--- _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 license: https://creativecommons.org/licenses/by/4.0/ 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 license: https://creativecommons.org/licenses/by-nc/4.0/ 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' ...