[{"day":"01","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2024-03-01T00:00:00Z","publication":"Science Advances","citation":{"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.","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).","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.","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","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.","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"},"article_type":"original","abstract":[{"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.","lang":"eng"}],"issue":"10","type":"journal_article","file":[{"file_id":"15185","relation":"main_file","date_updated":"2024-03-25T09:42:10Z","date_created":"2024-03-25T09:42:10Z","success":1,"checksum":"a19c43b260ea0bbaf895a29712e3153c","file_name":"2024_ScienceAdv_Palkina.pdf","access_level":"open_access","creator":"dernst","file_size":1499302,"content_type":"application/pdf"}],"oa_version":"Published Version","_id":"15179","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A hybrid pathway for self-sustained luminescence","ddc":["580"],"status":"public","intvolume":" 10","month":"03","publication_identifier":{"issn":["2375-2548"]},"doi":"10.1126/sciadv.adk1992","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","file_date_updated":"2024-03-25T09:42:10Z","article_number":"adk1992","author":[{"first_name":"Kseniia A.","last_name":"Palkina","full_name":"Palkina, Kseniia A."},{"full_name":"Karataeva, Tatiana A.","first_name":"Tatiana A.","last_name":"Karataeva"},{"first_name":"Maxim M.","last_name":"Perfilov","full_name":"Perfilov, Maxim M."},{"last_name":"Fakhranurova","first_name":"Liliia I.","full_name":"Fakhranurova, Liliia I."},{"full_name":"Markina, Nadezhda M.","last_name":"Markina","first_name":"Nadezhda M."},{"id":"4720D23C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9139-5383","first_name":"Louisa","last_name":"Gonzalez Somermeyer","full_name":"Gonzalez Somermeyer, Louisa"},{"first_name":"Elena","last_name":"Garcia-Perez","full_name":"Garcia-Perez, Elena"},{"full_name":"Vazquez-Vilar, Marta","last_name":"Vazquez-Vilar","first_name":"Marta"},{"last_name":"Rodriguez-Rodriguez","first_name":"Marta","full_name":"Rodriguez-Rodriguez, Marta"},{"full_name":"Vazquez-Vilriales, Victor","last_name":"Vazquez-Vilriales","first_name":"Victor"},{"full_name":"Shakhova, Ekaterina S.","first_name":"Ekaterina S.","last_name":"Shakhova"},{"full_name":"Mitiouchkina, Tatiana","first_name":"Tatiana","last_name":"Mitiouchkina"},{"full_name":"Belozerova, Olga A.","last_name":"Belozerova","first_name":"Olga A."},{"first_name":"Sergey I.","last_name":"Kovalchuk","full_name":"Kovalchuk, Sergey I."},{"full_name":"Alekberova, Anna","first_name":"Anna","last_name":"Alekberova"},{"first_name":"Alena K.","last_name":"Malyshevskaia","full_name":"Malyshevskaia, Alena K."},{"first_name":"Evgenia N.","last_name":"Bugaeva","full_name":"Bugaeva, Evgenia N."},{"full_name":"Guglya, Elena B.","last_name":"Guglya","first_name":"Elena B."},{"last_name":"Balakireva","first_name":"Anastasia","full_name":"Balakireva, Anastasia"},{"full_name":"Sytov, Nikita","last_name":"Sytov","first_name":"Nikita"},{"first_name":"Anastasia","last_name":"Bezlikhotnova","full_name":"Bezlikhotnova, Anastasia"},{"last_name":"Boldyreva","first_name":"Daria I.","full_name":"Boldyreva, Daria I."},{"full_name":"Babenko, Vladislav V.","last_name":"Babenko","first_name":"Vladislav V."},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"},{"last_name":"Choob","first_name":"Vladimir V.","full_name":"Choob, Vladimir V."},{"full_name":"Orzaez, Diego","last_name":"Orzaez","first_name":"Diego"},{"last_name":"Yampolsky","first_name":"Ilia V.","full_name":"Yampolsky, Ilia V."},{"full_name":"Mishin, Alexander S.","last_name":"Mishin","first_name":"Alexander S."},{"full_name":"Sarkisyan, Karen S.","first_name":"Karen S.","last_name":"Sarkisyan"}],"date_updated":"2024-03-25T09:44:53Z","date_created":"2024-03-25T08:54:33Z","volume":10,"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).","year":"2024","publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"FyKo"}]},{"file":[{"file_id":"12771","relation":"main_file","date_updated":"2023-03-27T07:09:08Z","date_created":"2023-03-27T07:09:08Z","success":1,"checksum":"0281bdfccf8d76c4e08dd011c603f6b6","file_name":"2023_PLoSOne_Pak.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":856625}],"oa_version":"Published Version","intvolume":" 18","status":"public","ddc":["570"],"title":"Using AlphaFold to predict the impact of single mutations on protein stability and function","_id":"12758","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"3","abstract":[{"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.","lang":"eng"}],"type":"journal_article","date_published":"2023-03-16T00:00:00Z","article_type":"original","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","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.","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","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.","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).","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.","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."},"publication":"PLoS ONE","has_accepted_license":"1","article_processing_charge":"No","day":"16","scopus_import":"1","volume":18,"date_updated":"2023-08-01T13:47:14Z","date_created":"2023-03-26T22:01:07Z","author":[{"first_name":"Marina A.","last_name":"Pak","full_name":"Pak, Marina A."},{"first_name":"Karina A.","last_name":"Markhieva","full_name":"Markhieva, Karina A."},{"full_name":"Novikova, Mariia S.","first_name":"Mariia S.","last_name":"Novikova"},{"full_name":"Petrov, Dmitry S.","last_name":"Petrov","first_name":"Dmitry S."},{"last_name":"Vorobyev","first_name":"Ilya S.","full_name":"Vorobyev, Ilya S."},{"full_name":"Maksimova, Ekaterina","last_name":"Maksimova","first_name":"Ekaterina","id":"2FBE0DE4-F248-11E8-B48F-1D18A9856A87"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"first_name":"Dmitry N.","last_name":"Ivankov","full_name":"Ivankov, Dmitry N."}],"department":[{"_id":"FyKo"},{"_id":"MaRo"}],"publisher":"Public Library of Science","publication_status":"published","year":"2023","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.","file_date_updated":"2023-03-27T07:09:08Z","article_number":"e0282689","language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0282689","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000985134400106"]},"publication_identifier":{"eissn":["1932-6203"]},"month":"03"},{"publication_identifier":{"eissn":["2041-1723"]},"month":"06","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001048208600023"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-39317-4","article_number":"3506","file_date_updated":"2023-06-26T10:26:04Z","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","publication_status":"published","year":"2023","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.","volume":14,"date_updated":"2023-12-13T11:26:34Z","date_created":"2023-06-25T22:00:45Z","author":[{"last_name":"Gert","first_name":"Krista R.B.","full_name":"Gert, Krista R.B."},{"first_name":"Karin","last_name":"Panser","full_name":"Panser, Karin"},{"full_name":"Surm, Joachim","last_name":"Surm","first_name":"Joachim"},{"first_name":"Benjamin S.","last_name":"Steinmetz","full_name":"Steinmetz, Benjamin S."},{"last_name":"Schleiffer","first_name":"Alexander","full_name":"Schleiffer, Alexander"},{"full_name":"Jovine, Luca","last_name":"Jovine","first_name":"Luca"},{"full_name":"Moran, Yehu","first_name":"Yehu","last_name":"Moran"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor"},{"last_name":"Pauli","first_name":"Andrea","full_name":"Pauli, Andrea"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"14","article_type":"original","citation":{"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","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.","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","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.","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).","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."},"publication":"Nature Communications","date_published":"2023-06-14T00:00:00Z","type":"journal_article","abstract":[{"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.","lang":"eng"}],"intvolume":" 14","ddc":["570"],"title":"Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13164","oa_version":"Published Version","file":[{"file_name":"2023_NatureComm_Gert.pdf","access_level":"open_access","creator":"dernst","file_size":1555006,"content_type":"application/pdf","file_id":"13172","relation":"main_file","date_created":"2023-06-26T10:26:04Z","date_updated":"2023-06-26T10:26:04Z","success":1,"checksum":"d6165f41c7f1c2c04b04256ec9f003fb"}]},{"language":[{"iso":"eng"}],"doi":"10.1093/gigascience/giad045","quality_controlled":"1","isi":1,"external_id":{"pmid":["37496156"],"isi":["001081086100001"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/gigascience/giad045"}],"oa":1,"month":"07","publication_identifier":{"eissn":["2047-217X"]},"date_updated":"2023-12-13T12:01:46Z","date_created":"2023-08-06T22:01:13Z","volume":12,"author":[{"full_name":"Wolfsberger, Walter","last_name":"Wolfsberger","first_name":"Walter"},{"first_name":"Karishma","last_name":"Chhugani","full_name":"Chhugani, Karishma"},{"last_name":"Shchubelka","first_name":"Khrystyna","full_name":"Shchubelka, Khrystyna"},{"full_name":"Frolova, Alina","last_name":"Frolova","first_name":"Alina"},{"full_name":"Salyha, Yuriy","last_name":"Salyha","first_name":"Yuriy"},{"last_name":"Zlenko","first_name":"Oksana","full_name":"Zlenko, Oksana"},{"full_name":"Arych, Mykhailo","first_name":"Mykhailo","last_name":"Arych"},{"first_name":"Dmytro","last_name":"Dziuba","full_name":"Dziuba, Dmytro"},{"first_name":"Andrii","last_name":"Parkhomenko","full_name":"Parkhomenko, Andrii"},{"first_name":"Volodymyr","last_name":"Smolanka","full_name":"Smolanka, Volodymyr"},{"last_name":"Gümüş","first_name":"Zeynep H.","full_name":"Gümüş, Zeynep H."},{"last_name":"Sezgin","first_name":"Efe","full_name":"Sezgin, Efe"},{"full_name":"Diaz-Lameiro, Alondra","last_name":"Diaz-Lameiro","first_name":"Alondra"},{"first_name":"Viktor R.","last_name":"Toth","full_name":"Toth, Viktor R."},{"full_name":"Maci, Megi","last_name":"Maci","first_name":"Megi"},{"full_name":"Bortz, Eric","first_name":"Eric","last_name":"Bortz"},{"full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"first_name":"Patricia M.","last_name":"Morton","full_name":"Morton, Patricia M."},{"last_name":"Łabaj","first_name":"Paweł P.","full_name":"Łabaj, Paweł P."},{"full_name":"Romero, Veronika","last_name":"Romero","first_name":"Veronika"},{"last_name":"Hlávka","first_name":"Jakub","full_name":"Hlávka, Jakub"},{"first_name":"Serghei","last_name":"Mangul","full_name":"Mangul, Serghei"},{"full_name":"Oleksyk, Taras K.","first_name":"Taras K.","last_name":"Oleksyk"}],"publication_status":"epub_ahead","publisher":"Oxford Academic","department":[{"_id":"FyKo"}],"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.","year":"2023","pmid":1,"date_published":"2023-07-27T00:00:00Z","article_type":"original","publication":"GigaScience","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","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.","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).","mla":"Wolfsberger, Walter, et al. “Scientists without Borders: Lessons from Ukraine.” GigaScience, vol. 12, Oxford Academic, 2023, doi: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."},"day":"27","article_processing_charge":"Yes","scopus_import":"1","oa_version":"Published Version","title":"Scientists without borders: Lessons from Ukraine","status":"public","intvolume":" 12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_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."}],"type":"journal_article"},{"type":"journal_article","abstract":[{"text":"Background: Antimicrobial resistance (AMR) poses a significant global health threat, and an accurate prediction of bacterial resistance patterns is critical for effective treatment and control strategies. In recent years, machine learning (ML) approaches have emerged as powerful tools for analyzing large-scale bacterial AMR data. However, ML methods often ignore evolutionary relationships among bacterial strains, which can greatly impact performance of the ML methods, especially if resistance-associated features are attempted to be detected. Genome-wide association studies (GWAS) methods like linear mixed models accounts for the evolutionary relationships in bacteria, but they uncover only highly significant variants which have already been reported in literature.\r\n\r\nResults: In this work, we introduce a novel phylogeny-related parallelism score (PRPS), which measures whether a certain feature is correlated with the population structure of a set of samples. We demonstrate that PRPS can be used, in combination with SVM- and random forest-based models, to reduce the number of features in the analysis, while simultaneously increasing models’ performance. We applied our pipeline to publicly available AMR data from PATRIC database for Mycobacterium tuberculosis against six common antibiotics.\r\n\r\nConclusions: Using our pipeline, we re-discovered known resistance-associated mutations as well as new candidate mutations which can be related to resistance and not previously reported in the literature. We demonstrated that taking into account phylogenetic relationships not only improves the model performance, but also yields more biologically relevant predicted most contributing resistance markers.","lang":"eng"}],"issue":"1","_id":"14716","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["570"],"title":"Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis","intvolume":" 23","file":[{"relation":"main_file","file_id":"14723","checksum":"7ff5e95f3496ff663301eb4a13a316d5","success":1,"date_created":"2024-01-02T09:09:32Z","date_updated":"2024-01-02T09:09:32Z","access_level":"open_access","file_name":"2023_BMCMicrobiology_Yurtseven.pdf","file_size":1979922,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication":"BMC Microbiology","citation":{"ama":"Yurtseven A, Buyanova S, Agrawal AAA, Bochkareva O, Kalinina OVV. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. 2023;23(1). doi:10.1186/s12866-023-03147-7","ista":"Yurtseven A, Buyanova S, Agrawal AAA, Bochkareva O, Kalinina OVV. 2023. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. 23(1), 404.","ieee":"A. Yurtseven, S. Buyanova, A. A. A. Agrawal, O. Bochkareva, and O. V. V. Kalinina, “Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis,” BMC Microbiology, vol. 23, no. 1. Springer Nature, 2023.","apa":"Yurtseven, A., Buyanova, S., Agrawal, A. A. A., Bochkareva, O., & Kalinina, O. V. V. (2023). Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. Springer Nature. https://doi.org/10.1186/s12866-023-03147-7","mla":"Yurtseven, Alper, et al. “Machine Learning and Phylogenetic Analysis Allow for Predicting Antibiotic Resistance in M. Tuberculosis.” BMC Microbiology, vol. 23, no. 1, 404, Springer Nature, 2023, doi:10.1186/s12866-023-03147-7.","short":"A. Yurtseven, S. Buyanova, A.A.A. Agrawal, O. Bochkareva, O.V.V. Kalinina, BMC Microbiology 23 (2023).","chicago":"Yurtseven, Alper, Sofia Buyanova, Amay Ajaykumar A. Agrawal, Olga Bochkareva, and Olga V V. Kalinina. “Machine Learning and Phylogenetic Analysis Allow for Predicting Antibiotic Resistance in M. Tuberculosis.” BMC Microbiology. Springer Nature, 2023. https://doi.org/10.1186/s12866-023-03147-7."},"article_type":"original","date_published":"2023-12-01T00:00:00Z","article_number":"404","file_date_updated":"2024-01-02T09:09:32Z","year":"2023","acknowledgement":"Open Access funding enabled and organized by Projekt DEAL. A.Y. and O.V.K. acknowledge financial support from the Klaus Faber Foundation. A.A.A. was funded by the Helmholtz AI project AMR-XAI. The work of O.O.B. is funded by Fonds zur Förderung der Wissenschaftlichen Forschung (FWF), Grant ESP 253-B.","pmid":1,"publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","author":[{"first_name":"Alper","last_name":"Yurtseven","full_name":"Yurtseven, Alper"},{"full_name":"Buyanova, Sofia","id":"2F54A7BC-3902-11EA-AC87-BC9F3DDC885E","last_name":"Buyanova","first_name":"Sofia"},{"full_name":"Agrawal, Amay Ajaykumar A.","first_name":"Amay Ajaykumar A.","last_name":"Agrawal"},{"first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"full_name":"Kalinina, Olga V V.","first_name":"Olga V V.","last_name":"Kalinina"}],"date_updated":"2024-01-02T09:20:57Z","date_created":"2023-12-31T23:01:02Z","volume":23,"month":"12","publication_identifier":{"eissn":["1471-2180"]},"external_id":{"pmid":["38124060"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1186/s12866-023-03147-7","language":[{"iso":"eng"}]},{"abstract":[{"text":"Motivation\r\nHigh plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions and duplications may independently occur in different strains, providing parallel adaptation or phenotypic diversity. Specifically, such rearrangements might be responsible for virulence, antibiotic resistance and antigenic variation. However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency.\r\nResults\r\nHere, we define the term ‘parallel rearrangements’ as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. We implement an algorithmic solution for the identification of parallel rearrangements in bacterial populations as a tool PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved. We demonstrated PaReBrick’s efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes.","lang":"eng"}],"issue":"2","type":"journal_article","file":[{"file_name":"2022_Bioinformatics_Zabelkin.pdf","access_level":"open_access","file_size":3425744,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"10930","date_updated":"2022-03-28T08:07:46Z","date_created":"2022-03-28T08:07:46Z","checksum":"4b5688ff9ac86180ccdf7f82fa33d926","success":1}],"oa_version":"Published Version","_id":"10927","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["000"],"title":"PaReBrick: PArallel REarrangements and BReaks identification toolkit","status":"public","intvolume":" 38","day":"15","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2022-01-15T00:00:00Z","publication":"Bioinformatics","citation":{"ama":"Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. PaReBrick: PArallel REarrangements and BReaks identification toolkit. Bioinformatics. 2022;38(2):357-363. doi:10.1093/bioinformatics/btab691","ista":"Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. 2022. PaReBrick: PArallel REarrangements and BReaks identification toolkit. Bioinformatics. 38(2), 357–363.","ieee":"A. Zabelkin, Y. Yakovleva, O. Bochkareva, and N. Alexeev, “PaReBrick: PArallel REarrangements and BReaks identification toolkit,” Bioinformatics, vol. 38, no. 2. Oxford Academic, pp. 357–363, 2022.","apa":"Zabelkin, A., Yakovleva, Y., Bochkareva, O., & Alexeev, N. (2022). PaReBrick: PArallel REarrangements and BReaks identification toolkit. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btab691","mla":"Zabelkin, Alexey, et al. “PaReBrick: PArallel REarrangements and BReaks Identification Toolkit.” Bioinformatics, vol. 38, no. 2, Oxford Academic, 2022, pp. 357–63, doi:10.1093/bioinformatics/btab691.","short":"A. Zabelkin, Y. Yakovleva, O. Bochkareva, N. Alexeev, Bioinformatics 38 (2022) 357–363.","chicago":"Zabelkin, Alexey, Yulia Yakovleva, Olga Bochkareva, and Nikita Alexeev. “PaReBrick: PArallel REarrangements and BReaks Identification Toolkit.” Bioinformatics. Oxford Academic, 2022. https://doi.org/10.1093/bioinformatics/btab691."},"article_type":"original","page":"357-363","file_date_updated":"2022-03-28T08:07:46Z","ec_funded":1,"author":[{"full_name":"Zabelkin, Alexey","last_name":"Zabelkin","first_name":"Alexey"},{"full_name":"Yakovleva, Yulia","last_name":"Yakovleva","first_name":"Yulia"},{"first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"first_name":"Nikita","last_name":"Alexeev","full_name":"Alexeev, Nikita"}],"related_material":{"link":[{"url":"https://github.com/ctlab/parallel-rearrangements","relation":"software"}]},"date_created":"2022-03-27T22:01:46Z","date_updated":"2023-08-03T06:21:46Z","volume":38,"acknowledgement":"The authors thank the 2020 student class of the Bioinformatics Institute, who\r\nused the first versions of the tool and provided many valuable suggestions to\r\nimprove usability. They also thank Louisa Gonzalez Somermeyer for manuscript proofreading\r\nThis work was supported by the National Center for Cognitive Research of\r\nITMO University and JetBrains Research [to A.Z and N.A.]; and the European\r\nUnion’s Horizon 2020 Research and Innovation Programme under the Marie\r\nSkłodowska-Curie [754411 to O.B.].\r\nPaReBrick is written in Python and is available on GitHub: https://github.com/ctlab/parallel-rearrangements.","year":"2022","publication_status":"published","publisher":"Oxford Academic","department":[{"_id":"FyKo"}],"month":"01","publication_identifier":{"eissn":["1460-2059"],"issn":["1367-4803"]},"doi":"10.1093/bioinformatics/btab691","language":[{"iso":"eng"}],"external_id":{"isi":["000743380100008"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}]},{"scopus_import":"1","article_processing_charge":"No","day":"08","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","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.","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","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.","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.","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.","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."},"publication":"Nature Methods","page":"374-380","article_type":"letter_note","date_published":"2022-04-08T00:00:00Z","type":"journal_article","issue":"4","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."}],"_id":"11187","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 19","title":"Unlocking capacities of genomics for the COVID-19 response and future pandemics","status":"public","oa_version":"Published Version","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"month":"04","oa":1,"external_id":{"isi":["000781199600011"],"pmid":["35396471"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41592-022-01444-z"}],"project":[{"name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41592-022-01444-z","language":[{"iso":"eng"}],"ec_funded":1,"pmid":1,"year":"2022","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).","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","publication_status":"published","author":[{"full_name":"Knyazev, Sergey","last_name":"Knyazev","first_name":"Sergey"},{"full_name":"Chhugani, Karishma","first_name":"Karishma","last_name":"Chhugani"},{"full_name":"Sarwal, Varuni","first_name":"Varuni","last_name":"Sarwal"},{"first_name":"Ram","last_name":"Ayyala","full_name":"Ayyala, Ram"},{"full_name":"Singh, Harman","first_name":"Harman","last_name":"Singh"},{"first_name":"Smruthi","last_name":"Karthikeyan","full_name":"Karthikeyan, Smruthi"},{"last_name":"Deshpande","first_name":"Dhrithi","full_name":"Deshpande, Dhrithi"},{"first_name":"Pelin Icer","last_name":"Baykal","full_name":"Baykal, Pelin Icer"},{"first_name":"Zoia","last_name":"Comarova","full_name":"Comarova, Zoia"},{"last_name":"Lu","first_name":"Angela","full_name":"Lu, Angela"},{"first_name":"Yuri","last_name":"Porozov","full_name":"Porozov, Yuri"},{"first_name":"Tetyana I.","last_name":"Vasylyeva","full_name":"Vasylyeva, Tetyana I."},{"first_name":"Joel O.","last_name":"Wertheim","full_name":"Wertheim, Joel O."},{"full_name":"Tierney, Braden T.","first_name":"Braden T.","last_name":"Tierney"},{"full_name":"Chiu, Charles Y.","last_name":"Chiu","first_name":"Charles Y."},{"first_name":"Ren","last_name":"Sun","full_name":"Sun, Ren"},{"full_name":"Wu, Aiping","first_name":"Aiping","last_name":"Wu"},{"full_name":"Abedalthagafi, Malak S.","last_name":"Abedalthagafi","first_name":"Malak S."},{"first_name":"Victoria M.","last_name":"Pak","full_name":"Pak, Victoria M."},{"full_name":"Nagaraj, Shivashankar H.","last_name":"Nagaraj","first_name":"Shivashankar H."},{"full_name":"Smith, Adam L.","first_name":"Adam L.","last_name":"Smith"},{"last_name":"Skums","first_name":"Pavel","full_name":"Skums, Pavel"},{"first_name":"Bogdan","last_name":"Pasaniuc","full_name":"Pasaniuc, Bogdan"},{"full_name":"Komissarov, Andrey","last_name":"Komissarov","first_name":"Andrey"},{"first_name":"Christopher E.","last_name":"Mason","full_name":"Mason, Christopher E."},{"full_name":"Bortz, Eric","first_name":"Eric","last_name":"Bortz"},{"full_name":"Lemey, Philippe","first_name":"Philippe","last_name":"Lemey"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor"},{"full_name":"Beerenwinkel, Niko","first_name":"Niko","last_name":"Beerenwinkel"},{"first_name":"Tommy Tsan Yuk","last_name":"Lam","full_name":"Lam, Tommy Tsan Yuk"},{"full_name":"Wu, Nicholas C.","last_name":"Wu","first_name":"Nicholas C."},{"first_name":"Alex","last_name":"Zelikovsky","full_name":"Zelikovsky, Alex"},{"full_name":"Knight, Rob","first_name":"Rob","last_name":"Knight"},{"last_name":"Crandall","first_name":"Keith A.","full_name":"Crandall, Keith A."},{"first_name":"Serghei","last_name":"Mangul","full_name":"Mangul, Serghei"}],"volume":19,"date_created":"2022-04-17T22:01:48Z","date_updated":"2023-08-03T06:46:09Z"},{"type":"journal_article","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."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11344","title":"Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia","ddc":["570"],"status":"public","intvolume":" 12","file":[{"access_level":"open_access","file_name":"2022_ScientificReports_Dranenko.pdf","file_size":3564155,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"11349","checksum":"12601b8a5c6b83bb618f92bcb963ecc9","success":1,"date_updated":"2022-05-02T09:05:20Z","date_created":"2022-05-02T09:05:20Z"}],"oa_version":"Published Version","scopus_import":"1","day":"27","has_accepted_license":"1","article_processing_charge":"No","publication":"Scientific Reports","citation":{"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.","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","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.","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","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.","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)."},"article_type":"original","date_published":"2022-04-27T00:00:00Z","article_number":"6868","file_date_updated":"2022-05-02T09:05:20Z","ec_funded":1,"year":"2022","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. ","pmid":1,"publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","author":[{"last_name":"Dranenko","first_name":"NO","full_name":"Dranenko, NO"},{"full_name":"Tutukina, MN","last_name":"Tutukina","first_name":"MN"},{"full_name":"Gelfand, MS","last_name":"Gelfand","first_name":"MS"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor"},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","first_name":"Olga","last_name":"Bochkareva","full_name":"Bochkareva, Olga"}],"date_updated":"2023-08-03T06:59:49Z","date_created":"2022-05-02T07:08:42Z","volume":12,"month":"04","publication_identifier":{"issn":["2045-2322"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["35477739"],"isi":["000788639400032"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"I05127","_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f","name":"Evolutionary analysis of gene regulation"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"doi":"10.1038/s41598-022-10827-3","language":[{"iso":"eng"}]},{"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.","year":"2022","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"FyKo"}],"publisher":"eLife Sciences Publications","author":[{"first_name":"Louisa","last_name":"Gonzalez Somermeyer","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9139-5383","full_name":"Gonzalez Somermeyer, Louisa"},{"first_name":"Aubin","last_name":"Fleiss","full_name":"Fleiss, Aubin"},{"first_name":"Alexander S","last_name":"Mishin","full_name":"Mishin, Alexander S"},{"full_name":"Bozhanova, Nina G","first_name":"Nina G","last_name":"Bozhanova"},{"full_name":"Igolkina, Anna A","first_name":"Anna A","last_name":"Igolkina"},{"first_name":"Jens","last_name":"Meiler","full_name":"Meiler, Jens"},{"first_name":"Maria-Elisenda","last_name":"Alaball Pujol","full_name":"Alaball Pujol, Maria-Elisenda"},{"first_name":"Ekaterina V","last_name":"Putintseva","full_name":"Putintseva, Ekaterina V"},{"full_name":"Sarkisyan, Karen S","last_name":"Sarkisyan","first_name":"Karen S"},{"full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-03T07:20:15Z","date_created":"2022-06-18T09:06:59Z","volume":11,"article_number":"75842","file_date_updated":"2022-06-20T07:44:19Z","ec_funded":1,"external_id":{"isi":["000799197200001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"doi":"10.7554/elife.75842","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"month":"05","publication_identifier":{"issn":["2050-084X"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11448","ddc":["570"],"title":"Heterogeneity of the GFP fitness landscape and data-driven protein design","status":"public","intvolume":" 11","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":5297213,"file_name":"2022_eLife_Somermeyer.pdf","access_level":"open_access","date_updated":"2022-06-20T07:44:19Z","date_created":"2022-06-20T07:44:19Z","success":1,"checksum":"7573c28f44028ab0cc81faef30039e44","file_id":"11454","relation":"main_file"}],"type":"journal_article","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."}],"publication":"eLife","citation":{"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.","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).","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.","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","ieee":"L. Gonzalez Somermeyer et al., “Heterogeneity of the GFP fitness landscape and data-driven protein design,” eLife, vol. 11. eLife Sciences Publications, 2022.","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"},"article_type":"original","date_published":"2022-05-05T00:00:00Z","scopus_import":"1","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"day":"05","article_processing_charge":"No","has_accepted_license":"1"},{"doi":"10.1186/s13059-022-02711-0","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000821915500002"]},"isi":1,"quality_controlled":"1","month":"07","publication_identifier":{"eissn":["1474-760X"]},"author":[{"full_name":"Zhang, Runxuan","first_name":"Runxuan","last_name":"Zhang"},{"full_name":"Kuo, Richard","first_name":"Richard","last_name":"Kuo"},{"last_name":"Coulter","first_name":"Max","full_name":"Coulter, Max"},{"full_name":"Calixto, Cristiane P.G.","first_name":"Cristiane P.G.","last_name":"Calixto"},{"last_name":"Entizne","first_name":"Juan Carlos","full_name":"Entizne, Juan Carlos"},{"first_name":"Wenbin","last_name":"Guo","full_name":"Guo, Wenbin"},{"full_name":"Marquez, Yamile","first_name":"Yamile","last_name":"Marquez"},{"last_name":"Milne","first_name":"Linda","full_name":"Milne, Linda"},{"full_name":"Riegler, Stefan","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","orcid":"0000-0003-3413-1343","first_name":"Stefan","last_name":"Riegler"},{"first_name":"Akihiro","last_name":"Matsui","full_name":"Matsui, Akihiro"},{"first_name":"Maho","last_name":"Tanaka","full_name":"Tanaka, Maho"},{"first_name":"Sarah","last_name":"Harvey","full_name":"Harvey, Sarah"},{"full_name":"Gao, Yubang","first_name":"Yubang","last_name":"Gao"},{"last_name":"Wießner-Kroh","first_name":"Theresa","full_name":"Wießner-Kroh, Theresa"},{"full_name":"Paniagua, Alejandro","last_name":"Paniagua","first_name":"Alejandro"},{"full_name":"Crespi, Martin","last_name":"Crespi","first_name":"Martin"},{"first_name":"Katherine","last_name":"Denby","full_name":"Denby, Katherine"},{"first_name":"Asa Ben","last_name":"Hur","full_name":"Hur, Asa Ben"},{"full_name":"Huq, Enamul","first_name":"Enamul","last_name":"Huq"},{"full_name":"Jantsch, Michael","first_name":"Michael","last_name":"Jantsch"},{"last_name":"Jarmolowski","first_name":"Artur","full_name":"Jarmolowski, Artur"},{"full_name":"Koester, Tino","last_name":"Koester","first_name":"Tino"},{"full_name":"Laubinger, Sascha","last_name":"Laubinger","first_name":"Sascha"},{"full_name":"Li, Qingshun Quinn","last_name":"Li","first_name":"Qingshun Quinn"},{"last_name":"Gu","first_name":"Lianfeng","full_name":"Gu, Lianfeng"},{"last_name":"Seki","first_name":"Motoaki","full_name":"Seki, Motoaki"},{"full_name":"Staiger, Dorothee","first_name":"Dorothee","last_name":"Staiger"},{"full_name":"Sunkar, Ramanjulu","first_name":"Ramanjulu","last_name":"Sunkar"},{"full_name":"Szweykowska-Kulinska, Zofia","first_name":"Zofia","last_name":"Szweykowska-Kulinska"},{"full_name":"Tu, Shih Long","last_name":"Tu","first_name":"Shih Long"},{"full_name":"Wachter, Andreas","first_name":"Andreas","last_name":"Wachter"},{"first_name":"Robbie","last_name":"Waugh","full_name":"Waugh, Robbie"},{"first_name":"Liming","last_name":"Xiong","full_name":"Xiong, Liming"},{"full_name":"Zhang, Xiao Ning","first_name":"Xiao Ning","last_name":"Zhang"},{"full_name":"Conesa, Ana","first_name":"Ana","last_name":"Conesa"},{"first_name":"Anireddy S.N.","last_name":"Reddy","full_name":"Reddy, Anireddy S.N."},{"full_name":"Barta, Andrea","first_name":"Andrea","last_name":"Barta"},{"full_name":"Kalyna, Maria","first_name":"Maria","last_name":"Kalyna"},{"full_name":"Brown, John W.S.","first_name":"John W.S.","last_name":"Brown"}],"date_updated":"2023-08-03T12:04:18Z","date_created":"2022-07-17T22:01:53Z","volume":23,"year":"2022","acknowledgement":"This work was jointly supported by funding from the Biotechnology and Biological Sciences Research Council (BBSRC) BB/P009751/1 to JB; BB/R014582/1 to RW and RZ; BB/S020160/1 to RZ; BB/S004610/1 (16 ERA-CAPS BARN) to RW; the Scottish Government Rural and Environment Science and Analytical Services division (RESAS) [to RZ, RW, and JB]; the\r\nNational Science Foundation (MCB-2014408) and the National Institute of Health (NIH) (GM-114297) to E.H.; S. H. was supported by funding to K.D. from the University of York; the Austrian Science Fund (FWF) SFB F43 to AB and MJ and [P26333] to MK; The French Agence Nationale de la Recherche grant ANR-16-CE12-0032 to MC; the Japan Science and\r\nTechnology Agency (JST), the Core Research for Evolutionary Science and Technology (CREST; Grant Number JPMJCR13B4) to M.S.; the National Science Foundation (Grant No. DBI1949036 to A.b.H and A.S.N.R, and Grant No. MCB 2014542 to E.H. and A.S.N.R.); and the DOE Office of Science, Office of Biological and Environmental Research (Grant\r\nNo. DE-SC0010733) to A.S.N.R and A.b.H.; the Deutsche Forschungsgemeinschaft (DFG) STA653/14-1 and STA653/15-1 to DS; the National Science Foundation grant (IOS-154173) to Q.Q.L.; the German Research Foundation (DFG) WA2167/8-1 to AW and SFB1101/C03 to AW and TWK; the Research Grants Council (RGC) of Hong Kong (GRF 12103020) to LX. NSF grant IOS-1849708 and NSF EPSCoR grant 1826836 to RS; the Academia Sinica to S.-L. T.","publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"BioMed Central","file_date_updated":"2022-07-18T08:15:24Z","article_number":"149","date_published":"2022-07-07T00:00:00Z","publication":"Genome Biology","citation":{"mla":"Zhang, Runxuan, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” Genome Biology, vol. 23, 149, BioMed Central, 2022, doi:10.1186/s13059-022-02711-0.","short":"R. Zhang, R. Kuo, M. Coulter, C.P.G. Calixto, J.C. Entizne, W. Guo, Y. Marquez, L. Milne, S. Riegler, A. Matsui, M. Tanaka, S. Harvey, Y. Gao, T. Wießner-Kroh, A. Paniagua, M. Crespi, K. Denby, A.B. Hur, E. Huq, M. Jantsch, A. Jarmolowski, T. Koester, S. Laubinger, Q.Q. Li, L. Gu, M. Seki, D. Staiger, R. Sunkar, Z. Szweykowska-Kulinska, S.L. Tu, A. Wachter, R. Waugh, L. Xiong, X.N. Zhang, A. Conesa, A.S.N. Reddy, A. Barta, M. Kalyna, J.W.S. Brown, Genome Biology 23 (2022).","chicago":"Zhang, Runxuan, Richard Kuo, Max Coulter, Cristiane P.G. Calixto, Juan Carlos Entizne, Wenbin Guo, Yamile Marquez, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” Genome Biology. BioMed Central, 2022. https://doi.org/10.1186/s13059-022-02711-0.","ama":"Zhang R, Kuo R, Coulter M, et al. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biology. 2022;23. doi:10.1186/s13059-022-02711-0","ista":"Zhang R, Kuo R, Coulter M, Calixto CPG, Entizne JC, Guo W, Marquez Y, Milne L, Riegler S, Matsui A, Tanaka M, Harvey S, Gao Y, Wießner-Kroh T, Paniagua A, Crespi M, Denby K, Hur AB, Huq E, Jantsch M, Jarmolowski A, Koester T, Laubinger S, Li QQ, Gu L, Seki M, Staiger D, Sunkar R, Szweykowska-Kulinska Z, Tu SL, Wachter A, Waugh R, Xiong L, Zhang XN, Conesa A, Reddy ASN, Barta A, Kalyna M, Brown JWS. 2022. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biology. 23, 149.","ieee":"R. Zhang et al., “A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis,” Genome Biology, vol. 23. BioMed Central, 2022.","apa":"Zhang, R., Kuo, R., Coulter, M., Calixto, C. P. G., Entizne, J. C., Guo, W., … Brown, J. W. S. (2022). A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-022-02711-0"},"article_type":"original","day":"07","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"creator":"dernst","content_type":"application/pdf","file_size":3146207,"access_level":"open_access","file_name":"2022_GenomeBiology_Zhang.pdf","success":1,"checksum":"2c30ef84151d257a6b835b4e069b70ac","date_created":"2022-07-18T08:15:24Z","date_updated":"2022-07-18T08:15:24Z","file_id":"11597","relation":"main_file"}],"oa_version":"Published Version","_id":"11587","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis","status":"public","ddc":["570"],"intvolume":" 23","abstract":[{"lang":"eng","text":"Background: Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis.\r\nResults: We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage.\r\nConclusions: AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species."}],"type":"journal_article"},{"publication_identifier":{"issn":["2059-0105"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.1038/s41541-022-00566-x","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000884278600004"],"pmid":["36379998"]},"file_date_updated":"2023-01-23T11:22:09Z","article_number":"145","volume":7,"date_updated":"2023-08-04T08:52:40Z","date_created":"2023-01-12T12:02:54Z","author":[{"full_name":"Byazrova, Maria G.","last_name":"Byazrova","first_name":"Maria G."},{"first_name":"Ekaterina A.","last_name":"Astakhova","full_name":"Astakhova, Ekaterina A."},{"id":"87DF77F0-1D9A-11EA-B6AE-CE443DDC885E","first_name":"Aygul","last_name":"Minnegalieva","full_name":"Minnegalieva, Aygul"},{"full_name":"Sukhova, Maria M.","last_name":"Sukhova","first_name":"Maria M."},{"full_name":"Mikhailov, Artem A.","first_name":"Artem A.","last_name":"Mikhailov"},{"full_name":"Prilipov, Alexey G.","last_name":"Prilipov","first_name":"Alexey G."},{"full_name":"Gorchakov, Andrey A.","first_name":"Andrey A.","last_name":"Gorchakov"},{"full_name":"Filatov, Alexander V.","last_name":"Filatov","first_name":"Alexander V."}],"department":[{"_id":"FyKo"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"acknowledgement":"We thank Sergey Kulemzin, Grigory Efimov, Yuri Lebedin, Alexander Taranin and Rudolf Valenta for providing reagents. Figures were created with the help of BioRender.com. This work was supported by the Russian Science Foundation (Project 21-15-00286). Byazrova M.G. was supported by the RUDN University Strategic Academic Leadership Program.","year":"2022","has_accepted_license":"1","article_processing_charge":"No","day":"15","keyword":["Pharmacology (medical)","Infectious Diseases","Pharmacology","Immunology","SARS-COV-2","COVID"],"scopus_import":"1","date_published":"2022-11-15T00:00:00Z","article_type":"original","citation":{"apa":"Byazrova, M. G., Astakhova, E. A., Minnegalieva, A., Sukhova, M. M., Mikhailov, A. A., Prilipov, A. G., … Filatov, A. V. (2022). Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination. Npj Vaccines. Springer Nature. https://doi.org/10.1038/s41541-022-00566-x","ieee":"M. G. Byazrova et al., “Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination,” npj Vaccines, vol. 7. Springer Nature, 2022.","ista":"Byazrova MG, Astakhova EA, Minnegalieva A, Sukhova MM, Mikhailov AA, Prilipov AG, Gorchakov AA, Filatov AV. 2022. Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination. npj Vaccines. 7, 145.","ama":"Byazrova MG, Astakhova EA, Minnegalieva A, et al. Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination. npj Vaccines. 2022;7. doi:10.1038/s41541-022-00566-x","chicago":"Byazrova, Maria G., Ekaterina A. Astakhova, Aygul Minnegalieva, Maria M. Sukhova, Artem A. Mikhailov, Alexey G. Prilipov, Andrey A. Gorchakov, and Alexander V. Filatov. “Anti-Ad26 Humoral Immunity Does Not Compromise SARS-COV-2 Neutralizing Antibody Responses Following Gam-COVID-Vac Booster Vaccination.” Npj Vaccines. Springer Nature, 2022. https://doi.org/10.1038/s41541-022-00566-x.","short":"M.G. Byazrova, E.A. Astakhova, A. Minnegalieva, M.M. Sukhova, A.A. Mikhailov, A.G. Prilipov, A.A. Gorchakov, A.V. Filatov, Npj Vaccines 7 (2022).","mla":"Byazrova, Maria G., et al. “Anti-Ad26 Humoral Immunity Does Not Compromise SARS-COV-2 Neutralizing Antibody Responses Following Gam-COVID-Vac Booster Vaccination.” Npj Vaccines, vol. 7, 145, Springer Nature, 2022, doi:10.1038/s41541-022-00566-x."},"publication":"npj Vaccines","abstract":[{"lang":"eng","text":"Replication-incompetent adenoviral vectors have been extensively used as a platform for vaccine design, with at least four anti-COVID-19 vaccines authorized to date. These vaccines elicit neutralizing antibody responses directed against SARS-CoV-2 Spike protein and confer significant level of protection against SARS-CoV-2 infection. Immunization with adenovirus-vectored vaccines is known to be accompanied by the production of anti-vector antibodies, which may translate into reduced efficacy of booster or repeated rounds of revaccination. Here, we used blood samples from patients who received an adenovirus-based Gam-COVID-Vac vaccine to address the question of whether anti-vector antibodies may influence the magnitude of SARS-CoV-2-specific humoral response after booster vaccination. We observed that rAd26-based prime vaccination with Gam-COVID-Vac induced the development of Ad26-neutralizing antibodies, which persisted in circulation for at least 9 months. Our analysis further indicates that high pre-boost Ad26 neutralizing antibody titers do not appear to affect the humoral immunogenicity of the Gam-COVID-Vac boost. The titers of anti-SARS-CoV-2 RBD IgGs and antibodies, which neutralized both the wild type and the circulating variants of concern of SARS-CoV-2 such as Delta and Omicron, were independent of the pre-boost levels of Ad26-neutralizing antibodies. Thus, our results support the development of repeated immunization schedule with adenovirus-based COVID-19 vaccines."}],"type":"journal_article","file":[{"success":1,"checksum":"ddaac096381565b2b4b7dcc34cdbc4ee","date_created":"2023-01-23T11:22:09Z","date_updated":"2023-01-23T11:22:09Z","file_id":"12347","relation":"main_file","creator":"dernst","file_size":1856046,"content_type":"application/pdf","access_level":"open_access","file_name":"2022_njpVaccines_Byazrova.pdf"}],"oa_version":"Published Version","intvolume":" 7","ddc":["570"],"status":"public","title":"Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination","_id":"12131","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"intvolume":" 14","ddc":["570"],"status":"public","title":"Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12173","oa_version":"Published Version","file":[{"checksum":"ee7681a17ae27645e9b5c1df61c15429","success":1,"date_created":"2023-01-26T10:56:51Z","date_updated":"2023-01-26T10:56:51Z","relation":"main_file","file_id":"12400","file_size":4075251,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2022_GutMicrobes_Baumgartner.pdf"}],"type":"journal_article","issue":"1","abstract":[{"text":"With increasing urbanization and industrialization, the prevalence of inflammatory bowel diseases (IBDs) has steadily been rising over the past two decades. IBD involves flares of gastrointestinal (GI) inflammation accompanied by microbiota perturbations. However, microbial mechanisms that trigger such flares remain elusive. Here, we analyzed the association of the emerging pathogen atypical enteropathogenic E. coli (aEPEC) with IBD disease activity. The presence of diarrheagenic E. coli was assessed in stool samples from 630 IBD patients and 234 age- and sex-matched controls without GI symptoms. Microbiota was analyzed with 16S ribosomal RNA gene amplicon sequencing, and 57 clinical aEPEC isolates were subjected to whole-genome sequencing and in vitro pathogenicity experiments including biofilm formation, epithelial barrier function and the ability to induce pro-inflammatory signaling. The presence of aEPEC correlated with laboratory, clinical and endoscopic disease activity in ulcerative colitis (UC), as well as microbiota dysbiosis. In vitro, aEPEC strains induce epithelial p21-activated kinases, disrupt the epithelial barrier and display potent biofilm formation. The effector proteins espV and espG2 distinguish aEPEC cultured from UC and Crohn’s disease patients, respectively. EspV-positive aEPEC harbor more virulence factors and have a higher pro-inflammatory potential, which is counteracted by 5-ASA. aEPEC may tip a fragile immune–microbiota homeostasis and thereby contribute to flares in UC. aEPEC isolates from UC patients display properties to disrupt the epithelial barrier and to induce pro-inflammatory signaling in vitro.","lang":"eng"}],"article_type":"original","citation":{"ama":"Baumgartner M, Zirnbauer R, Schlager S, et al. Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis. Gut Microbes. 2022;14(1). doi:10.1080/19490976.2022.2143218","apa":"Baumgartner, M., Zirnbauer, R., Schlager, S., Mertens, D., Gasche, N., Sladek, B., … Gasche, C. (2022). Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis. Gut Microbes. Taylor & Francis. https://doi.org/10.1080/19490976.2022.2143218","ieee":"M. Baumgartner et al., “Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis,” Gut Microbes, vol. 14, no. 1. Taylor & Francis, 2022.","ista":"Baumgartner M, Zirnbauer R, Schlager S, Mertens D, Gasche N, Sladek B, Herbold C, Bochkareva O, Emelianenko V, Vogelsang H, Lang M, Klotz A, Moik B, Makristathis A, Berry D, Dabsch S, Khare V, Gasche C. 2022. Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis. Gut Microbes. 14(1), e2143218.","short":"M. Baumgartner, R. Zirnbauer, S. Schlager, D. Mertens, N. Gasche, B. Sladek, C. Herbold, O. Bochkareva, V. Emelianenko, H. Vogelsang, M. Lang, A. Klotz, B. Moik, A. Makristathis, D. Berry, S. Dabsch, V. Khare, C. Gasche, Gut Microbes 14 (2022).","mla":"Baumgartner, Maximilian, et al. “Atypical Enteropathogenic E. Coli Are Associated with Disease Activity in Ulcerative Colitis.” Gut Microbes, vol. 14, no. 1, e2143218, Taylor & Francis, 2022, doi:10.1080/19490976.2022.2143218.","chicago":"Baumgartner, Maximilian, Rebecca Zirnbauer, Sabine Schlager, Daniel Mertens, Nikolaus Gasche, Barbara Sladek, Craig Herbold, et al. “Atypical Enteropathogenic E. Coli Are Associated with Disease Activity in Ulcerative Colitis.” Gut Microbes. Taylor & Francis, 2022. https://doi.org/10.1080/19490976.2022.2143218."},"publication":"Gut Microbes","date_published":"2022-11-22T00:00:00Z","keyword":["Infectious Diseases","Microbiology (medical)","Gastroenterology","Microbiology"],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"22","publisher":"Taylor & Francis","department":[{"_id":"FyKo"}],"publication_status":"published","acknowledgement":"We would like to acknowledge Anita Krnjic, Christina Gmainer, Marion Nehr, Helga Mock, and Sena Ecin for technical support in conducting the experiments.\r\nThis study was supported by the Austrian Science Fund (P 32302) and the Vienna Science and Technology Fund (LS18- 053; Austrian Science Fund (FWF)) [P 32302].","year":"2022","volume":14,"date_updated":"2023-08-04T09:10:18Z","date_created":"2023-01-12T12:11:36Z","author":[{"full_name":"Baumgartner, Maximilian","first_name":"Maximilian","last_name":"Baumgartner"},{"last_name":"Zirnbauer","first_name":"Rebecca","full_name":"Zirnbauer, Rebecca"},{"full_name":"Schlager, Sabine","first_name":"Sabine","last_name":"Schlager"},{"last_name":"Mertens","first_name":"Daniel","full_name":"Mertens, Daniel"},{"last_name":"Gasche","first_name":"Nikolaus","full_name":"Gasche, Nikolaus"},{"first_name":"Barbara","last_name":"Sladek","full_name":"Sladek, Barbara"},{"full_name":"Herbold, Craig","first_name":"Craig","last_name":"Herbold"},{"last_name":"Bochkareva","first_name":"Olga","full_name":"Bochkareva, Olga"},{"first_name":"Vera","last_name":"Emelianenko","id":"20152b9d-927a-11ed-8107-be36d740812d","full_name":"Emelianenko, Vera"},{"full_name":"Vogelsang, Harald","last_name":"Vogelsang","first_name":"Harald"},{"full_name":"Lang, Michaela","last_name":"Lang","first_name":"Michaela"},{"first_name":"Anton","last_name":"Klotz","full_name":"Klotz, Anton"},{"full_name":"Moik, Birgit","first_name":"Birgit","last_name":"Moik"},{"full_name":"Makristathis, Athanasios","first_name":"Athanasios","last_name":"Makristathis"},{"full_name":"Berry, David","first_name":"David","last_name":"Berry"},{"full_name":"Dabsch, Stefanie","last_name":"Dabsch","first_name":"Stefanie"},{"full_name":"Khare, Vineeta","last_name":"Khare","first_name":"Vineeta"},{"last_name":"Gasche","first_name":"Christoph","full_name":"Gasche, Christoph"}],"article_number":"e2143218","file_date_updated":"2023-01-26T10:56:51Z","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000889180100001"]},"language":[{"iso":"eng"}],"doi":"10.1080/19490976.2022.2143218","publication_identifier":{"issn":["1949-0976"],"eissn":["1949-0984"]},"month":"11"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12116","intvolume":" 378","title":"Remote opportunities for scholars in Ukraine","status":"public","oa_version":"Published Version","type":"journal_article","issue":"6626","abstract":[{"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.","lang":"eng"}],"citation":{"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.","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.","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.","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","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.","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"},"publication":"Science","page":"1285-1286","article_type":"letter_note","date_published":"2022-12-22T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"22","year":"2022","department":[{"_id":"FyKo"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","author":[{"first_name":"Karishma","last_name":"Chhugani","full_name":"Chhugani, Karishma"},{"full_name":"Frolova, Alina","last_name":"Frolova","first_name":"Alina"},{"first_name":"Yuriy","last_name":"Salyha","full_name":"Salyha, Yuriy"},{"first_name":"Andrada","last_name":"Fiscutean","full_name":"Fiscutean, Andrada"},{"first_name":"Oksana","last_name":"Zlenko","full_name":"Zlenko, Oksana"},{"first_name":"Sanita","last_name":"Reinsone","full_name":"Reinsone, Sanita"},{"full_name":"Wolfsberger, Walter W.","last_name":"Wolfsberger","first_name":"Walter W."},{"last_name":"Ivashchenko","first_name":"Oleksandra V.","full_name":"Ivashchenko, Oleksandra V."},{"last_name":"Maci","first_name":"Megi","full_name":"Maci, Megi"},{"full_name":"Dziuba, Dmytro","last_name":"Dziuba","first_name":"Dmytro"},{"last_name":"Parkhomenko","first_name":"Andrii","full_name":"Parkhomenko, Andrii"},{"full_name":"Bortz, Eric","first_name":"Eric","last_name":"Bortz"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor"},{"first_name":"Paweł P.","last_name":"Łabaj","full_name":"Łabaj, Paweł P."},{"full_name":"Romero, Veronika","first_name":"Veronika","last_name":"Romero"},{"last_name":"Hlávka","first_name":"Jakub","full_name":"Hlávka, Jakub"},{"full_name":"Oleksyk, Taras K.","first_name":"Taras K.","last_name":"Oleksyk"},{"full_name":"Mangul, Serghei","last_name":"Mangul","first_name":"Serghei"}],"volume":378,"date_created":"2023-01-12T11:56:30Z","date_updated":"2023-10-03T11:01:06Z","external_id":{"isi":["000963463700023"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1126/science.adg0797","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1126/science.adg0797","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"month":"12"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000629173100001"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1038/s41534-021-00387-1","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eissn":["2056-6387"]},"year":"2021","acknowledgement":"We would like to thank Robert Fickler for discussions about the experimental realization and Marek Sýs for running the NIST randomness test on the data we acquired in the experiment. We would like to thank Ugo Zanforlin, Gerald Buller, Daniel White, and Cristian Bonato for their help with the experiment. M. Pivoluska, M. Plesch, and M.M. acknowledge Czech-Austrian project MultiQUEST (I3053-N27 and GF17-33780L). M. Pivoluska and M. Plesch additionally acknowledge the support of VEGA project 2/0136/19. M.F. acknowledges support from the Polish NCN grant Sonata UMO-2014/14/E/ST2/00020, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program ERC AdG CERQUTE (grant agreement No 834266), the State Research Agency (AEI) TRANQI (PID2019-106888GB-I00/10.13039/501100011033), the Government of Spain (FIS2020-TRANQI; Severo Ochoa CEX2019-000910-S), Fundació Cellex, Fundació Mir-Puig, and Generalitat de Catalunya (CERCA, AGAUR). M.M., W.M., N.H.V., and C.F. acknowledge support from the QuantERA ERA-NET Co-fund (FWF Project I3773-N36) and the UK Engineering and Physical Sciences Research Council (EPSRC) (EP/P024114/1).","publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","author":[{"first_name":"Matej","last_name":"Pivoluska","full_name":"Pivoluska, Matej"},{"first_name":"Martin","last_name":"Plesch","full_name":"Plesch, Martin"},{"full_name":"Farkas, Máté","first_name":"Máté","last_name":"Farkas"},{"last_name":"Ruzickova","first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","full_name":"Ruzickova, Natalia"},{"last_name":"Flegel","first_name":"Clara","full_name":"Flegel, Clara"},{"last_name":"Valencia","first_name":"Natalia Herrera","full_name":"Valencia, Natalia Herrera"},{"last_name":"Mccutcheon","first_name":"Will","full_name":"Mccutcheon, Will"},{"full_name":"Malik, Mehul","first_name":"Mehul","last_name":"Malik"},{"last_name":"Aguilar","first_name":"Edgar A.","full_name":"Aguilar, Edgar A."}],"date_created":"2021-03-21T23:01:19Z","date_updated":"2023-08-07T14:17:26Z","volume":7,"article_number":"50","file_date_updated":"2021-03-22T11:09:34Z","publication":"npj Quantum Information","citation":{"mla":"Pivoluska, Matej, et al. “Semi-Device-Independent Random Number Generation with Flexible Assumptions.” Npj Quantum Information, vol. 7, 50, Springer Nature, 2021, doi:10.1038/s41534-021-00387-1.","short":"M. Pivoluska, M. Plesch, M. Farkas, N. Ruzickova, C. Flegel, N.H. Valencia, W. Mccutcheon, M. Malik, E.A. Aguilar, Npj Quantum Information 7 (2021).","chicago":"Pivoluska, Matej, Martin Plesch, Máté Farkas, Natalia Ruzickova, Clara Flegel, Natalia Herrera Valencia, Will Mccutcheon, Mehul Malik, and Edgar A. Aguilar. “Semi-Device-Independent Random Number Generation with Flexible Assumptions.” Npj Quantum Information. Springer Nature, 2021. https://doi.org/10.1038/s41534-021-00387-1.","ama":"Pivoluska M, Plesch M, Farkas M, et al. Semi-device-independent random number generation with flexible assumptions. npj Quantum Information. 2021;7. doi:10.1038/s41534-021-00387-1","ista":"Pivoluska M, Plesch M, Farkas M, Ruzickova N, Flegel C, Valencia NH, Mccutcheon W, Malik M, Aguilar EA. 2021. Semi-device-independent random number generation with flexible assumptions. npj Quantum Information. 7, 50.","apa":"Pivoluska, M., Plesch, M., Farkas, M., Ruzickova, N., Flegel, C., Valencia, N. H., … Aguilar, E. A. (2021). Semi-device-independent random number generation with flexible assumptions. Npj Quantum Information. Springer Nature. https://doi.org/10.1038/s41534-021-00387-1","ieee":"M. Pivoluska et al., “Semi-device-independent random number generation with flexible assumptions,” npj Quantum Information, vol. 7. Springer Nature, 2021."},"article_type":"original","date_published":"2021-03-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9255","ddc":["530"],"status":"public","title":"Semi-device-independent random number generation with flexible assumptions","intvolume":" 7","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_NPJQuantumInformation_Pivoluska.pdf","file_size":1360271,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"9274","checksum":"26d3f2a2c8c8fa8c1002028326b45f64","success":1,"date_created":"2021-03-22T11:09:34Z","date_updated":"2021-03-22T11:09:34Z"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Our ability to trust that a random number is truly random is essential for fields as diverse as cryptography and fundamental tests of quantum mechanics. Existing solutions both come with drawbacks—device-independent quantum random number generators (QRNGs) are highly impractical and standard semi-device-independent QRNGs are limited to a specific physical implementation and level of trust. Here we propose a framework for semi-device-independent randomness certification, using a source of trusted vacuum in the form of a signal shutter. It employs a flexible set of assumptions and levels of trust, allowing it to be applied in a wide range of physical scenarios involving both quantum and classical entropy sources. We experimentally demonstrate our protocol with a photonic setup and generate secure random bits under three different assumptions with varying degrees of security and resulting data rates."}]},{"file_date_updated":"2021-05-11T13:05:52Z","ec_funded":1,"article_number":"628622","author":[{"last_name":"Seferbekova","first_name":"Zaira","full_name":"Seferbekova, Zaira"},{"full_name":"Zabelkin, Alexey","first_name":"Alexey","last_name":"Zabelkin"},{"first_name":"Yulia","last_name":"Yakovleva","full_name":"Yakovleva, Yulia"},{"full_name":"Afasizhev, Robert","last_name":"Afasizhev","first_name":"Robert"},{"last_name":"Dranenko","first_name":"Natalia O.","full_name":"Dranenko, Natalia O."},{"last_name":"Alexeev","first_name":"Nikita","full_name":"Alexeev, Nikita"},{"full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S.","last_name":"Gelfand"},{"full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","first_name":"Olga"}],"date_created":"2021-05-09T22:01:38Z","date_updated":"2023-08-08T13:30:39Z","volume":12,"year":"2021","acknowledgement":"We thank Fyodor Kondrashov for valuable advice and manuscript proofreading. We also thank Alla Mikheenko for assistance with Circos.","publication_status":"published","publisher":"Frontiers","department":[{"_id":"FyKo"}],"month":"04","publication_identifier":{"eissn":["1664-302X"]},"doi":"10.3389/fmicb.2021.628622","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000643713300001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"abstract":[{"text":"Shigella are pathogens originating within the Escherichia lineage but frequently classified as a separate genus. Shigella genomes contain numerous insertion sequences (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess the contribution of genomic rearrangements to Shigella evolution. We found that Shigella experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic E. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in different Shigella lineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by all Shigella strains that also showed a high level of sequence conservation in the promoter and further in the 5′-intergenic region. In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli, we found a rate of genome rearrangements comparable to those in other E. coli and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These data indicate that the accumulation of ISs influenced many aspects of genome evolution and played an important role in the evolution of intracellular pathogens. Our research demonstrates the power of comparative genomics-based on synteny block composition and an important role of non-coding regions in the evolution of genomic islands.","lang":"eng"}],"type":"journal_article","file":[{"date_updated":"2021-05-11T13:05:52Z","date_created":"2021-05-11T13:05:52Z","checksum":"2f856543add59273a482a7f326fc0400","success":1,"relation":"main_file","file_id":"9384","file_size":14362316,"content_type":"application/pdf","creator":"kschuh","file_name":"2021_Frontiers_Microbiology_Seferbekova.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9380","title":"High rates of genome rearrangements and pathogenicity of Shigella spp","status":"public","ddc":["570"],"intvolume":" 12","day":"12","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2021-04-12T00:00:00Z","publication":"Frontiers in Microbiology","citation":{"ama":"Seferbekova Z, Zabelkin A, Yakovleva Y, et al. High rates of genome rearrangements and pathogenicity of Shigella spp. Frontiers in Microbiology. 2021;12. doi:10.3389/fmicb.2021.628622","ista":"Seferbekova Z, Zabelkin A, Yakovleva Y, Afasizhev R, Dranenko NO, Alexeev N, Gelfand MS, Bochkareva O. 2021. High rates of genome rearrangements and pathogenicity of Shigella spp. Frontiers in Microbiology. 12, 628622.","ieee":"Z. Seferbekova et al., “High rates of genome rearrangements and pathogenicity of Shigella spp,” Frontiers in Microbiology, vol. 12. Frontiers, 2021.","apa":"Seferbekova, Z., Zabelkin, A., Yakovleva, Y., Afasizhev, R., Dranenko, N. O., Alexeev, N., … Bochkareva, O. (2021). High rates of genome rearrangements and pathogenicity of Shigella spp. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2021.628622","mla":"Seferbekova, Zaira, et al. “High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.” Frontiers in Microbiology, vol. 12, 628622, Frontiers, 2021, doi:10.3389/fmicb.2021.628622.","short":"Z. Seferbekova, A. Zabelkin, Y. Yakovleva, R. Afasizhev, N.O. Dranenko, N. Alexeev, M.S. Gelfand, O. Bochkareva, Frontiers in Microbiology 12 (2021).","chicago":"Seferbekova, Zaira, Alexey Zabelkin, Yulia Yakovleva, Robert Afasizhev, Natalia O. Dranenko, Nikita Alexeev, Mikhail S. Gelfand, and Olga Bochkareva. “High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.” Frontiers in Microbiology. Frontiers, 2021. https://doi.org/10.3389/fmicb.2021.628622."},"article_type":"original"},{"language":[{"iso":"eng"}],"doi":"10.1038/s41431-021-00836-7","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209"}],"external_id":{"isi":["000625853200001"],"pmid":["33664501"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"07","publication_identifier":{"eissn":["14765438"],"issn":["10184813"]},"date_created":"2021-08-15T22:01:28Z","date_updated":"2023-08-11T10:33:42Z","volume":29,"author":[{"full_name":"Slavskii, Sergei A.","first_name":"Sergei A.","last_name":"Slavskii"},{"full_name":"Kuznetsov, Ivan A.","first_name":"Ivan A.","last_name":"Kuznetsov"},{"last_name":"Shashkova","first_name":"Tatiana I.","full_name":"Shashkova, Tatiana I."},{"full_name":"Bazykin, Georgii A.","last_name":"Bazykin","first_name":"Georgii A."},{"last_name":"Axenovich","first_name":"Tatiana I.","full_name":"Axenovich, Tatiana I."},{"first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"full_name":"Aulchenko, Yurii S.","first_name":"Yurii S.","last_name":"Aulchenko"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"year":"2021","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).","pmid":1,"file_date_updated":"2021-08-16T09:14:36Z","ec_funded":1,"date_published":"2021-07-01T00:00:00Z","article_type":"original","page":"1082-1091","publication":"European Journal of Human Genetics","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","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.","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","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.","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.","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."},"day":"01","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":"1","file":[{"file_size":1079395,"content_type":"application/pdf","creator":"asandaue","file_name":"2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf","access_level":"open_access","date_created":"2021-08-16T09:14:36Z","date_updated":"2021-08-16T09:14:36Z","checksum":"a676d76f91b0dbe0504c63e469129c2a","success":1,"relation":"main_file","file_id":"9921"}],"oa_version":"Published Version","ddc":["576"],"title":"The limits of normal approximation for adult height","status":"public","intvolume":" 29","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_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."}],"issue":"7","type":"journal_article"},{"publication_identifier":{"eissn":["20452322"]},"month":"07","doi":"10.1038/s41598-021-95025-3","language":[{"iso":"eng"}],"external_id":{"isi":["000683329100001"],"pmid":["34330988"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales"}],"isi":1,"quality_controlled":"1","ec_funded":1,"file_date_updated":"2021-08-16T11:36:49Z","article_number":"15729","related_material":{"link":[{"url":"https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/","relation":"press_release","description":"News on IST Website"}]},"author":[{"full_name":"Rella, Simon","last_name":"Rella","first_name":"Simon","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425"},{"first_name":"Yuliya A.","last_name":"Kulikova","full_name":"Kulikova, Yuliya A."},{"full_name":"Dermitzakis, Emmanouil T.","first_name":"Emmanouil T.","last_name":"Dermitzakis"},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"}],"volume":11,"date_updated":"2023-08-11T10:42:58Z","date_created":"2021-08-15T22:01:26Z","pmid":1,"year":"2021","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).","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","publication_status":"published","article_processing_charge":"Yes","has_accepted_license":"1","day":"30","scopus_import":"1","date_published":"2021-07-30T00:00:00Z","citation":{"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).","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.","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","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.","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","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."},"publication":"Scientific Reports","article_type":"original","issue":"1","abstract":[{"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.","lang":"eng"}],"type":"journal_article","file":[{"success":1,"checksum":"ac86892ed17e6724c7251844da5cef5c","date_created":"2021-08-16T11:36:49Z","date_updated":"2021-08-16T11:36:49Z","file_id":"9927","relation":"main_file","creator":"asandaue","content_type":"application/pdf","file_size":3432001,"access_level":"open_access","file_name":"2021_ScientificReports_Rella.pdf"}],"oa_version":"Published Version","_id":"9905","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 11","status":"public","ddc":["570","610"],"title":"Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains"},{"article_number":"91","file_date_updated":"2020-07-14T12:48:01Z","publisher":"Frontiers","department":[{"_id":"FyKo"}],"publication_status":"published","year":"2020","volume":11,"date_updated":"2023-08-18T07:05:18Z","date_created":"2020-03-22T23:00:46Z","author":[{"full_name":"Nimeth, Barbara Anna","first_name":"Barbara Anna","last_name":"Nimeth"},{"orcid":"0000-0003-3413-1343","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","last_name":"Riegler","first_name":"Stefan","full_name":"Riegler, Stefan"},{"last_name":"Kalyna","first_name":"Maria","full_name":"Kalyna, Maria"}],"publication_identifier":{"eissn":["1664462X"]},"month":"02","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000518903600001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3389/fpls.2020.00091","type":"journal_article","abstract":[{"text":"Plants are exposed to a variety of abiotic and biotic stresses that may result in DNA damage. Endogenous processes - such as DNA replication, DNA recombination, respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore essential to understand the strategies plants have developed for DNA damage detection, signaling, and repair. Alternative splicing (AS) is a key post-transcriptional process with a role in regulation of gene expression. Recent studies demonstrate that the majority of intron-containing genes in plants are alternatively spliced, highlighting the importance of AS in plant development and stress response. Not only does AS ensure a versatile proteome and influence the abundance and availability of proteins greatly, it has also emerged as an important player in the DNA damage response (DDR) in animals. Despite extensive studies of DDR carried out in plants, its regulation at the level of AS has not been comprehensively addressed. Here, we provide some insights into the interplay between AS and DDR in plants.","lang":"eng"}],"intvolume":" 11","title":"Alternative splicing and DNA damage response in plants","status":"public","ddc":["580"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7603","file":[{"relation":"main_file","file_id":"7607","checksum":"57c37209f7b6712ced86c0f11b2be74e","date_updated":"2020-07-14T12:48:01Z","date_created":"2020-03-23T09:03:40Z","access_level":"open_access","file_name":"2020_FrontiersPlants_Nimeth.pdf","file_size":507414,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"19","article_type":"original","citation":{"short":"B.A. Nimeth, S. Riegler, M. Kalyna, Frontiers in Plant Science 11 (2020).","mla":"Nimeth, Barbara Anna, et al. “Alternative Splicing and DNA Damage Response in Plants.” Frontiers in Plant Science, vol. 11, 91, Frontiers, 2020, doi:10.3389/fpls.2020.00091.","chicago":"Nimeth, Barbara Anna, Stefan Riegler, and Maria Kalyna. “Alternative Splicing and DNA Damage Response in Plants.” Frontiers in Plant Science. Frontiers, 2020. https://doi.org/10.3389/fpls.2020.00091.","ama":"Nimeth BA, Riegler S, Kalyna M. Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. 2020;11. doi:10.3389/fpls.2020.00091","ieee":"B. A. Nimeth, S. Riegler, and M. Kalyna, “Alternative splicing and DNA damage response in plants,” Frontiers in Plant Science, vol. 11. Frontiers, 2020.","apa":"Nimeth, B. A., Riegler, S., & Kalyna, M. (2020). Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2020.00091","ista":"Nimeth BA, Riegler S, Kalyna M. 2020. Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. 11, 91."},"publication":"Frontiers in Plant Science","date_published":"2020-02-19T00:00:00Z"},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"24","article_type":"original","citation":{"chicago":"Plesch, Martin, Samuel Plesník, and Natalia Ruzickova. “The IYPT and the ‘Ring Oiler’ Problem.” European Journal of Physics. IOP Publishing, 2020. https://doi.org/10.1088/1361-6404/ab6414.","mla":"Plesch, Martin, et al. “The IYPT and the ‘Ring Oiler’ Problem.” European Journal of Physics, vol. 41, no. 3, 034001, IOP Publishing, 2020, doi:10.1088/1361-6404/ab6414.","short":"M. Plesch, S. Plesník, N. Ruzickova, European Journal of Physics 41 (2020).","ista":"Plesch M, Plesník S, Ruzickova N. 2020. The IYPT and the ‘Ring Oiler’ problem. European Journal of Physics. 41(3), 034001.","apa":"Plesch, M., Plesník, S., & Ruzickova, N. (2020). The IYPT and the “Ring Oiler” problem. European Journal of Physics. IOP Publishing. https://doi.org/10.1088/1361-6404/ab6414","ieee":"M. Plesch, S. Plesník, and N. Ruzickova, “The IYPT and the ‘Ring Oiler’ problem,” European Journal of Physics, vol. 41, no. 3. IOP Publishing, 2020.","ama":"Plesch M, Plesník S, Ruzickova N. The IYPT and the “Ring Oiler” problem. European Journal of Physics. 2020;41(3). doi:10.1088/1361-6404/ab6414"},"publication":"European Journal of Physics","date_published":"2020-02-24T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"The International Young Physicists' Tournament (IYPT) continued in 2018 in Beijing, China and 2019 in Warsaw, Poland with its 31st and 32nd editions. The IYPT is a modern scientific competition for teams of high school students, also known as the Physics World Cup. It involves long-term theoretical and experimental work focused on solving 17 publicly announced open-ended problems in teams of five. On top of that, teams have to present their solutions in front of other teams and a scientific jury, and get opposed and reviewed by their peers. Here we present a brief information about the competition with a specific focus on one of the IYPT 2018 tasks, the 'Ring Oiler'. This seemingly simple mechanical problem appeared to be of such a complexity that even the dozens of participating teams and jurying scientists were not able to solve all of its subtleties."}],"intvolume":" 41","ddc":["530"],"title":"The IYPT and the 'Ring Oiler' problem","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7622","file":[{"date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-06T08:53:53Z","checksum":"47dda164e33b6c0c6c3ed14aad298376","file_id":"7641","relation":"main_file","creator":"dernst","file_size":1533672,"content_type":"application/pdf","file_name":"2020_EuropJourPhysics_Plesch.pdf","access_level":"open_access"}],"oa_version":"Published Version","publication_identifier":{"issn":["01430807"],"eissn":["13616404"]},"month":"02","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1910.03290"],"isi":["000537425400001"]},"language":[{"iso":"eng"}],"doi":"10.1088/1361-6404/ab6414","article_number":"034001","file_date_updated":"2020-07-14T12:48:01Z","publisher":"IOP Publishing","department":[{"_id":"FyKo"}],"publication_status":"published","year":"2020","volume":41,"date_updated":"2023-08-18T10:18:29Z","date_created":"2020-03-31T11:25:04Z","author":[{"full_name":"Plesch, Martin","first_name":"Martin","last_name":"Plesch"},{"full_name":"Plesník, Samuel","last_name":"Plesník","first_name":"Samuel"},{"full_name":"Ruzickova, Natalia","last_name":"Ruzickova","first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425"}]},{"publication_identifier":{"eissn":["20452322"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.1038/s41598-020-65406-1","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000560774200007"]},"file_date_updated":"2020-07-14T12:48:05Z","article_number":"8635","volume":10,"date_created":"2020-06-07T22:00:51Z","date_updated":"2023-08-21T07:00:17Z","author":[{"full_name":"Uroshlev, Leonid A.","last_name":"Uroshlev","first_name":"Leonid A."},{"full_name":"Abdullaev, Eldar T.","first_name":"Eldar T.","last_name":"Abdullaev"},{"last_name":"Umarova","first_name":"Iren R.","full_name":"Umarova, Iren R."},{"full_name":"Il’Icheva, Irina A.","last_name":"Il’Icheva","first_name":"Irina A."},{"last_name":"Panchenko","first_name":"Larisa A.","full_name":"Panchenko, Larisa A."},{"first_name":"Robert V.","last_name":"Polozov","full_name":"Polozov, Robert V."},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"},{"last_name":"Nechipurenko","first_name":"Yury D.","full_name":"Nechipurenko, Yury D."},{"full_name":"Grokhovsky, Sergei L.","last_name":"Grokhovsky","first_name":"Sergei L."}],"publisher":"Springer Nature","department":[{"_id":"FyKo"}],"publication_status":"published","year":"2020","has_accepted_license":"1","article_processing_charge":"No","day":"25","scopus_import":"1","date_published":"2020-05-25T00:00:00Z","article_type":"original","citation":{"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.","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","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.","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","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.","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).","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."},"publication":"Scientific Reports","abstract":[{"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.","lang":"eng"}],"type":"journal_article","file":[{"relation":"main_file","file_id":"7947","checksum":"099e51611a5b7ca04244d03b2faddf33","date_updated":"2020-07-14T12:48:05Z","date_created":"2020-06-08T06:27:32Z","access_level":"open_access","file_name":"2020_ScientificReports_Uroshlev.pdf","file_size":1001724,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","intvolume":" 10","ddc":["570"],"title":"A method for identification of the methylation level of CpG islands from NGS data","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7931"}]