{"id":"https://openalex.org/W2469263765","doi":"https://doi.org/10.1371/journal.pcbi.1004809","title":"QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks","display_name":"QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks","publication_year":2016,"publication_date":"2016-06-23","ids":{"openalex":"https://openalex.org/W2469263765","doi":"https://doi.org/10.1371/journal.pcbi.1004809","mag":"2469263765","pmid":"https://pubmed.ncbi.nlm.nih.gov/27336171"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004809","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004809","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004809&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.1004809&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022780099","display_name":"Asa Thibodeau","orcid":"https://orcid.org/0000-0003-2421-4225"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Asa Thibodeau","raw_affiliation_strings":["Department of Computer Science, University of Connecticut, Storrs, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Connecticut, Storrs, Connecticut, United States of America","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032360243","display_name":"Eladio J. M\u00e1rquez","orcid":"https://orcid.org/0000-0001-5548-5795"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]},{"id":"https://openalex.org/I4405260184","display_name":"The Jackson Laboratory for Genomic Medicine","ror":"https://ror.org/03cew3973","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256","https://openalex.org/I4405260184"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eladio J. M\u00e1rquez","raw_affiliation_strings":["The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I4210115256","https://openalex.org/I4405260184"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022945288","display_name":"Oscar Junhong Luo","orcid":"https://orcid.org/0000-0002-1266-3069"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]},{"id":"https://openalex.org/I4405260184","display_name":"The Jackson Laboratory for Genomic Medicine","ror":"https://ror.org/03cew3973","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256","https://openalex.org/I4405260184"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Oscar Luo","raw_affiliation_strings":["The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I4210115256","https://openalex.org/I4405260184"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028790437","display_name":"Yijun Ruan","orcid":"https://orcid.org/0000-0001-5881-569X"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]},{"id":"https://openalex.org/I4405260184","display_name":"The Jackson Laboratory for Genomic Medicine","ror":"https://ror.org/03cew3973","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256","https://openalex.org/I4405260184"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yijun Ruan","raw_affiliation_strings":["The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I4210115256","https://openalex.org/I4405260184"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078173518","display_name":"Francesca Menghi","orcid":"https://orcid.org/0000-0002-7209-251X"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]},{"id":"https://openalex.org/I4405260184","display_name":"The Jackson Laboratory for Genomic Medicine","ror":"https://ror.org/03cew3973","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256","https://openalex.org/I4405260184"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Francesca Menghi","raw_affiliation_strings":["The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-7209-251X","affiliations":[{"raw_affiliation_string":"The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I4210115256","https://openalex.org/I4405260184"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112474888","display_name":"Dong\u2010Guk Shin","orcid":"https://orcid.org/0009-0004-4649-7363"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dong-Guk Shin","raw_affiliation_strings":["Department of Computer Science, University of Connecticut, Storrs, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Connecticut, Storrs, Connecticut, United States of America","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079010434","display_name":"Michael L. Stitzel","orcid":"https://orcid.org/0000-0001-5630-559X"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]},{"id":"https://openalex.org/I4405260184","display_name":"The Jackson Laboratory for Genomic Medicine","ror":"https://ror.org/03cew3973","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256","https://openalex.org/I4405260184"]},{"id":"https://openalex.org/I75929689","display_name":"UConn Health","ror":"https://ror.org/02kzs4y22","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I75929689"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael L. Stitzel","raw_affiliation_strings":["Institute of Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, United States of America","The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I75929689"]},{"raw_affiliation_string":"The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I4210115256","https://openalex.org/I4405260184"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074945538","display_name":"Paola Vera\u2010Licona","orcid":"https://orcid.org/0000-0003-3970-2619"},"institutions":[{"id":"https://openalex.org/I75929689","display_name":"UConn Health","ror":"https://ror.org/02kzs4y22","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I75929689"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paola Vera-Licona","raw_affiliation_strings":["Center for Quantitative Medicine, Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut, United States of America","Institute of Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-3970-2619","affiliations":[{"raw_affiliation_string":"Center for Quantitative Medicine, Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I75929689"]},{"raw_affiliation_string":"Institute of Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I75929689"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081776556","display_name":"Duygu Ucar","orcid":"https://orcid.org/0000-0002-9772-3066"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]},{"id":"https://openalex.org/I4405260184","display_name":"The Jackson Laboratory for Genomic Medicine","ror":"https://ror.org/03cew3973","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256","https://openalex.org/I4405260184"]},{"id":"https://openalex.org/I75929689","display_name":"UConn Health","ror":"https://ror.org/02kzs4y22","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I75929689"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Duygu Ucar","raw_affiliation_strings":["Institute of Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, United States of America","The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I75929689"]},{"raw_affiliation_string":"The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America","institution_ids":["https://openalex.org/I4210115256","https://openalex.org/I4405260184"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5081776556"],"corresponding_institution_ids":["https://openalex.org/I4210115256","https://openalex.org/I4405260184","https://openalex.org/I75929689"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.4416,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.82056319,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"12","issue":"6","first_page":"e1004809","last_page":"e1004809"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9652000069618225,"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":0.9652000069618225,"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":0.02070000022649765,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.00139999995008111,"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/computer-science","display_name":"Computer science","score":0.6465046405792236},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.6235662698745728},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.48681876063346863},{"id":"https://openalex.org/keywords/javascript","display_name":"JavaScript","score":0.4504082500934601},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.44815126061439514},{"id":"https://openalex.org/keywords/centrality","display_name":"Centrality","score":0.42652615904808044},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4231681823730469},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41772329807281494},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4162350594997406},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.41368579864501953},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.39294156432151794},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30301007628440857},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.2910987436771393},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2440345585346222},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19332042336463928},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1574193835258484}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6465046405792236},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.6235662698745728},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.48681876063346863},{"id":"https://openalex.org/C544833334","wikidata":"https://www.wikidata.org/wiki/Q2005","display_name":"JavaScript","level":2,"score":0.4504082500934601},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.44815126061439514},{"id":"https://openalex.org/C53811970","wikidata":"https://www.wikidata.org/wiki/Q5062194","display_name":"Centrality","level":2,"score":0.42652615904808044},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4231681823730469},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41772329807281494},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4162350594997406},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.41368579864501953},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.39294156432151794},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30301007628440857},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.2910987436771393},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2440345585346222},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19332042336463928},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1574193835258484},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1004809","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004809","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004809&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:27336171","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27336171","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:europepmc.org:3903690","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4919057","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:bf5a8b5f969148eba9f21a6154f0656b","is_oa":true,"landing_page_url":"https://doaj.org/article/bf5a8b5f969148eba9f21a6154f0656b","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 12, Iss 6, p e1004809 (2016)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/3927462","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/QuIN_A_Web_Server_for_Querying_and_Visualizing_Chromatin_Interaction_Networks/3927462","pdf_url":null,"source":{"id":"https://openalex.org/S4306402621","display_name":"INDIGO (University of Illinois at Chicago)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I39422238","host_organization_name":"University of Illinois Chicago","host_organization_lineage":["https://openalex.org/I39422238"],"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":"","raw_type":"Dataset"},{"id":"pmh:oai:mouseion.jax.org:stfb2016-1161","is_oa":false,"landing_page_url":"https://mouseion.jax.org/stfb2016/164","pdf_url":null,"source":{"id":"https://openalex.org/S4377196421","display_name":"The Mouseion at the JAXlibrary (Jackson Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210115256","host_organization_name":"Jackson Laboratory","host_organization_lineage":["https://openalex.org/I4210115256"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Research 2016","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004809","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004809","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004809&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":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.5400000214576721}],"awards":[{"id":"https://openalex.org/G2771623481","display_name":null,"funder_award_id":"R01 CA186714","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G278894908","display_name":null,"funder_award_id":"P30CA034196","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2872294044","display_name":null,"funder_award_id":"R25 HG007631","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2469263765.pdf","grobid_xml":"https://content.openalex.org/works/W2469263765.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W272899539","https://openalex.org/W1805834977","https://openalex.org/W1926327739","https://openalex.org/W1985621639","https://openalex.org/W1986653602","https://openalex.org/W1987908519","https://openalex.org/W1991149014","https://openalex.org/W1996448420","https://openalex.org/W2009576540","https://openalex.org/W2010559811","https://openalex.org/W2011899558","https://openalex.org/W2014677321","https://openalex.org/W2030545812","https://openalex.org/W2031057223","https://openalex.org/W2031370629","https://openalex.org/W2052250375","https://openalex.org/W2072133788","https://openalex.org/W2073026107","https://openalex.org/W2079177924","https://openalex.org/W2083581022","https://openalex.org/W2090037139","https://openalex.org/W2096173332","https://openalex.org/W2097128336","https://openalex.org/W2102140136","https://openalex.org/W2111880238","https://openalex.org/W2115899293","https://openalex.org/W2116147219","https://openalex.org/W2116868464","https://openalex.org/W2117471298","https://openalex.org/W2117757143","https://openalex.org/W2118151336","https://openalex.org/W2119318600","https://openalex.org/W2122732537","https://openalex.org/W2128016314","https://openalex.org/W2137198307","https://openalex.org/W2145173401","https://openalex.org/W2149118429","https://openalex.org/W2154866190","https://openalex.org/W2158485828","https://openalex.org/W2159675211","https://openalex.org/W2165064122","https://openalex.org/W2175063164","https://openalex.org/W2259938310","https://openalex.org/W2313413464"],"related_works":["https://openalex.org/W2769306272","https://openalex.org/W2767823042","https://openalex.org/W2193871446","https://openalex.org/W2214256683","https://openalex.org/W2984808439","https://openalex.org/W3173734471","https://openalex.org/W2135425797","https://openalex.org/W3208534634","https://openalex.org/W3175249469","https://openalex.org/W4249628690"],"abstract_inverted_index":{"UNLABELLED:":[0],"Recent":[1],"studies":[2],"of":[3,49,65,73,86,94,106,127,134],"the":[4,81,132,226,232],"human":[5],"genome":[6],"have":[7],"indicated":[8],"that":[9,122],"regulatory":[10,52,67,193],"elements":[11,68],"(e.g.":[12],"promoters":[13],"and":[14,28,43,69,84,89,99,115,152,163,168,182,190,195,198,214,222,225],"enhancers)":[15],"at":[16,207],"distal":[17,62],"genomic":[18,87],"locations":[19],"can":[20,45,123],"interact":[21],"with":[22,160],"each":[23],"other":[24],"via":[25],"chromatin":[26,107,135,154],"folding":[27],"affect":[29],"gene":[30,63,177],"expression":[31],"levels.":[32],"Genomic":[33],"technologies":[34],"for":[35,76,131],"mapping":[36],"interactions":[37,50],"between":[38,51],"DNA":[39],"regions,":[40],"e.g.,":[41],"ChIA-PET":[42],"HiC,":[44],"generate":[46],"genome-wide":[47],"maps":[48,109],"elements.":[53],"These":[54],"interaction":[55,108,136,155,169],"datasets":[56,96],"are":[57],"important":[58,77],"resources":[59],"to":[60,70,188],"infer":[61],"targets":[64,194],"non-coding":[66],"facilitate":[71],"prioritization":[72],"critical":[74,192],"loci":[75],"cellular":[78],"functions.":[79],"With":[80],"increasing":[82],"diversity":[83],"complexity":[85],"information":[88],"public":[90],"ontologies,":[91],"making":[92],"sense":[93],"these":[95],"demands":[97],"integrative":[98],"easy-to-use":[100],"software":[101,121],"tools.":[102],"Moreover,":[103],"network":[104,128,173,185],"representation":[105],"enables":[110],"effective":[111],"data":[112],"visualization,":[113],"integration,":[114],"mining.":[116],"Currently,":[117],"there":[118],"is":[119,205,210,229],"no":[120],"take":[124],"full":[125],"advantage":[126],"theory":[129],"approaches":[130],"analysis":[133],"datasets.":[137],"To":[138],"fill":[139],"this":[140],"gap,":[141],"we":[142],"developed":[143,211],"a":[144],"web-based":[145],"application,":[146],"QuIN,":[147],"which":[148],"enables:":[149],"1)":[150],"building":[151],"visualizing":[153],"networks,":[156],"2)":[157],"annotating":[158],"networks":[159],"user-provided":[161],"private":[162],"publicly":[164],"available":[165,206,230,235],"functional":[166],"genomics":[167],"datasets,":[170],"3)":[171],"querying":[172],"components":[174],"based":[175,186],"on":[176,236],"name":[178],"or":[179],"chromosome":[180],"location,":[181],"4)":[183],"utilizing":[184,216],"measures":[187],"identify":[189],"prioritize":[191],"their":[196],"direct":[197],"indirect":[199],"interactions.":[200],"AVAILABILITY:":[201],"QuIN's":[202],"web":[203,220],"server":[204,221],"http://quin.jax.org":[208],"QuIN":[209],"in":[212],"Java":[213],"JavaScript,":[215],"an":[217],"Apache":[218],"Tomcat":[219],"MySQL":[223],"database":[224],"source":[227],"code":[228],"under":[231],"GPLV3":[233],"license":[234],"GitHub:":[237],"https://github.com/UcarLab/QuIN/.":[238]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":3}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
