{"id":"https://openalex.org/W4414432742","doi":"https://doi.org/10.1109/tcbbio.2025.3613657","title":"DISHIC: An Effective Method for Identifying Differential Interaction in Single-Cell Hi-C","display_name":"DISHIC: An Effective Method for Identifying Differential Interaction in Single-Cell Hi-C","publication_year":2025,"publication_date":"2025-09-23","ids":{"openalex":"https://openalex.org/W4414432742","doi":"https://doi.org/10.1109/tcbbio.2025.3613657","pmid":"https://pubmed.ncbi.nlm.nih.gov/40986587"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3613657","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3613657","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074611035","display_name":"Yichao Zhao","orcid":"https://orcid.org/0000-0001-8784-5361"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yichao Zhao","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044328870","display_name":"Ruiqing Zheng","orcid":"https://orcid.org/0000-0001-6372-6798"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruiqing Zheng","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100725456","display_name":"Li Tang","orcid":"https://orcid.org/0000-0002-2930-0862"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Li Tang","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112925021","display_name":"Pengzhen Jia","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pengzhen Jia","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"last","author":{"id":null,"display_name":"Min Li","orcid":"https://orcid.org/0000-0002-0188-1394"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Min Li","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5074611035"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.24926746,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"6","first_page":"3101","last_page":"3111"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10558","display_name":"Advancements in Semiconductor Devices and Circuit Design","score":0.949400007724762,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10558","display_name":"Advancements in Semiconductor Devices and Circuit Design","score":0.949400007724762,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.534600019454956},{"id":"https://openalex.org/keywords/covariate","display_name":"Covariate","score":0.5030999779701233},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.4632999897003174},{"id":"https://openalex.org/keywords/limit","display_name":"Limit (mathematics)","score":0.45739999413490295},{"id":"https://openalex.org/keywords/reliability","display_name":"Reliability (semiconductor)","score":0.4537000060081482},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.43860000371932983},{"id":"https://openalex.org/keywords/wavelet","display_name":"Wavelet","score":0.39169999957084656},{"id":"https://openalex.org/keywords/chromosome-conformation-capture","display_name":"Chromosome conformation capture","score":0.35260000824928284},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.29249998927116394}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6535000205039978},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5446000099182129},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.534600019454956},{"id":"https://openalex.org/C119043178","wikidata":"https://www.wikidata.org/wiki/Q320723","display_name":"Covariate","level":2,"score":0.5030999779701233},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.4632999897003174},{"id":"https://openalex.org/C151201525","wikidata":"https://www.wikidata.org/wiki/Q177239","display_name":"Limit (mathematics)","level":2,"score":0.45739999413490295},{"id":"https://openalex.org/C43214815","wikidata":"https://www.wikidata.org/wiki/Q7310987","display_name":"Reliability (semiconductor)","level":3,"score":0.4537000060081482},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.43860000371932983},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40639999508857727},{"id":"https://openalex.org/C47432892","wikidata":"https://www.wikidata.org/wiki/Q831390","display_name":"Wavelet","level":2,"score":0.39169999957084656},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3905999958515167},{"id":"https://openalex.org/C93946551","wikidata":"https://www.wikidata.org/wiki/Q5113914","display_name":"Chromosome conformation capture","level":5,"score":0.35260000824928284},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.29249998927116394},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.2874999940395355},{"id":"https://openalex.org/C160920958","wikidata":"https://www.wikidata.org/wiki/Q7662746","display_name":"Synthetic data","level":2,"score":0.28679999709129333},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.28119999170303345},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.2766999900341034},{"id":"https://openalex.org/C74750220","wikidata":"https://www.wikidata.org/wiki/Q2662197","display_name":"Differential evolution","level":2,"score":0.27480000257492065},{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.27480000257492065},{"id":"https://openalex.org/C175801342","wikidata":"https://www.wikidata.org/wiki/Q1988917","display_name":"Data analysis","level":2,"score":0.2718999981880188},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.26980000734329224},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.2655999958515167},{"id":"https://openalex.org/C87007009","wikidata":"https://www.wikidata.org/wiki/Q210832","display_name":"Statistical hypothesis testing","level":2,"score":0.25920000672340393},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.25839999318122864},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.2549000084400177},{"id":"https://openalex.org/C37616216","wikidata":"https://www.wikidata.org/wiki/Q3218363","display_name":"Lasso (programming language)","level":2,"score":0.25099998712539673}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"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":"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":"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":true},{"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},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3613657","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3613657","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40986587","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40986587","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":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8663586063","display_name":null,"funder_award_id":"62225209","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W1964672978","https://openalex.org/W1965863160","https://openalex.org/W1981030303","https://openalex.org/W2001810970","https://openalex.org/W2039521726","https://openalex.org/W2074661552","https://openalex.org/W2090037139","https://openalex.org/W2112616404","https://openalex.org/W2114104545","https://openalex.org/W2124940469","https://openalex.org/W2146512944","https://openalex.org/W2168602111","https://openalex.org/W2551092411","https://openalex.org/W2559588208","https://openalex.org/W2559702793","https://openalex.org/W2599773520","https://openalex.org/W2731989040","https://openalex.org/W2753502849","https://openalex.org/W2762506555","https://openalex.org/W2768310712","https://openalex.org/W2783644856","https://openalex.org/W2791759760","https://openalex.org/W2883453789","https://openalex.org/W2889244889","https://openalex.org/W2898577086","https://openalex.org/W2909032196","https://openalex.org/W2965970564","https://openalex.org/W3013777909","https://openalex.org/W3103000856","https://openalex.org/W3112600195","https://openalex.org/W3131450268","https://openalex.org/W3153853987","https://openalex.org/W3158393751","https://openalex.org/W3169952715","https://openalex.org/W3193986928","https://openalex.org/W3194691506","https://openalex.org/W4225491855","https://openalex.org/W4226185665","https://openalex.org/W4292722723","https://openalex.org/W4307432965","https://openalex.org/W4307845770","https://openalex.org/W4309944312","https://openalex.org/W4312211532","https://openalex.org/W4313454972","https://openalex.org/W4376872109","https://openalex.org/W4379792586","https://openalex.org/W4383113554","https://openalex.org/W4385812298","https://openalex.org/W4386305466","https://openalex.org/W4386471322","https://openalex.org/W4387701182","https://openalex.org/W4387966116","https://openalex.org/W4390206253","https://openalex.org/W4391291049","https://openalex.org/W4392874548","https://openalex.org/W4392899350","https://openalex.org/W4394813096","https://openalex.org/W4396894869","https://openalex.org/W4406259729","https://openalex.org/W4406259996"],"related_works":[],"abstract_inverted_index":{"Single-cell":[0],"three-dimensional":[1],"(3D)":[2],"genomics":[3],"plays":[4],"a":[5,132,252],"vital":[6],"role":[7],"in":[8,140,148,176,195],"understanding":[9],"the":[10,16,47,50,85,100,115,153,227,268],"spatial":[11],"organization":[12],"of":[13,46,104,114,229,262],"chromatin":[14,24,272],"within":[15],"cell":[17,37],"nucleus.":[18],"It":[19,171],"provides":[20],"insights":[21,281],"into":[22,282],"how":[23],"structures":[25],"influence":[26],"regulatory":[27,284],"mechanisms":[28],"and":[29,39,78,124,184,193,208,234,276],"cellular":[30],"functions":[31],"that":[32,83],"are":[33,74],"specific":[34,223],"to":[35,143,189,214,242],"different":[36],"types":[38,261],"states.":[40],"Analyzing":[41],"differential":[42,97,145,203],"interactions-the":[43],"fundamental":[44],"units":[45],"3D":[48,62],"genome-at":[49],"single-cell":[51,61,67,101,141],"level":[52],"is":[53],"crucial":[54],"for":[55,95,110,163],"extracting":[56],"this":[57,128],"valuable":[58],"information.":[59],"However,":[60],"genome":[63],"data":[64,73,167],"such":[65],"as":[66,218],"High-throughput":[68],"Chromatin":[69],"Conformation":[70],"Capture":[71],"(scHi-C)":[72],"inherently":[75],"sparse,":[76],"noisy":[77],"heterogeneous,":[79],"posing":[80],"significant":[81],"challenges":[82],"limit":[84],"downstream":[86],"analyses.":[87],"Although":[88],"existing":[89,243],"computational":[90],"methods":[91,245],"offer":[92],"helpful":[93],"solutions":[94],"identifying":[96],"interactions":[98,204],"at":[99],"level,":[102],"most":[103],"them":[105],"do":[106,118],"not":[107],"explicitly":[108],"account":[109],"intrinsic":[111],"statistical":[112,133],"properties":[113],"data,":[116],"nor":[117],"they":[119],"comprehensively":[120],"incorporate":[121],"both":[122,182,232],"within-sample":[123],"between-sample":[125],"covariates.":[126],"In":[127],"study,":[129],"we":[130,250],"developed":[131],"method":[134],"named":[135],"DISHIC":[136,151,230],"(Differential":[137],"Interaction":[138],"analysis":[139,147],"Hi-C)":[142],"perform":[144],"interaction":[146],"scHi-C":[149,197],"data.":[150,198],"leverages":[152],"Zero-Inflated":[154],"Negative":[155],"Binomial-based":[156],"Wavelet":[157],"(ZINB-WaVE)":[158],"model,":[159],"making":[160],"it":[161,188],"well-suited":[162],"high-dimensional":[164],"zero-inflated":[165],"count":[166],"with":[168,205],"high":[169],"dispersion.":[170],"models":[172],"each":[173,177],"bin":[174],"pair":[175],"sample":[178],"independently":[179],"while":[180,210],"incorporating":[181],"bin-pair-level":[183],"cell-level":[185],"covariates,":[186],"allowing":[187,212],"effectively":[190],"capture":[191],"noise":[192],"heterogeneity":[194],"sparse":[196],"This":[199,265],"approach":[200],"can":[201],"detect":[202],"greater":[206],"accuracy":[207],"reliability":[209],"also":[211],"users":[213],"flexibly":[215],"define":[216],"covariates":[217],"input":[219],"based":[220],"on":[221],"their":[222],"needs.":[224],"We":[225],"evaluated":[226],"performance":[228],"using":[231],"real":[233],"simulated":[235],"datasets,":[236],"demonstrating":[237],"its":[238],"enhanced":[239],"effectiveness":[240],"compared":[241],"state-of-the-art":[244],"under":[246],"various":[247],"conditions.":[248],"Furthermore,":[249],"conducted":[251],"comprehensive":[253],"case":[254],"study":[255,266],"analyzing":[256],"multi-omics":[257],"datasets":[258],"from":[259],"two":[260],"glial":[263],"cells.":[264],"explored":[267],"intricate":[269],"relationships":[270],"among":[271],"interactions,":[273],"gene":[274],"expressions,":[275],"epigenetic":[277],"modifications,":[278],"providing":[279],"new":[280],"cell-type-specific":[283],"mechanisms.":[285]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
