{"id":"https://openalex.org/W4408139937","doi":"https://doi.org/10.1093/bioinformatics/btaf026","title":"Significance in scale space for Hi-C data","display_name":"Significance in scale space for Hi-C data","publication_year":2025,"publication_date":"2025-02-27","ids":{"openalex":"https://openalex.org/W4408139937","doi":"https://doi.org/10.1093/bioinformatics/btaf026","pmid":"https://pubmed.ncbi.nlm.nih.gov/40036585"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf026","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf026","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/3/btaf026/62197507/btaf026.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/41/3/btaf026/62197507/btaf026.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111204673","display_name":"Rui Liu","orcid":"https://orcid.org/0009-0002-6467-8577"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rui Liu","raw_affiliation_strings":["Department of Statistics and Operations Research, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599,","Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States"],"raw_orcid":"https://orcid.org/0009-0002-6467-8577","affiliations":[{"raw_affiliation_string":"Department of Statistics and Operations Research, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599,","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050808730","display_name":"Zhengwu Zhang","orcid":"https://orcid.org/0000-0002-9047-8838"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhengwu Zhang","raw_affiliation_strings":["Department of Statistics and Operations Research, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599,","Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics and Operations Research, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599,","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053251909","display_name":"Hyejung Won","orcid":"https://orcid.org/0000-0003-3651-0566"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hyejung Won","raw_affiliation_strings":["Department of Genetics, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599,","Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599,","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053189482","display_name":"J. S. Marron","orcid":"https://orcid.org/0000-0003-2000-1476"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J S Marron","raw_affiliation_strings":["Department of Statistics and Operations Research, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599,","Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States"],"raw_orcid":"https://orcid.org/0000-0003-2000-1476","affiliations":[{"raw_affiliation_string":"Department of Statistics and Operations Research, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599,","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States","institution_ids":["https://openalex.org/I114027177"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I114027177"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.03200894,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9412000179290771,"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":0.9412000179290771,"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.02539999969303608,"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/T10885","display_name":"Gene expression and cancer classification","score":0.0027000000700354576,"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/scale","display_name":"Scale (ratio)","score":0.6453480124473572},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.5565707087516785},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5461855530738831},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.18381285667419434},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.15568849444389343},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.09688052535057068}],"concepts":[{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.6453480124473572},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.5565707087516785},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5461855530738831},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.18381285667419434},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.15568849444389343},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.09688052535057068}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"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":"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},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009457","descriptor_name":"Neuroglia","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009457","descriptor_name":"Neuroglia","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf026","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf026","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/3/btaf026/62197507/btaf026.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40036585","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40036585","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11879645","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11879645","pdf_url":null,"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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf026","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf026","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/3/btaf026/62197507/btaf026.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3685830080","display_name":null,"funder_award_id":"DMS-2113404","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"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4408139937.pdf"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1910205447","https://openalex.org/W1973062929","https://openalex.org/W1973976434","https://openalex.org/W2026148763","https://openalex.org/W2034917264","https://openalex.org/W2042243448","https://openalex.org/W2070021921","https://openalex.org/W2090037139","https://openalex.org/W2099416373","https://openalex.org/W2132685693","https://openalex.org/W2152605077","https://openalex.org/W2209806217","https://openalex.org/W2209883607","https://openalex.org/W2530292798","https://openalex.org/W2806216819","https://openalex.org/W2906147404","https://openalex.org/W2914685295","https://openalex.org/W2952664869","https://openalex.org/W2971932838","https://openalex.org/W3010189944","https://openalex.org/W3037015477","https://openalex.org/W3082989829","https://openalex.org/W3087339707","https://openalex.org/W3173670503","https://openalex.org/W3183404388","https://openalex.org/W3194691506","https://openalex.org/W4210888701","https://openalex.org/W4221095693","https://openalex.org/W4281651045","https://openalex.org/W4311662446","https://openalex.org/W4375859074","https://openalex.org/W6688387473"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"MOTIVATION:":[0],"Hi-C":[1,13,105,165],"technology":[2],"has":[3,214],"been":[4,16,58,216],"developed":[5],"to":[6,39,68,90,101,133,218],"profile":[7],"genome-wide":[8],"chromosome":[9],"conformation.":[10],"So":[11],"far":[12],"data":[14,92,166],"have":[15,57],"generated":[17],"from":[18],"a":[19,41,75],"large":[20],"compendium":[21],"of":[22,96,136],"different":[23,27,31,48,53,94],"cell":[24,49],"types":[25],"and":[26,103,140],"tissue":[28],"types.":[29,50],"Among":[30],"chromatin":[32,35],"conformation":[33],"units,":[34],"loops":[36,65,110,128,154],"were":[37,129],"found":[38,206],"play":[40],"key":[42],"role":[43],"in":[44,83,115,168,190,201,207],"gene":[45,117,134,158],"regulation":[46],"across":[47],"While":[51],"many":[52],"loop":[54,61,77,122],"calling":[55,78],"algorithms":[56],"developed,":[59],"most":[60],"callers":[62],"identified":[63],"shared":[64],"as":[66,125],"opposed":[67],"cell-type-specific":[69,116],"loops.":[70],"RESULTS:":[71],"We":[72],"propose":[73],"SSSHiC,":[74],"new":[76],"algorithm":[79],"based":[80],"on":[81],"significance":[82],"scale":[84],"space,":[85],"which":[86],"can":[87,151,171,204],"be":[88,172,205],"used":[89,167,200],"understand":[91],"at":[93,179,195],"levels":[95],"resolution.":[97],"By":[98],"applying":[99],"SSSHiC":[100,150],"neuronal":[102],"glial":[104],"data,":[106],"we":[107],"detected":[108],"more":[109,130,157],"that":[111,149,155],"are":[112],"potentially":[113],"engaged":[114],"regulation.":[118],"Compared":[119],"with":[120,221],"other":[121],"callers,":[123],"such":[124],"Mustache,":[126],"these":[127],"frequently":[131],"anchored":[132],"promoters":[135],"cellular":[137],"marker":[138],"genes":[139],"had":[141],"better":[142],"APA":[143],"scores.":[144],"Therefore,":[145],"our":[146],"results":[147],"suggest":[148],"effectively":[152],"capture":[153],"contain":[156],"regulatory":[159],"information.":[160],"AVAILABILITY":[161],"AND":[162],"IMPLEMENTATION:":[163],"The":[164,183,212],"this":[169,191,202],"study":[170,192],"accessed":[173],"through":[174],"the":[175,208,222],"PsychENCODE":[176],"Knowledge":[177],"Portal":[178],"https://www.synapse.org/#!":[180],"Synapse:":[181],"syn21760712.":[182],"code":[184,199,213],"utilized":[185],"for":[186],"Curvature":[187],"SSS":[188],"cited":[189],"is":[193],"available":[194],"https://github.com/jsmarron/MarronMatlabSoftware/blob/master/Matlab9/Matlab9Combined.zip.":[196],"All":[197],"custom":[198],"research":[203],"GitHub":[209],"repository:":[210],"https://github.com/jerryliu01998/HiC.":[211],"also":[215],"submitted":[217],"Code":[219],"Ocean":[220],"doi:":[223],"10.24433/CO.1912913.v1.":[224]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}