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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.","ieee":"O. M. Sigalova et al., “Additional file 19 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 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808835.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 19 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.9808835.v1","mla":"Sigalova, Olga M., et al. Additional File 19 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808835.v1."},"date_updated":"2023-08-30T06:20:21Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"first_name":"Olga M.","full_name":"Sigalova, Olga M.","last_name":"Sigalova"},{"last_name":"Chaplin","full_name":"Chaplin, Andrei V.","first_name":"Andrei V."},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","last_name":"Bochkareva"},{"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."},{"full_name":"Burskaia, Valentina","last_name":"Burskaia","first_name":"Valentina"},{"last_name":"Gelfand","full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S."}],"title":"Additional file 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","department":[{"_id":"FyKo"}],"_id":"9895","type":"research_data_reference","status":"public"},{"month":"09","publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808841.v1"}],"oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Summary of the analysed genomes. (CSV 24 kb)"}],"date_published":"2019-09-02T00:00:00Z","related_material":{"record":[{"id":"6898","status":"public","relation":"used_in_publication"}]},"doi":"10.6084/m9.figshare.9808841.v1","date_created":"2021-08-12T07:50:53Z","day":"02","year":"2019","status":"public","type":"research_data_reference","_id":"9896","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."},{"full_name":"Chaplin, Andrei V.","last_name":"Chaplin","first_name":"Andrei V."},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","last_name":"Bochkareva"},{"last_name":"Shelyakin","full_name":"Shelyakin, Pavel V.","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."}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"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.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","ieee":"O. M. Sigalova et al., “Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808841.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 1 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.9808841.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 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."},"date_updated":"2023-08-30T06:20:21Z"},{"quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"date_published":"2019-09-11T00:00:00Z","doi":"10.1038/s41467-019-12068-x","date_created":"2019-09-22T22:00:37Z","page":"4113","day":"11","publication":"Nature communications","isi":1,"has_accepted_license":"1","year":"2019","title":"Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions","author":[{"first_name":"Dorothee","full_name":"Bornhorst, Dorothee","last_name":"Bornhorst"},{"id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","first_name":"Peng","last_name":"Xia","orcid":"0000-0002-5419-7756","full_name":"Xia, Peng"},{"first_name":"Hiroyuki","full_name":"Nakajima, Hiroyuki","last_name":"Nakajima"},{"full_name":"Dingare, Chaitanya","last_name":"Dingare","first_name":"Chaitanya"},{"full_name":"Herzog, Wiebke","last_name":"Herzog","first_name":"Wiebke"},{"full_name":"Lecaudey, Virginie","last_name":"Lecaudey","first_name":"Virginie"},{"first_name":"Naoki","last_name":"Mochizuki","full_name":"Mochizuki, Naoki"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Deborah","last_name":"Yelon","full_name":"Yelon, Deborah"},{"full_name":"Abdelilah-Seyfried, Salim","last_name":"Abdelilah-Seyfried","first_name":"Salim"}],"external_id":{"pmid":["31511517"],"isi":["000485216800009"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Bornhorst D, Xia P, Nakajima H, Dingare C, Herzog W, Lecaudey V, Mochizuki N, Heisenberg C-PJ, Yelon D, Abdelilah-Seyfried S. 2019. Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature communications. 10(1), 4113.","chicago":"Bornhorst, Dorothee, Peng Xia, Hiroyuki Nakajima, Chaitanya Dingare, Wiebke Herzog, Virginie Lecaudey, Naoki Mochizuki, Carl-Philipp J Heisenberg, Deborah Yelon, and Salim Abdelilah-Seyfried. “Biomechanical Signaling within the Developing Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.” Nature Communications. Nature Publishing Group, 2019. https://doi.org/10.1038/s41467-019-12068-x.","apa":"Bornhorst, D., Xia, P., Nakajima, H., Dingare, C., Herzog, W., Lecaudey, V., … Abdelilah-Seyfried, S. (2019). Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-019-12068-x","ama":"Bornhorst D, Xia P, Nakajima H, et al. Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature communications. 2019;10(1):4113. doi:10.1038/s41467-019-12068-x","ieee":"D. Bornhorst et al., “Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions,” Nature communications, vol. 10, no. 1. Nature Publishing Group, p. 4113, 2019.","short":"D. Bornhorst, P. Xia, H. Nakajima, C. Dingare, W. Herzog, V. Lecaudey, N. Mochizuki, C.-P.J. Heisenberg, D. Yelon, S. Abdelilah-Seyfried, Nature Communications 10 (2019) 4113.","mla":"Bornhorst, Dorothee, et al. “Biomechanical Signaling within the Developing Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.” Nature Communications, vol. 10, no. 1, Nature Publishing Group, 2019, p. 4113, doi:10.1038/s41467-019-12068-x."},"month":"09","intvolume":" 10","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Intra-organ communication guides morphogenetic processes that are essential for an organ to carry out complex physiological functions. In the heart, the growth of the myocardium is tightly coupled to that of the endocardium, a specialized endothelial tissue that lines its interior. Several molecular pathways have been implicated in the communication between these tissues including secreted factors, components of the extracellular matrix, or proteins involved in cell-cell communication. Yet, it is unknown how the growth of the endocardium is coordinated with that of the myocardium. Here, we show that an increased expansion of the myocardial atrial chamber volume generates higher junctional forces within endocardial cells. This leads to biomechanical signaling involving VE-cadherin, triggering nuclear localization of the Hippo pathway transcriptional regulator Yap1 and endocardial proliferation. Our work suggests that the growth of the endocardium results from myocardial chamber volume expansion and ends when the tension on the tissue is relaxed.","lang":"eng"}],"volume":10,"issue":"1","license":"https://creativecommons.org/licenses/by/4.0/","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"62c2512712e16d27c1797d318d14ba9f","file_id":"6926","date_updated":"2020-07-14T12:47:44Z","file_size":3905793,"creator":"kschuh","date_created":"2019-10-01T11:18:50Z","file_name":"2019_Nature_Bornhorst.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20411723"]},"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":"6899","file_date_updated":"2020-07-14T12:47:44Z","department":[{"_id":"CaHe"}],"ddc":["570"],"date_updated":"2023-08-30T06:21:23Z"},{"article_number":"710","article_processing_charge":"No","external_id":{"isi":["000485256100001"]},"author":[{"full_name":"Sigalova, Olga M.","last_name":"Sigalova","first_name":"Olga M."},{"last_name":"Chaplin","full_name":"Chaplin, Andrei V.","first_name":"Andrei V."},{"orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","last_name":"Bochkareva","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"last_name":"Shelyakin","full_name":"Shelyakin, Pavel V.","first_name":"Pavel V."},{"first_name":"Vsevolod A.","last_name":"Filaretov","full_name":"Filaretov, Vsevolod A."},{"last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E.","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."}],"title":"Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","citation":{"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).","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.","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","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"BioMed Central","date_created":"2019-09-22T22:00:36Z","doi":"10.1186/s12864-019-6059-5","date_published":"2019-09-12T00:00:00Z","year":"2019","has_accepted_license":"1","isi":1,"publication":"BMC Genomics","day":"12","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","status":"public","_id":"6898","department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:47:44Z","date_updated":"2023-08-30T06:20:22Z","ddc":["570"],"scopus_import":"1","intvolume":" 20","month":"09","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","issue":"1","volume":20,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9731"},{"id":"9783","status":"public","relation":"research_data"},{"id":"9890","status":"public","relation":"research_data"},{"relation":"research_data","id":"9892","status":"public"},{"relation":"research_data","status":"public","id":"9893"},{"relation":"research_data","status":"public","id":"9894"},{"id":"9895","status":"public","relation":"research_data"},{"status":"public","id":"9896","relation":"research_data"},{"relation":"research_data","status":"public","id":"9897"},{"relation":"research_data","status":"public","id":"9898"},{"status":"public","id":"9899","relation":"research_data"},{"relation":"research_data","status":"public","id":"9900"},{"relation":"research_data","status":"public","id":"9901"}]},"publication_status":"published","publication_identifier":{"eissn":["14712164"]},"language":[{"iso":"eng"}],"file":[{"checksum":"b798773c5823012d31c812c9f7975da2","file_id":"6924","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-10-01T10:33:17Z","file_name":"2019_BioMed_Sigalova.pdf","creator":"kschuh","date_updated":"2020-07-14T12:47:44Z","file_size":4157175}]},{"page":"1312-1314","doi":"10.1016/j.molp.2019.09.003","date_published":"2019-10-07T00:00:00Z","date_created":"2019-09-30T10:00:40Z","isi":1,"year":"2019","day":"07","publication":"Molecular Plant","publisher":"Cell Press","quality_controlled":"1","author":[{"last_name":"Artner","full_name":"Artner, Christina","first_name":"Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"external_id":{"isi":["000489132500002"],"pmid":["31541740"]},"article_processing_charge":"No","title":"Ethylene and cytokinin - partners in root growth regulation","citation":{"mla":"Artner, Christina, and Eva Benková. “Ethylene and Cytokinin - Partners in Root Growth Regulation.” Molecular Plant, vol. 12, no. 10, Cell Press, 2019, pp. 1312–14, doi:10.1016/j.molp.2019.09.003.","ieee":"C. Artner and E. Benková, “Ethylene and cytokinin - partners in root growth regulation,” Molecular Plant, vol. 12, no. 10. Cell Press, pp. 1312–1314, 2019.","short":"C. Artner, E. Benková, Molecular Plant 12 (2019) 1312–1314.","ama":"Artner C, Benková E. Ethylene and cytokinin - partners in root growth regulation. Molecular Plant. 2019;12(10):1312-1314. doi:10.1016/j.molp.2019.09.003","apa":"Artner, C., & Benková, E. (2019). Ethylene and cytokinin - partners in root growth regulation. Molecular Plant. Cell Press. https://doi.org/10.1016/j.molp.2019.09.003","chicago":"Artner, Christina, and Eva Benková. “Ethylene and Cytokinin - Partners in Root Growth Regulation.” Molecular Plant. Cell Press, 2019. https://doi.org/10.1016/j.molp.2019.09.003.","ista":"Artner C, Benková E. 2019. Ethylene and cytokinin - partners in root growth regulation. Molecular Plant. 12(10), 1312–1314."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Hormonal regulation of plant adaptive responses to environmental signals","_id":"2685A872-B435-11E9-9278-68D0E5697425"}],"volume":12,"issue":"10","publication_identifier":{"issn":["1674-2052","1752-9867"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"10","intvolume":" 12","pmid":1,"oa_version":"None","department":[{"_id":"EvBe"}],"date_updated":"2023-08-30T06:55:02Z","type":"journal_article","article_type":"original","status":"public","_id":"6920"},{"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 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. Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808859.v1.","mla":"Sigalova, Olga M., et al. Additional File 21 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808859.v1.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","ieee":"O. M. 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.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808859.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 21 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.9808859.v1"},"date_updated":"2023-08-30T06:20:22Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Olga M.","full_name":"Sigalova, Olga M.","last_name":"Sigalova"},{"first_name":"Andrei V.","full_name":"Chaplin, Andrei V.","last_name":"Chaplin"},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga","last_name":"Bochkareva","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin","first_name":"Pavel V."},{"first_name":"Vsevolod A.","last_name":"Filaretov","full_name":"Filaretov, Vsevolod A."},{"full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov","first_name":"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","title":"Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","department":[{"_id":"FyKo"}],"_id":"9898","type":"research_data_reference","status":"public","year":"2019","day":"12","doi":"10.6084/m9.figshare.9808859.v1","date_published":"2019-09-12T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6898"}]},"date_created":"2021-08-12T08:10:23Z","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"}],"oa_version":"Published Version","publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808859.v1","open_access":"1"}],"oa":1,"month":"09"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Clusters of Orthologous Genes (COGs) and corresponding functional categories assigned to OGs. 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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"}],"article_processing_charge":"No","author":[{"full_name":"Sigalova, Olga M.","last_name":"Sigalova","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"},{"full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin","first_name":"Pavel V."},{"first_name":"Vsevolod A.","last_name":"Filaretov","full_name":"Filaretov, Vsevolod A."},{"full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov","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."}]},{"status":"public","type":"research_data_reference","_id":"9899","department":[{"_id":"FyKo"}],"title":"Additional file 2 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"},{"first_name":"Pavel V.","full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin"},{"last_name":"Filaretov","full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A."},{"first_name":"Evgeny E.","last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E."},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"article_processing_charge":"No","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 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.","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).","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","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"},"date_updated":"2023-08-30T06:20:22Z","month":"09","publisher":"Springer Nature","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808865.v1"}],"oa_version":"Published Version","abstract":[{"text":"Summary of orthologous groups (OGs) for 227 genomes of genus Chlamydia. (CSV 362 kb)","lang":"eng"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6898"}]},"doi":"10.6084/m9.figshare.9808865.v1","date_published":"2019-09-12T00:00:00Z","date_created":"2021-08-12T08:18:09Z","day":"12","year":"2019"},{"_id":"9900","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-30T06:20:22Z","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.","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","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)."},"title":"Additional file 5 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.","full_name":"Sigalova, Olga M.","last_name":"Sigalova"},{"full_name":"Chaplin, Andrei V.","last_name":"Chaplin","first_name":"Andrei V."},{"first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"last_name":"Filaretov","full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A."},{"first_name":"Evgeny E.","last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E."},{"first_name":"Valentina","full_name":"Burskaia, Valentina","last_name":"Burskaia"},{"last_name":"Gelfand","full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S."}],"oa_version":"Published Version","abstract":[{"text":"Pan-genome statistics by species. (CSV 3 kb)","lang":"eng"}],"month":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808886.v1"}],"oa":1,"publisher":"Springer Nature","day":"12","year":"2019","date_created":"2021-08-12T08:44:49Z","related_material":{"record":[{"status":"public","id":"6898","relation":"used_in_publication"}]},"doi":"10.6084/m9.figshare.9808886.v1","date_published":"2019-09-12T00:00:00Z"},{"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_processing_charge":"No","external_id":{"isi":["000486348700001"]},"author":[{"last_name":"Ovaskainen","full_name":"Ovaskainen, Otso","first_name":"Otso"},{"last_name":"Rybicki","full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel"},{"first_name":"Nerea","last_name":"Abrego","full_name":"Abrego, Nerea"}],"title":"What can observational data reveal about metacommunity processes?","citation":{"ista":"Ovaskainen O, Rybicki J, Abrego N. 2019. What can observational data reveal about metacommunity processes? Ecography. 42(11), 1877–1886.","chicago":"Ovaskainen, Otso, Joel Rybicki, and Nerea Abrego. “What Can Observational Data Reveal about Metacommunity Processes?” Ecography. Wiley, 2019. https://doi.org/10.1111/ecog.04444.","ieee":"O. Ovaskainen, J. Rybicki, and N. Abrego, “What can observational data reveal about metacommunity processes?,” Ecography, vol. 42, no. 11. Wiley, pp. 1877–1886, 2019.","short":"O. Ovaskainen, J. Rybicki, N. Abrego, Ecography 42 (2019) 1877–1886.","apa":"Ovaskainen, O., Rybicki, J., & Abrego, N. (2019). What can observational data reveal about metacommunity processes? Ecography. Wiley. https://doi.org/10.1111/ecog.04444","ama":"Ovaskainen O, Rybicki J, Abrego N. What can observational data reveal about metacommunity processes? Ecography. 2019;42(11):1877-1886. doi:10.1111/ecog.04444","mla":"Ovaskainen, Otso, et al. “What Can Observational Data Reveal about Metacommunity Processes?” Ecography, vol. 42, no. 11, Wiley, 2019, pp. 1877–86, doi:10.1111/ecog.04444."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"Wiley","page":"1877-1886","date_created":"2019-10-08T13:01:24Z","date_published":"2019-11-01T00:00:00Z","doi":"10.1111/ecog.04444","year":"2019","isi":1,"has_accepted_license":"1","publication":"Ecography","day":"01","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":"6936","file_date_updated":"2020-07-14T12:47:45Z","department":[{"_id":"DaAl"}],"date_updated":"2023-08-30T06:57:25Z","ddc":["577"],"scopus_import":"1","intvolume":" 42","month":"11","abstract":[{"lang":"eng","text":"A key challenge for community ecology is to understand to what extent observational data can be used to infer the underlying community assembly processes. As different processes can lead to similar or even identical patterns, statistical analyses of non‐manipulative observational data never yield undisputable causal inference on the underlying processes. Still, most empirical studies in community ecology are based on observational data, and hence understanding under which circumstances such data can shed light on assembly processes is a central concern for community ecologists. We simulated a spatial agent‐based model that generates variation in metacommunity dynamics across multiple axes, including the four classic metacommunity paradigms as special cases. We further simulated a virtual ecologist who analysed snapshot data sampled from the simulations using eighteen output metrics derived from beta‐diversity and habitat variation indices, variation partitioning and joint species distribution modelling. Our results indicated two main axes of variation in the output metrics. The first axis of variation described whether the landscape has patchy or continuous variation, and thus was essentially independent of the properties of the species community. The second axis of variation related to the level of predictability of the metacommunity. The most predictable communities were niche‐based metacommunities inhabiting static landscapes with marked environmental heterogeneity, such as metacommunities following the species sorting paradigm or the mass effects paradigm. The most unpredictable communities were neutral‐based metacommunities inhabiting dynamics landscapes with little spatial heterogeneity, such as metacommunities following the neutral or patch sorting paradigms. The output metrics from joint species distribution modelling yielded generally the highest resolution to disentangle among the simulated scenarios. Yet, the different types of statistical approaches utilized in this study carried complementary information, and thus our results suggest that the most comprehensive evaluation of metacommunity structure can be obtained by combining them.\r\n"}],"oa_version":"Published Version","ec_funded":1,"issue":"11","volume":42,"publication_status":"published","publication_identifier":{"eissn":["1600-0587"],"issn":["0906-7590"]},"language":[{"iso":"eng"}],"file":[{"checksum":"6c9fbbd5ea8ce10ae93e55ad560a7bf9","file_id":"6937","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"ecog.04444.pdf","date_created":"2019-10-08T13:07:44Z","creator":"jrybicki","file_size":1682718,"date_updated":"2020-07-14T12:47:45Z"}]}]