[{"project":[{"call_identifier":"FWF","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation"}],"type":"preprint","doi":"10.48550/arXiv.1912.08579","department":[{"_id":"GaTk"}],"article_number":"1912.08579","citation":{"ama":"Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1912.08579\">10.48550/arXiv.1912.08579</a>","ista":"Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv, 1912.08579.","short":"W. Bialek, T. Gregor, G. Tkačik, ArXiv (n.d.).","chicago":"Bialek, William, Thomas Gregor, and Gašper Tkačik. “Action at a Distance in Transcriptional Regulation.” <i>ArXiv</i>. ArXiv, n.d. <a href=\"https://doi.org/10.48550/arXiv.1912.08579\">https://doi.org/10.48550/arXiv.1912.08579</a>.","apa":"Bialek, W., Gregor, T., &#38; Tkačik, G. (n.d.). Action at a distance in transcriptional regulation. <i>arXiv</i>. ArXiv. <a href=\"https://doi.org/10.48550/arXiv.1912.08579\">https://doi.org/10.48550/arXiv.1912.08579</a>","ieee":"W. Bialek, T. Gregor, and G. Tkačik, “Action at a distance in transcriptional regulation,” <i>arXiv</i>. ArXiv.","mla":"Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.” <i>ArXiv</i>, 1912.08579, ArXiv, doi:<a href=\"https://doi.org/10.48550/arXiv.1912.08579\">10.48550/arXiv.1912.08579</a>."},"author":[{"full_name":"Bialek, William","last_name":"Bialek","first_name":"William"},{"full_name":"Gregor, Thomas","last_name":"Gregor","first_name":"Thomas"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"month":"12","date_published":"2019-12-18T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.08579"}],"article_processing_charge":"No","date_created":"2020-02-28T10:57:08Z","abstract":[{"lang":"eng","text":"There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but interacting sites are embedded in a liquid droplet of proteins which condenses out of the surrounding solution. We argue that droplet-mediated interactions can account for crucial features of gene regulation only if the droplet is poised at a non-generic point in its phase diagram. We explore a minimal model that embodies this idea, show that this model has a natural mechanism for self-tuning, and suggest direct experimental tests. "}],"oa_version":"Preprint","arxiv":1,"publisher":"ArXiv","language":[{"iso":"eng"}],"_id":"7552","day":"18","publication_status":"submitted","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-05-19T10:54:36Z","year":"2019","publication":"arXiv","status":"public","external_id":{"arxiv":["1912.08579"]},"title":"Action at a distance in transcriptional regulation"},{"month":"09","citation":{"apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 15 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.9808802.v1\">https://doi.org/10.6084/m9.figshare.9808802.v1</a>","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 15 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.9808802.v1\">https://doi.org/10.6084/m9.figshare.9808802.v1</a>.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808802.v1\">10.6084/m9.figshare.9808802.v1</a>","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 15 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.9808802.v1\">10.6084/m9.figshare.9808802.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).","mla":"Sigalova, Olga M., et al. <i>Additional File 15 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.9808802.v1\">10.6084/m9.figshare.9808802.v1</a>.","ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019."},"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","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga","orcid":"0000-0003-1006-6639"},{"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."},{"full_name":"Burskaia, Valentina","last_name":"Burskaia","first_name":"Valentina"},{"last_name":"Gelfand","full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S."}],"department":[{"_id":"FyKo"}],"doi":"10.6084/m9.figshare.9808802.v1","type":"research_data_reference","abstract":[{"lang":"eng","text":"Distribution of OGs with mosaic phyletic patterns across species (complete genomes only). (CSV 7 kb)"}],"publisher":"Springer Nature","oa_version":"Published Version","day":"12","_id":"9890","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808802.v1"}],"article_processing_charge":"No","date_published":"2019-09-12T00:00:00Z","related_material":{"record":[{"id":"6898","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-11T14:26:40Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2026-04-03T09:39:40Z","year":"2019","oa":1,"title":"Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public"},{"type":"research_data_reference","doi":"10.6084/m9.figshare.9808814.v1","department":[{"_id":"FyKo"}],"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"},{"full_name":"Bochkareva, Olga","last_name":"Bochkareva","first_name":"Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin","first_name":"Pavel V."},{"first_name":"Vsevolod A.","full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov"},{"last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E."},{"first_name":"Valentina","full_name":"Burskaia, Valentina","last_name":"Burskaia"},{"last_name":"Gelfand","full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S."}],"citation":{"ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","mla":"Sigalova, Olga M., et al. <i>Additional File 16 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.9808814.v1\">10.6084/m9.figshare.9808814.v1</a>.","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, <a href=\"https://doi.org/10.6084/m9.figshare.9808814.v1\">10.6084/m9.figshare.9808814.v1</a>.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808814.v1\">10.6084/m9.figshare.9808814.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).","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. <a href=\"https://doi.org/10.6084/m9.figshare.9808814.v1\">https://doi.org/10.6084/m9.figshare.9808814.v1</a>.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 16 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.9808814.v1\">https://doi.org/10.6084/m9.figshare.9808814.v1</a>"},"month":"09","date_published":"2019-09-12T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808814.v1","open_access":"1"}],"article_processing_charge":"No","date_created":"2021-08-12T07:11:53Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6898"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Distribution of OGs with mosaic phyletic patterns across species (all genomes). (CSV 10 kb)"}],"publisher":"Springer Nature","day":"12","_id":"9892","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2026-04-03T09:39:40Z","year":"2019","status":"public","title":"Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction"},{"year":"2019","date_updated":"2026-04-03T09:39:41Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"title":"Additional file 17 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","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"},{"last_name":"Bochkareva","full_name":"Bochkareva, Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga","orcid":"0000-0003-1006-6639"},{"last_name":"Shelyakin","full_name":"Shelyakin, Pavel V.","first_name":"Pavel V."},{"first_name":"Vsevolod A.","last_name":"Filaretov","full_name":"Filaretov, Vsevolod A."},{"first_name":"Evgeny E.","full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov"},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S.","last_name":"Gelfand"}],"citation":{"mla":"Sigalova, Olga M., et al. <i>Additional File 17 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.9808820.v1\">10.6084/m9.figshare.9808820.v1</a>.","ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 17 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 17 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.9808820.v1\">https://doi.org/10.6084/m9.figshare.9808820.v1</a>.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 17 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.9808820.v1\">https://doi.org/10.6084/m9.figshare.9808820.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).","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 17 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808820.v1\">10.6084/m9.figshare.9808820.v1</a>","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 17 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.9808820.v1\">10.6084/m9.figshare.9808820.v1</a>."},"month":"09","doi":"10.6084/m9.figshare.9808820.v1","type":"research_data_reference","department":[{"_id":"FyKo"}],"day":"12","_id":"9893","publisher":"Springer Nature","abstract":[{"text":"Summary of peripheral genesa phyletic patterns and tree concordance. (CSV 26 kb)","lang":"eng"}],"oa_version":"Published Version","date_created":"2021-08-12T07:20:10Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6898"}]},"date_published":"2019-09-12T00:00:00Z","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808820.v1"}]},{"oa":1,"year":"2019","date_updated":"2026-04-03T09:39:41Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Additional file 18 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","department":[{"_id":"FyKo"}],"doi":"10.6084/m9.figshare.9808826.v1","type":"research_data_reference","month":"09","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."},{"full_name":"Bochkareva, Olga","last_name":"Bochkareva","orcid":"0000-0003-1006-6639","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"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"},{"first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S.","last_name":"Gelfand"}],"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 18 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.9808826.v1\">https://doi.org/10.6084/m9.figshare.9808826.v1</a>.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 18 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.9808826.v1\">https://doi.org/10.6084/m9.figshare.9808826.v1</a>","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 18 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.9808826.v1\">10.6084/m9.figshare.9808826.v1</a>.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 18 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808826.v1\">10.6084/m9.figshare.9808826.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).","mla":"Sigalova, Olga M., et al. <i>Additional File 18 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.9808826.v1\">10.6084/m9.figshare.9808826.v1</a>.","ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 18 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019."},"related_material":{"record":[{"id":"6898","relation":"used_in_publication","status":"public"}]},"date_created":"2021-08-12T07:25:07Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808826.v1"}],"article_processing_charge":"No","date_published":"2019-09-12T00:00:00Z","_id":"9894","day":"12","publisher":"Springer Nature","oa_version":"Published Version","abstract":[{"text":"Orthologous families (OFs) derived by MCL clustering of OGs. (CSV 189 kb)","lang":"eng"}]},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2019","date_updated":"2026-04-03T09:39:41Z","oa":1,"title":"Additional file 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","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."},{"full_name":"Bochkareva, Olga","last_name":"Bochkareva","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639"},{"full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin","first_name":"Pavel V."},{"first_name":"Vsevolod A.","full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov"},{"full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov","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."}],"citation":{"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:<a href=\"https://doi.org/10.6084/m9.figshare.9808835.v1\">10.6084/m9.figshare.9808835.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 19 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.9808835.v1\">10.6084/m9.figshare.9808835.v1</a>.","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. <a href=\"https://doi.org/10.6084/m9.figshare.9808835.v1\">https://doi.org/10.6084/m9.figshare.9808835.v1</a>.","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. <a href=\"https://doi.org/10.6084/m9.figshare.9808835.v1\">https://doi.org/10.6084/m9.figshare.9808835.v1</a>","ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","mla":"Sigalova, Olga M., et al. <i>Additional File 19 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.9808835.v1\">10.6084/m9.figshare.9808835.v1</a>."},"month":"09","type":"research_data_reference","doi":"10.6084/m9.figshare.9808835.v1","department":[{"_id":"FyKo"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Additional information on proteins from OG1. (CSV 30 kb)"}],"publisher":"Springer Nature","day":"12","_id":"9895","date_published":"2019-09-12T00:00:00Z","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808835.v1","open_access":"1"}],"date_created":"2021-08-12T07:44:52Z","related_material":{"record":[{"id":"6898","relation":"used_in_publication","status":"public"}]}},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2026-04-03T09:39:41Z","year":"2019","oa":1,"title":"Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","month":"09","citation":{"mla":"Sigalova, Olga M., et al. <i>Additional File 1 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.9808841.v1\">10.6084/m9.figshare.9808841.v1</a>.","ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 1 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 1 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.9808841.v1\">https://doi.org/10.6084/m9.figshare.9808841.v1</a>.","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. <a href=\"https://doi.org/10.6084/m9.figshare.9808841.v1\">https://doi.org/10.6084/m9.figshare.9808841.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).","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:<a href=\"https://doi.org/10.6084/m9.figshare.9808841.v1\">10.6084/m9.figshare.9808841.v1</a>","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, <a href=\"https://doi.org/10.6084/m9.figshare.9808841.v1\">10.6084/m9.figshare.9808841.v1</a>."},"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","id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga","full_name":"Bochkareva, Olga","last_name":"Bochkareva"},{"last_name":"Shelyakin","full_name":"Shelyakin, Pavel V.","first_name":"Pavel V."},{"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","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S.","last_name":"Gelfand"}],"department":[{"_id":"FyKo"}],"doi":"10.6084/m9.figshare.9808841.v1","type":"research_data_reference","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Summary of the analysed genomes. (CSV 24 kb)"}],"publisher":"Springer Nature","_id":"9896","day":"02","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808841.v1","open_access":"1"}],"article_processing_charge":"No","date_published":"2019-09-02T00:00:00Z","related_material":{"record":[{"id":"6898","relation":"used_in_publication","status":"public"}]},"date_created":"2021-08-12T07:50:53Z"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808850.v1"}],"article_processing_charge":"No","date_published":"2019-09-12T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6898"}]},"date_created":"2021-08-12T07:58:15Z","publisher":"Springer Nature","abstract":[{"text":"Frameshift and nonsense mutations near homopolymeric tracts of OG1 genes. Only 374 genes with typical length and domain composition were considered. (CSV 6 kb)","lang":"eng"}],"oa_version":"Published Version","_id":"9897","day":"12","department":[{"_id":"FyKo"}],"doi":"10.6084/m9.figshare.9808850.v1","type":"research_data_reference","month":"09","citation":{"ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","mla":"Sigalova, Olga M., et al. <i>Additional File 20 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.9808850.v1\">10.6084/m9.figshare.9808850.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).","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808850.v1\">10.6084/m9.figshare.9808850.v1</a>","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 20 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.9808850.v1\">10.6084/m9.figshare.9808850.v1</a>.","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 20 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.9808850.v1\">https://doi.org/10.6084/m9.figshare.9808850.v1</a>.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 20 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.9808850.v1\">https://doi.org/10.6084/m9.figshare.9808850.v1</a>"},"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."},{"full_name":"Bochkareva, Olga","last_name":"Bochkareva","first_name":"Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"last_name":"Shelyakin","full_name":"Shelyakin, Pavel V.","first_name":"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."},{"last_name":"Burskaia","full_name":"Burskaia, Valentina","first_name":"Valentina"},{"full_name":"Gelfand, Mikhail S.","last_name":"Gelfand","first_name":"Mikhail S."}],"status":"public","title":"Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2019","date_updated":"2026-04-03T09:39:41Z"},{"citation":{"ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","mla":"Sigalova, Olga M., et al. <i>Additional File 21 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.9808859.v1\">10.6084/m9.figshare.9808859.v1</a>.","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:<a href=\"https://doi.org/10.6084/m9.figshare.9808859.v1\">10.6084/m9.figshare.9808859.v1</a>","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, <a href=\"https://doi.org/10.6084/m9.figshare.9808859.v1\">10.6084/m9.figshare.9808859.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).","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. <a href=\"https://doi.org/10.6084/m9.figshare.9808859.v1\">https://doi.org/10.6084/m9.figshare.9808859.v1</a>.","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. <a href=\"https://doi.org/10.6084/m9.figshare.9808859.v1\">https://doi.org/10.6084/m9.figshare.9808859.v1</a>"},"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","orcid":"0000-0003-1006-6639","last_name":"Bochkareva","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."},{"last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E."},{"last_name":"Burskaia","full_name":"Burskaia, Valentina","first_name":"Valentina"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"month":"09","doi":"10.6084/m9.figshare.9808859.v1","type":"research_data_reference","department":[{"_id":"FyKo"}],"_id":"9898","day":"12","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"}],"date_created":"2021-08-12T08:10:23Z","related_material":{"record":[{"id":"6898","relation":"used_in_publication","status":"public"}]},"date_published":"2019-09-12T00:00:00Z","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808859.v1"}],"year":"2019","date_updated":"2026-04-03T09:39:41Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"title":"Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public"},{"year":"2019","date_updated":"2026-04-03T09:39:41Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"title":"Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","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"},{"last_name":"Bochkareva","full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"last_name":"Shelyakin","full_name":"Shelyakin, Pavel V.","first_name":"Pavel V."},{"full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov","first_name":"Vsevolod A."},{"first_name":"Evgeny E.","last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E."},{"full_name":"Burskaia, Valentina","last_name":"Burskaia","first_name":"Valentina"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"citation":{"ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","mla":"Sigalova, Olga M., et al. <i>Additional File 2 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.9808865.v1\">10.6084/m9.figshare.9808865.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 2 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.9808865.v1\">10.6084/m9.figshare.9808865.v1</a>.","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:<a href=\"https://doi.org/10.6084/m9.figshare.9808865.v1\">10.6084/m9.figshare.9808865.v1</a>","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. <a href=\"https://doi.org/10.6084/m9.figshare.9808865.v1\">https://doi.org/10.6084/m9.figshare.9808865.v1</a>","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. <a href=\"https://doi.org/10.6084/m9.figshare.9808865.v1\">https://doi.org/10.6084/m9.figshare.9808865.v1</a>."},"month":"09","doi":"10.6084/m9.figshare.9808865.v1","type":"research_data_reference","department":[{"_id":"FyKo"}],"_id":"9899","day":"12","publisher":"Springer Nature","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Summary of orthologous groups (OGs) for 227 genomes of genus Chlamydia. (CSV 362 kb)"}],"date_created":"2021-08-12T08:18:09Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6898"}]},"date_published":"2019-09-12T00:00:00Z","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808865.v1","open_access":"1"}]},{"title":"Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","status":"public","year":"2019","date_updated":"2026-04-03T09:39:41Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"day":"12","_id":"9900","abstract":[{"lang":"eng","text":"Pan-genome statistics by species. (CSV 3 kb)"}],"publisher":"Springer Nature","oa_version":"Published Version","date_created":"2021-08-12T08:44:49Z","related_material":{"record":[{"id":"6898","relation":"used_in_publication","status":"public"}]},"date_published":"2019-09-12T00:00:00Z","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808886.v1"}],"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","last_name":"Bochkareva","full_name":"Bochkareva, Olga"},{"last_name":"Shelyakin","full_name":"Shelyakin, Pavel V.","first_name":"Pavel V."},{"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","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"last_name":"Gelfand","full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S."}],"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. <a href=\"https://doi.org/10.6084/m9.figshare.9808886.v1\">https://doi.org/10.6084/m9.figshare.9808886.v1</a>.","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. <a href=\"https://doi.org/10.6084/m9.figshare.9808886.v1\">https://doi.org/10.6084/m9.figshare.9808886.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 5 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.9808886.v1\">10.6084/m9.figshare.9808886.v1</a>.","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:<a href=\"https://doi.org/10.6084/m9.figshare.9808886.v1\">10.6084/m9.figshare.9808886.v1</a>","mla":"Sigalova, Olga M., et al. <i>Additional File 5 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.9808886.v1\">10.6084/m9.figshare.9808886.v1</a>.","ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019."},"month":"09","doi":"10.6084/m9.figshare.9808886.v1","type":"research_data_reference","department":[{"_id":"FyKo"}]},{"oa":1,"year":"2019","date_updated":"2026-04-03T09:39:41Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","department":[{"_id":"FyKo"}],"doi":"10.6084/m9.figshare.9808907.v1","type":"research_data_reference","month":"09","citation":{"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>.","ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 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 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\">https://doi.org/10.6084/m9.figshare.9808907.v1</a>","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. <a href=\"https://doi.org/10.6084/m9.figshare.9808907.v1\">https://doi.org/10.6084/m9.figshare.9808907.v1</a>.","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:<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>."},"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."},{"last_name":"Bochkareva","full_name":"Bochkareva, Olga","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639"},{"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","full_name":"Burskaia, Valentina","last_name":"Burskaia"},{"last_name":"Gelfand","full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S."}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6898"}]},"date_created":"2021-08-12T10:54:03Z","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808907.v1"}],"date_published":"2019-09-12T00:00:00Z","day":"12","_id":"9901","oa_version":"Published Version","publisher":"Springer Nature","abstract":[{"lang":"eng","text":"Clusters of Orthologous Genes (COGs) and corresponding functional categories assigned to OGs. (CSV 117 kb)"}]},{"publication":"Probability Theory and Related Fields","issue":"3-4","corr_author":"1","intvolume":"       173","oa":1,"has_accepted_license":"1","publication_status":"published","file_date_updated":"2020-07-14T12:46:03Z","year":"2019","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":173,"date_created":"2018-12-11T11:45:48Z","publist_id":"7546","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","language":[{"iso":"eng"}],"_id":"319","publisher":"Springer","department":[{"_id":"JaMa"}],"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"author":[{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","last_name":"Gerencser","full_name":"Gerencser, Mate"},{"last_name":"Hairer","full_name":"Hairer, Martin","first_name":"Martin"}],"status":"public","quality_controlled":"1","title":"Singular SPDEs in domains with boundaries","page":"697–758","external_id":{"isi":["000463613800001"]},"article_type":"original","ddc":["510"],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-04-03T09:45:34Z","acknowledgement":"MG thanks the support of the LMS Postdoctoral Mobility Grant.\r\n\r\n","file":[{"file_name":"2018_ProbTheory_Gerencser.pdf","date_updated":"2020-07-14T12:46:03Z","relation":"main_file","access_level":"open_access","creator":"dernst","checksum":"288d16ef7291242f485a9660979486e3","content_type":"application/pdf","file_id":"5722","file_size":893182,"date_created":"2018-12-17T16:25:24Z"}],"isi":1,"date_published":"2019-04-01T00:00:00Z","day":"01","abstract":[{"lang":"eng","text":"We study spaces of modelled distributions with singular behaviour near the boundary of a domain that, in the context of the theory of regularity structures, allow one to give robust solution theories for singular stochastic PDEs with boundary conditions. The calculus of modelled distributions established in Hairer (Invent Math 198(2):269–504, 2014. https://doi.org/10.1007/s00222-014-0505-4) is extended to this setting. We formulate and solve fixed point problems in these spaces with a class of kernels that is sufficiently large to cover in particular the Dirichlet and Neumann heat kernels. These results are then used to provide solution theories for the KPZ equation with Dirichlet and Neumann boundary conditions and for the 2D generalised parabolic Anderson model with Dirichlet boundary conditions. In the case of the KPZ equation with Neumann boundary conditions, we show that, depending on the class of mollifiers one considers, a “boundary renormalisation” takes place. In other words, there are situations in which a certain boundary condition is applied to an approximation to the KPZ equation, but the limiting process is the Hopf–Cole solution to the KPZ equation with a different boundary condition."}],"oa_version":"Published Version","type":"journal_article","doi":"10.1007/s00440-018-0841-1","month":"04","citation":{"apa":"Gerencser, M., &#38; Hairer, M. (2019). Singular SPDEs in domains with boundaries. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-018-0841-1\">https://doi.org/10.1007/s00440-018-0841-1</a>","chicago":"Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.” <i>Probability Theory and Related Fields</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s00440-018-0841-1\">https://doi.org/10.1007/s00440-018-0841-1</a>.","ama":"Gerencser M, Hairer M. Singular SPDEs in domains with boundaries. <i>Probability Theory and Related Fields</i>. 2019;173(3-4):697–758. doi:<a href=\"https://doi.org/10.1007/s00440-018-0841-1\">10.1007/s00440-018-0841-1</a>","ista":"Gerencser M, Hairer M. 2019. Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. 173(3–4), 697–758.","short":"M. Gerencser, M. Hairer, Probability Theory and Related Fields 173 (2019) 697–758.","mla":"Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.” <i>Probability Theory and Related Fields</i>, vol. 173, no. 3–4, Springer, 2019, pp. 697–758, doi:<a href=\"https://doi.org/10.1007/s00440-018-0841-1\">10.1007/s00440-018-0841-1</a>.","ieee":"M. Gerencser and M. Hairer, “Singular SPDEs in domains with boundaries,” <i>Probability Theory and Related Fields</i>, vol. 173, no. 3–4. Springer, pp. 697–758, 2019."},"publication_identifier":{"eissn":["1432-2064"],"issn":["0178-8051"]}},{"publication":"Linear Algebra and Its Applications","intvolume":"       576","corr_author":"1","publication_status":"published","ec_funded":1,"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":576,"year":"2019","publist_id":"7424","article_processing_charge":"No","scopus_import":"1","date_created":"2018-12-11T11:46:17Z","publisher":"Elsevier","_id":"405","language":[{"iso":"eng"}],"department":[{"_id":"LaEr"}],"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Virosztek","full_name":"Virosztek, Daniel","first_name":"Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1109-5511"}],"quality_controlled":"1","status":"public","page":"67-78","external_id":{"isi":["000470955300005"],"arxiv":["1712.05324"]},"title":"Jointly convex quantum Jensen divergences","article_type":"original","acknowledgement":"The author was supported by the ISTFELLOW program of the Institute of Science and Technology Austria (project code IC1027FELL01) and partially supported by the Hungarian National Research, Development and Innovation Office – NKFIH (grant no. K124152)","date_updated":"2025-04-15T06:50:00Z","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1712.05324","open_access":"1"}],"date_published":"2019-09-01T00:00:00Z","abstract":[{"lang":"eng","text":"We investigate the quantum Jensen divergences from the viewpoint of joint convexity. It turns out that the set of the functions which generate jointly convex quantum Jensen divergences on positive matrices coincides with the Matrix Entropy Class which has been introduced by Chen and Tropp quite recently."}],"oa_version":"Preprint","arxiv":1,"day":"01","doi":"10.1016/j.laa.2018.03.002","type":"journal_article","month":"09","citation":{"mla":"Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” <i>Linear Algebra and Its Applications</i>, vol. 576, Elsevier, 2019, pp. 67–78, doi:<a href=\"https://doi.org/10.1016/j.laa.2018.03.002\">10.1016/j.laa.2018.03.002</a>.","ieee":"D. Virosztek, “Jointly convex quantum Jensen divergences,” <i>Linear Algebra and Its Applications</i>, vol. 576. Elsevier, pp. 67–78, 2019.","chicago":"Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” <i>Linear Algebra and Its Applications</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.laa.2018.03.002\">https://doi.org/10.1016/j.laa.2018.03.002</a>.","apa":"Virosztek, D. (2019). Jointly convex quantum Jensen divergences. <i>Linear Algebra and Its Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.laa.2018.03.002\">https://doi.org/10.1016/j.laa.2018.03.002</a>","short":"D. Virosztek, Linear Algebra and Its Applications 576 (2019) 67–78.","ama":"Virosztek D. Jointly convex quantum Jensen divergences. <i>Linear Algebra and Its Applications</i>. 2019;576:67-78. doi:<a href=\"https://doi.org/10.1016/j.laa.2018.03.002\">10.1016/j.laa.2018.03.002</a>","ista":"Virosztek D. 2019. Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. 576, 67–78."}},{"_id":"429","language":[{"iso":"eng"}],"publisher":"Springer","date_created":"2018-12-11T11:46:25Z","article_processing_charge":"Yes (via OA deal)","publist_id":"7394","scopus_import":"1","author":[{"last_name":"Ajanki","full_name":"Ajanki, Oskari H","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","first_name":"Oskari H"},{"last_name":"Erdös","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László"},{"full_name":"Krüger, Torben H","last_name":"Krüger","first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297"}],"department":[{"_id":"LaEr"}],"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"intvolume":"       173","corr_author":"1","publication":"Probability Theory and Related Fields","issue":"1-2","file_date_updated":"2020-07-14T12:46:26Z","year":"2019","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":173,"oa":1,"has_accepted_license":"1","publication_status":"published","ec_funded":1,"day":"01","abstract":[{"text":"We consider real symmetric or complex hermitian random matrices with correlated entries. We prove local laws for the resolvent and universality of the local eigenvalue statistics in the bulk of the spectrum. The correlations have fast decay but are otherwise of general form. The key novelty is the detailed stability analysis of the corresponding matrix valued Dyson equation whose solution is the deterministic limit of the resolvent.","lang":"eng"}],"oa_version":"Published Version","file":[{"date_created":"2018-12-17T16:12:08Z","file_size":1201840,"file_id":"5720","content_type":"application/pdf","creator":"dernst","checksum":"f9354fa5c71f9edd17132588f0dc7d01","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:46:26Z","file_name":"2018_ProbTheory_Ajanki.pdf"}],"isi":1,"date_published":"2019-02-01T00:00:00Z","month":"02","publication_identifier":{"eissn":["1432-2064"],"issn":["0178-8051"]},"citation":{"mla":"Ajanki, Oskari H., et al. “Stability of the Matrix Dyson Equation and Random Matrices with Correlations.” <i>Probability Theory and Related Fields</i>, vol. 173, no. 1–2, Springer, 2019, pp. 293–373, doi:<a href=\"https://doi.org/10.1007/s00440-018-0835-z\">10.1007/s00440-018-0835-z</a>.","ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Stability of the matrix Dyson equation and random matrices with correlations,” <i>Probability Theory and Related Fields</i>, vol. 173, no. 1–2. Springer, pp. 293–373, 2019.","chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Stability of the Matrix Dyson Equation and Random Matrices with Correlations.” <i>Probability Theory and Related Fields</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s00440-018-0835-z\">https://doi.org/10.1007/s00440-018-0835-z</a>.","apa":"Ajanki, O. H., Erdös, L., &#38; Krüger, T. H. (2019). Stability of the matrix Dyson equation and random matrices with correlations. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-018-0835-z\">https://doi.org/10.1007/s00440-018-0835-z</a>","ama":"Ajanki OH, Erdös L, Krüger TH. Stability of the matrix Dyson equation and random matrices with correlations. <i>Probability Theory and Related Fields</i>. 2019;173(1-2):293–373. doi:<a href=\"https://doi.org/10.1007/s00440-018-0835-z\">10.1007/s00440-018-0835-z</a>","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 173 (2019) 293–373.","ista":"Ajanki OH, Erdös L, Krüger TH. 2019. Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. 173(1–2), 293–373."},"type":"journal_article","doi":"10.1007/s00440-018-0835-z","title":"Stability of the matrix Dyson equation and random matrices with correlations","page":"293–373","external_id":{"isi":["000459396500007"]},"status":"public","quality_controlled":"1","date_updated":"2026-04-03T09:46:51Z","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\n","article_type":"original","ddc":["510"],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"date_published":"2019-04-15T00:00:00Z","isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.01999"}],"oa_version":"Preprint","abstract":[{"text":"An upper bound sieve for rational points on suitable varieties isdeveloped, together with applications tocounting rational points in thin sets,to local solubility in families, and to the notion of “friable” rational pointswith respect to divisors. In the special case of quadrics, sharper estimates areobtained by developing a version of the Selberg sieve for rational points.","lang":"eng"}],"arxiv":1,"day":"15","type":"journal_article","doi":"10.1090/tran/7514","publication_identifier":{"issn":["0002-9947"],"eissn":["1088-6850"]},"citation":{"mla":"Browning, Timothy D., and Daniel Loughran. “Sieving Rational Points on Varieties.” <i>Transactions of the American Mathematical Society</i>, vol. 371, no. 8, American Mathematical Society, 2019, pp. 5757–85, doi:<a href=\"https://doi.org/10.1090/tran/7514\">10.1090/tran/7514</a>.","ieee":"T. D. Browning and D. Loughran, “Sieving rational points on varieties,” <i>Transactions of the American Mathematical Society</i>, vol. 371, no. 8. American Mathematical Society, pp. 5757–5785, 2019.","apa":"Browning, T. D., &#38; Loughran, D. (2019). Sieving rational points on varieties. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/7514\">https://doi.org/10.1090/tran/7514</a>","chicago":"Browning, Timothy D, and Daniel Loughran. “Sieving Rational Points on Varieties.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2019. <a href=\"https://doi.org/10.1090/tran/7514\">https://doi.org/10.1090/tran/7514</a>.","short":"T.D. Browning, D. Loughran, Transactions of the American Mathematical Society 371 (2019) 5757–5785.","ama":"Browning TD, Loughran D. Sieving rational points on varieties. <i>Transactions of the American Mathematical Society</i>. 2019;371(8):5757-5785. doi:<a href=\"https://doi.org/10.1090/tran/7514\">10.1090/tran/7514</a>","ista":"Browning TD, Loughran D. 2019. Sieving rational points on varieties. Transactions of the American Mathematical Society. 371(8), 5757–5785."},"month":"04","quality_controlled":"1","status":"public","external_id":{"arxiv":["1705.01999"],"isi":["000464034200019"]},"page":"5757-5785","title":"Sieving rational points on varieties","date_updated":"2025-07-10T11:51:20Z","scopus_import":"1","publist_id":"7746","article_processing_charge":"No","date_created":"2018-12-11T11:45:01Z","publisher":"American Mathematical Society","_id":"175","language":[{"iso":"eng"}],"department":[{"_id":"TiBr"}],"author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning","full_name":"Browning, Timothy D"},{"full_name":"Loughran, Daniel","last_name":"Loughran","first_name":"Daniel"}],"issue":"8","publication":"Transactions of the American Mathematical Society","intvolume":"       371","publication_status":"published","oa":1,"volume":371,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019"},{"oa":1,"publication_status":"published","year":"2019","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":4,"publication":"Proceedings of the ACM on Programming Languages","issue":"POPL","intvolume":"         4","author":[{"first_name":"Michael Joachim","id":"510d3901-2a03-11ee-914d-d9ae9011f0a7","last_name":"Sammler","full_name":"Sammler, Michael Joachim"},{"first_name":"Deepak","full_name":"Garg, Deepak","last_name":"Garg"},{"last_name":"Dreyer","full_name":"Dreyer, Derek","first_name":"Derek"},{"last_name":"Litak","full_name":"Litak, Tadeusz","first_name":"Tadeusz"}],"date_created":"2024-09-05T08:36:52Z","article_processing_charge":"No","scopus_import":"1","language":[{"iso":"eng"}],"_id":"17506","publisher":"Association for Computing Machinery","article_type":"original","date_updated":"2024-09-10T09:58:57Z","status":"public","quality_controlled":"1","title":"The high-level benefits of low-level sandboxing","page":"1-32","doi":"10.1145/3371100","type":"journal_article","extern":"1","month":"12","publication_identifier":{"issn":["2475-1421"]},"citation":{"mla":"Sammler, Michael Joachim, et al. “The High-Level Benefits of Low-Level Sandboxing.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 4, no. POPL, Association for Computing Machinery, 2019, pp. 1–32, doi:<a href=\"https://doi.org/10.1145/3371100\">10.1145/3371100</a>.","ieee":"M. J. Sammler, D. Garg, D. Dreyer, and T. Litak, “The high-level benefits of low-level sandboxing,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 4, no. POPL. Association for Computing Machinery, pp. 1–32, 2019.","chicago":"Sammler, Michael Joachim, Deepak Garg, Derek Dreyer, and Tadeusz Litak. “The High-Level Benefits of Low-Level Sandboxing.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2019. <a href=\"https://doi.org/10.1145/3371100\">https://doi.org/10.1145/3371100</a>.","apa":"Sammler, M. J., Garg, D., Dreyer, D., &#38; Litak, T. (2019). The high-level benefits of low-level sandboxing. <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3371100\">https://doi.org/10.1145/3371100</a>","ista":"Sammler MJ, Garg D, Dreyer D, Litak T. 2019. The high-level benefits of low-level sandboxing. Proceedings of the ACM on Programming Languages. 4(POPL), 1–32.","short":"M.J. Sammler, D. Garg, D. Dreyer, T. Litak, Proceedings of the ACM on Programming Languages 4 (2019) 1–32.","ama":"Sammler MJ, Garg D, Dreyer D, Litak T. The high-level benefits of low-level sandboxing. <i>Proceedings of the ACM on Programming Languages</i>. 2019;4(POPL):1-32. doi:<a href=\"https://doi.org/10.1145/3371100\">10.1145/3371100</a>"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3371100"}],"date_published":"2019-12-20T00:00:00Z","day":"20","abstract":[{"lang":"eng","text":"Sandboxing is a common technique that allows low-level, untrusted components to safely interact with trusted code. However, previous work has only investigated the low-level memory isolation guarantees of sandboxing, leaving open the question of the end-to-end guarantees that sandboxing affords programmers. In this paper, we fill this gap by showing that sandboxing enables reasoning about the known concept of robust safety, i.e., safety of the trusted code even in the presence of arbitrary untrusted code. To do this, we first present an idealized operational semantics for a language that combines trusted code with untrusted code. Sandboxing is built into our semantics. Then, we prove that safety properties of the trusted code (as enforced through a rich type system) are upheld in the presence of arbitrary untrusted code, so long as all interactions with untrusted code occur at the “any” type (a type inhabited by all values). Finally, to alleviate the burden of having to interact with untrusted code at only the “any” type, we formalize and prove safe several wrappers, which automatically convert values between the “any” type and much richer types. All our results are mechanized in the Coq proof assistant."}],"oa_version":"Published Version"},{"intvolume":"       486","publication":"Monthly Notices of the Royal Astronomical Society","issue":"2","year":"2019","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":486,"oa":1,"publication_status":"published","_id":"17510","language":[{"iso":"eng"}],"publisher":"Oxford University Press","date_created":"2024-09-05T08:49:24Z","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Abruzzo, Matthew W","last_name":"Abruzzo","first_name":"Matthew W"},{"full_name":"Haiman, Zoltán","last_name":"Haiman","first_name":"Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36"}],"title":"The impact of photometric redshift errors on lensing statistics in ray-tracing simulations","page":"2730-2753","status":"public","quality_controlled":"1","date_updated":"2024-09-10T12:49:04Z","article_type":"original","day":"18","oa_version":"Published Version","abstract":[{"text":"Weak lensing surveys are reaching sensitivities at which uncertainties in the galaxy redshift distributions n(z) from photo-z errors degrade cosmological constraints. We use ray-tracing simulations and a simple treatment of photo-z errors to assess cosmological parameter biases from uncertainties in n(z) in an LSST-like survey. We use lensing peak counts and the power spectrum to infer cosmological parameters, and find that the latter is somewhat more resilient to photo-z errors. We place conservative lower limits on the survey size at which different types of photo-z errors significantly degrade (${\\sim }50{{\\ \\rm per\\ cent}}$) ΛCDM (cold dark matter, wCDM) parameter constraints. A residual constant photo-z bias of |δz| &amp;lt; 0.003(1 + z), the current LSST requirement, does not significantly degrade surveys smaller than ≈1300 (≈490) deg2 using peaks and ≈6500 (≈4900) deg2 using the power spectrum. Surveys smaller than ≈920 (≈450) deg2 and ≈4600 (≈4000) deg2 avoid 25 per cent degradation. Adopting a recent prediction for LSST’s full photo-z probability distribution function (PDF), we find that simply approximating n(z) with the photo-z galaxy distribution computed from this PDF significantly degrades surveys as small as ≈60 (≈65) deg2 using peaks or the power spectrum. If the centroid bias in each tomographic bin is removed from the photo-z galaxy distribution, using peaks or the power spectrum still significantly degrades surveys larger than ≈200 (≈255) or ≈248 (≈315) deg2; 25 per cent degradations occur at survey sizes of ≈140 (≈180) deg2 or ≈165 (≈210) deg2. These results imply that the expected broad photo-z PDF significantly biases parameters, which must be further mitigated using more sophisticated photo-z treatments.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/mnras/stz1016"}],"date_published":"2019-04-18T00:00:00Z","extern":"1","month":"04","citation":{"apa":"Abruzzo, M. W., &#38; Haiman, Z. (2019). The impact of photometric redshift errors on lensing statistics in ray-tracing simulations. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stz1016\">https://doi.org/10.1093/mnras/stz1016</a>","chicago":"Abruzzo, Matthew W, and Zoltán Haiman. “The Impact of Photometric Redshift Errors on Lensing Statistics in Ray-Tracing Simulations.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/mnras/stz1016\">https://doi.org/10.1093/mnras/stz1016</a>.","ama":"Abruzzo MW, Haiman Z. The impact of photometric redshift errors on lensing statistics in ray-tracing simulations. <i>Monthly Notices of the Royal Astronomical Society</i>. 2019;486(2):2730-2753. doi:<a href=\"https://doi.org/10.1093/mnras/stz1016\">10.1093/mnras/stz1016</a>","short":"M.W. Abruzzo, Z. Haiman, Monthly Notices of the Royal Astronomical Society 486 (2019) 2730–2753.","ista":"Abruzzo MW, Haiman Z. 2019. The impact of photometric redshift errors on lensing statistics in ray-tracing simulations. Monthly Notices of the Royal Astronomical Society. 486(2), 2730–2753.","mla":"Abruzzo, Matthew W., and Zoltán Haiman. “The Impact of Photometric Redshift Errors on Lensing Statistics in Ray-Tracing Simulations.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 486, no. 2, Oxford University Press, 2019, pp. 2730–53, doi:<a href=\"https://doi.org/10.1093/mnras/stz1016\">10.1093/mnras/stz1016</a>.","ieee":"M. W. Abruzzo and Z. Haiman, “The impact of photometric redshift errors on lensing statistics in ray-tracing simulations,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 486, no. 2. Oxford University Press, pp. 2730–2753, 2019."},"publication_identifier":{"issn":["0035-8711","1365-2966"]},"type":"journal_article","doi":"10.1093/mnras/stz1016"},{"external_id":{"arxiv":["1812.08206"]},"title":"Constraining neutrino mass with weak lensing Minkowski Functionals","quality_controlled":"1","status":"public","date_updated":"2024-09-10T13:10:34Z","article_type":"original","arxiv":1,"oa_version":"Preprint","day":"07","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1812.08206","open_access":"1"}],"date_published":"2019-06-07T00:00:00Z","month":"06","publication_identifier":{"issn":["1475-7516"]},"citation":{"apa":"Marques, G. A., Liu, J., Matilla, J. M. Z., Haiman, Z., Bernui, A., &#38; Novaes, C. P. (2019). Constraining neutrino mass with weak lensing Minkowski Functionals. <i>Journal of Cosmology and Astroparticle Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1475-7516/2019/06/019\">https://doi.org/10.1088/1475-7516/2019/06/019</a>","chicago":"Marques, Gabriela A., Jia Liu, José Manuel Zorrilla Matilla, Zoltán Haiman, Armando Bernui, and Camila P. Novaes. “Constraining Neutrino Mass with Weak Lensing Minkowski Functionals.” <i>Journal of Cosmology and Astroparticle Physics</i>. IOP Publishing, 2019. <a href=\"https://doi.org/10.1088/1475-7516/2019/06/019\">https://doi.org/10.1088/1475-7516/2019/06/019</a>.","short":"G.A. Marques, J. Liu, J.M.Z. Matilla, Z. Haiman, A. Bernui, C.P. Novaes, Journal of Cosmology and Astroparticle Physics 2019 (2019).","ama":"Marques GA, Liu J, Matilla JMZ, Haiman Z, Bernui A, Novaes CP. Constraining neutrino mass with weak lensing Minkowski Functionals. <i>Journal of Cosmology and Astroparticle Physics</i>. 2019;2019(06). doi:<a href=\"https://doi.org/10.1088/1475-7516/2019/06/019\">10.1088/1475-7516/2019/06/019</a>","ista":"Marques GA, Liu J, Matilla JMZ, Haiman Z, Bernui A, Novaes CP. 2019. Constraining neutrino mass with weak lensing Minkowski Functionals. Journal of Cosmology and Astroparticle Physics. 2019(06), 019.","mla":"Marques, Gabriela A., et al. “Constraining Neutrino Mass with Weak Lensing Minkowski Functionals.” <i>Journal of Cosmology and Astroparticle Physics</i>, vol. 2019, no. 06, 019, IOP Publishing, 2019, doi:<a href=\"https://doi.org/10.1088/1475-7516/2019/06/019\">10.1088/1475-7516/2019/06/019</a>.","ieee":"G. A. Marques, J. Liu, J. M. Z. Matilla, Z. Haiman, A. Bernui, and C. P. Novaes, “Constraining neutrino mass with weak lensing Minkowski Functionals,” <i>Journal of Cosmology and Astroparticle Physics</i>, vol. 2019, no. 06. IOP Publishing, 2019."},"extern":"1","doi":"10.1088/1475-7516/2019/06/019","type":"journal_article","intvolume":"      2019","issue":"06","publication":"Journal of Cosmology and Astroparticle Physics","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":2019,"year":"2019","publication_status":"published","oa":1,"publisher":"IOP Publishing","language":[{"iso":"eng"}],"_id":"17511","article_processing_charge":"No","scopus_import":"1","date_created":"2024-09-05T08:50:20Z","author":[{"first_name":"Gabriela A.","last_name":"Marques","full_name":"Marques, Gabriela A."},{"full_name":"Liu, Jia","last_name":"Liu","first_name":"Jia"},{"last_name":"Matilla","full_name":"Matilla, José Manuel Zorrilla","first_name":"José Manuel Zorrilla"},{"full_name":"Haiman, Zoltán","last_name":"Haiman","first_name":"Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36"},{"first_name":"Armando","full_name":"Bernui, Armando","last_name":"Bernui"},{"first_name":"Camila P.","full_name":"Novaes, Camila P.","last_name":"Novaes"}],"article_number":"019"},{"author":[{"last_name":"Corley","full_name":"Corley, K Rainer","first_name":"K Rainer"},{"first_name":"Imre","full_name":"Bartos, Imre","last_name":"Bartos"},{"last_name":"Singer","full_name":"Singer, Leo P","first_name":"Leo P"},{"first_name":"Andrew R","last_name":"Williamson","full_name":"Williamson, Andrew R"},{"first_name":"Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","full_name":"Haiman, Zoltán","last_name":"Haiman"},{"first_name":"Bence","full_name":"Kocsis, Bence","last_name":"Kocsis"},{"first_name":"Samaya","full_name":"Nissanke, Samaya","last_name":"Nissanke"},{"last_name":"Márka","full_name":"Márka, Zsuzsa","first_name":"Zsuzsa"},{"first_name":"Szabolcs","last_name":"Márka","full_name":"Márka, Szabolcs"}],"date_created":"2024-09-05T08:51:22Z","article_processing_charge":"No","scopus_import":"1","_id":"17512","language":[{"iso":"eng"}],"publisher":"Oxford University Press","oa":1,"publication_status":"published","year":"2019","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":488,"publication":"Monthly Notices of the Royal Astronomical Society","issue":"3","intvolume":"       488","doi":"10.1093/mnras/stz2072","type":"journal_article","extern":"1","month":"07","citation":{"ieee":"K. R. Corley <i>et al.</i>, “Localization of binary black hole mergers with known inclination,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 488, no. 3. Oxford University Press, pp. 4459–4463, 2019.","mla":"Corley, K. Rainer, et al. “Localization of Binary Black Hole Mergers with Known Inclination.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 488, no. 3, Oxford University Press, 2019, pp. 4459–63, doi:<a href=\"https://doi.org/10.1093/mnras/stz2072\">10.1093/mnras/stz2072</a>.","short":"K.R. Corley, I. Bartos, L.P. Singer, A.R. Williamson, Z. Haiman, B. Kocsis, S. Nissanke, Z. Márka, S. Márka, Monthly Notices of the Royal Astronomical Society 488 (2019) 4459–4463.","ista":"Corley KR, Bartos I, Singer LP, Williamson AR, Haiman Z, Kocsis B, Nissanke S, Márka Z, Márka S. 2019. Localization of binary black hole mergers with known inclination. Monthly Notices of the Royal Astronomical Society. 488(3), 4459–4463.","ama":"Corley KR, Bartos I, Singer LP, et al. Localization of binary black hole mergers with known inclination. <i>Monthly Notices of the Royal Astronomical Society</i>. 2019;488(3):4459-4463. doi:<a href=\"https://doi.org/10.1093/mnras/stz2072\">10.1093/mnras/stz2072</a>","chicago":"Corley, K Rainer, Imre Bartos, Leo P Singer, Andrew R Williamson, Zoltán Haiman, Bence Kocsis, Samaya Nissanke, Zsuzsa Márka, and Szabolcs Márka. “Localization of Binary Black Hole Mergers with Known Inclination.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/mnras/stz2072\">https://doi.org/10.1093/mnras/stz2072</a>.","apa":"Corley, K. R., Bartos, I., Singer, L. P., Williamson, A. R., Haiman, Z., Kocsis, B., … Márka, S. (2019). Localization of binary black hole mergers with known inclination. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stz2072\">https://doi.org/10.1093/mnras/stz2072</a>"},"publication_identifier":{"issn":["0035-8711","1365-2966"]},"main_file_link":[{"url":"https://doi.org/10.1093/mnras/stz2072","open_access":"1"}],"date_published":"2019-07-30T00:00:00Z","day":"30","abstract":[{"text":"The localization of stellar-mass binary black hole mergers using gravitational waves is critical in understanding the properties of the binaries’ host galaxies, observing possible electromagnetic emission from the mergers, or using them as a cosmological distance ladder. The precision of this localization can be substantially increased with prior astrophysical information about the binary system. In particular, constraining the inclination of the binary can reduce the distance uncertainty of the source. Here, we present the first realistic set of localizations for binary black hole mergers, including different prior constraints on the binaries’ inclinations. We find that prior information on the inclination can reduce the localization volume by a factor of 3. We discuss two astrophysical scenarios of interest: (i) follow-up searches for beamed electromagnetic/neutrino counterparts and (ii) mergers in the accretion discs of active galactic nuclei.","lang":"eng"}],"oa_version":"Published Version","article_type":"original","date_updated":"2024-09-10T13:26:28Z","status":"public","quality_controlled":"1","title":"Localization of binary black hole mergers with known inclination","page":"4459-4463"}]