{"id":"https://openalex.org/W3155785778","doi":"https://doi.org/10.1186/s12859-021-04113-8","title":"Deciphering hierarchical organization of topologically associated domains through change-point testing","display_name":"Deciphering hierarchical organization of topologically associated domains through change-point testing","publication_year":2021,"publication_date":"2021-04-10","ids":{"openalex":"https://openalex.org/W3155785778","doi":"https://doi.org/10.1186/s12859-021-04113-8","mag":"3155785778","pmid":"https://pubmed.ncbi.nlm.nih.gov/33838653"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04113-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04113-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04113-8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04113-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090567392","display_name":"Haipeng Xing","orcid":"https://orcid.org/0000-0003-2048-2353"},"institutions":[{"id":"https://openalex.org/I1327163397","display_name":"State University of New York","ror":"https://ror.org/01q1z8k08","country_code":"US","type":"education","lineage":["https://openalex.org/I1327163397"]},{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Haipeng Xing","raw_affiliation_strings":["Department of Applied Mathematics and Statistics, State University of New York at Stony Brook, 100 Nicolls Rd, Stony Brook, NY, 11794, USA"],"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Statistics, State University of New York at Stony Brook, 100 Nicolls Rd, Stony Brook, NY, 11794, USA","institution_ids":["https://openalex.org/I59553526","https://openalex.org/I1327163397"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039197849","display_name":"Yingru Wu","orcid":"https://orcid.org/0000-0002-3714-6447"},"institutions":[{"id":"https://openalex.org/I1327163397","display_name":"State University of New York","ror":"https://ror.org/01q1z8k08","country_code":"US","type":"education","lineage":["https://openalex.org/I1327163397"]},{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yingru Wu","raw_affiliation_strings":["Department of Applied Mathematics and Statistics, State University of New York at Stony Brook, 100 Nicolls Rd, Stony Brook, NY, 11794, USA"],"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Statistics, State University of New York at Stony Brook, 100 Nicolls Rd, Stony Brook, NY, 11794, USA","institution_ids":["https://openalex.org/I59553526","https://openalex.org/I1327163397"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058814283","display_name":"Michael Q. Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I162577319","display_name":"The University of Texas at Dallas","ror":"https://ror.org/049emcs32","country_code":"US","type":"education","lineage":["https://openalex.org/I162577319"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Q. Zhang","raw_affiliation_strings":["Center for System Biology, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX, 75080, USA"],"affiliations":[{"raw_affiliation_string":"Center for System Biology, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX, 75080, USA","institution_ids":["https://openalex.org/I162577319"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057014050","display_name":"Yong Chen","orcid":"https://orcid.org/0000-0001-6827-4321"},"institutions":[{"id":"https://openalex.org/I44265643","display_name":"Rowan University","ror":"https://ror.org/049v69k10","country_code":"US","type":"education","lineage":["https://openalex.org/I44265643"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yong Chen","raw_affiliation_strings":["Department of Molecular and Cellular Biosciences, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ, 08028, USA. chenyong@rowan.edu","Department of Molecular and Cellular Biosciences, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ, 08028, USA"],"affiliations":[{"raw_affiliation_string":"Department of Molecular and Cellular Biosciences, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ, 08028, USA. chenyong@rowan.edu","institution_ids":["https://openalex.org/I44265643"]},{"raw_affiliation_string":"Department of Molecular and Cellular Biosciences, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ, 08028, USA","institution_ids":["https://openalex.org/I44265643"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5057014050"],"corresponding_institution_ids":["https://openalex.org/I44265643"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.2171,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.78456626,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":99},"biblio":{"volume":"22","issue":"1","first_page":"183","last_page":"183"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9952999949455261,"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":0.9952999949455261,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9714000225067139,"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":0.9513000249862671,"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/point","display_name":"Point (geometry)","score":0.47755107283592224},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4495863914489746},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44945091009140015},{"id":"https://openalex.org/keywords/hierarchical-organization","display_name":"Hierarchical organization","score":0.43755099177360535},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.33181333541870117},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33091700077056885},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.214793860912323}],"concepts":[{"id":"https://openalex.org/C28719098","wikidata":"https://www.wikidata.org/wiki/Q44946","display_name":"Point (geometry)","level":2,"score":0.47755107283592224},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4495863914489746},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44945091009140015},{"id":"https://openalex.org/C2780217385","wikidata":"https://www.wikidata.org/wiki/Q2389284","display_name":"Hierarchical organization","level":2,"score":0.43755099177360535},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.33181333541870117},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33091700077056885},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.214793860912323},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002467","descriptor_name":"Cell Nucleus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002467","descriptor_name":"Cell Nucleus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002467","descriptor_name":"Cell Nucleus","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":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-021-04113-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04113-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04113-8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33838653","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33838653","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:rdw.rowan.edu:csm_facpub-1260","is_oa":true,"landing_page_url":"https://rdw.rowan.edu/csm_facpub/260","pdf_url":null,"source":{"id":"https://openalex.org/S4377196130","display_name":"Rowan Digitals Works (Rowan University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I44265643","host_organization_name":"Rowan University","host_organization_lineage":["https://openalex.org/I44265643"],"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":"College of Science & Mathematics Departmental Research","raw_type":"article"},{"id":"pmh:oai:doaj.org/article:ba5b74a667a048c4bb71ea578ce8cd34","is_oa":true,"landing_page_url":"https://doaj.org/article/ba5b74a667a048c4bb71ea578ce8cd34","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-23 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8037919","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8037919","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04113-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04113-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04113-8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G174356194","display_name":null,"funder_award_id":"R01MH109616","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3845021963","display_name":null,"funder_award_id":"DMS-1612501","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3155785778.pdf","grobid_xml":"https://content.openalex.org/works/W3155785778.grobid-xml"},"referenced_works_count":86,"referenced_works":["https://openalex.org/W1491711721","https://openalex.org/W1518083799","https://openalex.org/W1831401007","https://openalex.org/W1862913282","https://openalex.org/W1964184081","https://openalex.org/W1972732851","https://openalex.org/W1973062929","https://openalex.org/W1979755874","https://openalex.org/W1989582360","https://openalex.org/W2001483697","https://openalex.org/W2021615423","https://openalex.org/W2026267776","https://openalex.org/W2028190503","https://openalex.org/W2030644393","https://openalex.org/W2036663020","https://openalex.org/W2037619809","https://openalex.org/W2038152407","https://openalex.org/W2041694722","https://openalex.org/W2042856568","https://openalex.org/W2070021921","https://openalex.org/W2073026107","https://openalex.org/W2078273711","https://openalex.org/W2087056061","https://openalex.org/W2100148696","https://openalex.org/W2106463809","https://openalex.org/W2109949710","https://openalex.org/W2114083195","https://openalex.org/W2117227640","https://openalex.org/W2118673550","https://openalex.org/W2138898429","https://openalex.org/W2146915571","https://openalex.org/W2150427470","https://openalex.org/W2152605077","https://openalex.org/W2153893972","https://openalex.org/W2160446587","https://openalex.org/W2161212572","https://openalex.org/W2163412235","https://openalex.org/W2168877341","https://openalex.org/W2185693210","https://openalex.org/W2227178360","https://openalex.org/W2310342073","https://openalex.org/W2324629078","https://openalex.org/W2401568148","https://openalex.org/W2416744721","https://openalex.org/W2523285811","https://openalex.org/W2530292798","https://openalex.org/W2573551764","https://openalex.org/W2581883027","https://openalex.org/W2616052794","https://openalex.org/W2625231465","https://openalex.org/W2749279500","https://openalex.org/W2755736028","https://openalex.org/W2757387674","https://openalex.org/W2768633047","https://openalex.org/W2784063494","https://openalex.org/W2792451492","https://openalex.org/W2798012365","https://openalex.org/W2800968671","https://openalex.org/W2808165720","https://openalex.org/W2810076504","https://openalex.org/W2811431585","https://openalex.org/W2887206273","https://openalex.org/W2888200508","https://openalex.org/W2890222565","https://openalex.org/W2891348030","https://openalex.org/W2898577086","https://openalex.org/W2904111278","https://openalex.org/W2904120442","https://openalex.org/W2935817721","https://openalex.org/W2950146685","https://openalex.org/W2951050465","https://openalex.org/W2955816935","https://openalex.org/W2955885837","https://openalex.org/W2977660404","https://openalex.org/W2991653202","https://openalex.org/W3005484567","https://openalex.org/W3011951807","https://openalex.org/W3012408807","https://openalex.org/W3020230577","https://openalex.org/W3024441585","https://openalex.org/W3103707579","https://openalex.org/W3120242712","https://openalex.org/W3120705677","https://openalex.org/W3124981602","https://openalex.org/W4212942074","https://openalex.org/W7002139687"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1971568933","https://openalex.org/W2117258802"],"abstract_inverted_index":{"HiCKey":[0],"is":[1],"optimized":[2],"for":[3,25],"processing":[4],"large":[5],"matrices":[6],"constructed":[7],"from":[8],"high-resolution":[9],"Hi-C":[10],"experiments.":[11],"The":[12],"method":[13],"and":[14],"theoretical":[15],"result":[16],"of":[17,28],"the":[18],"GLR":[19],"test":[20],"provide":[21],"a":[22],"general":[23,45],"framework":[24],"significance":[26],"testing":[27],"similar":[29],"experimental":[30],"chromatin":[31],"interaction":[32],"data":[33],"that":[34],"may":[35],"not":[36],"fully":[37],"follow":[38],"negative":[39],"binomial":[40],"distributions":[41],"but":[42],"rather":[43],"more":[44],"mixture":[46],"distributions.":[47]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":2}],"updated_date":"2026-03-29T08:15:47.926485","created_date":"2025-10-10T00:00:00"}
