{"id":"https://openalex.org/W2805027024","doi":"https://doi.org/10.1371/journal.pcbi.1006105","title":"A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data","display_name":"A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data","publication_year":2018,"publication_date":"2018-05-14","ids":{"openalex":"https://openalex.org/W2805027024","doi":"https://doi.org/10.1371/journal.pcbi.1006105","mag":"2805027024","pmid":"https://pubmed.ncbi.nlm.nih.gov/29758032"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1006105","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006105","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006105&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.1006105&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064329905","display_name":"Aaditya V. Rangan","orcid":"https://orcid.org/0000-0003-1579-7991"},"institutions":[{"id":"https://openalex.org/I4210153546","display_name":"Flatiron Health (United States)","ror":"https://ror.org/0508h6p74","country_code":"US","type":"company","lineage":["https://openalex.org/I4210153546"]},{"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":"Aaditya V. Rangan","raw_affiliation_strings":["Center for Computational Biology, Flatiron Institute, New York, New York, United States of America","Mathematics, New York University, New York, New York, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-1579-7991","affiliations":[{"raw_affiliation_string":"Center for Computational Biology, Flatiron Institute, New York, New York, United States of America","institution_ids":["https://openalex.org/I4210153546"]},{"raw_affiliation_string":"Mathematics, New York University, New York, New York, United States of America","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014652082","display_name":"Caroline C. McGrouther","orcid":null},"institutions":[{"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":"Caroline C. McGrouther","raw_affiliation_strings":["Mathematics, New York University, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mathematics, New York University, New York, New York, United States of America","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016043879","display_name":"John R. Kelsoe","orcid":"https://orcid.org/0000-0002-3013-2333"},"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":"John Kelsoe","raw_affiliation_strings":["Psychiatry, University of California, San Diego, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Psychiatry, University of California, San Diego, California, United States of America","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/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas Schork","raw_affiliation_strings":["Human Biology, J. Craig Venters Institute, La Jolla, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Biology, J. Craig Venters Institute, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I1301553790"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006966752","display_name":"Eli A. Stahl","orcid":"https://orcid.org/0000-0002-1192-0561"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Eli Stahl","raw_affiliation_strings":["Genetics and Genomic Sciences, Mount Sinai Medical School, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genetics and Genomic Sciences, Mount Sinai Medical School, New York, New York, United States of America","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100616624","display_name":"Qian Zhu","orcid":"https://orcid.org/0000-0001-7062-8221"},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qian Zhu","raw_affiliation_strings":["Computer Science, Princeton University, Princeton, New Jersey, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-7062-8221","affiliations":[{"raw_affiliation_string":"Computer Science, Princeton University, Princeton, New Jersey, United States of America","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053907733","display_name":"Arjun Krishnan","orcid":"https://orcid.org/0000-0002-7980-4110"},"institutions":[{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]},{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arjun Krishnan","raw_affiliation_strings":["Computational Mathematics Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Mathematics Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America","institution_ids":["https://openalex.org/I87216513","https://openalex.org/I4210111179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006247664","display_name":"Vicky Yao","orcid":"https://orcid.org/0000-0002-3201-9983"},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vicky Yao","raw_affiliation_strings":["Computer Science, Princeton University, Princeton, New Jersey, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-3201-9983","affiliations":[{"raw_affiliation_string":"Computer Science, Princeton University, Princeton, New Jersey, United States of America","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025250742","display_name":"Olga G. Troyanskaya","orcid":"https://orcid.org/0000-0002-5676-5737"},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]},{"id":"https://openalex.org/I4210153546","display_name":"Flatiron Health (United States)","ror":"https://ror.org/0508h6p74","country_code":"US","type":"company","lineage":["https://openalex.org/I4210153546"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Olga Troyanskaya","raw_affiliation_strings":["Center for Computational Biology, Flatiron Institute, New York, New York, United States of America","Computer Science, Princeton University, Princeton, New Jersey, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, Flatiron Institute, New York, New York, United States of America","institution_ids":["https://openalex.org/I4210153546"]},{"raw_affiliation_string":"Computer Science, Princeton University, Princeton, New Jersey, United States of America","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050630351","display_name":"Seda Bilaloglu","orcid":"https://orcid.org/0000-0002-0242-8348"},"institutions":[{"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":"Seda Bilaloglu","raw_affiliation_strings":["Department of Rehabilitation Medicine, New York University Medical School, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Rehabilitation Medicine, New York University Medical School, New York, New York, United States of America","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019962521","display_name":"Preeti Raghavan","orcid":"https://orcid.org/0000-0002-7852-5005"},"institutions":[{"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":"Preeti Raghavan","raw_affiliation_strings":["Department of Rehabilitation Medicine, New York University Medical School, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Rehabilitation Medicine, New York University Medical School, New York, New York, United States of America","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046910847","display_name":"Sarah E. Bergen","orcid":"https://orcid.org/0000-0002-5888-0034"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Sarah Bergen","raw_affiliation_strings":["Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-5888-0034","affiliations":[{"raw_affiliation_string":"Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064331176","display_name":"Anders Jur\u00e9us","orcid":"https://orcid.org/0000-0002-8922-6377"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]},{"id":"https://openalex.org/I881427289","display_name":"University of Gothenburg","ror":"https://ror.org/01tm6cn81","country_code":"SE","type":"education","lineage":["https://openalex.org/I881427289"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Anders Jureus","raw_affiliation_strings":["Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden","Physiology and Biophysics, University of Gothenburg, Gothenburg, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden","institution_ids":["https://openalex.org/I28166907"]},{"raw_affiliation_string":"Physiology and Biophysics, University of Gothenburg, Gothenburg, Sweden","institution_ids":["https://openalex.org/I881427289"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023024313","display_name":"Mikael Land\u00e9n","orcid":null},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Mikael Landen","raw_affiliation_strings":["Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden","institution_ids":["https://openalex.org/I28166907"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":14,"corresponding_author_ids":["https://openalex.org/A5064329905"],"corresponding_institution_ids":["https://openalex.org/I4210153546","https://openalex.org/I57206974"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.1856,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.52957295,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"14","issue":"5","first_page":"e1006105","last_page":"e1006105"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9994000196456909,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9994000196456909,"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":0.9914000034332275,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9854000210762024,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/covariate","display_name":"Covariate","score":0.802891731262207},{"id":"https://openalex.org/keywords/biclustering","display_name":"Biclustering","score":0.6969043016433716},{"id":"https://openalex.org/keywords/rank","display_name":"Rank (graph theory)","score":0.49117276072502136},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.44422829151153564},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44289296865463257},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37937256693840027},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.3590910732746124},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32988783717155457},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2726603150367737},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.17323195934295654},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.09893065690994263}],"concepts":[{"id":"https://openalex.org/C119043178","wikidata":"https://www.wikidata.org/wiki/Q320723","display_name":"Covariate","level":2,"score":0.802891731262207},{"id":"https://openalex.org/C144817290","wikidata":"https://www.wikidata.org/wiki/Q2976575","display_name":"Biclustering","level":5,"score":0.6969043016433716},{"id":"https://openalex.org/C164226766","wikidata":"https://www.wikidata.org/wiki/Q7293202","display_name":"Rank (graph theory)","level":2,"score":0.49117276072502136},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.44422829151153564},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44289296865463257},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37937256693840027},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3590910732746124},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32988783717155457},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2726603150367737},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.17323195934295654},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.09893065690994263},{"id":"https://openalex.org/C94641424","wikidata":"https://www.wikidata.org/wiki/Q5172845","display_name":"Correlation clustering","level":3,"score":0.0},{"id":"https://openalex.org/C33704608","wikidata":"https://www.wikidata.org/wiki/Q5014717","display_name":"CURE data clustering algorithm","level":4,"score":0.0}],"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":"D001714","descriptor_name":"Bipolar Disorder","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001714","descriptor_name":"Bipolar Disorder","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001714","descriptor_name":"Bipolar Disorder","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1006105","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006105","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006105&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:29758032","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29758032","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:RePEc:plo:pcbi00:1006105","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006105","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:3516fd8d65ac40969c8cda7731788d4e","is_oa":true,"landing_page_url":"https://doaj.org/article/3516fd8d65ac40969c8cda7731788d4e","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 14, Iss 5, p e1006105 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4962794","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC5997363","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":"","raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/6266759","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/A_loop-counting_method_for_covariate-corrected_low-rank_biclustering_of_gene-expression_and_genome-wide_association_study_data/6266759","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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:pubmedcentral.nih.gov:5997363","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5997363","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1006105","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006105","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006105&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":[],"awards":[{"id":"https://openalex.org/G2219584700","display_name":null,"funder_award_id":"24-74501-X0096-R9834","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306164","display_name":"Simons Foundation","ror":"https://ror.org/01cmst727"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2805027024.pdf","grobid_xml":"https://content.openalex.org/works/W2805027024.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W93530381","https://openalex.org/W564855521","https://openalex.org/W1486996222","https://openalex.org/W1593486402","https://openalex.org/W1829669249","https://openalex.org/W1868454717","https://openalex.org/W1984238247","https://openalex.org/W1986010539","https://openalex.org/W1988615302","https://openalex.org/W1992918752","https://openalex.org/W2023416945","https://openalex.org/W2036328877","https://openalex.org/W2043905333","https://openalex.org/W2048971937","https://openalex.org/W2065303476","https://openalex.org/W2066459155","https://openalex.org/W2079361215","https://openalex.org/W2080278541","https://openalex.org/W2090257125","https://openalex.org/W2091551287","https://openalex.org/W2098290597","https://openalex.org/W2113055609","https://openalex.org/W2117730787","https://openalex.org/W2126877147","https://openalex.org/W2130158951","https://openalex.org/W2133149215","https://openalex.org/W2133576408","https://openalex.org/W2135105223","https://openalex.org/W2136107412","https://openalex.org/W2144544802","https://openalex.org/W2148125505","https://openalex.org/W2150718242","https://openalex.org/W2151933617","https://openalex.org/W2158309583","https://openalex.org/W2159998236","https://openalex.org/W2164061579","https://openalex.org/W2165232124","https://openalex.org/W2166602562","https://openalex.org/W2166661751","https://openalex.org/W2169387435","https://openalex.org/W2493031458","https://openalex.org/W2911293880","https://openalex.org/W2950358183","https://openalex.org/W2952259914","https://openalex.org/W2964207886","https://openalex.org/W3100951886","https://openalex.org/W4285719527","https://openalex.org/W6635743399","https://openalex.org/W6823353385","https://openalex.org/W6989532433"],"related_works":["https://openalex.org/W1974340769","https://openalex.org/W2900595096","https://openalex.org/W4289277241","https://openalex.org/W2979322793","https://openalex.org/W2765801824","https://openalex.org/W2188068678","https://openalex.org/W2157302779","https://openalex.org/W4236723217","https://openalex.org/W4226363062","https://openalex.org/W2109980432"],"abstract_inverted_index":{"A":[0],"common":[1],"goal":[2],"in":[3,58,76,85,113],"data-analysis":[4],"is":[5,96],"to":[6,103,122],"sift":[7],"through":[8,66],"a":[9,21,27,77,155],"large":[10],"data-matrix":[11,55],"and":[12,47,51,68,127,150],"detect":[13],"any":[14],"significant":[15],"submatrices":[16,41],"(i.e.,":[17,42],"biclusters)":[18],"that":[19,56,70,97],"have":[20],"low":[22],"numerical":[23],"rank.":[24],"We":[25,64,136],"present":[26],"simple":[28,82],"algorithm":[29,36,118],"for":[30,105,124],"tackling":[31],"this":[32,71],"biclustering":[33],"problem.":[34],"Our":[35],"accumulates":[37],"information":[38],"about":[39],"2-by-2":[40],"'loops')":[43],"within":[44,133],"the":[45,54,134,144,151],"data-matrix,":[46],"focuses":[48],"on":[49],"rows":[50],"columns":[52],"of":[53,61,79,88,93,107],"participate":[57],"an":[59],"abundance":[60],"low-rank":[62],"loops.":[63],"demonstrate,":[65],"analysis":[67,149],"numerical-experiments,":[69],"loop-counting":[72],"method":[73,95],"performs":[74],"well":[75,130],"variety":[78],"scenarios,":[80],"outperforming":[81],"spectral":[83],"methods":[84],"many":[86],"situations":[87],"interest.":[89],"Another":[90],"important":[91],"feature":[92],"our":[94,117],"it":[98],"can":[99,119],"easily":[100],"be":[101,120],"modified":[102,121],"account":[104],"aspects":[106],"experimental":[108],"design":[109],"which":[110],"commonly":[111],"arise":[112],"practice.":[114],"For":[115],"example,":[116],"correct":[123],"controls,":[125],"categorical-":[126],"continuous-covariates,":[128],"as":[129,131],"sparsity":[132],"data.":[135],"demonstrate":[137],"these":[138],"practical":[139],"features":[140],"with":[141],"two":[142],"examples;":[143],"first":[145],"drawn":[146,153],"from":[147,154],"gene-expression":[148],"second":[152],"much":[156],"larger":[157],"genome-wide-association-study":[158],"(GWAS).":[159]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}