fitness of a genotype is determined by fitness potential, a single intermediate variable to which all loci contribute additively, so that new alleles can accumulate in any order. Individual-based simulations of sexual and asexual populations reveal that under generic selection, sex often retards adaptive evolution. When new alleles are beneficial only if they accumulate in a prescribed order, a sexual population may evolve two or more times slower than an asexual population because only asexual reproduction allows some overlap of successive allele replacements. Many other fitness surfaces lead to an even greater disadvantage of sex. Thus, either sex exists in spite of its impact on the rate of adaptive allele replacements, or natural fitness surfaces have rather specific properties, at least at the scale of intrapopulation genetic variability. article_processing_charge: No article_type: original author: - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Alexey full_name: Kondrashov, Alexey last_name: Kondrashov citation: ama: Kondrashov F, Kondrashov A. Multidimensional epistasis and the disadvantage of sex. PNAS. 2001;98(21):12089-12092. doi:10.1073/pnas.211214298 apa: Kondrashov, F., & Kondrashov, A. (2001). Multidimensional epistasis and the disadvantage of sex. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.211214298 chicago: Kondrashov, Fyodor, and Alexey Kondrashov. “Multidimensional Epistasis and the Disadvantage of Sex.” PNAS. National Academy of Sciences, 2001. https://doi.org/10.1073/pnas.211214298. ieee: F. Kondrashov and A. Kondrashov, “Multidimensional epistasis and the disadvantage of sex,” PNAS, vol. 98, no. 21. National Academy of Sciences, pp. 12089–12092, 2001. ista: Kondrashov F, Kondrashov A. 2001. Multidimensional epistasis and the disadvantage of sex. PNAS. 98(21), 12089–12092. mla: Kondrashov, Fyodor, and Alexey Kondrashov. “Multidimensional Epistasis and the Disadvantage of Sex.” PNAS, vol. 98, no. 21, National Academy of Sciences, 2001, pp. 12089–92, doi:10.1073/pnas.211214298. short: F. Kondrashov, A. Kondrashov, PNAS 98 (2001) 12089–12092. date_created: 2018-12-11T11:48:58Z date_published: 2001-10-09T00:00:00Z date_updated: 2023-06-02T08:18:22Z day: '09' doi: 10.1073/pnas.211214298 extern: '1' external_id: pmid: - '11593020' intvolume: ' 98' issue: '21' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59772/ month: '10' oa: 1 oa_version: Published Version page: 12089 - 12092 pmid: 1 publication: PNAS publication_identifier: issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences publist_id: '6774' quality_controlled: '1' scopus_import: '1' status: public title: Multidimensional epistasis and the disadvantage of sex type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 98 year: '2001' ... --- _id: '867' abstract: - lang: eng text: Genes with new functions often evolve by gene duplication. Alternative splicing is another means of evolutionary innovation in eukaryotes, which allows a single gene to encode functionally diverse proteins. We investigate a connection between these two evolutionary phenomena. For ∼10% of the described cases of substitution alternative splicing, such that either one or another amino acid sequence is included into the protein, evidence of origin by tandem exon duplication was found. This is a conservative estimate because alternative exons are typically short and, on many occasions, duplicates may have diverged beyond recognition. Dating exon duplications through a combination of the available experimental data on alternative splicing in orthologous genes from different species and computational analysis indicates that most of the duplications antedate at least the radiation of mammalian orders or even the radiation of vertebrate classes. At present, tandem exon duplication is the only mechanism of evolution of substitution alternative splicing that can be specifically demonstrated. Along with gene duplication, this could be a major route for generating functional diversity during evolution of multicellular eukaryotes. article_processing_charge: No article_type: original author: - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Eugene full_name: Koonin, Eugene last_name: Koonin citation: ama: Kondrashov F, Koonin E. Origin of alternative splicing by tandem exon duplication. Human Molecular Genetics. 2001;10(23):2661-2669. doi:10.1093/hmg/10.23.2661 apa: Kondrashov, F., & Koonin, E. (2001). Origin of alternative splicing by tandem exon duplication. Human Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/10.23.2661 chicago: Kondrashov, Fyodor, and Eugene Koonin. “Origin of Alternative Splicing by Tandem Exon Duplication.” Human Molecular Genetics. Oxford University Press, 2001. https://doi.org/10.1093/hmg/10.23.2661. ieee: F. Kondrashov and E. Koonin, “Origin of alternative splicing by tandem exon duplication,” Human Molecular Genetics, vol. 10, no. 23. Oxford University Press, pp. 2661–2669, 2001. ista: Kondrashov F, Koonin E. 2001. Origin of alternative splicing by tandem exon duplication. Human Molecular Genetics. 10(23), 2661–2669. mla: Kondrashov, Fyodor, and Eugene Koonin. “Origin of Alternative Splicing by Tandem Exon Duplication.” Human Molecular Genetics, vol. 10, no. 23, Oxford University Press, 2001, pp. 2661–69, doi:10.1093/hmg/10.23.2661. short: F. Kondrashov, E. Koonin, Human Molecular Genetics 10 (2001) 2661–2669. date_created: 2018-12-11T11:48:55Z date_published: 2001-11-01T00:00:00Z date_updated: 2023-06-02T08:39:47Z day: '01' doi: 10.1093/hmg/10.23.2661 extern: '1' external_id: pmid: - '11726553' intvolume: ' 10' issue: '23' language: - iso: eng month: '11' oa_version: Published Version page: 2661 - 2669 pmid: 1 publication: Human Molecular Genetics publication_identifier: issn: - 0964-6906 publication_status: published publisher: Oxford University Press publist_id: '6777' quality_controlled: '1' scopus_import: '1' status: public title: Origin of alternative splicing by tandem exon duplication type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 10 year: '2001' ... --- _id: '851' abstract: - lang: eng text: 'The study and comparison of mutation(al) spectra is an important problem in molecular biology, because these spectra often reflect on important features of mutations and their fixation. Such features include the interaction of DNA with various mutagens, the function of repair/replication enzymes, and properties of target proteins. It is known that mutability varies significantly along nucleotide sequences, such that mutations often concentrate at certain positions, called "hotspots," in a sequence. In this paper, we discuss in detail two approaches for mutation spectra analysis: the comparison of mutation spectra with a HG-PUBL program, (FTP: sunsite.unc.edu/pub/academic/ biology/dna-mutations/hyperg) and hotspot prediction with the CLUSTERM program (www.itba.mi.cnr.it/webmutation; ftp.bionet.nsc.ru/pub/biology/dbms/clusterm.zip). Several other approaches for mutational spectra analysis, such as the analysis of a target protein structure, hotspot context revealing, multiple spectra comparisons, as well as a number of mutation databases are briefly described. Mutation spectra in the lacI gene of E. coli and the human p53 gene are used for illustration of various difficulties of such analysis.' acknowledgement: 'Russian Fund of Fundamental Research. Grant Number: 99-04-49535. NIH. Grant Number: GM 20293. NASA. Grant Number: NCC2-1057' article_processing_charge: No article_type: original author: - first_name: Igor full_name: Rogozin, Igor last_name: Rogozin - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Galina full_name: Glazko, Galina last_name: Glazko citation: ama: Rogozin I, Kondrashov F, Glazko G. Use of mutation spectra analysis software. Human Mutation. 2001;17(2):83-102. doi:10.1002/1098-1004(200102)17:2&lt;83::AID-HUMU1&gt;3.0.CO;2-E apa: Rogozin, I., Kondrashov, F., & Glazko, G. (2001). Use of mutation spectra analysis software. Human Mutation. Wiley-Blackwell. https://doi.org/10.1002/1098-1004(200102)17:2&lt;83::AID-HUMU1&gt;3.0.CO;2-E chicago: Rogozin, Igor, Fyodor Kondrashov, and Galina Glazko. “Use of Mutation Spectra Analysis Software.” Human Mutation. Wiley-Blackwell, 2001. https://doi.org/10.1002/1098-1004(200102)17:2&lt;83::AID-HUMU1&gt;3.0.CO;2-E. ieee: I. Rogozin, F. Kondrashov, and G. Glazko, “Use of mutation spectra analysis software,” Human Mutation, vol. 17, no. 2. Wiley-Blackwell, pp. 83–102, 2001. ista: Rogozin I, Kondrashov F, Glazko G. 2001. Use of mutation spectra analysis software. Human Mutation. 17(2), 83–102. mla: Rogozin, Igor, et al. “Use of Mutation Spectra Analysis Software.” Human Mutation, vol. 17, no. 2, Wiley-Blackwell, 2001, pp. 83–102, doi:10.1002/1098-1004(200102)17:2&lt;83::AID-HUMU1&gt;3.0.CO;2-E. short: I. Rogozin, F. Kondrashov, G. Glazko, Human Mutation 17 (2001) 83–102. date_created: 2018-12-11T11:48:50Z date_published: 2001-01-01T00:00:00Z date_updated: 2023-06-02T09:22:17Z day: '01' doi: 10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E extern: '1' external_id: pmid: - '11180592' intvolume: ' 17' issue: '2' language: - iso: eng month: '01' oa_version: None page: 83 - 102 pmid: 1 publication: Human Mutation publication_identifier: issn: - 1059-7794 publication_status: published publisher: Wiley-Blackwell publist_id: '6796' quality_controlled: '1' scopus_import: '1' status: public title: Use of mutation spectra analysis software type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 17 year: '2001' ... --- _id: '841' article_processing_charge: No article_type: original author: - first_name: Yuri full_name: Wolf, Yuri last_name: Wolf - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Eugene full_name: Koonin, Eugene last_name: Koonin citation: ama: 'Wolf Y, Kondrashov F, Koonin E. Footprints of primordial introns on the eukaryotic genome: still no clear traces . Trends in Genetics. 2001;17(9):499-501. doi:10.1016/S0168-9525(01)02376-9' apa: 'Wolf, Y., Kondrashov, F., & Koonin, E. (2001). Footprints of primordial introns on the eukaryotic genome: still no clear traces . Trends in Genetics. Elsevier. https://doi.org/10.1016/S0168-9525(01)02376-9' chicago: 'Wolf, Yuri, Fyodor Kondrashov, and Eugene Koonin. “Footprints of Primordial Introns on the Eukaryotic Genome: Still No Clear Traces .” Trends in Genetics. Elsevier, 2001. https://doi.org/10.1016/S0168-9525(01)02376-9.' ieee: 'Y. Wolf, F. Kondrashov, and E. Koonin, “Footprints of primordial introns on the eukaryotic genome: still no clear traces ,” Trends in Genetics, vol. 17, no. 9. Elsevier, pp. 499–501, 2001.' ista: 'Wolf Y, Kondrashov F, Koonin E. 2001. Footprints of primordial introns on the eukaryotic genome: still no clear traces . Trends in Genetics. 17(9), 499–501.' mla: 'Wolf, Yuri, et al. “Footprints of Primordial Introns on the Eukaryotic Genome: Still No Clear Traces .” Trends in Genetics, vol. 17, no. 9, Elsevier, 2001, pp. 499–501, doi:10.1016/S0168-9525(01)02376-9.' short: Y. Wolf, F. Kondrashov, E. Koonin, Trends in Genetics 17 (2001) 499–501. date_created: 2018-12-11T11:48:47Z date_published: 2001-09-01T00:00:00Z date_updated: 2023-06-02T09:38:37Z day: '01' doi: 10.1016/S0168-9525(01)02376-9 extern: '1' external_id: pmid: - '11721681' intvolume: ' 17' issue: '9' language: - iso: eng month: '09' oa_version: None page: 499 - 501 pmid: 1 publication: Trends in Genetics publication_identifier: issn: - 0168-9479 publication_status: published publisher: Elsevier publist_id: '6805' quality_controlled: '1' scopus_import: '1' status: public title: 'Footprints of primordial introns on the eukaryotic genome: still no clear traces ' type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 17 year: '2001' ... --- _id: '842' article_processing_charge: No article_type: original author: - first_name: Yuri full_name: Wolf, Yuri last_name: Wolf - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Eugene full_name: Koonin, Eugene last_name: Koonin citation: ama: Wolf Y, Kondrashov F, Koonin E. No footprints of primordial introns in a eukaryotic genome. Trends in Genetics. 2000;16(8):333-334. doi:10.1016/S0168-9525(00)02059-X apa: Wolf, Y., Kondrashov, F., & Koonin, E. (2000). No footprints of primordial introns in a eukaryotic genome. Trends in Genetics. Elsevier. https://doi.org/10.1016/S0168-9525(00)02059-X chicago: Wolf, Yuri, Fyodor Kondrashov, and Eugene Koonin. “No Footprints of Primordial Introns in a Eukaryotic Genome.” Trends in Genetics. Elsevier, 2000. https://doi.org/10.1016/S0168-9525(00)02059-X. ieee: Y. Wolf, F. Kondrashov, and E. Koonin, “No footprints of primordial introns in a eukaryotic genome,” Trends in Genetics, vol. 16, no. 8. Elsevier, pp. 333–334, 2000. ista: Wolf Y, Kondrashov F, Koonin E. 2000. No footprints of primordial introns in a eukaryotic genome. Trends in Genetics. 16(8), 333–334. mla: Wolf, Yuri, et al. “No Footprints of Primordial Introns in a Eukaryotic Genome.” Trends in Genetics, vol. 16, no. 8, Elsevier, 2000, pp. 333–34, doi:10.1016/S0168-9525(00)02059-X. short: Y. Wolf, F. Kondrashov, E. Koonin, Trends in Genetics 16 (2000) 333–334. date_created: 2018-12-11T11:48:48Z date_published: 2000-08-01T00:00:00Z date_updated: 2023-05-08T09:22:03Z day: '01' doi: 10.1016/S0168-9525(00)02059-X extern: '1' external_id: pmid: - '10904260 ' intvolume: ' 16' issue: '8' language: - iso: eng month: '08' oa_version: None page: 333 - 334 pmid: 1 publication: Trends in Genetics publication_identifier: issn: - 0168-9479 publication_status: published publisher: Elsevier publist_id: '6806' quality_controlled: '1' scopus_import: '1' status: public title: No footprints of primordial introns in a eukaryotic genome type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 16 year: '2000' ... --- _id: '883' abstract: - lang: eng text: Sympatric speciation, the origin of two or more species from a single local population, has almost certainly been involved in formation of several species flocks, and may be fairly common in nature. The most straightforward scenario for sympatric speciation requires disruptive selection favouring two substantially different phenotypes, and consists of the evolution of reproductive isolation between them followed by the elimination of all intermediate phenotypes. Here we use the hypergeometric phenotypic model to show that sympatric speciation is possible even when fitness and mate choice depend on different quantitative traits, so that speciation must involve formation of covariance between these traits. The increase in the number of variable loci affecting fitness facilitates sympatric speciation, whereas the increase in the number of variable loci affecting mate choice has the opposite effect. These predictions may enable more cases of sympatric speciation to be identified. acknowledgement: This study was supported by a grant from the NSF. article_processing_charge: No article_type: original author: - first_name: Alexey full_name: Kondrashov, Alexey last_name: Kondrashov - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kondrashov A, Kondrashov F. Interactions among quantitative traits in the course of sympatric speciation. Nature. 1999;400(6742):351-354. doi:10.1038/22514 apa: Kondrashov, A., & Kondrashov, F. (1999). Interactions among quantitative traits in the course of sympatric speciation. Nature. Nature Publishing Group. https://doi.org/10.1038/22514 chicago: Kondrashov, Alexey, and Fyodor Kondrashov. “Interactions among Quantitative Traits in the Course of Sympatric Speciation.” Nature. Nature Publishing Group, 1999. https://doi.org/10.1038/22514. ieee: A. Kondrashov and F. Kondrashov, “Interactions among quantitative traits in the course of sympatric speciation,” Nature, vol. 400, no. 6742. Nature Publishing Group, pp. 351–354, 1999. ista: Kondrashov A, Kondrashov F. 1999. Interactions among quantitative traits in the course of sympatric speciation. Nature. 400(6742), 351–354. mla: Kondrashov, Alexey, and Fyodor Kondrashov. “Interactions among Quantitative Traits in the Course of Sympatric Speciation.” Nature, vol. 400, no. 6742, Nature Publishing Group, 1999, pp. 351–54, doi:10.1038/22514. short: A. Kondrashov, F. Kondrashov, Nature 400 (1999) 351–354. date_created: 2018-12-11T11:49:00Z date_published: 1999-07-01T00:00:00Z date_updated: 2023-04-13T10:33:44Z day: '01' doi: 10.1038/22514 extern: '1' external_id: pmid: - '10432111' intvolume: ' 400' issue: '6742' language: - iso: eng month: '07' oa_version: None page: 351 - 354 pmid: 1 publication: Nature publication_identifier: issn: - 0028-0836 publication_status: published publisher: Nature Publishing Group publist_id: '6761' quality_controlled: '1' scopus_import: '1' status: public title: Interactions among quantitative traits in the course of sympatric speciation type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 400 year: '1999' ...