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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. <a href=\"https://doi.org/10.6084/m9.figshare.9808907.v1\">https://doi.org/10.6084/m9.figshare.9808907.v1</a>.","mla":"Sigalova, Olga M., et al. <i>Additional File 9 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>. Springer Nature, 2019, doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808907.v1\">10.6084/m9.figshare.9808907.v1</a>.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","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, <a href=\"https://doi.org/10.6084/m9.figshare.9808907.v1\">10.6084/m9.figshare.9808907.v1</a>."},"year":"2019","date_updated":"2023-08-30T06:20:22Z","oa":1,"abstract":[{"lang":"eng","text":"Clusters of Orthologous Genes (COGs) and corresponding functional categories assigned to OGs. (CSV 117 kb)"}],"day":"12","doi":"10.6084/m9.figshare.9808907.v1","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6898"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808907.v1"}]},{"date_published":"2018-05-31T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publist_id":"7620","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","relation":"research_data","id":"9811"},{"status":"public","relation":"research_data","id":"9812"}]},"status":"public","file":[{"content_type":"application/pdf","file_name":"2018_GenomeBiology_Zapata.pdf","date_updated":"2020-07-14T12:45:47Z","file_size":1414722,"checksum":"f3e4922486bd9bf1483271bdbed394a7","date_created":"2018-12-17T14:05:01Z","creator":"dernst","file_id":"5708","access_level":"open_access","relation":"main_file"}],"publication":"Genome Biology","has_accepted_license":"1","month":"05","article_number":"67","oa_version":"Published Version","project":[{"grant_number":"335980","name":"Systematic investigation of epistasis in molecular evolution","_id":"26120F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"isi":1,"external_id":{"isi":["000433986200001"]},"date_updated":"2023-09-13T09:01:32Z","citation":{"short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018).","mla":"Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” <i>Genome Biology</i>, vol. 19, 67, BioMed Central, 2018, doi:<a href=\"https://doi.org/10.1186/s13059-018-1434-0\">10.1186/s13059-018-1434-0</a>.","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.","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. <i>Genome Biology</i>. 2018;19. doi:<a href=\"https://doi.org/10.1186/s13059-018-1434-0\">10.1186/s13059-018-1434-0</a>","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-018-1434-0\">https://doi.org/10.1186/s13059-018-1434-0</a>","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.” <i>Genome Biology</i>. BioMed Central, 2018. <a href=\"https://doi.org/10.1186/s13059-018-1434-0\">https://doi.org/10.1186/s13059-018-1434-0</a>.","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,” <i>Genome Biology</i>, vol. 19. BioMed Central, 2018."},"year":"2018","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."}],"doi":"10.1186/s13059-018-1434-0","day":"31","ddc":["570"],"volume":19,"author":[{"first_name":"Luis","last_name":"Zapata","full_name":"Zapata, Luis"},{"full_name":"Pich, Oriol","first_name":"Oriol","last_name":"Pich"},{"full_name":"Serrano, Luis","last_name":"Serrano","first_name":"Luis"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor"},{"last_name":"Ossowski","first_name":"Stephan","full_name":"Ossowski, Stephan"},{"first_name":"Martin","last_name":"Schaefer","full_name":"Schaefer, Martin"}],"_id":"279","scopus_import":"1","title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","intvolume":"        19","publication_status":"published","date_created":"2018-12-11T11:45:35Z","department":[{"_id":"FyKo"}],"article_processing_charge":"No","file_date_updated":"2020-07-14T12:45:47Z","quality_controlled":"1","ec_funded":1,"publisher":"BioMed Central"},{"scopus_import":"1","_id":"5780","issue":"50","author":[{"first_name":"Alexey A.","last_name":"Kotlobay","full_name":"Kotlobay, Alexey A."},{"id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5375-6341","full_name":"Sarkisyan, Karen","first_name":"Karen","last_name":"Sarkisyan"},{"last_name":"Mokrushina","first_name":"Yuliana A.","full_name":"Mokrushina, Yuliana A."},{"full_name":"Marcet-Houben, Marina","first_name":"Marina","last_name":"Marcet-Houben"},{"first_name":"Ekaterina O.","last_name":"Serebrovskaya","full_name":"Serebrovskaya, Ekaterina O."},{"full_name":"Markina, Nadezhda M.","first_name":"Nadezhda M.","last_name":"Markina"},{"id":"4720D23C-F248-11E8-B48F-1D18A9856A87","last_name":"Gonzalez Somermeyer","first_name":"Louisa","full_name":"Gonzalez Somermeyer, Louisa","orcid":"0000-0001-9139-5383"},{"first_name":"Andrey Y.","last_name":"Gorokhovatsky","full_name":"Gorokhovatsky, Andrey Y."},{"last_name":"Vvedensky","first_name":"Andrey","full_name":"Vvedensky, Andrey"},{"full_name":"Purtov, Konstantin V.","last_name":"Purtov","first_name":"Konstantin V."},{"full_name":"Petushkov, Valentin N.","first_name":"Valentin N.","last_name":"Petushkov"},{"last_name":"Rodionova","first_name":"Natalja S.","full_name":"Rodionova, Natalja S."},{"last_name":"Chepurnyh","first_name":"Tatiana V.","full_name":"Chepurnyh, Tatiana V."},{"full_name":"Fakhranurova, Liliia","last_name":"Fakhranurova","first_name":"Liliia"},{"full_name":"Guglya, Elena B.","first_name":"Elena B.","last_name":"Guglya"},{"full_name":"Ziganshin, Rustam","last_name":"Ziganshin","first_name":"Rustam"},{"full_name":"Tsarkova, Aleksandra S.","last_name":"Tsarkova","first_name":"Aleksandra S."},{"full_name":"Kaskova, Zinaida M.","last_name":"Kaskova","first_name":"Zinaida M."},{"last_name":"Shender","first_name":"Victoria","full_name":"Shender, Victoria"},{"last_name":"Abakumov","first_name":"Maxim","full_name":"Abakumov, Maxim"},{"full_name":"Abakumova, Tatiana O.","last_name":"Abakumova","first_name":"Tatiana O."},{"full_name":"Povolotskaya, Inna S.","last_name":"Povolotskaya","first_name":"Inna S."},{"first_name":"Fedor M.","last_name":"Eroshkin","full_name":"Eroshkin, Fedor M."},{"last_name":"Zaraisky","first_name":"Andrey G.","full_name":"Zaraisky, Andrey G."},{"last_name":"Mishin","first_name":"Alexander S.","full_name":"Mishin, Alexander S."},{"full_name":"Dolgov, Sergey V.","first_name":"Sergey V.","last_name":"Dolgov"},{"full_name":"Mitiouchkina, Tatiana Y.","first_name":"Tatiana Y.","last_name":"Mitiouchkina"},{"full_name":"Kopantzev, Eugene P.","last_name":"Kopantzev","first_name":"Eugene P."},{"first_name":"Hans E.","last_name":"Waldenmaier","full_name":"Waldenmaier, Hans E."},{"last_name":"Oliveira","first_name":"Anderson G.","full_name":"Oliveira, Anderson G."},{"full_name":"Oba, Yuichi","first_name":"Yuichi","last_name":"Oba"},{"first_name":"Ekaterina","last_name":"Barsova","full_name":"Barsova, Ekaterina"},{"first_name":"Ekaterina A.","last_name":"Bogdanova","full_name":"Bogdanova, Ekaterina A."},{"full_name":"Gabaldón, Toni","last_name":"Gabaldón","first_name":"Toni"},{"full_name":"Stevani, Cassius V.","last_name":"Stevani","first_name":"Cassius V."},{"last_name":"Lukyanov","first_name":"Sergey","full_name":"Lukyanov, Sergey"},{"first_name":"Ivan V.","last_name":"Smirnov","full_name":"Smirnov, Ivan V."},{"full_name":"Gitelson, Josef I.","first_name":"Josef I.","last_name":"Gitelson"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"},{"full_name":"Yampolsky, Ilia V.","last_name":"Yampolsky","first_name":"Ilia V."}],"date_created":"2018-12-23T22:59:18Z","department":[{"_id":"FyKo"}],"article_processing_charge":"No","publication_status":"published","intvolume":"       115","title":"Genetically encodable bioluminescent system from fungi","quality_controlled":"1","page":"12728-12732","file_date_updated":"2020-07-14T12:47:11Z","publisher":"National Academy of Sciences","year":"2018","citation":{"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.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1803615115\">https://doi.org/10.1073/pnas.1803615115</a>.","ieee":"A. A. Kotlobay <i>et al.</i>, “Genetically encodable bioluminescent system from fungi,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 50. National Academy of Sciences, pp. 12728–12732, 2018.","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. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1803615115\">https://doi.org/10.1073/pnas.1803615115</a>","ama":"Kotlobay AA, Sarkisyan K, Mokrushina YA, et al. Genetically encodable bioluminescent system from fungi. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2018;115(50):12728-12732. doi:<a href=\"https://doi.org/10.1073/pnas.1803615115\">10.1073/pnas.1803615115</a>","ista":"Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 115(50), 12728–12732.","mla":"Kotlobay, Alexey A., et al. “Genetically Encodable Bioluminescent System from Fungi.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 50, National Academy of Sciences, 2018, pp. 12728–32, doi:<a href=\"https://doi.org/10.1073/pnas.1803615115\">10.1073/pnas.1803615115</a>.","short":"A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya, N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov, V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya, R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova, I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y. Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova, E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson, F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 12728–12732."},"date_updated":"2023-09-11T14:04:05Z","external_id":{"isi":["000452866000068"]},"isi":1,"day":"11","doi":"10.1073/pnas.1803615115","abstract":[{"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.","lang":"eng"}],"volume":115,"ddc":["580"],"has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","oa_version":"Published Version","month":"12","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","date_published":"2018-12-11T00:00:00Z","publication_identifier":{"issn":["00278424"]},"oa":1,"file":[{"date_created":"2019-02-05T15:21:40Z","file_size":1271988,"checksum":"46b2c12185eb2ddb598f4c7b4bd267bf","date_updated":"2020-07-14T12:47:11Z","content_type":"application/pdf","file_name":"2018_PNAS_Kotlobay.pdf","access_level":"open_access","relation":"main_file","file_id":"5926","creator":"dernst"}],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"creator":"kschuh","file_id":"5997","relation":"main_file","access_level":"open_access","file_name":"2018_Oxford_Usmanova.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:15Z","file_size":291969,"checksum":"7e0495153f44211479674601d7f6ee03","date_created":"2019-02-14T13:00:55Z"}],"date_published":"2018-11-01T00:00:00Z","type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"oa":1,"publication_identifier":{"issn":["1367-4803","1460-2059"]},"language":[{"iso":"eng"}],"publication":"Bioinformatics","has_accepted_license":"1","month":"11","oa_version":"Published Version","project":[{"grant_number":"335980","name":"Systematic investigation of epistasis in molecular evolution","call_identifier":"FP7","_id":"26120F5C-B435-11E9-9278-68D0E5697425"}],"ddc":["570"],"volume":34,"isi":1,"external_id":{"pmid":["29722803"],"isi":["000450038900008"]},"date_updated":"2023-09-19T14:31:13Z","citation":{"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.","mla":"Usmanova, Dinara R., et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” <i>Bioinformatics</i>, vol. 34, no. 21, Oxford University Press , 2018, pp. 3653–58, doi:<a href=\"https://doi.org/10.1093/bioinformatics/bty340\">10.1093/bioinformatics/bty340</a>.","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.","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. <i>Bioinformatics</i>. Oxford University Press . <a href=\"https://doi.org/10.1093/bioinformatics/bty340\">https://doi.org/10.1093/bioinformatics/bty340</a>","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. <i>Bioinformatics</i>. 2018;34(21):3653-3658. doi:<a href=\"https://doi.org/10.1093/bioinformatics/bty340\">10.1093/bioinformatics/bty340</a>","ieee":"D. R. Usmanova <i>et al.</i>, “Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation,” <i>Bioinformatics</i>, vol. 34, no. 21. Oxford University Press , pp. 3653–3658, 2018.","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.” <i>Bioinformatics</i>. Oxford University Press , 2018. <a href=\"https://doi.org/10.1093/bioinformatics/bty340\">https://doi.org/10.1093/bioinformatics/bty340</a>."},"year":"2018","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"}],"doi":"10.1093/bioinformatics/bty340","day":"01","file_date_updated":"2020-07-14T12:47:15Z","page":"3653-3658","quality_controlled":"1","ec_funded":1,"publisher":"Oxford University Press ","author":[{"full_name":"Usmanova, Dinara R","last_name":"Usmanova","first_name":"Dinara R"},{"last_name":"Bogatyreva","first_name":"Natalya S","full_name":"Bogatyreva, Natalya S"},{"full_name":"Ariño Bernad, Joan","last_name":"Ariño Bernad","first_name":"Joan"},{"full_name":"Eremina, Aleksandra A","first_name":"Aleksandra A","last_name":"Eremina"},{"last_name":"Gorshkova","first_name":"Anastasiya A","full_name":"Gorshkova, Anastasiya A"},{"full_name":"Kanevskiy, German M","first_name":"German M","last_name":"Kanevskiy"},{"full_name":"Lonishin, Lyubov R","first_name":"Lyubov R","last_name":"Lonishin"},{"full_name":"Meister, Alexander V","last_name":"Meister","first_name":"Alexander V"},{"last_name":"Yakupova","first_name":"Alisa G","full_name":"Yakupova, Alisa G"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor"},{"id":"49FF1036-F248-11E8-B48F-1D18A9856A87","last_name":"Ivankov","first_name":"Dmitry","full_name":"Ivankov, Dmitry"}],"issue":"21","_id":"5995","pmid":1,"scopus_import":"1","title":"Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation","intvolume":"        34","publication_status":"published","article_processing_charge":"No","date_created":"2019-02-14T12:48:00Z","department":[{"_id":"FyKo"}]},{"month":"12","title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","oa_version":"Published Version","article_processing_charge":"No","date_created":"2023-05-23T16:08:20Z","department":[{"_id":"FyKo"}],"author":[{"last_name":"Garriga","first_name":"Edgar","full_name":"Garriga, Edgar"},{"full_name":"di Tommaso, Paolo","last_name":"di Tommaso","first_name":"Paolo"},{"full_name":"Magis, Cedrik","last_name":"Magis","first_name":"Cedrik"},{"full_name":"Erb, Ionas","last_name":"Erb","first_name":"Ionas"},{"first_name":"Leila","last_name":"Mansouri","full_name":"Mansouri, Leila"},{"last_name":"Baltzis","first_name":"Athanasios","full_name":"Baltzis, Athanasios"},{"full_name":"Laayouni, Hafid","first_name":"Hafid","last_name":"Laayouni"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov"},{"last_name":"Floden","first_name":"Evan","full_name":"Floden, Evan"},{"last_name":"Notredame","first_name":"Cedric","full_name":"Notredame, Cedric"}],"_id":"13059","publisher":"Zenodo","abstract":[{"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).","lang":"eng"}],"oa":1,"doi":"10.5281/ZENODO.2025846","day":"07","date_published":"2018-12-07T00:00:00Z","type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2023-09-06T14:32:51Z","citation":{"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, <a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>.","short":"E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018).","mla":"Garriga, Edgar, et al. <i>Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method</i>. Zenodo, 2018, doi:<a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>.","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. <a href=\"https://doi.org/10.5281/ZENODO.2025846\">https://doi.org/10.5281/ZENODO.2025846</a>.","ieee":"E. Garriga <i>et al.</i>, “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.","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. <a href=\"https://doi.org/10.5281/ZENODO.2025846\">https://doi.org/10.5281/ZENODO.2025846</a>","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:<a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>"},"year":"2018","ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"7181","relation":"used_in_publication","status":"public"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.3271452"}]},{"publisher":"Springer Nature","_id":"9811","author":[{"first_name":"Luis","last_name":"Zapata","full_name":"Zapata, Luis"},{"full_name":"Pich, Oriol","last_name":"Pich","first_name":"Oriol"},{"full_name":"Serrano, Luis","last_name":"Serrano","first_name":"Luis"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov"},{"first_name":"Stephan","last_name":"Ossowski","full_name":"Ossowski, Stephan"},{"full_name":"Schaefer, Martin","first_name":"Martin","last_name":"Schaefer"}],"oa_version":"Preprint","article_processing_charge":"No","department":[{"_id":"FyKo"}],"date_created":"2021-08-06T12:53:49Z","month":"05","title":"Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.6401390.v1"}],"status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"status":"public","id":"279","relation":"used_in_publication"}]},"date_updated":"2023-09-13T09:01:31Z","citation":{"ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:<a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">10.6084/m9.figshare.6401390.v1</a>","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer, M. (2018). Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">https://doi.org/10.6084/m9.figshare.6401390.v1</a>","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. <a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">https://doi.org/10.6084/m9.figshare.6401390.v1</a>.","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.","mla":"Zapata, Luis, et al. <i>Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome</i>. Springer Nature, 2018, doi:<a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">10.6084/m9.figshare.6401390.v1</a>.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">10.6084/m9.figshare.6401390.v1</a>."},"year":"2018","date_published":"2018-05-31T00:00:00Z","type":"research_data_reference","doi":"10.6084/m9.figshare.6401390.v1","day":"31","abstract":[{"lang":"eng","text":"This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb)"}],"oa":1},{"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.6401414.v1","open_access":"1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","related_material":{"record":[{"status":"public","id":"279","relation":"used_in_publication"}]},"day":"31","doi":"10.6084/m9.figshare.6401414.v1","oa":1,"abstract":[{"text":"This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb)","lang":"eng"}],"citation":{"mla":"Zapata, Luis, et al. <i>Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome</i>. Springer Nature, 2018, doi:<a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">10.6084/m9.figshare.6401414.v1</a>.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">10.6084/m9.figshare.6401414.v1</a>.","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:<a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">10.6084/m9.figshare.6401414.v1</a>","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer, M. (2018). Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">https://doi.org/10.6084/m9.figshare.6401414.v1</a>","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. <a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">https://doi.org/10.6084/m9.figshare.6401414.v1</a>.","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."},"year":"2018","date_updated":"2023-09-13T09:01:31Z","type":"research_data_reference","date_published":"2018-05-31T00:00:00Z","publisher":"Springer Nature","date_created":"2021-08-06T12:58:25Z","department":[{"_id":"FyKo"}],"article_processing_charge":"No","oa_version":"Published Version","title":"Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","month":"05","_id":"9812","author":[{"full_name":"Zapata, Luis","first_name":"Luis","last_name":"Zapata"},{"first_name":"Oriol","last_name":"Pich","full_name":"Pich, Oriol"},{"first_name":"Luis","last_name":"Serrano","full_name":"Serrano, Luis"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stephan","last_name":"Ossowski","full_name":"Ossowski, Stephan"},{"last_name":"Schaefer","first_name":"Martin","full_name":"Schaefer, Martin"}]},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2018-03-01T00:00:00Z","oa":1,"publist_id":"7445","file":[{"checksum":"458a7c2c2e79528567edfeb0f326cbe0","file_size":691602,"date_created":"2018-12-12T10:08:07Z","content_type":"application/pdf","file_name":"IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf","date_updated":"2020-07-14T12:46:16Z","relation":"main_file","access_level":"open_access","creator":"system","file_id":"4667"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","has_accepted_license":"1","publication":"Genome Biology and Evolution","oa_version":"Published Version","month":"03","language":[{"iso":"eng"}],"year":"2018","citation":{"apa":"Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., &#38; Frishman, D. (2018). Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evy049\">https://doi.org/10.1093/gbe/evy049</a>","ama":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. <i>Genome Biology and Evolution</i>. 2018;10(3):928-938. doi:<a href=\"https://doi.org/10.1093/gbe/evy049\">10.1093/gbe/evy049</a>","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,” <i>Genome Biology and Evolution</i>, vol. 10, no. 3. Oxford University Press, pp. 928–938, 2018.","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.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/gbe/evy049\">https://doi.org/10.1093/gbe/evy049</a>.","short":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome Biology and Evolution 10 (2018) 928–938.","mla":"Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” <i>Genome Biology and Evolution</i>, vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:<a href=\"https://doi.org/10.1093/gbe/evy049\">10.1093/gbe/evy049</a>.","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."},"date_updated":"2023-09-11T13:56:52Z","external_id":{"isi":["000429483700022"]},"isi":1,"day":"01","doi":"10.1093/gbe/evy049","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."}],"volume":10,"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","ddc":["576"],"scopus_import":"1","_id":"384","issue":"3","author":[{"full_name":"Hönigschmid, Peter","first_name":"Peter","last_name":"Hönigschmid"},{"full_name":"Bykova, Nadya","last_name":"Bykova","first_name":"Nadya"},{"last_name":"Schneider","first_name":"René","full_name":"Schneider, René"},{"full_name":"Ivankov, Dmitry","first_name":"Dmitry","last_name":"Ivankov","id":"49FF1036-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Frishman, Dmitrij","first_name":"Dmitrij","last_name":"Frishman"}],"article_processing_charge":"No","department":[{"_id":"FyKo"}],"date_created":"2018-12-11T11:46:10Z","publication_status":"published","intvolume":"        10","title":"Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss","pubrep_id":"999","quality_controlled":"1","page":"928 - 938","file_date_updated":"2020-07-14T12:46:16Z","publisher":"Oxford University Press"},{"date_created":"2018-12-11T12:05:05Z","department":[{"_id":"FyKo"}],"publication_status":"published","oa_version":"None","intvolume":"       102","title":"Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.","month":"02","scopus_import":1,"_id":"3771","publication":"Biological Journal of the Linnean Society","issue":"3","author":[{"full_name":"Pavan, Ana","first_name":"Ana","last_name":"Pavan"},{"last_name":"Martins","first_name":"Felipe","full_name":"Martins, Felipe"},{"full_name":"Santos, Fabrício","last_name":"Santos","first_name":"Fabrício"},{"full_name":"Ditchfield, Albert","first_name":"Albert","last_name":"Ditchfield"},{"id":"409D5C96-F248-11E8-B48F-1D18A9856A87","last_name":"Fernandes Redondo","first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793"}],"publisher":"Wiley-Blackwell","quality_controlled":"1","page":"527 - 539","language":[{"iso":"eng"}],"day":"10","doi":"10.1111/j.1095-8312.2010.01601.x","publist_id":"2456","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."}],"citation":{"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. <i>Biological Journal of the Linnean Society</i>. 2011;102(3):527-539. doi:<a href=\"https://doi.org/10.1111/j.1095-8312.2010.01601.x\">10.1111/j.1095-8312.2010.01601.x</a>","apa":"Pavan, A., Martins, F., Santos, F., Ditchfield, A., &#38; 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. <i>Biological Journal of the Linnean Society</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1095-8312.2010.01601.x\">https://doi.org/10.1111/j.1095-8312.2010.01601.x</a>","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.” <i>Biological Journal of the Linnean Society</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/10.1111/j.1095-8312.2010.01601.x\">https://doi.org/10.1111/j.1095-8312.2010.01601.x</a>.","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.,” <i>Biological Journal of the Linnean Society</i>, vol. 102, no. 3. Wiley-Blackwell, pp. 527–539, 2011.","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.” <i>Biological Journal of the Linnean Society</i>, vol. 102, no. 3, Wiley-Blackwell, 2011, pp. 527–39, doi:<a href=\"https://doi.org/10.1111/j.1095-8312.2010.01601.x\">10.1111/j.1095-8312.2010.01601.x</a>.","short":"A. Pavan, F. Martins, F. Santos, A. Ditchfield, R.A. Fernandes Redondo, Biological Journal of the Linnean Society 102 (2011) 527–539.","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."},"year":"2011","date_updated":"2021-01-12T07:52:05Z","type":"journal_article","date_published":"2011-02-10T00:00:00Z","volume":102,"status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"}]