[{"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"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 10","month":"03","publication_status":"published","publication_identifier":{"issn":["2375-2548"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"15185","checksum":"a19c43b260ea0bbaf895a29712e3153c","success":1,"creator":"dernst","date_updated":"2024-03-25T09:42:10Z","file_size":1499302,"date_created":"2024-03-25T09:42:10Z","file_name":"2024_ScienceAdv_Palkina.pdf"}],"issue":"10","volume":10,"_id":"15179","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2024-03-25T09:44:53Z","ddc":["580"],"department":[{"_id":"FyKo"}],"file_date_updated":"2024-03-25T09:42:10Z","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).","oa":1,"publisher":"American Association for the Advancement of Science","quality_controlled":"1","year":"2024","has_accepted_license":"1","publication":"Science Advances","day":"01","date_created":"2024-03-25T08:54:33Z","doi":"10.1126/sciadv.adk1992","date_published":"2024-03-01T00:00:00Z","article_number":"adk1992","citation":{"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.","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.","ama":"Palkina KA, Karataeva TA, Perfilov MM, et al. A hybrid pathway for self-sustained luminescence. Science Advances. 2024;10(10). doi:10.1126/sciadv.adk1992","apa":"Palkina, K. A., Karataeva, T. A., Perfilov, M. M., Fakhranurova, L. I., Markina, N. M., Gonzalez Somermeyer, L., … Sarkisyan, K. S. (2024). A hybrid pathway for self-sustained luminescence. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adk1992","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).","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","author":[{"first_name":"Kseniia A.","full_name":"Palkina, Kseniia A.","last_name":"Palkina"},{"first_name":"Tatiana A.","last_name":"Karataeva","full_name":"Karataeva, Tatiana A."},{"full_name":"Perfilov, Maxim M.","last_name":"Perfilov","first_name":"Maxim M."},{"first_name":"Liliia I.","full_name":"Fakhranurova, Liliia I.","last_name":"Fakhranurova"},{"first_name":"Nadezhda M.","last_name":"Markina","full_name":"Markina, Nadezhda M."},{"id":"4720D23C-F248-11E8-B48F-1D18A9856A87","first_name":"Louisa","full_name":"Gonzalez Somermeyer, Louisa","orcid":"0000-0001-9139-5383","last_name":"Gonzalez Somermeyer"},{"first_name":"Elena","full_name":"Garcia-Perez, Elena","last_name":"Garcia-Perez"},{"first_name":"Marta","last_name":"Vazquez-Vilar","full_name":"Vazquez-Vilar, Marta"},{"full_name":"Rodriguez-Rodriguez, Marta","last_name":"Rodriguez-Rodriguez","first_name":"Marta"},{"full_name":"Vazquez-Vilriales, Victor","last_name":"Vazquez-Vilriales","first_name":"Victor"},{"first_name":"Ekaterina S.","full_name":"Shakhova, Ekaterina S.","last_name":"Shakhova"},{"last_name":"Mitiouchkina","full_name":"Mitiouchkina, Tatiana","first_name":"Tatiana"},{"last_name":"Belozerova","full_name":"Belozerova, Olga A.","first_name":"Olga A."},{"first_name":"Sergey I.","full_name":"Kovalchuk, Sergey I.","last_name":"Kovalchuk"},{"full_name":"Alekberova, Anna","last_name":"Alekberova","first_name":"Anna"},{"full_name":"Malyshevskaia, Alena K.","last_name":"Malyshevskaia","first_name":"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."},{"first_name":"Anastasia","last_name":"Balakireva","full_name":"Balakireva, Anastasia"},{"last_name":"Sytov","full_name":"Sytov, Nikita","first_name":"Nikita"},{"first_name":"Anastasia","last_name":"Bezlikhotnova","full_name":"Bezlikhotnova, Anastasia"},{"full_name":"Boldyreva, Daria I.","last_name":"Boldyreva","first_name":"Daria I."},{"last_name":"Babenko","full_name":"Babenko, Vladislav V.","first_name":"Vladislav V."},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov"},{"first_name":"Vladimir V.","full_name":"Choob, Vladimir V.","last_name":"Choob"},{"last_name":"Orzaez","full_name":"Orzaez, Diego","first_name":"Diego"},{"first_name":"Ilia V.","last_name":"Yampolsky","full_name":"Yampolsky, Ilia V."},{"full_name":"Mishin, Alexander S.","last_name":"Mishin","first_name":"Alexander S."},{"full_name":"Sarkisyan, Karen S.","last_name":"Sarkisyan","first_name":"Karen S."}],"title":"A hybrid pathway for self-sustained luminescence"},{"title":"Using AlphaFold to predict the impact of single mutations on protein stability and function","author":[{"last_name":"Pak","full_name":"Pak, Marina A.","first_name":"Marina A."},{"first_name":"Karina A.","full_name":"Markhieva, Karina A.","last_name":"Markhieva"},{"last_name":"Novikova","full_name":"Novikova, Mariia S.","first_name":"Mariia S."},{"first_name":"Dmitry S.","last_name":"Petrov","full_name":"Petrov, Dmitry S."},{"first_name":"Ilya S.","full_name":"Vorobyev, Ilya S.","last_name":"Vorobyev"},{"id":"2FBE0DE4-F248-11E8-B48F-1D18A9856A87","first_name":"Ekaterina","full_name":"Maksimova, Ekaterina","last_name":"Maksimova"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dmitry N.","last_name":"Ivankov","full_name":"Ivankov, Dmitry N."}],"article_processing_charge":"No","external_id":{"isi":["000985134400106"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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).","ama":"Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 2023;18(3). doi:10.1371/journal.pone.0282689","apa":"Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I. S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0282689","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.","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.","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."},"article_number":"e0282689","doi":"10.1371/journal.pone.0282689","date_published":"2023-03-16T00:00:00Z","date_created":"2023-03-26T22:01:07Z","day":"16","publication":"PLoS ONE","isi":1,"has_accepted_license":"1","year":"2023","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"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.","department":[{"_id":"FyKo"},{"_id":"MaRo"}],"file_date_updated":"2023-03-27T07:09:08Z","ddc":["570"],"date_updated":"2023-08-01T13:47:14Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"12758","volume":18,"issue":"3","file":[{"date_updated":"2023-03-27T07:09:08Z","file_size":856625,"creator":"dernst","date_created":"2023-03-27T07:09:08Z","file_name":"2023_PLoSOne_Pak.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"12771","checksum":"0281bdfccf8d76c4e08dd011c603f6b6","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1932-6203"]},"publication_status":"published","month":"03","intvolume":" 18","scopus_import":"1","oa_version":"Published Version","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"}]},{"external_id":{"isi":["001048208600023"]},"article_processing_charge":"No","author":[{"last_name":"Gert","full_name":"Gert, Krista R.B.","first_name":"Krista R.B."},{"full_name":"Panser, Karin","last_name":"Panser","first_name":"Karin"},{"last_name":"Surm","full_name":"Surm, Joachim","first_name":"Joachim"},{"last_name":"Steinmetz","full_name":"Steinmetz, Benjamin S.","first_name":"Benjamin S."},{"first_name":"Alexander","last_name":"Schleiffer","full_name":"Schleiffer, Alexander"},{"first_name":"Luca","full_name":"Jovine, Luca","last_name":"Jovine"},{"last_name":"Moran","full_name":"Moran, Yehu","first_name":"Yehu"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov"},{"last_name":"Pauli","full_name":"Pauli, Andrea","first_name":"Andrea"}],"title":"Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries","citation":{"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.","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).","ama":"Gert KRB, Panser K, Surm J, et al. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. 2023;14. doi:10.1038/s41467-023-39317-4","apa":"Gert, K. R. B., Panser, K., Surm, J., Steinmetz, B. S., Schleiffer, A., Jovine, L., … Pauli, A. (2023). Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-39317-4","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"3506","date_created":"2023-06-25T22:00:45Z","doi":"10.1038/s41467-023-39317-4","date_published":"2023-06-14T00:00:00Z","year":"2023","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"14","oa":1,"publisher":"Springer Nature","quality_controlled":"1","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.","file_date_updated":"2023-06-26T10:26:04Z","department":[{"_id":"FyKo"}],"date_updated":"2023-12-13T11:26:34Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"13164","volume":14,"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2023-06-26T10:26:04Z","file_name":"2023_NatureComm_Gert.pdf","creator":"dernst","date_updated":"2023-06-26T10:26:04Z","file_size":1555006,"checksum":"d6165f41c7f1c2c04b04256ec9f003fb","file_id":"13172","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"scopus_import":"1","intvolume":" 14","month":"06","abstract":[{"lang":"eng","text":"Molecular compatibility between gametes is a prerequisite for successful fertilization. As long as a sperm and egg can recognize and bind each other via their surface proteins, gamete fusion may occur even between members of separate species, resulting in hybrids that can impact speciation. The egg membrane protein Bouncer confers species specificity to gamete interactions between medaka and zebrafish, preventing their cross-fertilization. Here, we leverage this specificity to uncover distinct amino acid residues and N-glycosylation patterns that differentially influence the function of medaka and zebrafish Bouncer and contribute to cross-species incompatibility. Curiously, in contrast to the specificity observed for medaka and zebrafish Bouncer, seahorse and fugu Bouncer are compatible with both zebrafish and medaka sperm, in line with the pervasive purifying selection that dominates Bouncer’s evolution. The Bouncer-sperm interaction is therefore the product of seemingly opposing evolutionary forces that, for some species, restrict fertilization to closely related fish, and for others, allow broad gamete compatibility that enables hybridization."}],"oa_version":"Published Version"},{"article_type":"original","type":"journal_article","status":"public","_id":"13976","department":[{"_id":"FyKo"}],"date_updated":"2023-12-13T12:01:46Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/gigascience/giad045"}],"scopus_import":"1","intvolume":" 12","month":"07","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","volume":12,"publication_status":"epub_ahead","publication_identifier":{"eissn":["2047-217X"]},"language":[{"iso":"eng"}],"article_processing_charge":"Yes","external_id":{"pmid":["37496156"],"isi":["001081086100001"]},"author":[{"full_name":"Wolfsberger, Walter","last_name":"Wolfsberger","first_name":"Walter"},{"full_name":"Chhugani, Karishma","last_name":"Chhugani","first_name":"Karishma"},{"first_name":"Khrystyna","full_name":"Shchubelka, Khrystyna","last_name":"Shchubelka"},{"first_name":"Alina","full_name":"Frolova, Alina","last_name":"Frolova"},{"first_name":"Yuriy","full_name":"Salyha, Yuriy","last_name":"Salyha"},{"first_name":"Oksana","full_name":"Zlenko, Oksana","last_name":"Zlenko"},{"full_name":"Arych, Mykhailo","last_name":"Arych","first_name":"Mykhailo"},{"first_name":"Dmytro","full_name":"Dziuba, Dmytro","last_name":"Dziuba"},{"first_name":"Andrii","full_name":"Parkhomenko, Andrii","last_name":"Parkhomenko"},{"first_name":"Volodymyr","full_name":"Smolanka, Volodymyr","last_name":"Smolanka"},{"first_name":"Zeynep H.","last_name":"Gümüş","full_name":"Gümüş, Zeynep H."},{"full_name":"Sezgin, Efe","last_name":"Sezgin","first_name":"Efe"},{"first_name":"Alondra","last_name":"Diaz-Lameiro","full_name":"Diaz-Lameiro, Alondra"},{"first_name":"Viktor R.","full_name":"Toth, Viktor R.","last_name":"Toth"},{"first_name":"Megi","full_name":"Maci, Megi","last_name":"Maci"},{"full_name":"Bortz, Eric","last_name":"Bortz","first_name":"Eric"},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"first_name":"Patricia M.","full_name":"Morton, Patricia M.","last_name":"Morton"},{"full_name":"Łabaj, Paweł P.","last_name":"Łabaj","first_name":"Paweł P."},{"first_name":"Veronika","full_name":"Romero, Veronika","last_name":"Romero"},{"first_name":"Jakub","full_name":"Hlávka, Jakub","last_name":"Hlávka"},{"first_name":"Serghei","last_name":"Mangul","full_name":"Mangul, Serghei"},{"first_name":"Taras K.","full_name":"Oleksyk, Taras K.","last_name":"Oleksyk"}],"title":"Scientists without borders: Lessons from Ukraine","citation":{"mla":"Wolfsberger, Walter, et al. “Scientists without Borders: Lessons from Ukraine.” GigaScience, vol. 12, Oxford Academic, 2023, doi:10.1093/gigascience/giad045.","ieee":"W. Wolfsberger et al., “Scientists without borders: Lessons from Ukraine,” GigaScience, vol. 12. Oxford Academic, 2023.","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).","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","ama":"Wolfsberger W, Chhugani K, Shchubelka K, et al. Scientists without borders: Lessons from Ukraine. GigaScience. 2023;12. 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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Oxford Academic","quality_controlled":"1","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.","date_created":"2023-08-06T22:01:13Z","doi":"10.1093/gigascience/giad045","date_published":"2023-07-27T00:00:00Z","year":"2023","isi":1,"publication":"GigaScience","day":"27"},{"citation":{"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.","short":"A. Yurtseven, S. Buyanova, A.A.A. Agrawal, O. Bochkareva, O.V.V. Kalinina, BMC Microbiology 23 (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","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Alper","last_name":"Yurtseven","full_name":"Yurtseven, Alper"},{"id":"2F54A7BC-3902-11EA-AC87-BC9F3DDC885E","first_name":"Sofia","last_name":"Buyanova","full_name":"Buyanova, Sofia"},{"first_name":"Amay Ajaykumar A.","last_name":"Agrawal","full_name":"Agrawal, Amay Ajaykumar A."},{"orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga"},{"first_name":"Olga V V.","full_name":"Kalinina, Olga V V.","last_name":"Kalinina"}],"external_id":{"pmid":["38124060"]},"article_processing_charge":"Yes (via OA deal)","title":"Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis","article_number":"404","has_accepted_license":"1","year":"2023","day":"01","publication":"BMC Microbiology","doi":"10.1186/s12866-023-03147-7","date_published":"2023-12-01T00:00:00Z","date_created":"2023-12-31T23:01:02Z","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.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"date_updated":"2024-01-02T09:20:57Z","ddc":["570"],"department":[{"_id":"FyKo"}],"file_date_updated":"2024-01-02T09:09:32Z","_id":"14716","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["1471-2180"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"7ff5e95f3496ff663301eb4a13a316d5","file_id":"14723","success":1,"date_updated":"2024-01-02T09:09:32Z","file_size":1979922,"creator":"dernst","date_created":"2024-01-02T09:09:32Z","file_name":"2023_BMCMicrobiology_Yurtseven.pdf"}],"language":[{"iso":"eng"}],"issue":"1","volume":23,"abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"12","intvolume":" 23"},{"file_date_updated":"2022-03-28T08:07:46Z","department":[{"_id":"FyKo"}],"ddc":["000"],"date_updated":"2023-08-03T06:21:46Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10927","issue":"2","volume":38,"related_material":{"link":[{"url":"https://github.com/ctlab/parallel-rearrangements","relation":"software"}]},"ec_funded":1,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"10930","checksum":"4b5688ff9ac86180ccdf7f82fa33d926","creator":"dernst","file_size":3425744,"date_updated":"2022-03-28T08:07:46Z","file_name":"2022_Bioinformatics_Zabelkin.pdf","date_created":"2022-03-28T08:07:46Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1367-4803"],"eissn":["1460-2059"]},"publication_status":"published","month":"01","intvolume":" 38","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"title":"PaReBrick: PArallel REarrangements and BReaks identification toolkit","author":[{"first_name":"Alexey","last_name":"Zabelkin","full_name":"Zabelkin, Alexey"},{"first_name":"Yulia","last_name":"Yakovleva","full_name":"Yakovleva, Yulia"},{"last_name":"Bochkareva","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"first_name":"Nikita","full_name":"Alexeev, Nikita","last_name":"Alexeev"}],"article_processing_charge":"No","external_id":{"isi":["000743380100008"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","ista":"Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. 2022. PaReBrick: PArallel REarrangements and BReaks identification toolkit. Bioinformatics. 38(2), 357–363.","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.","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.","short":"A. Zabelkin, Y. Yakovleva, O. Bochkareva, N. Alexeev, Bioinformatics 38 (2022) 357–363.","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","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"},"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"doi":"10.1093/bioinformatics/btab691","date_published":"2022-01-15T00:00:00Z","date_created":"2022-03-27T22:01:46Z","page":"357-363","day":"15","publication":"Bioinformatics","isi":1,"has_accepted_license":"1","year":"2022","publisher":"Oxford Academic","quality_controlled":"1","oa":1,"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."},{"publication_status":"published","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"4","volume":19,"abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1038/s41592-022-01444-z","open_access":"1"}],"scopus_import":"1","intvolume":" 19","month":"04","date_updated":"2023-08-03T06:46:09Z","department":[{"_id":"FyKo"}],"_id":"11187","article_type":"letter_note","type":"journal_article","status":"public","year":"2022","isi":1,"publication":"Nature Methods","day":"08","page":"374-380","date_created":"2022-04-17T22:01:48Z","date_published":"2022-04-08T00:00:00Z","doi":"10.1038/s41592-022-01444-z","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).","oa":1,"quality_controlled":"1","publisher":"Springer Nature","citation":{"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.","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","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["35396471"],"isi":["000781199600011"]},"author":[{"full_name":"Knyazev, Sergey","last_name":"Knyazev","first_name":"Sergey"},{"first_name":"Karishma","full_name":"Chhugani, Karishma","last_name":"Chhugani"},{"full_name":"Sarwal, Varuni","last_name":"Sarwal","first_name":"Varuni"},{"first_name":"Ram","full_name":"Ayyala, Ram","last_name":"Ayyala"},{"first_name":"Harman","last_name":"Singh","full_name":"Singh, Harman"},{"first_name":"Smruthi","last_name":"Karthikeyan","full_name":"Karthikeyan, Smruthi"},{"first_name":"Dhrithi","last_name":"Deshpande","full_name":"Deshpande, Dhrithi"},{"first_name":"Pelin Icer","full_name":"Baykal, Pelin Icer","last_name":"Baykal"},{"first_name":"Zoia","last_name":"Comarova","full_name":"Comarova, Zoia"},{"full_name":"Lu, Angela","last_name":"Lu","first_name":"Angela"},{"last_name":"Porozov","full_name":"Porozov, Yuri","first_name":"Yuri"},{"first_name":"Tetyana I.","last_name":"Vasylyeva","full_name":"Vasylyeva, Tetyana I."},{"last_name":"Wertheim","full_name":"Wertheim, Joel O.","first_name":"Joel O."},{"first_name":"Braden T.","full_name":"Tierney, Braden T.","last_name":"Tierney"},{"first_name":"Charles Y.","last_name":"Chiu","full_name":"Chiu, Charles Y."},{"last_name":"Sun","full_name":"Sun, Ren","first_name":"Ren"},{"first_name":"Aiping","full_name":"Wu, Aiping","last_name":"Wu"},{"first_name":"Malak S.","full_name":"Abedalthagafi, Malak S.","last_name":"Abedalthagafi"},{"first_name":"Victoria M.","full_name":"Pak, Victoria M.","last_name":"Pak"},{"last_name":"Nagaraj","full_name":"Nagaraj, Shivashankar H.","first_name":"Shivashankar H."},{"last_name":"Smith","full_name":"Smith, Adam L.","first_name":"Adam L."},{"full_name":"Skums, Pavel","last_name":"Skums","first_name":"Pavel"},{"first_name":"Bogdan","last_name":"Pasaniuc","full_name":"Pasaniuc, Bogdan"},{"full_name":"Komissarov, Andrey","last_name":"Komissarov","first_name":"Andrey"},{"full_name":"Mason, Christopher E.","last_name":"Mason","first_name":"Christopher E."},{"first_name":"Eric","full_name":"Bortz, Eric","last_name":"Bortz"},{"first_name":"Philippe","last_name":"Lemey","full_name":"Lemey, Philippe"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"},{"last_name":"Beerenwinkel","full_name":"Beerenwinkel, Niko","first_name":"Niko"},{"first_name":"Tommy Tsan Yuk","full_name":"Lam, Tommy Tsan Yuk","last_name":"Lam"},{"first_name":"Nicholas C.","full_name":"Wu, Nicholas C.","last_name":"Wu"},{"first_name":"Alex","last_name":"Zelikovsky","full_name":"Zelikovsky, Alex"},{"full_name":"Knight, Rob","last_name":"Knight","first_name":"Rob"},{"first_name":"Keith A.","full_name":"Crandall, Keith A.","last_name":"Crandall"},{"first_name":"Serghei","full_name":"Mangul, Serghei","last_name":"Mangul"}],"title":"Unlocking capacities of genomics for the COVID-19 response and future pandemics","project":[{"call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales"}]},{"publication_identifier":{"issn":["2045-2322"]},"publication_status":"published","file":[{"success":1,"checksum":"12601b8a5c6b83bb618f92bcb963ecc9","file_id":"11349","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2022_ScientificReports_Dranenko.pdf","date_created":"2022-05-02T09:05:20Z","creator":"dernst","file_size":3564155,"date_updated":"2022-05-02T09:05:20Z"}],"language":[{"iso":"eng"}],"volume":12,"ec_funded":1,"abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 12","date_updated":"2023-08-03T06:59:49Z","ddc":["570"],"file_date_updated":"2022-05-02T09:05:20Z","department":[{"_id":"FyKo"}],"_id":"11344","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","isi":1,"has_accepted_license":"1","year":"2022","day":"27","publication":"Scientific Reports","date_published":"2022-04-27T00:00:00Z","doi":"10.1038/s41598-022-10827-3","date_created":"2022-05-02T07:08:42Z","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. ","publisher":"Springer Nature","quality_controlled":"1","oa":1,"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.","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.","short":"N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, O. Bochkareva, Scientific Reports 12 (2022).","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Dranenko","full_name":"Dranenko, NO","first_name":"NO"},{"first_name":"MN","full_name":"Tutukina, MN","last_name":"Tutukina"},{"full_name":"Gelfand, MS","last_name":"Gelfand","first_name":"MS"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"last_name":"Bochkareva","full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425"}],"article_processing_charge":"No","external_id":{"pmid":["35477739"],"isi":["000788639400032"]},"title":"Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia","article_number":"6868","project":[{"grant_number":"I05127","name":"Evolutionary analysis of gene regulation","_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"_id":"11448","department":[{"_id":"GradSch"},{"_id":"FyKo"}],"file_date_updated":"2022-06-20T07:44:19Z","date_updated":"2023-08-03T07:20:15Z","ddc":["570"],"scopus_import":"1","month":"05","intvolume":" 11","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"oa_version":"Published Version","volume":11,"ec_funded":1,"publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","file":[{"success":1,"file_id":"11454","checksum":"7573c28f44028ab0cc81faef30039e44","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2022_eLife_Somermeyer.pdf","date_created":"2022-06-20T07:44:19Z","creator":"dernst","file_size":5297213,"date_updated":"2022-06-20T07:44:19Z"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"article_number":"75842","author":[{"full_name":"Gonzalez Somermeyer, Louisa","orcid":"0000-0001-9139-5383","last_name":"Gonzalez Somermeyer","first_name":"Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fleiss, Aubin","last_name":"Fleiss","first_name":"Aubin"},{"first_name":"Alexander S","last_name":"Mishin","full_name":"Mishin, Alexander S"},{"full_name":"Bozhanova, Nina G","last_name":"Bozhanova","first_name":"Nina G"},{"full_name":"Igolkina, Anna A","last_name":"Igolkina","first_name":"Anna A"},{"first_name":"Jens","full_name":"Meiler, Jens","last_name":"Meiler"},{"full_name":"Alaball Pujol, Maria-Elisenda","last_name":"Alaball Pujol","first_name":"Maria-Elisenda"},{"last_name":"Putintseva","full_name":"Putintseva, Ekaterina V","first_name":"Ekaterina V"},{"first_name":"Karen S","last_name":"Sarkisyan","full_name":"Sarkisyan, Karen S"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000799197200001"]},"article_processing_charge":"No","title":"Heterogeneity of the GFP fitness landscape and data-driven protein design","citation":{"ama":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP fitness landscape and data-driven protein design. eLife. 2022;11. doi:10.7554/elife.75842","apa":"Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina, A. A., Meiler, J., … Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape and data-driven protein design. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.75842","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).","ieee":"L. Gonzalez Somermeyer et al., “Heterogeneity of the GFP fitness landscape and data-driven protein design,” eLife, vol. 11. eLife Sciences Publications, 2022.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"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.","doi":"10.7554/elife.75842","date_published":"2022-05-05T00:00:00Z","date_created":"2022-06-18T09:06:59Z","isi":1,"has_accepted_license":"1","year":"2022","day":"05","publication":"eLife"},{"article_number":"149","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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).","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.","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","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"},"title":"A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis","author":[{"last_name":"Zhang","full_name":"Zhang, Runxuan","first_name":"Runxuan"},{"full_name":"Kuo, Richard","last_name":"Kuo","first_name":"Richard"},{"first_name":"Max","last_name":"Coulter","full_name":"Coulter, Max"},{"first_name":"Cristiane P.G.","last_name":"Calixto","full_name":"Calixto, Cristiane P.G."},{"last_name":"Entizne","full_name":"Entizne, Juan Carlos","first_name":"Juan Carlos"},{"first_name":"Wenbin","full_name":"Guo, Wenbin","last_name":"Guo"},{"first_name":"Yamile","last_name":"Marquez","full_name":"Marquez, Yamile"},{"full_name":"Milne, Linda","last_name":"Milne","first_name":"Linda"},{"id":"FF6018E0-D806-11E9-8E43-0B14E6697425","first_name":"Stefan","full_name":"Riegler, Stefan","orcid":"0000-0003-3413-1343","last_name":"Riegler"},{"last_name":"Matsui","full_name":"Matsui, Akihiro","first_name":"Akihiro"},{"full_name":"Tanaka, Maho","last_name":"Tanaka","first_name":"Maho"},{"last_name":"Harvey","full_name":"Harvey, Sarah","first_name":"Sarah"},{"full_name":"Gao, Yubang","last_name":"Gao","first_name":"Yubang"},{"full_name":"Wießner-Kroh, Theresa","last_name":"Wießner-Kroh","first_name":"Theresa"},{"first_name":"Alejandro","full_name":"Paniagua, Alejandro","last_name":"Paniagua"},{"first_name":"Martin","last_name":"Crespi","full_name":"Crespi, Martin"},{"first_name":"Katherine","last_name":"Denby","full_name":"Denby, Katherine"},{"last_name":"Hur","full_name":"Hur, Asa Ben","first_name":"Asa Ben"},{"first_name":"Enamul","full_name":"Huq, Enamul","last_name":"Huq"},{"last_name":"Jantsch","full_name":"Jantsch, Michael","first_name":"Michael"},{"first_name":"Artur","full_name":"Jarmolowski, Artur","last_name":"Jarmolowski"},{"full_name":"Koester, Tino","last_name":"Koester","first_name":"Tino"},{"full_name":"Laubinger, Sascha","last_name":"Laubinger","first_name":"Sascha"},{"first_name":"Qingshun Quinn","full_name":"Li, Qingshun Quinn","last_name":"Li"},{"first_name":"Lianfeng","last_name":"Gu","full_name":"Gu, Lianfeng"},{"first_name":"Motoaki","last_name":"Seki","full_name":"Seki, Motoaki"},{"first_name":"Dorothee","last_name":"Staiger","full_name":"Staiger, Dorothee"},{"last_name":"Sunkar","full_name":"Sunkar, Ramanjulu","first_name":"Ramanjulu"},{"last_name":"Szweykowska-Kulinska","full_name":"Szweykowska-Kulinska, Zofia","first_name":"Zofia"},{"full_name":"Tu, Shih Long","last_name":"Tu","first_name":"Shih Long"},{"full_name":"Wachter, Andreas","last_name":"Wachter","first_name":"Andreas"},{"first_name":"Robbie","full_name":"Waugh, Robbie","last_name":"Waugh"},{"full_name":"Xiong, Liming","last_name":"Xiong","first_name":"Liming"},{"first_name":"Xiao Ning","full_name":"Zhang, Xiao Ning","last_name":"Zhang"},{"first_name":"Ana","full_name":"Conesa, Ana","last_name":"Conesa"},{"first_name":"Anireddy S.N.","last_name":"Reddy","full_name":"Reddy, Anireddy S.N."},{"full_name":"Barta, Andrea","last_name":"Barta","first_name":"Andrea"},{"first_name":"Maria","last_name":"Kalyna","full_name":"Kalyna, Maria"},{"full_name":"Brown, John W.S.","last_name":"Brown","first_name":"John W.S."}],"article_processing_charge":"No","external_id":{"isi":["000821915500002"]},"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.","publisher":"BioMed Central","quality_controlled":"1","oa":1,"day":"07","publication":"Genome Biology","isi":1,"has_accepted_license":"1","year":"2022","date_published":"2022-07-07T00:00:00Z","doi":"10.1186/s13059-022-02711-0","date_created":"2022-07-17T22:01:53Z","_id":"11587","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-08-03T12:04:18Z","department":[{"_id":"FyKo"}],"file_date_updated":"2022-07-18T08:15:24Z","oa_version":"Published Version","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."}],"month":"07","intvolume":" 23","scopus_import":"1","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"2c30ef84151d257a6b835b4e069b70ac","file_id":"11597","file_size":3146207,"date_updated":"2022-07-18T08:15:24Z","creator":"dernst","file_name":"2022_GenomeBiology_Zhang.pdf","date_created":"2022-07-18T08:15:24Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1474-760X"]},"publication_status":"published","volume":23},{"citation":{"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.","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.","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.","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).","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Maria G.","full_name":"Byazrova, Maria G.","last_name":"Byazrova"},{"last_name":"Astakhova","full_name":"Astakhova, Ekaterina A.","first_name":"Ekaterina A."},{"first_name":"Aygul","id":"87DF77F0-1D9A-11EA-B6AE-CE443DDC885E","last_name":"Minnegalieva","full_name":"Minnegalieva, Aygul"},{"first_name":"Maria M.","last_name":"Sukhova","full_name":"Sukhova, Maria M."},{"first_name":"Artem A.","last_name":"Mikhailov","full_name":"Mikhailov, Artem A."},{"last_name":"Prilipov","full_name":"Prilipov, Alexey G.","first_name":"Alexey G."},{"last_name":"Gorchakov","full_name":"Gorchakov, Andrey A.","first_name":"Andrey A."},{"first_name":"Alexander V.","last_name":"Filatov","full_name":"Filatov, Alexander V."}],"external_id":{"pmid":["36379998"],"isi":["000884278600004"]},"article_processing_charge":"No","title":"Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination","article_number":"145","isi":1,"has_accepted_license":"1","year":"2022","day":"15","publication":"npj Vaccines","doi":"10.1038/s41541-022-00566-x","date_published":"2022-11-15T00:00:00Z","date_created":"2023-01-12T12:02:54Z","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.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"date_updated":"2023-08-04T08:52:40Z","ddc":["570"],"department":[{"_id":"FyKo"}],"file_date_updated":"2023-01-23T11:22:09Z","_id":"12131","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Pharmacology (medical)","Infectious Diseases","Pharmacology","Immunology","SARS-COV-2","COVID"],"publication_identifier":{"issn":["2059-0105"]},"publication_status":"published","file":[{"success":1,"file_id":"12347","checksum":"ddaac096381565b2b4b7dcc34cdbc4ee","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2022_njpVaccines_Byazrova.pdf","date_created":"2023-01-23T11:22:09Z","file_size":1856046,"date_updated":"2023-01-23T11:22:09Z","creator":"dernst"}],"language":[{"iso":"eng"}],"volume":7,"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."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"11","intvolume":" 7"},{"article_number":"e2143218","citation":{"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.","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","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).","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Maximilian","full_name":"Baumgartner, Maximilian","last_name":"Baumgartner"},{"full_name":"Zirnbauer, Rebecca","last_name":"Zirnbauer","first_name":"Rebecca"},{"first_name":"Sabine","full_name":"Schlager, Sabine","last_name":"Schlager"},{"full_name":"Mertens, Daniel","last_name":"Mertens","first_name":"Daniel"},{"first_name":"Nikolaus","full_name":"Gasche, Nikolaus","last_name":"Gasche"},{"first_name":"Barbara","full_name":"Sladek, Barbara","last_name":"Sladek"},{"first_name":"Craig","last_name":"Herbold","full_name":"Herbold, Craig"},{"full_name":"Bochkareva, Olga","last_name":"Bochkareva","first_name":"Olga"},{"first_name":"Vera","id":"20152b9d-927a-11ed-8107-be36d740812d","full_name":"Emelianenko, Vera","last_name":"Emelianenko"},{"first_name":"Harald","full_name":"Vogelsang, Harald","last_name":"Vogelsang"},{"full_name":"Lang, Michaela","last_name":"Lang","first_name":"Michaela"},{"last_name":"Klotz","full_name":"Klotz, Anton","first_name":"Anton"},{"full_name":"Moik, Birgit","last_name":"Moik","first_name":"Birgit"},{"first_name":"Athanasios","last_name":"Makristathis","full_name":"Makristathis, Athanasios"},{"last_name":"Berry","full_name":"Berry, David","first_name":"David"},{"last_name":"Dabsch","full_name":"Dabsch, Stefanie","first_name":"Stefanie"},{"first_name":"Vineeta","last_name":"Khare","full_name":"Khare, Vineeta"},{"full_name":"Gasche, Christoph","last_name":"Gasche","first_name":"Christoph"}],"article_processing_charge":"No","external_id":{"isi":["000889180100001"]},"title":"Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis","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].","quality_controlled":"1","publisher":"Taylor & Francis","oa":1,"has_accepted_license":"1","isi":1,"year":"2022","day":"22","publication":"Gut Microbes","date_published":"2022-11-22T00:00:00Z","doi":"10.1080/19490976.2022.2143218","date_created":"2023-01-12T12:11:36Z","_id":"12173","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Infectious Diseases","Microbiology (medical)","Gastroenterology","Microbiology"],"date_updated":"2023-08-04T09:10:18Z","ddc":["570"],"file_date_updated":"2023-01-26T10:56:51Z","department":[{"_id":"FyKo"}],"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"}],"oa_version":"Published Version","scopus_import":"1","month":"11","intvolume":" 14","publication_identifier":{"eissn":["1949-0984"],"issn":["1949-0976"]},"publication_status":"published","file":[{"checksum":"ee7681a17ae27645e9b5c1df61c15429","file_id":"12400","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-01-26T10:56:51Z","file_name":"2022_GutMicrobes_Baumgartner.pdf","creator":"dernst","date_updated":"2023-01-26T10:56:51Z","file_size":4075251}],"language":[{"iso":"eng"}],"volume":14,"issue":"1"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Russia’s unprovoked attack on Ukraine has destroyed civilian infrastructure, including universities, research centers, and other academic infrastructure (1). Many Ukrainian scholars and researchers remain in Ukraine, and their work has suffered from major setbacks (2–4). We call on international scientists and institutions to support them."}],"month":"12","intvolume":" 378","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.adg0797"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"publication_status":"published","volume":378,"issue":"6626","_id":"12116","status":"public","type":"journal_article","article_type":"letter_note","date_updated":"2023-10-03T11:01:06Z","department":[{"_id":"FyKo"}],"quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"day":"22","publication":"Science","isi":1,"year":"2022","doi":"10.1126/science.adg0797","date_published":"2022-12-22T00:00:00Z","date_created":"2023-01-12T11:56:30Z","page":"1285-1286","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","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.","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.","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."},"title":"Remote opportunities for scholars in Ukraine","author":[{"first_name":"Karishma","full_name":"Chhugani, Karishma","last_name":"Chhugani"},{"first_name":"Alina","full_name":"Frolova, Alina","last_name":"Frolova"},{"full_name":"Salyha, Yuriy","last_name":"Salyha","first_name":"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"},{"first_name":"Walter W.","last_name":"Wolfsberger","full_name":"Wolfsberger, Walter W."},{"last_name":"Ivashchenko","full_name":"Ivashchenko, Oleksandra V.","first_name":"Oleksandra V."},{"full_name":"Maci, Megi","last_name":"Maci","first_name":"Megi"},{"first_name":"Dmytro","full_name":"Dziuba, Dmytro","last_name":"Dziuba"},{"first_name":"Andrii","full_name":"Parkhomenko, Andrii","last_name":"Parkhomenko"},{"last_name":"Bortz","full_name":"Bortz, Eric","first_name":"Eric"},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"first_name":"Paweł P.","last_name":"Łabaj","full_name":"Łabaj, Paweł P."},{"first_name":"Veronika","full_name":"Romero, Veronika","last_name":"Romero"},{"full_name":"Hlávka, Jakub","last_name":"Hlávka","first_name":"Jakub"},{"first_name":"Taras K.","last_name":"Oleksyk","full_name":"Oleksyk, Taras K."},{"full_name":"Mangul, Serghei","last_name":"Mangul","first_name":"Serghei"}],"external_id":{"isi":["000963463700023"]},"article_processing_charge":"No"},{"volume":7,"publication_identifier":{"eissn":["2056-6387"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"26d3f2a2c8c8fa8c1002028326b45f64","file_id":"9274","file_size":1360271,"date_updated":"2021-03-22T11:09:34Z","creator":"dernst","file_name":"2021_NPJQuantumInformation_Pivoluska.pdf","date_created":"2021-03-22T11:09:34Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","intvolume":" 7","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."}],"oa_version":"Published Version","file_date_updated":"2021-03-22T11:09:34Z","department":[{"_id":"FyKo"}],"date_updated":"2023-08-07T14:17:26Z","ddc":["530"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9255","date_published":"2021-03-15T00:00:00Z","doi":"10.1038/s41534-021-00387-1","date_created":"2021-03-21T23:01:19Z","has_accepted_license":"1","isi":1,"year":"2021","day":"15","publication":"npj Quantum Information","quality_controlled":"1","publisher":"Springer Nature","oa":1,"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).","author":[{"full_name":"Pivoluska, Matej","last_name":"Pivoluska","first_name":"Matej"},{"first_name":"Martin","last_name":"Plesch","full_name":"Plesch, Martin"},{"first_name":"Máté","full_name":"Farkas, Máté","last_name":"Farkas"},{"first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","full_name":"Ruzickova, Natalia","last_name":"Ruzickova"},{"full_name":"Flegel, Clara","last_name":"Flegel","first_name":"Clara"},{"full_name":"Valencia, Natalia Herrera","last_name":"Valencia","first_name":"Natalia Herrera"},{"last_name":"Mccutcheon","full_name":"Mccutcheon, Will","first_name":"Will"},{"last_name":"Malik","full_name":"Malik, Mehul","first_name":"Mehul"},{"full_name":"Aguilar, Edgar A.","last_name":"Aguilar","first_name":"Edgar A."}],"article_processing_charge":"No","external_id":{"isi":["000629173100001"]},"title":"Semi-device-independent random number generation with flexible assumptions","citation":{"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.","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.","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).","ieee":"M. Pivoluska et al., “Semi-device-independent random number generation with flexible assumptions,” npj Quantum Information, vol. 7. Springer Nature, 2021.","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"50"},{"publication_identifier":{"eissn":["1664-302X"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"2f856543add59273a482a7f326fc0400","file_id":"9384","creator":"kschuh","file_size":14362316,"date_updated":"2021-05-11T13:05:52Z","file_name":"2021_Frontiers_Microbiology_Seferbekova.pdf","date_created":"2021-05-11T13:05:52Z"}],"language":[{"iso":"eng"}],"volume":12,"ec_funded":1,"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 12","date_updated":"2023-08-08T13:30:39Z","ddc":["570"],"department":[{"_id":"FyKo"}],"file_date_updated":"2021-05-11T13:05:52Z","_id":"9380","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","isi":1,"has_accepted_license":"1","year":"2021","day":"12","publication":"Frontiers in Microbiology","date_published":"2021-04-12T00:00:00Z","doi":"10.3389/fmicb.2021.628622","date_created":"2021-05-09T22:01:38Z","acknowledgement":"We thank Fyodor Kondrashov for valuable advice and manuscript proofreading. We also thank Alla Mikheenko for assistance with Circos.","quality_controlled":"1","publisher":"Frontiers","oa":1,"citation":{"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.","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.","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.","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","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","short":"Z. Seferbekova, A. Zabelkin, Y. Yakovleva, R. Afasizhev, N.O. Dranenko, N. Alexeev, M.S. Gelfand, O. Bochkareva, Frontiers in Microbiology 12 (2021).","ieee":"Z. Seferbekova et al., “High rates of genome rearrangements and pathogenicity of Shigella spp,” Frontiers in Microbiology, vol. 12. Frontiers, 2021."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Zaira","full_name":"Seferbekova, Zaira","last_name":"Seferbekova"},{"first_name":"Alexey","full_name":"Zabelkin, Alexey","last_name":"Zabelkin"},{"first_name":"Yulia","full_name":"Yakovleva, Yulia","last_name":"Yakovleva"},{"first_name":"Robert","full_name":"Afasizhev, Robert","last_name":"Afasizhev"},{"first_name":"Natalia O.","last_name":"Dranenko","full_name":"Dranenko, Natalia O."},{"last_name":"Alexeev","full_name":"Alexeev, Nikita","first_name":"Nikita"},{"first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S.","last_name":"Gelfand"},{"first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639"}],"article_processing_charge":"No","external_id":{"isi":["000643713300001"]},"title":"High rates of genome rearrangements and pathogenicity of Shigella spp","article_number":"628622","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","ista":"Slavskii SA, Kuznetsov IA, Shashkova TI, Bazykin GA, Axenovich TI, Kondrashov F, Aulchenko YS. 2021. The limits of normal approximation for adult height. European Journal of Human Genetics. 29(7), 1082–1091.","mla":"Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.” European Journal of Human Genetics, vol. 29, no. 7, Springer Nature, 2021, pp. 1082–91, doi:10.1038/s41431-021-00836-7.","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.","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.","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","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"},"title":"The limits of normal approximation for adult height","external_id":{"isi":["000625853200001"],"pmid":["33664501"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"Sergei A.","last_name":"Slavskii","full_name":"Slavskii, Sergei A."},{"first_name":"Ivan A.","last_name":"Kuznetsov","full_name":"Kuznetsov, Ivan A."},{"last_name":"Shashkova","full_name":"Shashkova, Tatiana I.","first_name":"Tatiana I."},{"last_name":"Bazykin","full_name":"Bazykin, Georgii A.","first_name":"Georgii A."},{"last_name":"Axenovich","full_name":"Axenovich, Tatiana I.","first_name":"Tatiana I."},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"last_name":"Aulchenko","full_name":"Aulchenko, Yurii S.","first_name":"Yurii S."}],"project":[{"_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales"}],"publication":"European Journal of Human Genetics","day":"01","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-08-15T22:01:28Z","doi":"10.1038/s41431-021-00836-7","date_published":"2021-07-01T00:00:00Z","page":"1082-1091","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).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","ddc":["576"],"date_updated":"2023-08-11T10:33:42Z","file_date_updated":"2021-08-16T09:14:36Z","department":[{"_id":"FyKo"}],"_id":"9910","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"checksum":"a676d76f91b0dbe0504c63e469129c2a","file_id":"9921","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-08-16T09:14:36Z","file_name":"2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf","creator":"asandaue","date_updated":"2021-08-16T09:14:36Z","file_size":1079395}],"publication_status":"published","publication_identifier":{"eissn":["14765438"],"issn":["10184813"]},"ec_funded":1,"volume":29,"issue":"7","pmid":1,"oa_version":"Published Version","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."}],"intvolume":" 29","month":"07","scopus_import":"1"},{"year":"2021","has_accepted_license":"1","isi":1,"publication":"Scientific Reports","day":"30","date_created":"2021-08-15T22:01:26Z","doi":"10.1038/s41598-021-95025-3","date_published":"2021-07-30T00:00:00Z","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).","oa":1,"quality_controlled":"1","publisher":"Springer Nature","citation":{"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.","ista":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 11(1), 15729.","mla":"Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” Scientific Reports, vol. 11, no. 1, 15729, Springer Nature, 2021, doi:10.1038/s41598-021-95025-3.","ama":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 2021;11(1). doi:10.1038/s41598-021-95025-3","apa":"Rella, S., Kulikova, Y. A., Dermitzakis, E. T., & Kondrashov, F. (2021). Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-95025-3","short":"S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports 11 (2021).","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes","external_id":{"pmid":["34330988"],"isi":["000683329100001"]},"author":[{"full_name":"Rella, Simon","last_name":"Rella","first_name":"Simon","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425"},{"first_name":"Yuliya A.","full_name":"Kulikova, Yuliya A.","last_name":"Kulikova"},{"first_name":"Emmanouil T.","full_name":"Dermitzakis, Emmanouil T.","last_name":"Dermitzakis"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"}],"title":"Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains","article_number":"15729","project":[{"call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209"}],"publication_status":"published","publication_identifier":{"eissn":["20452322"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9927","checksum":"ac86892ed17e6724c7251844da5cef5c","success":1,"date_updated":"2021-08-16T11:36:49Z","file_size":3432001,"creator":"asandaue","date_created":"2021-08-16T11:36:49Z","file_name":"2021_ScientificReports_Rella.pdf"}],"ec_funded":1,"related_material":{"link":[{"description":"News on IST Website","relation":"press_release","url":"https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/"}]},"volume":11,"issue":"1","abstract":[{"lang":"eng","text":"Vaccines are thought to be the best available solution for controlling the ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains may come too rapidly for current vaccine developments to alleviate the health, economic and social consequences of the pandemic. To quantify and characterize the risk of such a scenario, we created a SIR-derived model with initial stochastic dynamics of the vaccine-resistant strain to study the probability of its emergence and establishment. Using parameters realistically resembling SARS-CoV-2 transmission, we model a wave-like pattern of the pandemic and consider the impact of the rate of vaccination and the strength of non-pharmaceutical intervention measures on the probability of emergence of a resistant strain. As expected, we found that a fast rate of vaccination decreases the probability of emergence of a resistant strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions happened at a time when most individuals of the population have already been vaccinated the probability of emergence of a resistant strain was greatly increased. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment. Our results suggest that policymakers and individuals should consider maintaining non-pharmaceutical interventions and transmission-reducing behaviours throughout the entire vaccination period."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 11","month":"07","date_updated":"2023-08-11T10:42:58Z","ddc":["570","610"],"department":[{"_id":"FyKo"}],"file_date_updated":"2021-08-16T11:36:49Z","_id":"9905","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public"},{"intvolume":" 11","month":"02","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"volume":11,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7607","checksum":"57c37209f7b6712ced86c0f11b2be74e","creator":"dernst","file_size":507414,"date_updated":"2020-07-14T12:48:01Z","file_name":"2020_FrontiersPlants_Nimeth.pdf","date_created":"2020-03-23T09:03:40Z"}],"publication_status":"published","publication_identifier":{"eissn":["1664462X"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"7603","file_date_updated":"2020-07-14T12:48:01Z","department":[{"_id":"FyKo"}],"ddc":["580"],"date_updated":"2023-08-18T07:05:18Z","oa":1,"publisher":"Frontiers","quality_controlled":"1","date_created":"2020-03-22T23:00:46Z","date_published":"2020-02-19T00:00:00Z","doi":"10.3389/fpls.2020.00091","publication":"Frontiers in Plant Science","day":"19","year":"2020","isi":1,"has_accepted_license":"1","article_number":"91","title":"Alternative splicing and DNA damage response in plants","external_id":{"isi":["000518903600001"]},"article_processing_charge":"No","author":[{"first_name":"Barbara Anna","full_name":"Nimeth, Barbara Anna","last_name":"Nimeth"},{"last_name":"Riegler","full_name":"Riegler, Stefan","orcid":"0000-0003-3413-1343","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","first_name":"Stefan"},{"last_name":"Kalyna","full_name":"Kalyna, Maria","first_name":"Maria"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Nimeth BA, Riegler S, Kalyna M. 2020. Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. 11, 91.","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.","short":"B.A. Nimeth, S. Riegler, M. Kalyna, Frontiers in Plant Science 11 (2020).","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.","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","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","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."}},{"publication":"European Journal of Physics","day":"24","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2020-03-31T11:25:04Z","date_published":"2020-02-24T00:00:00Z","doi":"10.1088/1361-6404/ab6414","oa":1,"publisher":"IOP Publishing","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Plesch M, Plesník S, Ruzickova N. 2020. The IYPT and the ‘Ring Oiler’ problem. European Journal of Physics. 41(3), 034001.","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.","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.","short":"M. Plesch, S. Plesník, N. Ruzickova, European Journal of Physics 41 (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","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","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."},"title":"The IYPT and the 'Ring Oiler' problem","article_processing_charge":"No","external_id":{"arxiv":["1910.03290"],"isi":["000537425400001"]},"author":[{"last_name":"Plesch","full_name":"Plesch, Martin","first_name":"Martin"},{"full_name":"Plesník, Samuel","last_name":"Plesník","first_name":"Samuel"},{"full_name":"Ruzickova, Natalia","last_name":"Ruzickova","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","first_name":"Natalia"}],"article_number":"034001","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7641","checksum":"47dda164e33b6c0c6c3ed14aad298376","file_size":1533672,"date_updated":"2020-07-14T12:48:01Z","creator":"dernst","file_name":"2020_EuropJourPhysics_Plesch.pdf","date_created":"2020-04-06T08:53:53Z"}],"publication_status":"published","publication_identifier":{"issn":["01430807"],"eissn":["13616404"]},"issue":"3","volume":41,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"intvolume":" 41","month":"02","scopus_import":"1","ddc":["530"],"date_updated":"2023-08-18T10:18:29Z","file_date_updated":"2020-07-14T12:48:01Z","department":[{"_id":"FyKo"}],"_id":"7622","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original"},{"volume":10,"publication_status":"published","publication_identifier":{"eissn":["20452322"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7947","checksum":"099e51611a5b7ca04244d03b2faddf33","file_size":1001724,"date_updated":"2020-07-14T12:48:05Z","creator":"dernst","file_name":"2020_ScientificReports_Uroshlev.pdf","date_created":"2020-06-08T06:27:32Z"}],"scopus_import":"1","intvolume":" 10","month":"05","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"}],"oa_version":"Published Version","department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:48:05Z","date_updated":"2023-08-21T07:00:17Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"7931","date_created":"2020-06-07T22:00:51Z","doi":"10.1038/s41598-020-65406-1","date_published":"2020-05-25T00:00:00Z","year":"2020","isi":1,"has_accepted_license":"1","publication":"Scientific Reports","day":"25","oa":1,"publisher":"Springer Nature","quality_controlled":"1","external_id":{"isi":["000560774200007"]},"article_processing_charge":"No","author":[{"last_name":"Uroshlev","full_name":"Uroshlev, Leonid A.","first_name":"Leonid A."},{"first_name":"Eldar T.","full_name":"Abdullaev, Eldar T.","last_name":"Abdullaev"},{"full_name":"Umarova, Iren R.","last_name":"Umarova","first_name":"Iren R."},{"last_name":"Il’Icheva","full_name":"Il’Icheva, Irina A.","first_name":"Irina A."},{"first_name":"Larisa A.","last_name":"Panchenko","full_name":"Panchenko, Larisa A."},{"first_name":"Robert V.","full_name":"Polozov, Robert V.","last_name":"Polozov"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"full_name":"Nechipurenko, Yury D.","last_name":"Nechipurenko","first_name":"Yury D."},{"last_name":"Grokhovsky","full_name":"Grokhovsky, Sergei L.","first_name":"Sergei L."}],"title":"A method for identification of the methylation level of CpG islands from NGS data","citation":{"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.","ista":"Uroshlev LA, Abdullaev ET, Umarova IR, Il’Icheva IA, Panchenko LA, Polozov RV, Kondrashov F, Nechipurenko YD, Grokhovsky SL. 2020. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 10, 8635.","mla":"Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” Scientific Reports, vol. 10, 8635, Springer Nature, 2020, doi:10.1038/s41598-020-65406-1.","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.","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).","ama":"Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 2020;10. doi:10.1038/s41598-020-65406-1","apa":"Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko, L. A., Polozov, R. V., … Grokhovsky, S. L. (2020). A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-65406-1"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"8635"},{"acknowledgement":"We would like to thank our co-workers and members of the Alkalaeva lab for participating in discussions about the topics covered in this essay.","publisher":"Springer Nature","quality_controlled":"1","year":"2020","isi":1,"publication":"Molecular Biology","day":"19","page":"475-484","date_created":"2020-08-30T22:01:11Z","date_published":"2020-08-19T00:00:00Z","doi":"10.1134/S0026893320040111","citation":{"chicago":"Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320040111.","ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 54(4), 475–484.","mla":"Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” Molecular Biology, vol. 54, no. 4, Springer Nature, 2020, pp. 475–84, doi:10.1134/S0026893320040111.","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320040111","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 2020;54(4):475-484. doi:10.1134/S0026893320040111","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molecular Biology, vol. 54, no. 4. Springer Nature, pp. 475–484, 2020.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molecular Biology 54 (2020) 475–484."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000562110300001"]},"article_processing_charge":"No","author":[{"first_name":"S. A.","last_name":"Mukba","full_name":"Mukba, S. A."},{"id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","full_name":"Vlasov, Petr","last_name":"Vlasov"},{"full_name":"Kolosov, P. M.","last_name":"Kolosov","first_name":"P. M."},{"first_name":"E. Y.","full_name":"Shuvalova, E. Y.","last_name":"Shuvalova"},{"last_name":"Egorova","full_name":"Egorova, T. V.","first_name":"T. V."},{"first_name":"E. Z.","full_name":"Alkalaeva, E. Z.","last_name":"Alkalaeva"}],"title":"Expanding the genetic code: Unnatural base pairs in biological systems","abstract":[{"lang":"eng","text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications."}],"oa_version":"None","scopus_import":"1","intvolume":" 54","month":"08","publication_status":"published","publication_identifier":{"eissn":["16083245"],"issn":["00268933"]},"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"original","id":"8321","status":"public"}]},"volume":54,"issue":"4","_id":"8320","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-22T09:01:03Z","department":[{"_id":"FyKo"}]},{"language":[{"iso":"rus"}],"publication_status":"published","publication_identifier":{"issn":["00268984"]},"related_material":{"record":[{"status":"public","id":"8320","relation":"translation"}]},"volume":54,"issue":"4","pmid":1,"oa_version":"None","abstract":[{"text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications.","lang":"eng"}],"intvolume":" 54","month":"07","scopus_import":"1","date_updated":"2023-08-22T09:01:02Z","department":[{"_id":"FyKo"}],"_id":"8321","status":"public","type":"journal_article","article_type":"original","publication":"Molekuliarnaia biologiia","day":"01","year":"2020","date_created":"2020-08-30T22:01:11Z","doi":"10.31857/S0026898420040126","date_published":"2020-07-01T00:00:00Z","page":"531-541","publisher":"Russian Academy of Sciences","quality_controlled":"1","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 54(4), 531–541.","chicago":"Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the genetic code: Unnatural base pairs in biological systems.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420040126.","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molekuliarnaia biologiia, vol. 54, no. 4. Russian Academy of Sciences, pp. 531–541, 2020.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 531–541.","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 2020;54(4):531-541. doi:10.31857/S0026898420040126","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. Russian Academy of Sciences. https://doi.org/10.31857/S0026898420040126","mla":"Mukba, S. A., et al. “Expanding the genetic code: Unnatural base pairs in biological systems.” Molekuliarnaia biologiia, vol. 54, no. 4, Russian Academy of Sciences, 2020, pp. 531–41, doi:10.31857/S0026898420040126."},"title":"Expanding the genetic code: Unnatural base pairs in biological systems","external_id":{"pmid":["32799218"]},"article_processing_charge":"No","author":[{"first_name":"S. A.","last_name":"Mukba","full_name":"Mukba, S. A."},{"full_name":"Vlasov, Petr","last_name":"Vlasov","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"},{"first_name":"P. M.","last_name":"Kolosov","full_name":"Kolosov, P. M."},{"last_name":"Shuvalova","full_name":"Shuvalova, E. Y.","first_name":"E. Y."},{"first_name":"T. V.","last_name":"Egorova","full_name":"Egorova, T. V."},{"full_name":"Alkalaeva, E. Z.","last_name":"Alkalaeva","first_name":"E. Z."}]},{"citation":{"ista":"Esteban LA, Lonishin LR, Bobrovskiy DM, Leleytner G, Bogatyreva NS, Kondrashov F, Ivankov DN. 2020. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 36(6), 1960–1962.","chicago":"Esteban, Laura A, Lyubov R Lonishin, Daniil M Bobrovskiy, Gregory Leleytner, Natalya S Bogatyreva, Fyodor Kondrashov, and Dmitry N Ivankov. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics. Oxford Academic, 2020. https://doi.org/10.1093/bioinformatics/btz841.","ieee":"L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially complete datasets from a single experiment,” Bioinformatics, vol. 36, no. 6. Oxford Academic, pp. 1960–1962, 2020.","short":"L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva, F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962.","ama":"Esteban LA, Lonishin LR, Bobrovskiy DM, et al. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 2020;36(6):1960-1962. doi:10.1093/bioinformatics/btz841","apa":"Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva, N. S., Kondrashov, F., & Ivankov, D. N. (2020). HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btz841","mla":"Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics, vol. 36, no. 6, Oxford Academic, 2020, pp. 1960–62, doi:10.1093/bioinformatics/btz841."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Esteban, Laura A","last_name":"Esteban","first_name":"Laura A"},{"full_name":"Lonishin, Lyubov R","last_name":"Lonishin","first_name":"Lyubov R"},{"first_name":"Daniil M","full_name":"Bobrovskiy, Daniil M","last_name":"Bobrovskiy"},{"first_name":"Gregory","last_name":"Leleytner","full_name":"Leleytner, Gregory"},{"last_name":"Bogatyreva","full_name":"Bogatyreva, Natalya S","first_name":"Natalya S"},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"first_name":"Dmitry N ","full_name":"Ivankov, Dmitry N ","last_name":"Ivankov"}],"external_id":{"pmid":["31742320"],"isi":["000538696800054"]},"article_processing_charge":"No","title":"HypercubeME: Two hundred million combinatorially complete datasets from a single experiment","project":[{"_id":"26120F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Systematic investigation of epistasis in molecular evolution","grant_number":"335980"}],"isi":1,"has_accepted_license":"1","year":"2020","day":"15","publication":"Bioinformatics","page":"1960-1962","date_published":"2020-03-15T00:00:00Z","doi":"10.1093/bioinformatics/btz841","date_created":"2020-10-11T22:01:14Z","acknowledgement":"This work was supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013, ERC grant agreement 335980_EinME) and Startup package to the Ivankov laboratory at Skolkovo Institute of Science and Technology. The work was started at the School of Molecular and Theoretical Biology 2017 supported by the Zimin Foundation. N.S.B. was supported by the Woman Scientists Support Grant in Centre for Genomic Regulation (CRG). ","publisher":"Oxford Academic","quality_controlled":"1","oa":1,"date_updated":"2023-08-22T09:57:29Z","ddc":["000","570"],"file_date_updated":"2020-10-12T12:02:09Z","department":[{"_id":"FyKo"}],"_id":"8645","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","publication_identifier":{"issn":["1367-4803"],"eissn":["1460-2059"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"21d6f71839deb3b83e4a356193f72767","file_id":"8649","success":1,"creator":"dernst","date_updated":"2020-10-12T12:02:09Z","file_size":308341,"date_created":"2020-10-12T12:02:09Z","file_name":"2020_Bioinformatics_Esteban.pdf"}],"language":[{"iso":"eng"}],"issue":"6","volume":36,"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","abstract":[{"text":"Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a ‘combinatorially complete dataset’. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199 847 053 unique combinatorially complete genotype combinations of dimensionality ranging from 2 to 12. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"03","intvolume":" 36"},{"type":"journal_article","article_type":"original","status":"public","_id":"8707","department":[{"_id":"FyKo"}],"date_updated":"2023-08-22T10:37:10Z","scopus_import":"1","month":"10","intvolume":" 52","abstract":[{"text":"Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data.","lang":"eng"}],"pmid":1,"oa_version":"None","volume":52,"publication_identifier":{"issn":["10614036"],"eissn":["15461718"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"first_name":"Silvia","last_name":" Galan","full_name":" Galan, Silvia"},{"id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","first_name":"Nick N","last_name":"Machnik","full_name":"Machnik, Nick N","orcid":"0000-0001-6617-9742"},{"first_name":"Kai","full_name":"Kruse, Kai","last_name":"Kruse"},{"full_name":"Díaz, Noelia","last_name":"Díaz","first_name":"Noelia"},{"last_name":"Marti-Renom","full_name":"Marti-Renom, Marc A","first_name":"Marc A"},{"last_name":"Vaquerizas","full_name":"Vaquerizas, Juan M","first_name":"Juan M"}],"external_id":{"pmid":["33077914"],"isi":["000579693500004"]},"article_processing_charge":"No","title":"CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction","citation":{"short":"S. Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas, Nature Genetics 52 (2020) 1247–1255.","ieee":"S. Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M. Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction,” Nature Genetics, vol. 52. Springer Nature, pp. 1247–1255, 2020.","ama":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 2020;52:1247-1255. doi:10.1038/s41588-020-00712-y","apa":"Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., & Vaquerizas, J. M. (2020). CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-020-00712-y","mla":"Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” Nature Genetics, vol. 52, Springer Nature, 2020, pp. 1247–55, doi:10.1038/s41588-020-00712-y.","ista":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 52, 1247–1255.","chicago":"Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom, and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” Nature Genetics. Springer Nature, 2020. https://doi.org/10.1038/s41588-020-00712-y."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"Work in the Vaquerizas laboratory is funded by the Max Planck Society, the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN to J.M.V.) and the Medical Research Council in the UK. This research was partially funded by the European Union’s H2020 Framework Programme through the European Research Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R. The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia, Innovación y Universidades to the European Molecular Biology Laboratory partnership, the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208, the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from the European Regional Development Fund corresponding to the 2014–2020 Smart Growth Operating Program. S.G. thanks the support from the Company of Biologists (grant no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship programme.","page":"1247-1255","doi":"10.1038/s41588-020-00712-y","date_published":"2020-10-19T00:00:00Z","date_created":"2020-10-25T23:01:20Z","isi":1,"year":"2020","day":"19","publication":"Nature Genetics"},{"publication":"Molecular Biology","day":"01","year":"2020","isi":1,"date_created":"2020-10-25T23:01:17Z","date_published":"2020-09-01T00:00:00Z","doi":"10.1134/S0026893320050088","page":"739-748","acknowledgement":"We would like to thank the staff of CCU Genome for sequencing, Tat’yana Pestova, Christopher Helen, and Lyudmila Yur’evna Frolova for the plasmids provided, as well as the laboratory staff for productive discussion of the results. We also thank former laboratory employees Yuliya Vladimirovna Bocharova and Polina Nikolaevna Kryuchkova for the exceptional contribution to the present work.","quality_controlled":"1","publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320050088.","ista":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. 54(5), 739–748.","mla":"Sokolova, E. E., et al. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” Molecular Biology, vol. 54, no. 5, Springer Nature, 2020, pp. 739–48, doi:10.1134/S0026893320050088.","apa":"Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320050088","ama":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. 2020;54(5):739-748. doi:10.1134/S0026893320050088","ieee":"E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” Molecular Biology, vol. 54, no. 5. Springer Nature, pp. 739–748, 2020.","short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molecular Biology 54 (2020) 739–748."},"title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","article_processing_charge":"No","external_id":{"isi":["000579441200009"]},"author":[{"first_name":"E. E.","last_name":"Sokolova","full_name":"Sokolova, E. E."},{"id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Vlasov","full_name":"Vlasov, Petr"},{"last_name":"Egorova","full_name":"Egorova, T. V.","first_name":"T. V."},{"first_name":"A. V.","full_name":"Shuvalov, A. V.","last_name":"Shuvalov"},{"first_name":"E. Z.","full_name":"Alkalaeva, E. Z.","last_name":"Alkalaeva"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["16083245"],"issn":["00268933"]},"related_material":{"record":[{"relation":"original","status":"public","id":"8701"}]},"issue":"5","volume":54,"oa_version":"None","abstract":[{"text":"Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency.","lang":"eng"}],"intvolume":" 54","month":"09","scopus_import":"1","date_updated":"2023-08-22T10:39:38Z","department":[{"_id":"FyKo"}],"_id":"8700","status":"public","article_type":"original","type":"journal_article"},{"title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","author":[{"first_name":"E. E.","full_name":"Sokolova, E. E.","last_name":"Sokolova"},{"last_name":"Vlasov","full_name":"Vlasov, Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"},{"last_name":"Egorova","full_name":"Egorova, T. V.","first_name":"T. V."},{"first_name":"A. V.","full_name":"Shuvalov, A. V.","last_name":"Shuvalov"},{"last_name":"Alkalaeva","full_name":"Alkalaeva, E. Z.","first_name":"E. Z."}],"article_processing_charge":"No","external_id":{"pmid":["33009793"]},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"mla":"Sokolova, E. E., et al. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” Molekuliarnaia biologiia, vol. 54, no. 5, Russian Academy of Sciences, 2020, pp. 837–48, doi:10.31857/S0026898420050080.","ieee":"E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” Molekuliarnaia biologiia, vol. 54, no. 5. Russian Academy of Sciences, pp. 837–848, 2020.","short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 837–848.","apa":"Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. Russian Academy of Sciences. https://doi.org/10.31857/S0026898420050080","ama":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. 2020;54(5):837-848. doi:10.31857/S0026898420050080","chicago":"Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420050080.","ista":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. 54(5), 837–848."},"publisher":"Russian Academy of Sciences","quality_controlled":"1","doi":"10.31857/S0026898420050080","date_published":"2020-09-01T00:00:00Z","date_created":"2020-10-25T23:01:17Z","page":"837-848","day":"01","publication":"Molekuliarnaia biologiia","year":"2020","status":"public","type":"journal_article","article_type":"original","_id":"8701","department":[{"_id":"FyKo"}],"date_updated":"2023-08-22T10:39:37Z","month":"09","intvolume":" 54","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency."}],"volume":54,"related_material":{"record":[{"relation":"translation","id":"8700","status":"public"}]},"issue":"5","language":[{"iso":"rus"}],"publication_identifier":{"issn":["00268984"]},"publication_status":"published"},{"publication":"Proceedings of 1st International Electronic Conference on Microbiology","day":"02","year":"2020","has_accepted_license":"1","date_created":"2024-03-04T11:41:31Z","date_published":"2020-11-02T00:00:00Z","doi":"10.3390/ecm2020-07116","acknowledgement":"The work was supported by of Russian Foundation of Basic Research: grant № 19-04-00831 for Viktoria Shcherbakova and Olga Troshina, grant № 18-34-00334 for Viktoriia Oshurkova and Vladimir Trubitsyn. \r\nWe thank Dr Natalia Suzina (IBPM RAS, Federal Research Center Pushchino Center for\r\nBiological Research RAS) for the help with the microscopic studies, respectively; Dr. Margarita Meyer (Division of Genetics, Department of Medicine, BWH and HMS, USA) and Dr Fedor Kondrashov (IST, Austria) for their help in obtaining the genomic sequence of strain JL01. ","oa":1,"publisher":"MDPI","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Oshurkova, Viktoriia, et al. “Characterization of Methanosarcina Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta Associata GLS2T.” Proceedings of 1st International Electronic Conference on Microbiology, MDPI, 2020, doi:10.3390/ecm2020-07116.","ama":"Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova V. Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. In: Proceedings of 1st International Electronic Conference on Microbiology. MDPI; 2020. doi:10.3390/ecm2020-07116","apa":"Oshurkova, V., Troshina, O., Trubitsyn, V., Ryzhmanova, Y., Bochkareva, O., & Shcherbakova, V. (2020). Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. In Proceedings of 1st International Electronic Conference on Microbiology. Virtual: MDPI. https://doi.org/10.3390/ecm2020-07116","ieee":"V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, and V. Shcherbakova, “Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T,” in Proceedings of 1st International Electronic Conference on Microbiology, Virtual, 2020.","short":"V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, V. Shcherbakova, in:, Proceedings of 1st International Electronic Conference on Microbiology, MDPI, 2020.","chicago":"Oshurkova, Viktoriia, Olga Troshina, Vladimir Trubitsyn, Yana Ryzhmanova, Olga Bochkareva, and Viktoria Shcherbakova. “Characterization of Methanosarcina Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta Associata GLS2T.” In Proceedings of 1st International Electronic Conference on Microbiology. MDPI, 2020. https://doi.org/10.3390/ecm2020-07116.","ista":"Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova V. 2020. Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. Proceedings of 1st International Electronic Conference on Microbiology. ECM: Electronic Conference on Microbiology."},"title":"Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T","article_processing_charge":"Yes","author":[{"last_name":"Oshurkova","full_name":"Oshurkova, Viktoriia","first_name":"Viktoriia"},{"last_name":"Troshina","full_name":"Troshina, Olga","first_name":"Olga"},{"first_name":"Vladimir","last_name":"Trubitsyn","full_name":"Trubitsyn, Vladimir"},{"full_name":"Ryzhmanova, Yana","last_name":"Ryzhmanova","first_name":"Yana"},{"full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga"},{"first_name":"Viktoria","full_name":"Shcherbakova, Viktoria","last_name":"Shcherbakova"}],"language":[{"iso":"eng"}],"file":[{"file_name":"2020_ECM_Oshurkova.pdf","date_created":"2024-03-20T08:05:46Z","file_size":595543,"date_updated":"2024-03-20T08:05:46Z","creator":"dernst","success":1,"file_id":"15127","checksum":"d1914af7811a21a4b2744eb51b5834e3","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","oa_version":"Published Version","abstract":[{"lang":"eng","text":"A mesophilic methanogenic culture, designated JL01, was isolated from Holocene permafrost in the Russian Arctic [1]. After long-term extensive cultivation at 15°C it turned out to be a tied binary culture of archaeal (JL01) and bacterial (Sphaerochaeta associata GLS2) strains.\r\nStrain JL01 was a strict anaerobe and grew on methanol, acetate and methylamines as energy and carbon sources. Cells were irregular coccoid, non-motile, non-spore-forming, and Gram-stainpositive. Optimum conditions for growth were 24-28 oC, pH 6.8–7.3 and 0.075-0.1 M NaCl.\r\nPhylogenetic tree reconstructions based on 16S rRNA and concatenated alignment of broadly\r\nconserved protein-coding genes revealed its close relation to Methanosarcina mazei S-6\r\nT (similarity 99.5%). The comparison of whole genomic sequences (ANI) of the isolate and the type strain of M.mazei was 98.5%, which is higher than the values recommended for new species. Thus strain JL01 (=VKM B-2370=JCM 31898) represents the first M. mazei isolated from permanently subzero Arcticsediments. The long-term co-cultivation of JL01 with S. associata GLS2T showed the methane production without any additional carbon and energy sources. Genome analysis of S. associata GLS2T revealed putative genes involved in methanochondroithin catabolism."}],"month":"11","ddc":["570"],"date_updated":"2024-03-20T08:06:22Z","file_date_updated":"2024-03-20T08:05:46Z","department":[{"_id":"FyKo"}],"_id":"15071","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"ECM: Electronic Conference on Microbiology","start_date":"2020-11-02","end_date":"2020-11-30","location":"Virtual"},"type":"conference"},{"status":"public","article_type":"original","type":"journal_article","_id":"7889","file_date_updated":"2021-03-02T23:30:03Z","department":[{"_id":"FyKo"}],"ddc":["570"],"date_updated":"2023-09-05T15:30:34Z","month":"04","intvolume":" 38","scopus_import":"1","pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Autoluminescent plants engineered to express a bacterial bioluminescence gene cluster in plastids have not been widely adopted because of low light output. We engineered tobacco plants with a fungal bioluminescence system that converts caffeic acid (present in all plants) into luciferin and report self-sustained luminescence that is visible to the naked eye. Our findings could underpin development of a suite of imaging tools for plants.","lang":"eng"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41587-020-0578-0"}]},"volume":38,"ec_funded":1,"file":[{"creator":"dernst","file_size":1180086,"date_updated":"2021-03-02T23:30:03Z","file_name":"2020_NatureBiotech_Mitiouchkina.pdf","date_created":"2020-08-28T08:57:07Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2021-03-01","file_id":"8316","checksum":"1b30467500ec6277229a875b06e196d0"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"publication_status":"published","project":[{"grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425"}],"title":"Plants with genetically encoded autoluminescence","author":[{"last_name":"Mitiouchkina","full_name":"Mitiouchkina, Tatiana","first_name":"Tatiana"},{"last_name":"Mishin","full_name":"Mishin, Alexander S.","first_name":"Alexander S."},{"id":"4720D23C-F248-11E8-B48F-1D18A9856A87","first_name":"Louisa","full_name":"Gonzalez Somermeyer, Louisa","orcid":"0000-0001-9139-5383","last_name":"Gonzalez Somermeyer"},{"first_name":"Nadezhda M.","full_name":"Markina, Nadezhda M.","last_name":"Markina"},{"full_name":"Chepurnyh, Tatiana V.","last_name":"Chepurnyh","first_name":"Tatiana V."},{"first_name":"Elena B.","full_name":"Guglya, Elena B.","last_name":"Guglya"},{"first_name":"Tatiana A.","full_name":"Karataeva, Tatiana A.","last_name":"Karataeva"},{"full_name":"Palkina, Kseniia A.","last_name":"Palkina","first_name":"Kseniia A."},{"last_name":"Shakhova","full_name":"Shakhova, Ekaterina S.","first_name":"Ekaterina S."},{"last_name":"Fakhranurova","full_name":"Fakhranurova, Liliia I.","first_name":"Liliia I."},{"last_name":"Chekova","full_name":"Chekova, Sofia V.","first_name":"Sofia V."},{"first_name":"Aleksandra S.","last_name":"Tsarkova","full_name":"Tsarkova, Aleksandra S."},{"first_name":"Yaroslav V.","full_name":"Golubev, Yaroslav V.","last_name":"Golubev"},{"last_name":"Negrebetsky","full_name":"Negrebetsky, Vadim V.","first_name":"Vadim V."},{"last_name":"Dolgushin","full_name":"Dolgushin, Sergey A.","first_name":"Sergey A."},{"first_name":"Pavel V.","last_name":"Shalaev","full_name":"Shalaev, Pavel V."},{"first_name":"Dmitry","last_name":"Shlykov","full_name":"Shlykov, Dmitry"},{"first_name":"Olesya A.","full_name":"Melnik, Olesya A.","last_name":"Melnik"},{"first_name":"Victoria O.","full_name":"Shipunova, Victoria O.","last_name":"Shipunova"},{"last_name":"Deyev","full_name":"Deyev, Sergey M.","first_name":"Sergey M."},{"first_name":"Andrey I.","full_name":"Bubyrev, Andrey I.","last_name":"Bubyrev"},{"full_name":"Pushin, Alexander S.","last_name":"Pushin","first_name":"Alexander S."},{"last_name":"Choob","full_name":"Choob, Vladimir V.","first_name":"Vladimir V."},{"first_name":"Sergey V.","full_name":"Dolgov, Sergey V.","last_name":"Dolgov"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"},{"first_name":"Ilia V.","full_name":"Yampolsky, Ilia V.","last_name":"Yampolsky"},{"first_name":"Karen S.","last_name":"Sarkisyan","full_name":"Sarkisyan, Karen S."}],"article_processing_charge":"No","external_id":{"pmid":["32341562"],"isi":["000529298800003"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Mitiouchkina, Tatiana, Alexander S. Mishin, Louisa Gonzalez Somermeyer, Nadezhda M. Markina, Tatiana V. Chepurnyh, Elena B. Guglya, Tatiana A. Karataeva, et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology. Springer Nature, 2020. https://doi.org/10.1038/s41587-020-0500-9.","ista":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, Markina NM, Chepurnyh TV, Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV, Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D, Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV, Kondrashov F, Yampolsky IV, Sarkisyan KS. 2020. Plants with genetically encoded autoluminescence. Nature Biotechnology. 38, 944–946.","mla":"Mitiouchkina, Tatiana, et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology, vol. 38, Springer Nature, 2020, pp. 944–46, doi:10.1038/s41587-020-0500-9.","ama":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, et al. Plants with genetically encoded autoluminescence. Nature Biotechnology. 2020;38:944-946. doi:10.1038/s41587-020-0500-9","apa":"Mitiouchkina, T., Mishin, A. S., Gonzalez Somermeyer, L., Markina, N. M., Chepurnyh, T. V., Guglya, E. B., … Sarkisyan, K. S. (2020). Plants with genetically encoded autoluminescence. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-020-0500-9","short":"T. Mitiouchkina, A.S. Mishin, L. Gonzalez Somermeyer, N.M. Markina, T.V. Chepurnyh, E.B. Guglya, T.A. Karataeva, K.A. Palkina, E.S. Shakhova, L.I. Fakhranurova, S.V. Chekova, A.S. Tsarkova, Y.V. Golubev, V.V. Negrebetsky, S.A. Dolgushin, P.V. Shalaev, D. Shlykov, O.A. Melnik, V.O. Shipunova, S.M. Deyev, A.I. Bubyrev, A.S. Pushin, V.V. Choob, S.V. Dolgov, F. Kondrashov, I.V. Yampolsky, K.S. Sarkisyan, Nature Biotechnology 38 (2020) 944–946.","ieee":"T. Mitiouchkina et al., “Plants with genetically encoded autoluminescence,” Nature Biotechnology, vol. 38. Springer Nature, pp. 944–946, 2020."},"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"This study was designed, performed and funded by Planta LLC. We thank K. Wood for assisting in manuscript development. Planta acknowledges support from the Skolkovo Innovation Centre. We thank D. Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure. We thank S. Shakhov for providing\r\nphotography equipment. The Synthetic Biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0, K.S.S.). K.S.S. is supported by an Imperial College Research Fellowship. Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy\r\nof Sciences Сore Facility (CKP IBCH; supported by the Russian Ministry of Education and Science Grant RFMEFI62117X0018). The F.A.K. lab is supported by ERC grant agreement 771209—CharFL. This project received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie\r\nGrant Agreement 665385. K.S.S. acknowledges support by President’s Grant 075-15-2019-411. Design and assembly of some of the plasmids was supported by Russian Science Foundation grant 19-74-10102. Imaging experiments were partially supported by Russian Science Foundation grant 17-14-01169p. LC-MS/MS analyses of extracts were\r\nsupported by Russian Science Foundation grant 16-14-00052p. Design and assembly of plasmids was partially supported by grant 075-15-2019-1789 from the Ministry of Science and Higher Education of the Russian Federation allocated to the Center for Precision Genome Editing and Genetic Technologies for Biomedicine. The authors\r\nwould like to acknowledge the work of Genomics Core Facility of the Skolkovo Institute of Science and Technology, which performed the sequencing and bioinformatic analysis.","doi":"10.1038/s41587-020-0500-9","date_published":"2020-04-27T00:00:00Z","date_created":"2020-05-25T15:02:00Z","page":"944-946","day":"27","publication":"Nature Biotechnology","isi":1,"has_accepted_license":"1","year":"2020"},{"month":"04","intvolume":" 15","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible.","lang":"eng"}],"volume":15,"issue":"4","related_material":{"record":[{"relation":"research_data","status":"public","id":"9789"},{"status":"public","id":"9790","relation":"research_data"},{"id":"9797","status":"public","relation":"research_data"}]},"ec_funded":1,"file":[{"file_name":"2019_PLOSGenetics_Pokusaeva.pdf","date_created":"2019-05-14T08:26:08Z","file_size":3726017,"date_updated":"2020-07-14T12:47:30Z","creator":"dernst","file_id":"6445","checksum":"cf3889c8a8a16053dacf9c3776cbe217","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15537404"]},"publication_status":"published","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"6419","file_date_updated":"2020-07-14T12:47:30Z","department":[{"_id":"FyKo"}],"ddc":["570"],"date_updated":"2023-08-25T10:30:37Z","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"doi":"10.1371/journal.pgen.1008079","date_published":"2019-04-10T00:00:00Z","date_created":"2019-05-13T07:58:38Z","day":"10","publication":"PLoS Genetics","isi":1,"has_accepted_license":"1","year":"2019","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"article_number":"e1008079","title":"An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape","author":[{"id":"3184041C-F248-11E8-B48F-1D18A9856A87","first_name":"Victoria","orcid":"0000-0001-7660-444X","full_name":"Pokusaeva, Victoria","last_name":"Pokusaeva"},{"last_name":"Usmanova","full_name":"Usmanova, Dinara R.","first_name":"Dinara R."},{"last_name":"Putintseva","full_name":"Putintseva, Ekaterina V.","first_name":"Ekaterina V."},{"first_name":"Lorena","full_name":"Espinar, Lorena","last_name":"Espinar"},{"first_name":"Karen","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5375-6341","full_name":"Sarkisyan, Karen","last_name":"Sarkisyan"},{"last_name":"Mishin","full_name":"Mishin, Alexander S.","first_name":"Alexander S."},{"last_name":"Bogatyreva","full_name":"Bogatyreva, Natalya S.","first_name":"Natalya S."},{"id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry","last_name":"Ivankov","full_name":"Ivankov, Dmitry"},{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan"},{"last_name":"Avvakumov","full_name":"Avvakumov, Sergey","first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Inna S.","full_name":"Povolotskaya, Inna S.","last_name":"Povolotskaya"},{"first_name":"Guillaume J.","last_name":"Filion","full_name":"Filion, Guillaume J."},{"full_name":"Carey, Lucas B.","last_name":"Carey","first_name":"Lucas B."},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"}],"article_processing_charge":"No","external_id":{"isi":["000466866000029"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.","ieee":"V. Pokusaeva et al., “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS Genetics, vol. 15, no. 4. Public Library of Science, 2019.","short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019).","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 2019;15(4). doi:10.1371/journal.pgen.1008079","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics. Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 15(4), e1008079."}},{"status":"public","type":"research_data_reference","_id":"9790","title":"A statistical summary of segment libraries and sequencing results","department":[{"_id":"FyKo"}],"article_processing_charge":"No","author":[{"last_name":"Pokusaeva","full_name":"Pokusaeva, Victoria","orcid":"0000-0001-7660-444X","first_name":"Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dinara R.","last_name":"Usmanova","full_name":"Usmanova, Dinara R."},{"first_name":"Ekaterina V.","last_name":"Putintseva","full_name":"Putintseva, Ekaterina V."},{"first_name":"Lorena","full_name":"Espinar, Lorena","last_name":"Espinar"},{"full_name":"Sarkisyan, Karen","orcid":"0000-0002-5375-6341","last_name":"Sarkisyan","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","first_name":"Karen"},{"first_name":"Alexander S.","last_name":"Mishin","full_name":"Mishin, Alexander S."},{"full_name":"Bogatyreva, Natalya S.","last_name":"Bogatyreva","first_name":"Natalya S."},{"last_name":"Ivankov","full_name":"Ivankov, Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry"},{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan"},{"full_name":"Avvakumov, Sergey","last_name":"Avvakumov","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey"},{"last_name":"Povolotskaya","full_name":"Povolotskaya, Inna S.","first_name":"Inna S."},{"first_name":"Guillaume J.","full_name":"Filion, Guillaume J.","last_name":"Filion"},{"last_name":"Carey","full_name":"Carey, Lucas B.","first_name":"Lucas B."},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A Statistical Summary of Segment Libraries and Sequencing Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011.","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing results, Public Library of Science, 10.1371/journal.pgen.1008079.s011.","mla":"Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011","ieee":"V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019.","short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. 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Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing results, Public Library of Science, 10.1371/journal.pgen.1008079.s011.","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A Statistical Summary of Segment Libraries and Sequencing Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"status":"public","type":"research_data_reference","_id":"9789","department":[{"_id":"FyKo"}],"title":"Multiple alignment of His3 orthologues","author":[{"last_name":"Pokusaeva","full_name":"Pokusaeva, Victoria","orcid":"0000-0001-7660-444X","id":"3184041C-F248-11E8-B48F-1D18A9856A87","first_name":"Victoria"},{"last_name":"Usmanova","full_name":"Usmanova, Dinara R.","first_name":"Dinara R."},{"first_name":"Ekaterina V.","last_name":"Putintseva","full_name":"Putintseva, Ekaterina V."},{"first_name":"Lorena","full_name":"Espinar, Lorena","last_name":"Espinar"},{"orcid":"0000-0002-5375-6341","full_name":"Sarkisyan, Karen","last_name":"Sarkisyan","first_name":"Karen","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mishin","full_name":"Mishin, Alexander S.","first_name":"Alexander S."},{"full_name":"Bogatyreva, Natalya S.","last_name":"Bogatyreva","first_name":"Natalya S."},{"first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","full_name":"Ivankov, Dmitry","last_name":"Ivankov"},{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan"},{"full_name":"Avvakumov, Sergey","last_name":"Avvakumov","first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Povolotskaya","full_name":"Povolotskaya, Inna S.","first_name":"Inna S."},{"first_name":"Guillaume J.","full_name":"Filion, Guillaume J.","last_name":"Filion"},{"full_name":"Carey, Lucas B.","last_name":"Carey","first_name":"Lucas B."},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “Multiple Alignment of His3 Orthologues.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s010.","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. Multiple alignment of His3 orthologues, Public Library of Science, 10.1371/journal.pgen.1008079.s010.","mla":"Pokusaeva, Victoria, et al. Multiple Alignment of His3 Orthologues. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s010.","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. Multiple alignment of His3 orthologues. 2019. doi:10.1371/journal.pgen.1008079.s010","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). Multiple alignment of His3 orthologues. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s010","short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019).","ieee":"V. Pokusaeva et al., “Multiple alignment of His3 orthologues.” Public Library of Science, 2019."},"date_updated":"2023-08-25T10:30:36Z","month":"04","publisher":"Public Library of Science","oa_version":"Published Version","related_material":{"record":[{"id":"6419","status":"public","relation":"used_in_publication"}]},"date_published":"2019-04-10T00:00:00Z","doi":"10.1371/journal.pgen.1008079.s010","date_created":"2021-08-06T08:38:50Z","day":"10","year":"2019"},{"type":"journal_article","article_type":"original","status":"public","_id":"6506","department":[{"_id":"FyKo"}],"date_updated":"2023-08-28T08:39:47Z","scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/340828v2","open_access":"1"}],"month":"07","intvolume":" 4","abstract":[{"text":"How does environmental complexity affect the evolution of single genes? Here, we measured the effects of a set of Bacillus subtilis glutamate dehydrogenase mutants across 19 different environments—from phenotypically homogeneous single-cell populations in liquid media to heterogeneous biofilms, plant roots and soil populations. The effects of individual gene mutations on organismal fitness were highly reproducible in liquid cultures. However, 84% of the tested alleles showed opposing fitness effects under different growth conditions (sign environmental pleiotropy). In colony biofilms and soil samples, different alleles dominated in parallel replica experiments. Accordingly, we found that in these heterogeneous cell populations the fate of mutations was dictated by a combination of selection and drift. The latter relates to programmed prophage excisions that occurred during biofilm development. Overall, for each condition, a wide range of glutamate dehydrogenase mutations persisted and sometimes fixated as a result of the combined action of selection, pleiotropy and chance. However, over longer periods and in multiple environments, nearly all of this diversity would be lost—across all the environments and conditions that we tested, the wild type was the fittest allele.","lang":"eng"}],"oa_version":"Preprint","volume":4,"issue":"7","publication_identifier":{"issn":["2058-5276"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"last_name":"Noda-García","full_name":"Noda-García, Lianet","first_name":"Lianet"},{"first_name":"Dan","full_name":"Davidi, Dan","last_name":"Davidi"},{"last_name":"Korenblum","full_name":"Korenblum, Elisa","first_name":"Elisa"},{"last_name":"Elazar","full_name":"Elazar, Assaf","first_name":"Assaf"},{"first_name":"Ekaterina","id":"2EF67C84-F248-11E8-B48F-1D18A9856A87","last_name":"Putintseva","full_name":"Putintseva, Ekaterina"},{"first_name":"Asaph","last_name":"Aharoni","full_name":"Aharoni, Asaph"},{"last_name":"Tawfik","full_name":"Tawfik, Dan S.","first_name":"Dan S."}],"article_processing_charge":"No","external_id":{"isi":["000480348200017"]},"title":"Chance and pleiotropy dominate genetic diversity in complex bacterial environments","citation":{"ieee":"L. Noda-García et al., “Chance and pleiotropy dominate genetic diversity in complex bacterial environments,” Nature Microbiology, vol. 4, no. 7. Springer Nature, pp. 1221–1230, 2019.","short":"L. Noda-García, D. Davidi, E. Korenblum, A. Elazar, E. Putintseva, A. Aharoni, D.S. Tawfik, Nature Microbiology 4 (2019) 1221–1230.","ama":"Noda-García L, Davidi D, Korenblum E, et al. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 2019;4(7):1221–1230. doi:10.1038/s41564-019-0412-y","apa":"Noda-García, L., Davidi, D., Korenblum, E., Elazar, A., Putintseva, E., Aharoni, A., & Tawfik, D. S. (2019). Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0412-y","mla":"Noda-García, Lianet, et al. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology, vol. 4, no. 7, Springer Nature, 2019, pp. 1221–1230, doi:10.1038/s41564-019-0412-y.","ista":"Noda-García L, Davidi D, Korenblum E, Elazar A, Putintseva E, Aharoni A, Tawfik DS. 2019. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 4(7), 1221–1230.","chicago":"Noda-García, Lianet, Dan Davidi, Elisa Korenblum, Assaf Elazar, Ekaterina Putintseva, Asaph Aharoni, and Dan S. Tawfik. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology. Springer Nature, 2019. https://doi.org/10.1038/s41564-019-0412-y."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Springer Nature","oa":1,"page":"1221–1230","doi":"10.1038/s41564-019-0412-y","date_published":"2019-07-01T00:00:00Z","date_created":"2019-05-29T13:03:30Z","isi":1,"year":"2019","day":"01","publication":"Nature Microbiology"},{"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808772.v1","open_access":"1"}],"oa":1,"publisher":"Springer Nature","month":"09","abstract":[{"lang":"eng","text":"OGs with putative pseudogenes by the number of affected genomes in different chlamydial species. Frameshift and nonsense mutations located less than 60 bp upstreamof the gene end or present in a single genome from the corresponding OG were excluded. (CSV 31 kb)"}],"oa_version":"Published Version","date_created":"2021-07-27T14:09:11Z","doi":"10.6084/m9.figshare.9808772.v1","related_material":{"record":[{"id":"6898","status":"public","relation":"used_in_publication"}]},"date_published":"2019-09-12T00:00:00Z","year":"2019","day":"12","type":"research_data_reference","status":"public","_id":"9731","article_processing_charge":"No","author":[{"full_name":"Sigalova, Olga","last_name":"Sigalova","first_name":"Olga"},{"first_name":"Andrei","last_name":"Chaplin","full_name":"Chaplin, Andrei"},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga","last_name":"Bochkareva","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"first_name":"Pavel","full_name":"Shelyakin, Pavel","last_name":"Shelyakin"},{"first_name":"Vsevolod","full_name":"Filaretov, Vsevolod","last_name":"Filaretov"},{"first_name":"Evgeny","last_name":"Akkuratov","full_name":"Akkuratov, Evgeny"},{"first_name":"Valentina","full_name":"Burskaia, Valentina","last_name":"Burskaia"},{"full_name":"Gelfand, Mikhail S.","last_name":"Gelfand","first_name":"Mikhail S."}],"department":[{"_id":"FyKo"}],"title":"Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","citation":{"mla":"Sigalova, Olga, et al. Additional File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808772.v1.","ieee":"O. Sigalova et al., “Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","short":"O. Sigalova, A. Chaplin, O. Bochkareva, P. Shelyakin, V. Filaretov, E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","ama":"Sigalova O, Chaplin A, Bochkareva O, et al. Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808772.v1","apa":"Sigalova, O., Chaplin, A., Bochkareva, O., Shelyakin, P., Filaretov, V., Akkuratov, E., … Gelfand, M. S. (2019). Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808772.v1","chicago":"Sigalova, Olga, Andrei Chaplin, Olga Bochkareva, Pavel Shelyakin, Vsevolod Filaretov, Evgeny Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808772.v1.","ista":"Sigalova O, Chaplin A, Bochkareva O, Shelyakin P, Filaretov V, Akkuratov E, Burskaia V, Gelfand MS. 2019. Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808772.v1."},"date_updated":"2023-08-30T06:20:21Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"day":"12","year":"2019","date_created":"2021-08-06T07:59:56Z","date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808760.v1","related_material":{"record":[{"id":"6898","status":"public","relation":"used_in_publication"}]},"oa_version":"Published Version","abstract":[{"text":"Predicted frameshift and nonsense mutations in Chlamydial pan-genome. For the analysis of putative pseudogenes, events located less than 60 bp. away from gene end or present in a single genome from the corresponding OG were excluded. (CSV 600 kb)","lang":"eng"}],"month":"09","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808760.v1"}],"publisher":"Springer Nature","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-30T06:20:21Z","citation":{"chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808760.v1.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808760.v1.","mla":"Sigalova, Olga M., et al. 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Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019)."},"title":"Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","department":[{"_id":"FyKo"}],"article_processing_charge":"No","author":[{"first_name":"Olga M.","last_name":"Sigalova","full_name":"Sigalova, Olga M."},{"first_name":"Andrei V.","last_name":"Chaplin","full_name":"Chaplin, Andrei V."},{"full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","last_name":"Bochkareva","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"first_name":"Pavel V.","full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin"},{"full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov","first_name":"Vsevolod A."},{"first_name":"Evgeny E.","full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov"},{"first_name":"Valentina","full_name":"Burskaia, Valentina","last_name":"Burskaia"},{"last_name":"Gelfand","full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S."}],"_id":"9783","status":"public","type":"research_data_reference"},{"department":[{"_id":"FyKo"}],"title":"Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","author":[{"full_name":"Sigalova, Olga M.","last_name":"Sigalova","first_name":"Olga M."},{"first_name":"Andrei V.","last_name":"Chaplin","full_name":"Chaplin, Andrei V."},{"orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","last_name":"Bochkareva","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin","first_name":"Pavel V."},{"full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov","first_name":"Vsevolod A."},{"last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E."},{"first_name":"Valentina","full_name":"Burskaia, Valentina","last_name":"Burskaia"},{"first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S.","last_name":"Gelfand"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. 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(CSV 6 kb)"}]},{"status":"public","type":"research_data_reference","_id":"9890","department":[{"_id":"FyKo"}],"title":"Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","article_processing_charge":"No","author":[{"last_name":"Sigalova","full_name":"Sigalova, Olga M.","first_name":"Olga M."},{"last_name":"Chaplin","full_name":"Chaplin, Andrei V.","first_name":"Andrei V."},{"full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga"},{"first_name":"Pavel V.","full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin"},{"first_name":"Vsevolod A.","full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov"},{"first_name":"Evgeny E.","full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov"},{"first_name":"Valentina","full_name":"Burskaia, Valentina","last_name":"Burskaia"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. 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Gelfand. “Additional File 15 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808802.v1."},"date_updated":"2023-08-30T06:20:21Z","month":"09","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808802.v1","open_access":"1"}],"oa":1,"publisher":"Springer Nature","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Distribution of OGs with mosaic phyletic patterns across species (complete genomes only). (CSV 7 kb)"}],"date_created":"2021-08-11T14:26:40Z","doi":"10.6084/m9.figshare.9808802.v1","date_published":"2019-09-12T00:00:00Z","related_material":{"record":[{"id":"6898","status":"public","relation":"used_in_publication"}]},"day":"12","year":"2019"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-30T06:20:21Z","citation":{"chicago":"Sigalova, Olga M., Andrei V Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 16 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808814.v1.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808814.v1.","mla":"Sigalova, Olga M., et al. Additional File 16 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808814.v1.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. 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Gelfand, (2019)."},"title":"Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","department":[{"_id":"FyKo"}],"author":[{"first_name":"Olga M.","full_name":"Sigalova, Olga M.","last_name":"Sigalova"},{"first_name":"Andrei V","last_name":"Chaplin","full_name":"Chaplin, Andrei V"},{"orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","last_name":"Bochkareva","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"first_name":"Vsevolod A.","full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov"},{"first_name":"Evgeny E.","last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E."},{"first_name":"Valentina","full_name":"Burskaia, Valentina","last_name":"Burskaia"},{"full_name":"Gelfand, Mikhail S.","last_name":"Gelfand","first_name":"Mikhail S."}],"article_processing_charge":"No","_id":"9892","status":"public","type":"research_data_reference","day":"12","year":"2019","doi":"10.6084/m9.figshare.9808814.v1","related_material":{"record":[{"relation":"used_in_publication","id":"6898","status":"public"}]},"date_published":"2019-09-12T00:00:00Z","date_created":"2021-08-12T07:11:53Z","oa_version":"Published Version","abstract":[{"text":"Distribution of OGs with mosaic phyletic patterns across species (all genomes). 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Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 19 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808835.v1.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. 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(CSV 30 kb)"}],"oa_version":"Published Version"},{"department":[{"_id":"FyKo"}],"title":"Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","author":[{"full_name":"Sigalova, Olga M.","last_name":"Sigalova","first_name":"Olga M."},{"first_name":"Andrei V.","full_name":"Chaplin, Andrei V.","last_name":"Chaplin"},{"full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga"},{"full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin","first_name":"Pavel V."},{"full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov","first_name":"Vsevolod A."},{"full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov","first_name":"Evgeny E."},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S.","last_name":"Gelfand"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-30T06:20:21Z","citation":{"chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 1 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808841.v1.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808841.v1.","mla":"Sigalova, Olga M., et al. Additional File 1 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808841.v1.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. 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Gelfand, (2019)."},"status":"public","type":"research_data_reference","_id":"9896","related_material":{"record":[{"status":"public","id":"6898","relation":"used_in_publication"}]},"date_published":"2019-09-02T00:00:00Z","doi":"10.6084/m9.figshare.9808841.v1","date_created":"2021-08-12T07:50:53Z","day":"02","year":"2019","month":"09","publisher":"Springer Nature","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808841.v1"}],"oa_version":"Published Version","abstract":[{"text":"Summary of the analysed genomes. (CSV 24 kb)","lang":"eng"}]},{"_id":"6898","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-30T06:20:22Z","ddc":["570"],"department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:47:44Z","abstract":[{"lang":"eng","text":"Background\r\n\r\nChlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria.\r\nResults\r\n\r\nWe report pan-genomic analysis of sixteen species from genus Chlamydia including identification and functional annotation of orthologous genes, and characterization of gene gains, losses, and rearrangements. We demonstrate the overall genome stability of these bacteria as indicated by a large fraction of common genes with conserved genomic locations. On the other hand, extreme evolvability is confined to several paralogous gene families such as polymorphic membrane proteins and phospholipase D, and likely is caused by the pressure from the host immune system.\r\nConclusions\r\n\r\nThis combination of a large, conserved core genome and a small, evolvable periphery likely reflect the balance between the selective pressure towards genome reduction and the need to adapt to escape from the host immunity."}],"oa_version":"Published Version","scopus_import":"1","month":"09","intvolume":" 20","publication_identifier":{"eissn":["14712164"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"b798773c5823012d31c812c9f7975da2","file_id":"6924","creator":"kschuh","file_size":4157175,"date_updated":"2020-07-14T12:47:44Z","file_name":"2019_BioMed_Sigalova.pdf","date_created":"2019-10-01T10:33:17Z"}],"language":[{"iso":"eng"}],"issue":"1","volume":20,"related_material":{"record":[{"id":"9731","status":"public","relation":"research_data"},{"relation":"research_data","id":"9783","status":"public"},{"relation":"research_data","id":"9890","status":"public"},{"status":"public","id":"9892","relation":"research_data"},{"relation":"research_data","id":"9893","status":"public"},{"status":"public","id":"9894","relation":"research_data"},{"relation":"research_data","id":"9895","status":"public"},{"relation":"research_data","id":"9896","status":"public"},{"status":"public","id":"9897","relation":"research_data"},{"id":"9898","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9899"},{"id":"9900","status":"public","relation":"research_data"},{"id":"9901","status":"public","relation":"research_data"}]},"article_number":"710","citation":{"mla":"Sigalova, Olga M., et al. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” BMC Genomics, vol. 20, no. 1, 710, BioMed Central, 2019, doi:10.1186/s12864-019-6059-5.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. 2019;20(1). doi:10.1186/s12864-019-6059-5","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-019-6059-5","ieee":"O. M. Sigalova et al., “Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction,” BMC Genomics, vol. 20, no. 1. BioMed Central, 2019.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, BMC Genomics 20 (2019).","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” BMC Genomics. BioMed Central, 2019. https://doi.org/10.1186/s12864-019-6059-5.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. 20(1), 710."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Olga M.","last_name":"Sigalova","full_name":"Sigalova, Olga M."},{"first_name":"Andrei V.","full_name":"Chaplin, Andrei V.","last_name":"Chaplin"},{"first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","last_name":"Bochkareva"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov","first_name":"Vsevolod A."},{"last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E."},{"full_name":"Burskaia, Valentina","last_name":"Burskaia","first_name":"Valentina"},{"full_name":"Gelfand, Mikhail S.","last_name":"Gelfand","first_name":"Mikhail S."}],"external_id":{"isi":["000485256100001"]},"article_processing_charge":"No","title":"Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","publisher":"BioMed Central","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2019","day":"12","publication":"BMC Genomics","date_published":"2019-09-12T00:00:00Z","doi":"10.1186/s12864-019-6059-5","date_created":"2019-09-22T22:00:36Z"},{"date_created":"2021-08-12T08:10:23Z","date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808859.v1","related_material":{"record":[{"status":"public","id":"6898","relation":"used_in_publication"}]},"day":"12","year":"2019","month":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808859.v1"}],"oa":1,"publisher":"Springer Nature","oa_version":"Published Version","abstract":[{"text":"All polyN tracts of length 5 or more nucleotides in sequences of genes from OG1. Sequences were extracted and scanned prior to automatic correction for frameshifts implemented in the RAST pipeline. (CSV 133 kb)","lang":"eng"}],"department":[{"_id":"FyKo"}],"title":"Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","article_processing_charge":"No","author":[{"first_name":"Olga M.","full_name":"Sigalova, Olga M.","last_name":"Sigalova"},{"first_name":"Andrei V.","last_name":"Chaplin","full_name":"Chaplin, Andrei V."},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga","full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","last_name":"Bochkareva"},{"first_name":"Pavel V.","full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin"},{"last_name":"Filaretov","full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A."},{"last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E."},{"first_name":"Valentina","full_name":"Burskaia, Valentina","last_name":"Burskaia"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-30T06:20:22Z","citation":{"mla":"Sigalova, Olga M., et al. 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Sigalova et al., “Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 21 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808859.v1.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. 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V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808907.v1","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808907.v1","ieee":"O. M. Sigalova et al., “Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","mla":"Sigalova, Olga M., et al. Additional File 9 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808907.v1.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808907.v1.","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 9 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808907.v1."},"title":"Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","department":[{"_id":"FyKo"}],"author":[{"last_name":"Sigalova","full_name":"Sigalova, Olga M.","first_name":"Olga M."},{"last_name":"Chaplin","full_name":"Chaplin, Andrei V.","first_name":"Andrei V."},{"last_name":"Bochkareva","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"first_name":"Pavel V.","full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin"},{"first_name":"Vsevolod A.","last_name":"Filaretov","full_name":"Filaretov, Vsevolod A."},{"last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E."},{"last_name":"Burskaia","full_name":"Burskaia, Valentina","first_name":"Valentina"},{"last_name":"Gelfand","full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S."}],"article_processing_charge":"No","_id":"9901","status":"public","type":"research_data_reference"},{"article_processing_charge":"No","author":[{"first_name":"Olga M.","last_name":"Sigalova","full_name":"Sigalova, Olga M."},{"full_name":"Chaplin, Andrei V.","last_name":"Chaplin","first_name":"Andrei V."},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga","last_name":"Bochkareva","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"first_name":"Pavel V.","full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin"},{"last_name":"Filaretov","full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A."},{"full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov","first_name":"Evgeny E."},{"full_name":"Burskaia, Valentina","last_name":"Burskaia","first_name":"Valentina"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"department":[{"_id":"FyKo"}],"title":"Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","citation":{"mla":"Sigalova, Olga M., et al. Additional File 2 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808865.v1.","ieee":"O. M. Sigalova et al., “Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808865.v1","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808865.v1","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 2 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808865.v1.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808865.v1."},"date_updated":"2023-08-30T06:20:22Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9899","date_created":"2021-08-12T08:18:09Z","date_published":"2019-09-12T00:00:00Z","related_material":{"record":[{"id":"6898","status":"public","relation":"used_in_publication"}]},"doi":"10.6084/m9.figshare.9808865.v1","year":"2019","day":"12","oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808865.v1","open_access":"1"}],"publisher":"Springer Nature","month":"09","abstract":[{"lang":"eng","text":"Summary of orthologous groups (OGs) for 227 genomes of genus Chlamydia. (CSV 362 kb)"}],"oa_version":"Published Version"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Pan-genome statistics by species. (CSV 3 kb)"}],"month":"09","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808886.v1"}],"publisher":"Springer Nature","day":"12","year":"2019","date_created":"2021-08-12T08:44:49Z","date_published":"2019-09-12T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"6898","status":"public"}]},"doi":"10.6084/m9.figshare.9808886.v1","_id":"9900","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808886.v1.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808886.v1.","mla":"Sigalova, Olga M., et al. Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808886.v1.","ieee":"O. M. Sigalova et al., “Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808886.v1","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808886.v1"},"date_updated":"2023-08-30T06:20:22Z","department":[{"_id":"FyKo"}],"title":"Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","article_processing_charge":"No","author":[{"last_name":"Sigalova","full_name":"Sigalova, Olga M.","first_name":"Olga M."},{"first_name":"Andrei V.","last_name":"Chaplin","full_name":"Chaplin, Andrei V."},{"first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","last_name":"Bochkareva"},{"full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin","first_name":"Pavel V."},{"last_name":"Filaretov","full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A."},{"full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov","first_name":"Evgeny E."},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"last_name":"Gelfand","full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S."}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41587-019-0333-6.","ista":"Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2019. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 37(12), 1466–1470.","mla":"Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology, vol. 37, no. 12, Springer Nature, 2019, pp. 1466–70, doi:10.1038/s41587-019-0333-6.","apa":"Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-019-0333-6","ama":"Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 2019;37(12):1466-1470. doi:10.1038/s41587-019-0333-6","short":"E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019) 1466–1470.","ieee":"E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf regressive method,” Nature Biotechnology, vol. 37, no. 12. Springer Nature, pp. 1466–1470, 2019."},"title":"Large multiple sequence alignments with a root-to-leaf regressive method","author":[{"first_name":"Edgar","last_name":"Garriga","full_name":"Garriga, Edgar"},{"first_name":"Paolo","last_name":"Di Tommaso","full_name":"Di Tommaso, Paolo"},{"first_name":"Cedrik","last_name":"Magis","full_name":"Magis, Cedrik"},{"first_name":"Ionas","full_name":"Erb, Ionas","last_name":"Erb"},{"first_name":"Leila","full_name":"Mansouri, Leila","last_name":"Mansouri"},{"first_name":"Athanasios","last_name":"Baltzis","full_name":"Baltzis, Athanasios"},{"full_name":"Laayouni, Hafid","last_name":"Laayouni","first_name":"Hafid"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"first_name":"Evan","full_name":"Floden, Evan","last_name":"Floden"},{"first_name":"Cedric","last_name":"Notredame","full_name":"Notredame, Cedric"}],"external_id":{"pmid":["31792410"],"isi":["000500748900021"]},"article_processing_charge":"No","project":[{"call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209"}],"day":"01","publication":"Nature Biotechnology","isi":1,"year":"2019","date_published":"2019-12-01T00:00:00Z","doi":"10.1038/s41587-019-0333-6","date_created":"2019-12-15T23:00:43Z","page":"1466-1470","publisher":"Springer Nature","quality_controlled":"1","oa":1,"date_updated":"2023-09-06T14:32:52Z","department":[{"_id":"FyKo"}],"_id":"7181","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["10870156"],"eissn":["15461696"]},"publication_status":"published","issue":"12","related_material":{"record":[{"status":"public","id":"13059","relation":"research_data"}]},"volume":37,"ec_funded":1,"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy declines substantially as the number of sequences is scaled up5. We introduce a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard workstation and substantially improves accuracy on datasets larger than 10,000 sequences. Our regressive algorithm works the other way around to the progressive algorithm and begins by aligning the most dissimilar sequences. It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their original complexity. Our approach will enable analyses of extremely large genomic datasets such as the recently announced Earth BioGenome Project, which comprises 1.5 million eukaryotic genomes6."}],"month":"12","intvolume":" 37","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/","open_access":"1"}]},{"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-06T14:32:51Z","citation":{"mla":"Garriga, Edgar, et al. Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method. Zenodo, 2018, doi:10.5281/ZENODO.2025846.","apa":"Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo. https://doi.org/10.5281/ZENODO.2025846","ama":"Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. 2018. doi:10.5281/ZENODO.2025846","ieee":"E. Garriga et al., “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.","short":"E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018).","chicago":"Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.2025846.","ista":"Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method, Zenodo, 10.5281/ZENODO.2025846."},"title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","department":[{"_id":"FyKo"}],"article_processing_charge":"No","author":[{"full_name":"Garriga, Edgar","last_name":"Garriga","first_name":"Edgar"},{"last_name":"di Tommaso","full_name":"di Tommaso, Paolo","first_name":"Paolo"},{"first_name":"Cedrik","last_name":"Magis","full_name":"Magis, Cedrik"},{"full_name":"Erb, Ionas","last_name":"Erb","first_name":"Ionas"},{"first_name":"Leila","last_name":"Mansouri","full_name":"Mansouri, Leila"},{"full_name":"Baltzis, Athanasios","last_name":"Baltzis","first_name":"Athanasios"},{"last_name":"Laayouni","full_name":"Laayouni, Hafid","first_name":"Hafid"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"first_name":"Evan","full_name":"Floden, Evan","last_name":"Floden"},{"first_name":"Cedric","full_name":"Notredame, Cedric","last_name":"Notredame"}],"_id":"13059","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","day":"07","year":"2018","date_created":"2023-05-23T16:08:20Z","doi":"10.5281/ZENODO.2025846","related_material":{"record":[{"status":"public","id":"7181","relation":"used_in_publication"}]},"date_published":"2018-12-07T00:00:00Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript.\r\nThe repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee)."}],"month":"12","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.3271452","open_access":"1"}],"publisher":"Zenodo"},{"date_updated":"2023-09-11T13:56:52Z","ddc":["576"],"department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:46:16Z","_id":"384","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"999","status":"public","publication_status":"published","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"458a7c2c2e79528567edfeb0f326cbe0","file_id":"4667","creator":"system","file_size":691602,"date_updated":"2020-07-14T12:46:16Z","file_name":"IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf","date_created":"2018-12-12T10:08:07Z"}],"issue":"3","volume":10,"abstract":[{"lang":"eng","text":"Can orthologous proteins differ in terms of their ability to be secreted? To answer this question, we investigated the distribution of signal peptides within the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons revealed a large number of signal peptide gain and loss events, in which signal peptides emerge or disappear in the course of evolution. Signal peptide losses prevail over gains, an effect which is especially pronounced in the transition from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate decline in the number of signal peptide-containing proteins in endosymbionts cannot be explained by the overall reduction of their genomes. Signal peptides can be gained and lost either by acquisition/elimination of the corresponding N-terminal regions or by gradual accumulation of mutations. The evolutionary dynamics of signal peptides in bacterial proteins represents a powerful mechanism of functional diversification."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 10","month":"03","citation":{"ieee":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, and D. Frishman, “Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University Press, pp. 928–938, 2018.","short":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome Biology and Evolution 10 (2018) 928–938.","apa":"Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., & Frishman, D. (2018). Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evy049","ama":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 2018;10(3):928-938. doi:10.1093/gbe/evy049","mla":"Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution, vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:10.1093/gbe/evy049.","ista":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. 2018. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 10(3), 928–938.","chicago":"Hönigschmid, Peter, Nadya Bykova, René Schneider, Dmitry Ivankov, and Dmitrij Frishman. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/gbe/evy049."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000429483700022"]},"article_processing_charge":"No","author":[{"first_name":"Peter","full_name":"Hönigschmid, Peter","last_name":"Hönigschmid"},{"first_name":"Nadya","full_name":"Bykova, Nadya","last_name":"Bykova"},{"first_name":"René","last_name":"Schneider","full_name":"Schneider, René"},{"id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry","full_name":"Ivankov, Dmitry","last_name":"Ivankov"},{"last_name":"Frishman","full_name":"Frishman, Dmitrij","first_name":"Dmitrij"}],"publist_id":"7445","title":"Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss","year":"2018","has_accepted_license":"1","isi":1,"publication":"Genome Biology and Evolution","day":"01","page":"928 - 938","date_created":"2018-12-11T11:46:10Z","doi":"10.1093/gbe/evy049","date_published":"2018-03-01T00:00:00Z","acknowledgement":"his work was supported by the Deutsche Forschungsgemeinschaft (grant number FR 1411/9-1). This work was supported by the German Research Foundation (DFG) and the Technical University of Munich within the fund- ing programme Open Access Publish\r\nWe thank Goar Frishman for help with the annotation of the\r\nsymbiont status of the organisms and Michael Galperin for\r\nuseful comments. T","oa":1,"quality_controlled":"1","publisher":"Oxford University Press"},{"department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:47:11Z","date_updated":"2023-09-11T14:04:05Z","ddc":["580"],"type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"5780","issue":"50","volume":115,"publication_identifier":{"issn":["00278424"]},"publication_status":"published","file":[{"file_id":"5926","checksum":"46b2c12185eb2ddb598f4c7b4bd267bf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_PNAS_Kotlobay.pdf","date_created":"2019-02-05T15:21:40Z","creator":"dernst","file_size":1271988,"date_updated":"2020-07-14T12:47:11Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"12","intvolume":" 115","abstract":[{"lang":"eng","text":"Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in full, which is found only in bacteria. Here, we report identification of the fungal luciferase and three other key enzymes that together form the biosynthetic cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite. Introduction of the identified genes into the genome of the yeast Pichia pastoris along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis cycle and found that fungal bioluminescence emerged through a series of events that included two independent gene duplications. The retention of the duplicated enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication was followed by functional sequence divergence of enzymes of at least one gene in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence proceeded through several closely related stepping stone nonluminescent biochemical reactions with adaptive roles. The availability of a complete eukaryotic luciferin biosynthesis pathway provides several applications in biomedicine and bioengineering."}],"oa_version":"Published Version","author":[{"last_name":"Kotlobay","full_name":"Kotlobay, Alexey A.","first_name":"Alexey A."},{"id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","last_name":"Sarkisyan","orcid":"0000-0002-5375-6341","full_name":"Sarkisyan, Karen"},{"first_name":"Yuliana A.","last_name":"Mokrushina","full_name":"Mokrushina, Yuliana A."},{"first_name":"Marina","full_name":"Marcet-Houben, Marina","last_name":"Marcet-Houben"},{"full_name":"Serebrovskaya, Ekaterina O.","last_name":"Serebrovskaya","first_name":"Ekaterina O."},{"full_name":"Markina, Nadezhda M.","last_name":"Markina","first_name":"Nadezhda M."},{"last_name":"Gonzalez Somermeyer","orcid":"0000-0001-9139-5383","full_name":"Gonzalez Somermeyer, Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","first_name":"Louisa"},{"first_name":"Andrey Y.","full_name":"Gorokhovatsky, Andrey Y.","last_name":"Gorokhovatsky"},{"last_name":"Vvedensky","full_name":"Vvedensky, Andrey","first_name":"Andrey"},{"first_name":"Konstantin V.","last_name":"Purtov","full_name":"Purtov, Konstantin V."},{"full_name":"Petushkov, Valentin N.","last_name":"Petushkov","first_name":"Valentin N."},{"full_name":"Rodionova, Natalja S.","last_name":"Rodionova","first_name":"Natalja S."},{"last_name":"Chepurnyh","full_name":"Chepurnyh, Tatiana V.","first_name":"Tatiana V."},{"first_name":"Liliia","last_name":"Fakhranurova","full_name":"Fakhranurova, Liliia"},{"first_name":"Elena B.","full_name":"Guglya, Elena B.","last_name":"Guglya"},{"last_name":"Ziganshin","full_name":"Ziganshin, Rustam","first_name":"Rustam"},{"first_name":"Aleksandra S.","last_name":"Tsarkova","full_name":"Tsarkova, Aleksandra S."},{"full_name":"Kaskova, Zinaida M.","last_name":"Kaskova","first_name":"Zinaida M."},{"first_name":"Victoria","last_name":"Shender","full_name":"Shender, Victoria"},{"full_name":"Abakumov, Maxim","last_name":"Abakumov","first_name":"Maxim"},{"first_name":"Tatiana O.","last_name":"Abakumova","full_name":"Abakumova, Tatiana O."},{"first_name":"Inna S.","last_name":"Povolotskaya","full_name":"Povolotskaya, Inna S."},{"full_name":"Eroshkin, Fedor M.","last_name":"Eroshkin","first_name":"Fedor M."},{"last_name":"Zaraisky","full_name":"Zaraisky, Andrey G.","first_name":"Andrey G."},{"first_name":"Alexander S.","full_name":"Mishin, Alexander S.","last_name":"Mishin"},{"last_name":"Dolgov","full_name":"Dolgov, Sergey V.","first_name":"Sergey V."},{"full_name":"Mitiouchkina, Tatiana Y.","last_name":"Mitiouchkina","first_name":"Tatiana Y."},{"full_name":"Kopantzev, Eugene P.","last_name":"Kopantzev","first_name":"Eugene P."},{"first_name":"Hans E.","last_name":"Waldenmaier","full_name":"Waldenmaier, Hans E."},{"full_name":"Oliveira, Anderson G.","last_name":"Oliveira","first_name":"Anderson G."},{"first_name":"Yuichi","last_name":"Oba","full_name":"Oba, Yuichi"},{"full_name":"Barsova, Ekaterina","last_name":"Barsova","first_name":"Ekaterina"},{"first_name":"Ekaterina A.","last_name":"Bogdanova","full_name":"Bogdanova, Ekaterina A."},{"first_name":"Toni","last_name":"Gabaldón","full_name":"Gabaldón, Toni"},{"first_name":"Cassius V.","last_name":"Stevani","full_name":"Stevani, Cassius V."},{"first_name":"Sergey","last_name":"Lukyanov","full_name":"Lukyanov, Sergey"},{"first_name":"Ivan V.","last_name":"Smirnov","full_name":"Smirnov, Ivan V."},{"last_name":"Gitelson","full_name":"Gitelson, Josef I.","first_name":"Josef I."},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"first_name":"Ilia V.","last_name":"Yampolsky","full_name":"Yampolsky, Ilia V."}],"external_id":{"isi":["000452866000068"]},"article_processing_charge":"No","title":"Genetically encodable bioluminescent system from fungi","citation":{"ista":"Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 115(50), 12728–12732.","chicago":"Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben, Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1803615115.","apa":"Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya, E. O., Markina, N. M., … Yampolsky, I. V. (2018). Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1803615115","ama":"Kotlobay AA, Sarkisyan K, Mokrushina YA, et al. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(50):12728-12732. doi:10.1073/pnas.1803615115","ieee":"A. A. Kotlobay et al., “Genetically encodable bioluminescent system from fungi,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50. National Academy of Sciences, pp. 12728–12732, 2018.","short":"A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya, N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov, V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya, R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova, I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y. Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova, E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson, F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 12728–12732.","mla":"Kotlobay, Alexey A., et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50, National Academy of Sciences, 2018, pp. 12728–32, doi:10.1073/pnas.1803615115."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"12728-12732","date_published":"2018-12-11T00:00:00Z","doi":"10.1073/pnas.1803615115","date_created":"2018-12-23T22:59:18Z","isi":1,"has_accepted_license":"1","year":"2018","day":"11","publication":"Proceedings of the National Academy of Sciences of the United States of America","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1},{"date_published":"2018-05-31T00:00:00Z","doi":"10.1186/s13059-018-1434-0","date_created":"2018-12-11T11:45:35Z","has_accepted_license":"1","isi":1,"year":"2018","day":"31","publication":"Genome Biology","publisher":"BioMed Central","quality_controlled":"1","oa":1,"author":[{"last_name":"Zapata","full_name":"Zapata, Luis","first_name":"Luis"},{"first_name":"Oriol","full_name":"Pich, Oriol","last_name":"Pich"},{"last_name":"Serrano","full_name":"Serrano, Luis","first_name":"Luis"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov"},{"first_name":"Stephan","last_name":"Ossowski","full_name":"Ossowski, Stephan"},{"last_name":"Schaefer","full_name":"Schaefer, Martin","first_name":"Martin"}],"publist_id":"7620","article_processing_charge":"No","external_id":{"isi":["000433986200001"]},"title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","citation":{"mla":"Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology, vol. 19, 67, BioMed Central, 2018, doi:10.1186/s13059-018-1434-0.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 2018;19. doi:10.1186/s13059-018-1434-0","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1434-0","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018).","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” Genome Biology, vol. 19. BioMed Central, 2018.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1434-0.","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19, 67."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"26120F5C-B435-11E9-9278-68D0E5697425","grant_number":"335980","name":"Systematic investigation of epistasis in molecular evolution"}],"article_number":"67","volume":19,"related_material":{"record":[{"id":"9811","status":"public","relation":"research_data"},{"relation":"research_data","id":"9812","status":"public"}]},"ec_funded":1,"publication_status":"published","file":[{"file_name":"2018_GenomeBiology_Zapata.pdf","date_created":"2018-12-17T14:05:01Z","file_size":1414722,"date_updated":"2020-07-14T12:45:47Z","creator":"dernst","file_id":"5708","checksum":"f3e4922486bd9bf1483271bdbed394a7","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 19","abstract":[{"lang":"eng","text":"Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments."}],"oa_version":"Published Version","department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:45:47Z","date_updated":"2023-09-13T09:01:32Z","ddc":["570"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"279"},{"author":[{"last_name":"Zapata","full_name":"Zapata, Luis","first_name":"Luis"},{"last_name":"Pich","full_name":"Pich, Oriol","first_name":"Oriol"},{"full_name":"Serrano, Luis","last_name":"Serrano","first_name":"Luis"},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"full_name":"Ossowski, Stephan","last_name":"Ossowski","first_name":"Stephan"},{"first_name":"Martin","last_name":"Schaefer","full_name":"Schaefer, Martin"}],"article_processing_charge":"No","department":[{"_id":"FyKo"}],"title":"Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","date_updated":"2023-09-13T09:01:31Z","citation":{"ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401414.v1","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401414.v1","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","mla":"Zapata, Luis, et al. Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1.","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401414.v1.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401414.v1."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9812","date_published":"2018-05-31T00:00:00Z","related_material":{"record":[{"status":"public","id":"279","relation":"used_in_publication"}]},"doi":"10.6084/m9.figshare.6401414.v1","date_created":"2021-08-06T12:58:25Z","year":"2018","day":"31","publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.6401414.v1","open_access":"1"}],"oa":1,"month":"05","abstract":[{"lang":"eng","text":"This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb)"}],"oa_version":"Published Version"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.6401390.v1"}],"oa":1,"publisher":"Springer Nature","month":"05","abstract":[{"text":"This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb)","lang":"eng"}],"oa_version":"Preprint","date_created":"2021-08-06T12:53:49Z","date_published":"2018-05-31T00:00:00Z","doi":"10.6084/m9.figshare.6401390.v1","related_material":{"record":[{"relation":"used_in_publication","id":"279","status":"public"}]},"year":"2018","day":"31","type":"research_data_reference","status":"public","_id":"9811","article_processing_charge":"No","author":[{"full_name":"Zapata, Luis","last_name":"Zapata","first_name":"Luis"},{"last_name":"Pich","full_name":"Pich, Oriol","first_name":"Oriol"},{"last_name":"Serrano","full_name":"Serrano, Luis","first_name":"Luis"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"last_name":"Ossowski","full_name":"Ossowski, Stephan","first_name":"Stephan"},{"first_name":"Martin","full_name":"Schaefer, Martin","last_name":"Schaefer"}],"department":[{"_id":"FyKo"}],"title":"Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","citation":{"short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401390.v1","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401390.v1","mla":"Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1.","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401390.v1.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401390.v1."},"date_updated":"2023-09-13T09:01:31Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"project":[{"call_identifier":"FP7","_id":"26120F5C-B435-11E9-9278-68D0E5697425","name":"Systematic investigation of epistasis in molecular evolution","grant_number":"335980"}],"article_processing_charge":"No","external_id":{"pmid":["29722803"],"isi":["000450038900008"]},"author":[{"last_name":"Usmanova","full_name":"Usmanova, Dinara R","first_name":"Dinara R"},{"full_name":"Bogatyreva, Natalya S","last_name":"Bogatyreva","first_name":"Natalya S"},{"first_name":"Joan","last_name":"Ariño Bernad","full_name":"Ariño Bernad, Joan"},{"last_name":"Eremina","full_name":"Eremina, Aleksandra A","first_name":"Aleksandra A"},{"full_name":"Gorshkova, Anastasiya A","last_name":"Gorshkova","first_name":"Anastasiya A"},{"full_name":"Kanevskiy, German M","last_name":"Kanevskiy","first_name":"German M"},{"first_name":"Lyubov R","full_name":"Lonishin, Lyubov R","last_name":"Lonishin"},{"first_name":"Alexander V","full_name":"Meister, Alexander V","last_name":"Meister"},{"full_name":"Yakupova, Alisa G","last_name":"Yakupova","first_name":"Alisa G"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ivankov, Dmitry","last_name":"Ivankov","first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87"}],"title":"Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation","citation":{"ista":"Usmanova DR, Bogatyreva NS, Ariño Bernad J, Eremina AA, Gorshkova AA, Kanevskiy GM, Lonishin LR, Meister AV, Yakupova AG, Kondrashov F, Ivankov D. 2018. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 34(21), 3653–3658.","chicago":"Usmanova, Dinara R, Natalya S Bogatyreva, Joan Ariño Bernad, Aleksandra A Eremina, Anastasiya A Gorshkova, German M Kanevskiy, Lyubov R Lonishin, et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics. Oxford University Press , 2018. https://doi.org/10.1093/bioinformatics/bty340.","ieee":"D. R. Usmanova et al., “Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation,” Bioinformatics, vol. 34, no. 21. Oxford University Press , pp. 3653–3658, 2018.","short":"D.R. Usmanova, N.S. Bogatyreva, J. Ariño Bernad, A.A. Eremina, A.A. Gorshkova, G.M. Kanevskiy, L.R. Lonishin, A.V. Meister, A.G. Yakupova, F. Kondrashov, D. Ivankov, Bioinformatics 34 (2018) 3653–3658.","ama":"Usmanova DR, Bogatyreva NS, Ariño Bernad J, et al. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 2018;34(21):3653-3658. doi:10.1093/bioinformatics/bty340","apa":"Usmanova, D. R., Bogatyreva, N. S., Ariño Bernad, J., Eremina, A. A., Gorshkova, A. A., Kanevskiy, G. M., … Ivankov, D. (2018). Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. Oxford University Press . https://doi.org/10.1093/bioinformatics/bty340","mla":"Usmanova, Dinara R., et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics, vol. 34, no. 21, Oxford University Press , 2018, pp. 3653–58, doi:10.1093/bioinformatics/bty340."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"quality_controlled":"1","publisher":"Oxford University Press ","page":"3653-3658","date_created":"2019-02-14T12:48:00Z","date_published":"2018-11-01T00:00:00Z","doi":"10.1093/bioinformatics/bty340","year":"2018","has_accepted_license":"1","isi":1,"publication":"Bioinformatics","day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","status":"public","_id":"5995","department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:47:15Z","date_updated":"2023-09-19T14:31:13Z","ddc":["570"],"scopus_import":"1","intvolume":" 34","month":"11","abstract":[{"text":"Motivation\r\nComputational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic shift of the predicted change of stability, has been noted as an issue for several methods, but has not been investigated systematically. Presence of the bias may lead to misleading results especially when exploring the effects of combination of different mutations.\r\n\r\nResults\r\nHere we use a protocol to measure the bias as a function of the number of introduced mutations. It is based on a self-consistency test of the reciprocity the effect of a mutation. An advantage of the used approach is that it relies solely on crystal structures without experimentally measured stability values. We applied the protocol to four popular algorithms predicting change of protein stability upon mutation, FoldX, Eris, Rosetta and I-Mutant, and found an inherent bias. For one program, FoldX, we manage to substantially reduce the bias using additional relaxation by Modeller. Authors using algorithms for predicting effects of mutations should be aware of the bias described here.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"ec_funded":1,"issue":"21","volume":34,"publication_status":"published","publication_identifier":{"issn":["1367-4803","1460-2059"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-02-14T13:00:55Z","file_name":"2018_Oxford_Usmanova.pdf","date_updated":"2020-07-14T12:47:15Z","file_size":291969,"creator":"kschuh","file_id":"5997","checksum":"7e0495153f44211479674601d7f6ee03","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}]},{"month":"02","intvolume":" 102","publisher":"Wiley-Blackwell","scopus_import":1,"quality_controlled":"1","oa_version":"None","abstract":[{"lang":"eng","text":"The small-sized frugivorous bat Carollia perspicillata is an understory specialist and occurs in a wide range of lowland habitats, tending to be more common in tropical dry or moist forests of South and Central America. Its sister species, Carollia brevicauda, occurs almost exclusively in the Amazon rainforest. A recent phylogeographic study proposed a hypothesis of origin and subsequent diversification for C. perspicillata along the Atlantic coastal forest of Brazil. Additionally, it also found two allopatric clades for C. brevicauda separated by the Amazon Basin. We used cytochrome b gene sequences and a more extensive sampling to test hypotheses related to the origin and diversification of C. perspicillata plus C. brevicauda clade in South America. The results obtained indicate that there are two sympatric evolutionary lineages within each species. In C. perspicillata, one lineage is limited to the Southern Atlantic Forest, whereas the other is widely distributed. Coalescent analysis points to a simultaneous origin for C. perspicillata and C. brevicauda, although no place for the diversification of each species can be firmly suggested. The phylogeographic pattern shown by C. perspicillata is also congruent with the Pleistocene refugia hypothesis as a likely vicariant phenomenon shaping the present distribution of its intraspecific lineages."}],"volume":102,"doi":"10.1111/j.1095-8312.2010.01601.x","issue":"3","date_published":"2011-02-10T00:00:00Z","date_created":"2018-12-11T12:05:05Z","page":"527 - 539","day":"10","language":[{"iso":"eng"}],"publication":"Biological Journal of the Linnean Society","publication_status":"published","year":"2011","status":"public","type":"journal_article","_id":"3771","title":"Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.","department":[{"_id":"FyKo"}],"publist_id":"2456","author":[{"first_name":"Ana","last_name":"Pavan","full_name":"Pavan, Ana"},{"first_name":"Felipe","last_name":"Martins","full_name":"Martins, Felipe"},{"last_name":"Santos","full_name":"Santos, Fabrício","first_name":"Fabrício"},{"first_name":"Albert","last_name":"Ditchfield","full_name":"Ditchfield, Albert"},{"first_name":"Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793","last_name":"Fernandes Redondo"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"A. Pavan, F. Martins, F. Santos, A. Ditchfield, and R. A. Fernandes Redondo, “Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.,” Biological Journal of the Linnean Society, vol. 102, no. 3. Wiley-Blackwell, pp. 527–539, 2011.","short":"A. Pavan, F. Martins, F. Santos, A. Ditchfield, R.A. Fernandes Redondo, Biological Journal of the Linnean Society 102 (2011) 527–539.","ama":"Pavan A, Martins F, Santos F, Ditchfield A, Fernandes Redondo RA. Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests. Biological Journal of the Linnean Society. 2011;102(3):527-539. doi:10.1111/j.1095-8312.2010.01601.x","apa":"Pavan, A., Martins, F., Santos, F., Ditchfield, A., & Fernandes Redondo, R. A. (2011). Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests. Biological Journal of the Linnean Society. Wiley-Blackwell. https://doi.org/10.1111/j.1095-8312.2010.01601.x","mla":"Pavan, Ana, et al. “Patterns of Diversification in Two Species of Short-Tailed Bats (Carollia Gray, 1838): The Effects of Historical Fragmentation of Brazilian Rainforests.” Biological Journal of the Linnean Society, vol. 102, no. 3, Wiley-Blackwell, 2011, pp. 527–39, doi:10.1111/j.1095-8312.2010.01601.x.","ista":"Pavan A, Martins F, Santos F, Ditchfield A, Fernandes Redondo RA. 2011. Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests. Biological Journal of the Linnean Society. 102(3), 527–539.","chicago":"Pavan, Ana, Felipe Martins, Fabrício Santos, Albert Ditchfield, and Rodrigo A Fernandes Redondo. “Patterns of Diversification in Two Species of Short-Tailed Bats (Carollia Gray, 1838): The Effects of Historical Fragmentation of Brazilian Rainforests.” Biological Journal of the Linnean Society. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1095-8312.2010.01601.x."},"date_updated":"2021-01-12T07:52:05Z"}]