{"id":"https://openalex.org/W4403863248","doi":"https://doi.org/10.1109/tcbb.2024.3487434","title":"Detecting Boolean Asymmetric Relationships With a Loop Counting Technique and its Implications for Analyzing Heterogeneity Within Gene Expression Datasets","display_name":"Detecting Boolean Asymmetric Relationships With a Loop Counting Technique and its Implications for Analyzing Heterogeneity Within Gene Expression Datasets","publication_year":2024,"publication_date":"2024-10-29","ids":{"openalex":"https://openalex.org/W4403863248","doi":"https://doi.org/10.1109/tcbb.2024.3487434","pmid":"https://pubmed.ncbi.nlm.nih.gov/39471117"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2024.3487434","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3487434","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":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12037869/pdf/nihms-2043603.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101911636","display_name":"Haosheng Zhou","orcid":"https://orcid.org/0000-0001-8062-9818"},"institutions":[{"id":"https://openalex.org/I36672615","display_name":"Courant Institute of Mathematical Sciences","ror":"https://ror.org/037tm7f56","country_code":"US","type":"education","lineage":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Haosheng Zhou","raw_affiliation_strings":["Courant Institute of Mathematical Sciences, New York University, New York, NY, USA","Courant Institute of Mathematical Sciences, New York University, NY, USA"],"raw_orcid":"https://orcid.org/0000-0001-8062-9818","affiliations":[{"raw_affiliation_string":"Courant Institute of Mathematical Sciences, New York University, New York, NY, USA","institution_ids":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"raw_affiliation_string":"Courant Institute of Mathematical Sciences, New York University, NY, USA","institution_ids":["https://openalex.org/I36672615","https://openalex.org/I57206974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100665430","display_name":"Wei Lin","orcid":"https://orcid.org/0000-0002-7506-3466"},"institutions":[{"id":"https://openalex.org/I1284308235","display_name":"Translational Genomics Research Institute","ror":"https://ror.org/02hfpnk21","country_code":"US","type":"facility","lineage":["https://openalex.org/I1284308235"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Lin","raw_affiliation_strings":["Translational Genomics Research Institute, Quantitative Medicine and Systems Biology, Phoenix, AZ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Translational Genomics Research Institute, Quantitative Medicine and Systems Biology, Phoenix, AZ, USA","institution_ids":["https://openalex.org/I1284308235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086410837","display_name":"Sergio R. Labra","orcid":"https://orcid.org/0000-0002-4072-1131"},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sergio R. Labra","raw_affiliation_strings":["Scripps Research Institute, Department of Molecular Medicine and Chemistry, La Jolla, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-4072-1131","affiliations":[{"raw_affiliation_string":"Scripps Research Institute, Department of Molecular Medicine and Chemistry, La Jolla, CA, USA","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066753734","display_name":"Stuart A. Lipton","orcid":"https://orcid.org/0000-0002-3490-1259"},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stuart A. Lipton","raw_affiliation_strings":["Scripps Research Institute, Neurodegeneration New Medicines Center, Department of Molecular Medicine, La Jolla, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-3490-1259","affiliations":[{"raw_affiliation_string":"Scripps Research Institute, Neurodegeneration New Medicines Center, Department of Molecular Medicine, La Jolla, CA, USA","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017640298","display_name":"Jeremy A. Elman","orcid":"https://orcid.org/0000-0002-5840-1769"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremy A. Elman","raw_affiliation_strings":["Department of Psychiatry, University of California San Diego, La Jolla, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-5840-1769","affiliations":[{"raw_affiliation_string":"Department of Psychiatry, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077225971","display_name":"Nicholas J. Schork","orcid":"https://orcid.org/0000-0003-0920-5013"},"institutions":[{"id":"https://openalex.org/I1284308235","display_name":"Translational Genomics Research Institute","ror":"https://ror.org/02hfpnk21","country_code":"US","type":"facility","lineage":["https://openalex.org/I1284308235"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas J. Schork","raw_affiliation_strings":["Translational Genomics Research Institute, Quantitative Medicine and Systems Biology, Phoenix, AZ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Translational Genomics Research Institute, Quantitative Medicine and Systems Biology, Phoenix, AZ, USA","institution_ids":["https://openalex.org/I1284308235"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064329905","display_name":"Aaditya V. Rangan","orcid":"https://orcid.org/0000-0003-1579-7991"},"institutions":[{"id":"https://openalex.org/I36672615","display_name":"Courant Institute of Mathematical Sciences","ror":"https://ror.org/037tm7f56","country_code":"US","type":"education","lineage":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaditya V. Rangan","raw_affiliation_strings":["Courant Institute of Mathematical Sciences, New York University, New York, NY, USA","Courant Institute of Mathematical Sciences, New York University, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Courant Institute of Mathematical Sciences, New York University, New York, NY, USA","institution_ids":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"raw_affiliation_string":"Courant Institute of Mathematical Sciences, New York University, NY, USA","institution_ids":["https://openalex.org/I36672615","https://openalex.org/I57206974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5101911636"],"corresponding_institution_ids":["https://openalex.org/I36672615","https://openalex.org/I57206974"],"apc_list":null,"apc_paid":null,"fwci":0.2227,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.58095189,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"22","issue":"1","first_page":"27","last_page":"38"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9979000091552734,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9979000091552734,"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":0.995199978351593,"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":0.9883000254631042,"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/expression","display_name":"Expression (computer science)","score":0.5575418472290039},{"id":"https://openalex.org/keywords/loop","display_name":"Loop (graph theory)","score":0.45887553691864014},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4318593442440033},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39275094866752625},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3364362120628357},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.332153856754303},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3295212984085083},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2634180188179016},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.11990854144096375}],"concepts":[{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5575418472290039},{"id":"https://openalex.org/C184670325","wikidata":"https://www.wikidata.org/wiki/Q512604","display_name":"Loop (graph theory)","level":2,"score":0.45887553691864014},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4318593442440033},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39275094866752625},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3364362120628357},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.332153856754303},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3295212984085083},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2634180188179016},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.11990854144096375},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbb.2024.3487434","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3487434","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:39471117","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39471117","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},{"id":"pmh:oai:pubmedcentral.nih.gov:12037869","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12037869/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12037869/pdf/nihms-2043603.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Trans Comput Biol Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:12037869","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12037869/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12037869/pdf/nihms-2043603.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Trans Comput Biol Bioinform","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G20805340","display_name":null,"funder_award_id":"UH3AG064706","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2244907097","display_name":null,"funder_award_id":"AG065169","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6723679444","display_name":null,"funder_award_id":"U19 AG065169","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"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/W4403863248.pdf","grobid_xml":"https://content.openalex.org/works/W4403863248.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W1600339875","https://openalex.org/W1637197683","https://openalex.org/W1891744697","https://openalex.org/W1895263298","https://openalex.org/W1964854862","https://openalex.org/W1987881263","https://openalex.org/W1992120851","https://openalex.org/W2005936873","https://openalex.org/W2034784092","https://openalex.org/W2043905333","https://openalex.org/W2048971937","https://openalex.org/W2051201963","https://openalex.org/W2055849881","https://openalex.org/W2056297380","https://openalex.org/W2060406328","https://openalex.org/W2068805767","https://openalex.org/W2080374853","https://openalex.org/W2081324564","https://openalex.org/W2084251771","https://openalex.org/W2085116222","https://openalex.org/W2089500151","https://openalex.org/W2090867005","https://openalex.org/W2109195117","https://openalex.org/W2120696420","https://openalex.org/W2131681506","https://openalex.org/W2135000328","https://openalex.org/W2141012957","https://openalex.org/W2144544802","https://openalex.org/W2149031002","https://openalex.org/W2159480644","https://openalex.org/W2160533336","https://openalex.org/W2162752924","https://openalex.org/W2169387435","https://openalex.org/W2301536592","https://openalex.org/W2343876552","https://openalex.org/W2559479590","https://openalex.org/W2782262358","https://openalex.org/W2805027024","https://openalex.org/W2895694428","https://openalex.org/W2904130550","https://openalex.org/W2910528791","https://openalex.org/W2946121087","https://openalex.org/W2989784226","https://openalex.org/W3016206855","https://openalex.org/W3108760242","https://openalex.org/W3126301796","https://openalex.org/W3184070303","https://openalex.org/W4283729936","https://openalex.org/W4293093121","https://openalex.org/W4306730220","https://openalex.org/W4311457559","https://openalex.org/W4386568734","https://openalex.org/W6629329278","https://openalex.org/W6698232373","https://openalex.org/W6748816842"],"related_works":["https://openalex.org/W24774503","https://openalex.org/W2014821076","https://openalex.org/W1990620319","https://openalex.org/W1965744717","https://openalex.org/W2111234595","https://openalex.org/W3216334292","https://openalex.org/W1883238101","https://openalex.org/W2481821631","https://openalex.org/W1536525683","https://openalex.org/W2482256034"],"abstract_inverted_index":{"Many":[0],"traditional":[1,164,200],"methods":[2],"for":[3,30,84,122],"analyzing":[4],"gene-gene":[5,100],"relationships":[6,52,87],"focus":[7],"on":[8,109],"positive":[9],"and":[10,175,187],"negative":[11],"correlations,":[12],"both":[13],"of":[14,19,32,40,79,106,139,173],"which":[15,81,194],"are":[16,82],"a":[17,38,62,137,146],"kind":[18],"'symmetric'":[20],"relationship.":[21],"Biclustering":[22],"is":[23,96],"one":[24,107,189],"such":[25,49],"technique":[26],"that":[27,66,76,95,120,133,151],"typically":[28],"searches":[29],"subsets":[31,78,172],"genes":[33,43,80],"exhibiting":[34],"correlated":[35],"expression":[36],"among":[37,136],"subset":[39,138],"samples.":[41,140],"However,":[42],"can":[44,67,91,129,190],"also":[45],"exhibit":[46],"'asymmetric'":[47],"relationships,":[48],"as":[50],"'if-then'":[51],"used":[53,69],"in":[54],"boolean":[55],"circuits.":[56],"In":[57],"this":[58],"paper":[59],"we":[60],"develop":[61],"very":[63],"general":[64],"method":[65,144],"be":[68],"to":[70,93,145],"detect":[71,130],"biclusters":[72],"within":[73,161,179],"gene-expression":[74],"data":[75],"involve":[77,170],"enriched":[83],"these":[85],"'boolean-asymmetric'":[86],"(BARs).":[88],"These":[89],"BAR-biclusters":[90,128,154,169],"correspond":[92],"heterogeneity":[94],"driven":[97],"by":[98,183],"asymmetric":[99,131],"interactions,":[101],"e.g.,":[102],"reflecting":[103],"regulatory":[104],"effects":[105],"gene":[108],"another,":[110],"rather":[111],"than":[112],"more":[113,163],"standard":[114],"symmetric":[115],"interactions.":[116],"Unlike":[117],"typical":[118],"approaches":[119],"search":[121],"BARs":[123],"across":[124],"the":[125,152,162,168,180,185],"entire":[126],"population,":[127],"interactions":[132],"only":[134,199],"occur":[135],"We":[141],"apply":[142],"our":[143],"single-cell":[147],"RNA-sequencing":[148],"data-set,":[149],"demonstrating":[150],"statistically-significant":[153],"indeed":[155],"contain":[156],"additional":[157],"information":[158],"not":[159],"present":[160],"'boolean-symmetric'-biclusters.":[165],"For":[166],"example,":[167],"different":[171,177],"cells,":[174],"highlight":[176],"gene-pathways":[178],"data-set.":[181],"Moreover,":[182],"combining":[184],"boolean-asymmetric-":[186],"boolean-symmetric-signals,":[188],"build":[191],"linear":[192],"classifiers":[193],"outperform":[195],"those":[196],"built":[197],"using":[198],"boolean-symmetric":[201],"signals.":[202]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2025-12-22T23:10:17.713674","created_date":"2025-10-10T00:00:00"}
