{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T11:22:22Z","timestamp":1773660142166,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2019,5,22]],"date-time":"2019-05-22T00:00:00Z","timestamp":1558483200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["17-74-10143"],"award-info":[{"award-number":["17-74-10143"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Recent development of Hi-C technique, a biochemical method to study 3D genome architecture, provided large amount of information describing spatial organization of chromosomes in different cell types and species. While multiple tools are available for analysis and comparison of Hi-C data of different cell types, there are almost no resources for systematic interspecies comparison.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To fill this gap, we developed C-InterSecture, a computational pipeline allowing systematic comparison of genome architecture between species. C-InterSecture allows statistical comparison of contact frequencies of individual pairs of loci, as well as interspecies comparison of contacts pattern within defined genomic regions, i.e. topologically associated domains. We employed C-InterSecture to compare mammalian and avian genome organization and showed how evolutionary changes of genomic distance affect 3D architecture of vertebrate\u2019s genome.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>C-InterSecture is implemented as a collection of python scripts freely available on GitHub repository at https:\/\/github.com\/NuriddinovMA\/C-InterSecture. Jucebox-compatible .hic files produced by C-InterSecture are available at http:\/\/genedev.bionet.nsc.ru\/site\/CIntersecture.html.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz415","type":"journal-article","created":{"date-parts":[[2019,5,14]],"date-time":"2019-05-14T11:42:11Z","timestamp":1557834131000},"page":"4912-4921","source":"Crossref","is-referenced-by-count":16,"title":["C-InterSecture\u2014a computational tool for interspecies comparison of genome architecture"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2417-8263","authenticated-orcid":false,"given":"M","family":"Nuriddinov","sequence":"first","affiliation":[{"name":"Institute of Cytology and Genetics"}]},{"given":"V","family":"Fishman","sequence":"additional","affiliation":[{"name":"Institute of Cytology and Genetics"},{"name":"Novosibirsk State University , Novosibirsk, Russia"}]}],"member":"286","published-online":{"date-parts":[[2019,5,22]]},"reference":[{"key":"2023013108304661200_btz415-B1","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1186\/s13059-015-0642-0","article-title":"Comparison of the 3D organization of sperm and fibroblast genomes using the Hi-C approach","volume":"16","author":"Battulin","year":"2015","journal-title":"Genome Biol"},{"key":"2023013108304661200_btz415-B2","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1016\/j.cell.2017.09.043","article-title":"Multiscale 3D genome rewiring during mouse neural development","volume":"171","author":"Bonev","year":"2017","journal-title":"Cell"},{"key":"2023013108304661200_btz415-B3","doi-asserted-by":"crossref","first-page":"E4504","DOI":"10.1073\/pnas.1609643113","article-title":"Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture","volume":"113","author":"Darrow","year":"2016","journal-title":"Proc. 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