{"id":"https://openalex.org/W2119318600","doi":"https://doi.org/10.1093/bioinformatics/btt120","title":"CytoHiC: a cytoscape plugin for visual comparison of Hi-C networks","display_name":"CytoHiC: a cytoscape plugin for visual comparison of Hi-C networks","publication_year":2013,"publication_date":"2013-03-18","ids":{"openalex":"https://openalex.org/W2119318600","doi":"https://doi.org/10.1093/bioinformatics/btt120","mag":"2119318600","pmid":"https://pubmed.ncbi.nlm.nih.gov/23508968"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt120","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt120","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/9/1206/48895700/bioinformatics_29_9_1206.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/9/1206/48895700/bioinformatics_29_9_1206.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006953572","display_name":"Yoli Shavit","orcid":"https://orcid.org/0000-0002-3393-6070"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Yoli Shavit","raw_affiliation_strings":["Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, UK","[Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD, UK]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, UK","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"[Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD, UK]","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056748708","display_name":"P\u00edetro Li\u00f3","orcid":"https://orcid.org/0000-0002-0540-5053"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Pietro Lio'","raw_affiliation_strings":["Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, UK","[Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD, UK]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, UK","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"[Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD, UK]","institution_ids":["https://openalex.org/I241749"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5006953572"],"corresponding_institution_ids":["https://openalex.org/I241749"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":1.3744,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.80751046,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"29","issue":"9","first_page":"1206","last_page":"1207"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8043000102043152,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8043000102043152,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11841","display_name":"Nuclear Structure and Function","score":0.04259999841451645,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.030400000512599945,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.9325000047683716},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7337636947631836},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.7146137952804565},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6780463457107544},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5946455001831055},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4334113597869873},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4222729206085205},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3494280278682709},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1546134650707245}],"concepts":[{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.9325000047683716},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7337636947631836},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7146137952804565},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6780463457107544},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5946455001831055},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4334113597869873},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4222729206085205},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3494280278682709},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1546134650707245}],"mesh":[{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btt120","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt120","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/9/1206/48895700/bioinformatics_29_9_1206.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23508968","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23508968","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt120","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt120","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/9/1206/48895700/bioinformatics_29_9_1206.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2119318600.pdf","grobid_xml":"https://content.openalex.org/works/W2119318600.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W2001576815","https://openalex.org/W2090037139","https://openalex.org/W2097798909","https://openalex.org/W2105778988","https://openalex.org/W2107935250","https://openalex.org/W2108615748","https://openalex.org/W2120718521","https://openalex.org/W2128106349","https://openalex.org/W2132882607","https://openalex.org/W2159675211","https://openalex.org/W6676055941"],"related_works":["https://openalex.org/W4287378204","https://openalex.org/W2981957539","https://openalex.org/W47352601","https://openalex.org/W2545422590","https://openalex.org/W4240705470","https://openalex.org/W2945311252","https://openalex.org/W631546281","https://openalex.org/W4213354039","https://openalex.org/W2266220644","https://openalex.org/W88292646"],"abstract_inverted_index":{"SUMMARY:":[0],"With":[1],"the":[2,5,13,31,42,47],"introduction":[3],"of":[4,12,46,56,108,124,129],"Hi-C":[6,57,77,114,125],"method":[7],"new":[8,63],"and":[9,35,64,104,127,143],"fundamental":[10],"properties":[11],"nuclear":[14],"architecture":[15],"are":[16,145],"emerging.":[17],"The":[18,134],"ability":[19],"to":[20,29,102,119],"interpret":[21],"data":[22,58,126],"generated":[23],"by":[24,89],"this":[25],"method,":[26],"which":[27,99],"aims":[28],"capture":[30],"physical":[32],"proximity":[33],"between":[34,76],"within":[36],"chromosomes,":[37],"is":[38],"crucial":[39],"for":[40,53],"uncovering":[41],"three":[43],"dimensional":[44],"structure":[45],"nucleus.":[48],"Providing":[49],"researchers":[50],"with":[51],"tools":[52],"interactive":[54],"visualization":[55],"can":[59,70],"help":[60],"in":[61,73],"gaining":[62],"important":[65],"insights.":[66],"Specifically,":[67],"visual":[68,122],"comparison":[69,123],"pinpoint":[71],"changes":[72],"spatial":[74,106],"organization":[75],"datasets,":[78],"originating":[79],"from":[80],"different":[81,85,90],"cell":[82],"lines":[83],"or":[84,87],"species,":[86],"normalized":[88,113],"methods.":[91],"Here,":[92],"we":[93],"present":[94],"CytoHiC,":[95],"a":[96],"Cytsocape":[97],"plugin,":[98,136],"allow":[100],"users":[101],"view":[103],"compare":[105],"maps":[107],"genomic":[109,131],"landmarks,":[110],"based":[111],"on":[112],"datasets.":[115],"CytoHiC":[116,135],"was":[117],"developed":[118],"support":[120],"intuitive":[121],"integration":[128],"additional":[130],"annotations.":[132],"AVAILABILITY:":[133],"source":[137],"code,":[138],"user":[139],"manual,":[140],"example":[141],"files":[142],"documentation":[144],"available":[146],"at:":[147],"http://apps.cytoscape.org/apps/cytohicplugin":[148]},"counts_by_year":[{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
