{"id":"https://openalex.org/W4396667339","doi":"https://doi.org/10.1371/journal.pcbi.1012067","title":"Cooltools: Enabling high-resolution Hi-C analysis in Python","display_name":"Cooltools: Enabling high-resolution Hi-C analysis in Python","publication_year":2024,"publication_date":"2024-05-06","ids":{"openalex":"https://openalex.org/W4396667339","doi":"https://doi.org/10.1371/journal.pcbi.1012067","pmid":"https://pubmed.ncbi.nlm.nih.gov/38709825"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1012067","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012067","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012067&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012067&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Open2C","orcid":null},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Open2C","raw_affiliation_strings":["Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America","Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America","institution_ids":["https://openalex.org/I166722992"]},{"raw_affiliation_string":"Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America","institution_ids":["https://openalex.org/I166722992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056094388","display_name":"Nezar Abdennur","orcid":"https://orcid.org/0000-0001-5814-0864"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nezar Abdennur","raw_affiliation_strings":["Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076507430","display_name":"Sameer Abraham","orcid":"https://orcid.org/0000-0002-7460-2771"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sameer Abraham","raw_affiliation_strings":["Department of Computational and Quantitative Biology, University of Southern California, Los Angeles, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational and Quantitative Biology, University of Southern California, Los Angeles, California, United States of America","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007945510","display_name":"Geoffrey Fudenberg","orcid":"https://orcid.org/0000-0001-5905-6517"},"institutions":[{"id":"https://openalex.org/I860889466","display_name":"Friedrich Miescher Institute","ror":"https://ror.org/01bmjkv45","country_code":"CH","type":"facility","lineage":["https://openalex.org/I860889466"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Geoffrey Fudenberg","raw_affiliation_strings":["Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0001-5905-6517","affiliations":[{"raw_affiliation_string":"Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland","institution_ids":["https://openalex.org/I860889466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021382553","display_name":"Ilya M. Flyamer","orcid":"https://orcid.org/0000-0002-4892-4208"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ilya M. Flyamer","raw_affiliation_strings":["Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-4892-4208","affiliations":[{"raw_affiliation_string":"Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038716685","display_name":"Aleksandra A. Galitsyna","orcid":"https://orcid.org/0000-0001-8969-5694"},"institutions":[{"id":"https://openalex.org/I125523173","display_name":"Institute of Molecular Biotechnology","ror":"https://ror.org/01zqrxf85","country_code":"AT","type":"facility","lineage":["https://openalex.org/I125523173","https://openalex.org/I138211613"]},{"id":"https://openalex.org/I138211613","display_name":"Austrian Academy of Sciences","ror":"https://ror.org/03anc3s24","country_code":"AT","type":"government","lineage":["https://openalex.org/I138211613"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Aleksandra A. Galitsyna","raw_affiliation_strings":["Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria","institution_ids":["https://openalex.org/I125523173","https://openalex.org/I138211613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038907259","display_name":"Anton Goloborodko","orcid":"https://orcid.org/0000-0002-2210-8616"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Anton Goloborodko","raw_affiliation_strings":["Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090127511","display_name":"Maxim Imakaev","orcid":"https://orcid.org/0000-0002-5320-2728"},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Maxim Imakaev","raw_affiliation_strings":["Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America","institution_ids":["https://openalex.org/I166722992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009962743","display_name":"Bet\u00fcl Akg\u00f6l Oksuz","orcid":"https://orcid.org/0000-0002-0177-4193"},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Betul A. Oksuz","raw_affiliation_strings":["Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America","institution_ids":["https://openalex.org/I166722992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024015487","display_name":"Sergey V. Venev","orcid":"https://orcid.org/0000-0002-1507-7460"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sergey V. Venev","raw_affiliation_strings":["Department of Computational and Quantitative Biology, University of Southern California, Los Angeles, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational and Quantitative Biology, University of Southern California, Los Angeles, California, United States of America","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100701344","display_name":"Yao Xiao","orcid":"https://orcid.org/0000-0002-8258-0736"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yao Xiao","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5007945510","https://openalex.org/A5009962743","https://openalex.org/A5021382553","https://openalex.org/A5024015487","https://openalex.org/A5038716685","https://openalex.org/A5038907259","https://openalex.org/A5056094388","https://openalex.org/A5076507430","https://openalex.org/A5090127511"],"corresponding_institution_ids":["https://openalex.org/I1174212","https://openalex.org/I125523173","https://openalex.org/I138211613","https://openalex.org/I166722992","https://openalex.org/I63966007","https://openalex.org/I860889466"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":43.1083,"has_fulltext":true,"cited_by_count":254,"citation_normalized_percentile":{"value":0.99940239,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"20","issue":"5","first_page":"e1012067","last_page":"e1012067"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9997000098228455,"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":0.9997000098228455,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9955000281333923,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8481616973876953},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7597304582595825},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7138653993606567},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5509013533592224},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.5187783241271973},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5085111856460571},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.4597187042236328},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.4286803901195526},{"id":"https://openalex.org/keywords/pace","display_name":"Pace","score":0.4138324558734894},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.26055479049682617},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.19386491179466248},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.1619318425655365}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8481616973876953},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7597304582595825},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7138653993606567},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5509013533592224},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.5187783241271973},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5085111856460571},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.4597187042236328},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.4286803901195526},{"id":"https://openalex.org/C2777526511","wikidata":"https://www.wikidata.org/wiki/Q691543","display_name":"Pace","level":2,"score":0.4138324558734894},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26055479049682617},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.19386491179466248},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.1619318425655365},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"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":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1012067","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012067","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012067&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:38709825","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38709825","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11098495","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11098495","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11098495/pdf/pcbi.1012067.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:70d4fa2637ed41ecb2f8c041c46c5ff4","is_oa":true,"landing_page_url":"https://doaj.org/article/70d4fa2637ed41ecb2f8c041c46c5ff4","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 20, Iss 5, p e1012067 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1012067","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012067","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012067&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1569544241","display_name":null,"funder_award_id":"R01 HG003143","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G1704165282","display_name":null,"funder_award_id":"R35 GM143116-01","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G1846104044","display_name":null,"funder_award_id":"UM1HG011536","funder_id":"https://openalex.org/F4320338403","funder_display_name":"Common Fund"},{"id":"https://openalex.org/G6387550307","display_name":null,"funder_award_id":"R35 GM143116","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7636947132","display_name":null,"funder_award_id":"GM143116-01","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8017732303","display_name":null,"funder_award_id":"UM1 HG011536","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320321004","display_name":"\u00d6sterreichischen Akademie der Wissenschaften","ror":"https://ror.org/03anc3s24"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320338403","display_name":"Common Fund","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4396667339.pdf"},"referenced_works_count":65,"referenced_works":["https://openalex.org/W1965863160","https://openalex.org/W1973062929","https://openalex.org/W2001576815","https://openalex.org/W2015159529","https://openalex.org/W2090037139","https://openalex.org/W2097798909","https://openalex.org/W2101234009","https://openalex.org/W2245493112","https://openalex.org/W2247766769","https://openalex.org/W2481029670","https://openalex.org/W2584394140","https://openalex.org/W2738924259","https://openalex.org/W2745958356","https://openalex.org/W2757387674","https://openalex.org/W2782774915","https://openalex.org/W2796109902","https://openalex.org/W2888425844","https://openalex.org/W2904120442","https://openalex.org/W2915661059","https://openalex.org/W2945281272","https://openalex.org/W2946393337","https://openalex.org/W2951575223","https://openalex.org/W2953105755","https://openalex.org/W2960979937","https://openalex.org/W2978425787","https://openalex.org/W2978734876","https://openalex.org/W2980782218","https://openalex.org/W2982127583","https://openalex.org/W2987911680","https://openalex.org/W2994756760","https://openalex.org/W3002052930","https://openalex.org/W3003257820","https://openalex.org/W3003909932","https://openalex.org/W3013167866","https://openalex.org/W3013371767","https://openalex.org/W3017099913","https://openalex.org/W3017323102","https://openalex.org/W3027849952","https://openalex.org/W3032387589","https://openalex.org/W3035965352","https://openalex.org/W3087813728","https://openalex.org/W3088572354","https://openalex.org/W3092624702","https://openalex.org/W3094879970","https://openalex.org/W3099165428","https://openalex.org/W3099878876","https://openalex.org/W3103145119","https://openalex.org/W3106437999","https://openalex.org/W3112752014","https://openalex.org/W3120518704","https://openalex.org/W3129040860","https://openalex.org/W3165253641","https://openalex.org/W3198476511","https://openalex.org/W3202988924","https://openalex.org/W3209575515","https://openalex.org/W4210254079","https://openalex.org/W4211071958","https://openalex.org/W4212902261","https://openalex.org/W4307492587","https://openalex.org/W4312114373","https://openalex.org/W4320913817","https://openalex.org/W4392173297","https://openalex.org/W6675354045","https://openalex.org/W6747441544","https://openalex.org/W6912753541"],"related_works":["https://openalex.org/W3023169329","https://openalex.org/W4389470870","https://openalex.org/W2782165897","https://openalex.org/W1582950852","https://openalex.org/W4300438041","https://openalex.org/W2054104202","https://openalex.org/W2139703748","https://openalex.org/W2761254753","https://openalex.org/W1024825291","https://openalex.org/W2188981919"],"abstract_inverted_index":{"Chromosome":[0],"conformation":[1],"capture":[2],"(3C)":[3],"technologies":[4],"reveal":[5],"the":[6,103,146,150],"incredible":[7],"complexity":[8],"of":[9,13,39,86,96,149],"genome":[10,24,154],"organization.":[11],"Maps":[12],"increasing":[14],"size,":[15],"depth,":[16],"and":[17,30,44,93,110,123,137,152],"resolution":[18],"are":[19],"now":[20],"used":[21],"to":[22,47],"probe":[23],"architecture":[25],"across":[26],"cell":[27],"states,":[28],"types,":[29],"organisms.":[31],"Larger":[32],"datasets":[33],"add":[34],"challenges":[35],"at":[36],"each":[37],"step":[38],"computational":[40,87],"analysis,":[41],"from":[42],"storage":[43,109],"memory":[45],"constraints":[46],"researchers'":[48],"time;":[49],"however,":[50],"analysis":[51,71,95,140],"tools":[52,65,88],"that":[53,89],"meet":[54],"these":[55],"increased":[56],"resource":[57],"demands":[58],"have":[59],"not":[60],"kept":[61],"pace.":[62],"Furthermore,":[63],"existing":[64],"offer":[66],"limited":[67],"support":[68],"for":[69,72,112],"customizing":[70],"specific":[73],"use":[74,148],"cases":[75],"or":[76],"new":[77],"biology.":[78],"Here":[79],"we":[80],"introduce":[81],"cooltools":[82,144],"(https://github.com/open2c/cooltools),":[83],"a":[84,117],"suite":[85],"enables":[90,145],"flexible,":[91],"scalable,":[92],"reproducible":[94],"high-resolution":[97,113],"contact":[98],"frequency":[99],"data.":[100],"Cooltools":[101,115],"leverages":[102],"widely-adopted":[104],"cooler":[105],"format":[106],"which":[107,129],"handles":[108],"access":[111],"datasets.":[114,156],"provides":[116],"paired":[118],"command":[119],"line":[120],"interface":[121,127],"(CLI)":[122],"Python":[124],"application":[125],"programming":[126],"(API),":[128],"respectively":[130],"facilitate":[131],"workflows":[132],"on":[133],"high-performance":[134],"computing":[135],"clusters":[136],"in":[138],"interactive":[139],"environments.":[141],"In":[142],"short,":[143],"effective":[147],"latest":[151],"largest":[153],"folding":[155]},"counts_by_year":[{"year":2026,"cited_by_count":62},{"year":2025,"cited_by_count":109},{"year":2024,"cited_by_count":60},{"year":2023,"cited_by_count":22},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2024-05-07T00:00:00"}
