{"id":"https://openalex.org/W2586464090","doi":"https://doi.org/10.1093/bioinformatics/btx058","title":"PatternMarkers &amp; GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF","display_name":"PatternMarkers &amp; GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF","publication_year":2017,"publication_date":"2017-01-30","ids":{"openalex":"https://openalex.org/W2586464090","doi":"https://doi.org/10.1093/bioinformatics/btx058","mag":"2586464090","pmid":"https://pubmed.ncbi.nlm.nih.gov/28174896"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx058","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx058","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/12/1892/25155541/btx058.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/12/1892/25155541/btx058.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069366529","display_name":"Genevieve Stein-O\u2019Brien","orcid":"https://orcid.org/0000-0001-8681-9110"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]},{"id":"https://openalex.org/I4210151493","display_name":"Lieber Institute for Brain Development","ror":"https://ror.org/04q36wn27","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210151493"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Genevieve L Stein-O\u2019Brien","raw_affiliation_strings":["Lieber Institute for Brain Development, Baltimore, MD, USA","McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lieber Institute for Brain Development, Baltimore, MD, USA","institution_ids":["https://openalex.org/I4210151493"]},{"raw_affiliation_string":"McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071206854","display_name":"Jacob Carey","orcid":"https://orcid.org/0000-0001-9462-206X"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jacob L Carey","raw_affiliation_strings":["Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040159274","display_name":"Wai Shing Lee","orcid":null},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wai Shing Lee","raw_affiliation_strings":["Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031000000","display_name":"Michael Considine","orcid":"https://orcid.org/0000-0002-4468-6820"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Considine","raw_affiliation_strings":["Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080546333","display_name":"Alexander V. Favorov","orcid":"https://orcid.org/0000-0003-2595-1091"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]},{"id":"https://openalex.org/I4210148309","display_name":"Vavilov Institute of General Genetics","ror":"https://ror.org/05ermrg42","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210148309"]},{"id":"https://openalex.org/I4210163576","display_name":"Genetika","ror":"https://ror.org/05hr7qe62","country_code":"RU","type":"facility","lineage":["https://openalex.org/I4210163576"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"Alexander V Favorov","raw_affiliation_strings":["Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA","Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia","Vavilov Institute of General Genetics, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"]},{"raw_affiliation_string":"Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia","institution_ids":["https://openalex.org/I4210163576"]},{"raw_affiliation_string":"Vavilov Institute of General Genetics, Moscow, Russia","institution_ids":["https://openalex.org/I4210148309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033962716","display_name":"Emily Flam","orcid":"https://orcid.org/0000-0001-6262-1126"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emily Flam","raw_affiliation_strings":["Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022815817","display_name":"Theresa Guo","orcid":"https://orcid.org/0000-0002-1689-3275"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Theresa Guo","raw_affiliation_strings":["Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100698035","display_name":"Sijia Li","orcid":"https://orcid.org/0000-0002-2244-7327"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sijia Li","raw_affiliation_strings":["Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079978893","display_name":"Luigi Marchionni","orcid":"https://orcid.org/0000-0002-7336-8071"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Luigi Marchionni","raw_affiliation_strings":["Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057519297","display_name":"Thomas D. Sherman","orcid":null},"institutions":[{"id":"https://openalex.org/I64281891","display_name":"College of New Jersey","ror":"https://ror.org/02nx5r318","country_code":"US","type":"education","lineage":["https://openalex.org/I64281891"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas Sherman","raw_affiliation_strings":["Department of Mathematics and Statistics, The College of New Jersey, Ewing Township, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, The College of New Jersey, Ewing Township, NJ, USA","institution_ids":["https://openalex.org/I64281891"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027765178","display_name":"Shawn Sivy","orcid":null},"institutions":[{"id":"https://openalex.org/I64281891","display_name":"College of New Jersey","ror":"https://ror.org/02nx5r318","country_code":"US","type":"education","lineage":["https://openalex.org/I64281891"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shawn Sivy","raw_affiliation_strings":["Department of Mathematics and Statistics, The College of New Jersey, Ewing Township, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, The College of New Jersey, Ewing Township, NJ, USA","institution_ids":["https://openalex.org/I64281891"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052817116","display_name":"Daria A. Gaykalova","orcid":"https://orcid.org/0000-0001-5037-0147"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daria A Gaykalova","raw_affiliation_strings":["Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113433650","display_name":"Ronald D.G. McKay","orcid":null},"institutions":[{"id":"https://openalex.org/I4210151493","display_name":"Lieber Institute for Brain Development","ror":"https://ror.org/04q36wn27","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210151493"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ronald D McKay","raw_affiliation_strings":["Lieber Institute for Brain Development, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lieber Institute for Brain Development, Baltimore, MD, USA","institution_ids":["https://openalex.org/I4210151493"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014591184","display_name":"Michael F. Ochs","orcid":null},"institutions":[{"id":"https://openalex.org/I64281891","display_name":"College of New Jersey","ror":"https://ror.org/02nx5r318","country_code":"US","type":"education","lineage":["https://openalex.org/I64281891"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael F Ochs","raw_affiliation_strings":["Department of Mathematics and Statistics, The College of New Jersey, Ewing Township, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, The College of New Jersey, Ewing Township, NJ, USA","institution_ids":["https://openalex.org/I64281891"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080758121","display_name":"Carlo Colantuoni","orcid":"https://orcid.org/0000-0001-6818-6380"},"institutions":[{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]},{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Carlo Colantuoni","raw_affiliation_strings":["Department of Neurology and Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA","Institute for Genome Sciences, University of Maryland School of Medicine"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neurology and Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"]},{"raw_affiliation_string":"Institute for Genome Sciences, University of Maryland School of Medicine","institution_ids":["https://openalex.org/I126744593"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027701541","display_name":"Elana J. Fertig","orcid":"https://orcid.org/0000-0003-3204-342X"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Elana J Fertig","raw_affiliation_strings":["Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5027701541","https://openalex.org/A5069366529","https://openalex.org/A5080758121"],"corresponding_institution_ids":["https://openalex.org/I126744593","https://openalex.org/I145311948","https://openalex.org/I2799853436","https://openalex.org/I4210151493"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.5141,"has_fulltext":false,"cited_by_count":63,"citation_normalized_percentile":{"value":0.89853864,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"33","issue":"12","first_page":"1892","last_page":"1894"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.3206000030040741,"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":0.3206000030040741,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.21279999613761902,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.18809999525547028,"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/transcriptome","display_name":"Transcriptome","score":0.715200662612915},{"id":"https://openalex.org/keywords/non-negative-matrix-factorization","display_name":"Non-negative matrix factorization","score":0.6078736782073975},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6022866368293762},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5001492500305176},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3488786220550537},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20948928594589233},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11936306953430176},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1149362325668335},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.095767080783844},{"id":"https://openalex.org/keywords/matrix-decomposition","display_name":"Matrix decomposition","score":0.09039363265037537},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.06360706686973572}],"concepts":[{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.715200662612915},{"id":"https://openalex.org/C152671427","wikidata":"https://www.wikidata.org/wiki/Q10843505","display_name":"Non-negative matrix factorization","level":4,"score":0.6078736782073975},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6022866368293762},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5001492500305176},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3488786220550537},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20948928594589233},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11936306953430176},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1149362325668335},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.095767080783844},{"id":"https://openalex.org/C42355184","wikidata":"https://www.wikidata.org/wiki/Q1361088","display_name":"Matrix decomposition","level":3,"score":0.09039363265037537},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.06360706686973572},{"id":"https://openalex.org/C158693339","wikidata":"https://www.wikidata.org/wiki/Q190524","display_name":"Eigenvalues and eigenvectors","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"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":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btx058","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx058","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/12/1892/25155541/btx058.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28174896","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28174896","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:5860188","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860188","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx058","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx058","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/12/1892/25155541/btx058.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.5,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G2761940219","display_name":null,"funder_award_id":"T32 GM007814","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6325397735","display_name":null,"funder_award_id":"R01 CA177669","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320315857","display_name":"Lieber Institute for Brain Development","ror":"https://ror.org/04q36wn27"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1533942137","https://openalex.org/W1538685017","https://openalex.org/W1768527575","https://openalex.org/W1816176398","https://openalex.org/W1963846748","https://openalex.org/W1982946814","https://openalex.org/W2001895044","https://openalex.org/W2008251891","https://openalex.org/W2036099373","https://openalex.org/W2039033307","https://openalex.org/W2056701536","https://openalex.org/W2101502746","https://openalex.org/W2130410032","https://openalex.org/W2136787567","https://openalex.org/W2156508863","https://openalex.org/W2158146385","https://openalex.org/W2170083890"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4399648768","https://openalex.org/W2101428145","https://openalex.org/W4297433825","https://openalex.org/W4318261659","https://openalex.org/W2122823937","https://openalex.org/W3215340255","https://openalex.org/W2048687561"],"abstract_inverted_index":{"SUMMARY:":[0],"Non-negative":[1],"Matrix":[2],"Factorization":[3],"(NMF)":[4],"algorithms":[5],"associate":[6],"gene":[7,54],"expression":[8],"with":[9,19,56,113,134],"biological":[10,42],"processes":[11],"(e.g.":[12],"time-course":[13],"dynamics":[14],"or":[15,170,172],"disease":[16],"subtypes).":[17],"Compared":[18],"univariate":[20],"associations,":[21],"the":[22,72,80,90,107,121,159,165],"relative":[23],"weights":[24],"of":[25,47,89,120,145],"NMF":[26,48,78,115],"solutions":[27],"can":[28,110],"obscure":[29],"biomarkers.":[30],"Therefore,":[31,61],"we":[32,62,126],"developed":[33,64],"a":[34,86,100],"novel":[35,51],"patternMarkers":[36,57,143],"statistic":[37],"to":[38],"extract":[39],"genes":[40],"for":[41,117],"validation":[43],"and":[44,52,95,130,142],"enhanced":[45],"visualization":[46,96],"results.":[49],"Finding":[50],"unbiased":[53],"markers":[55],"requires":[58],"whole-genome":[59,149],"data.":[60,150],"also":[63],"Genome-Wide":[65],"CoGAPS":[66,160],"Analysis":[67],"in":[68,106,137,158],"Parallel":[69],"Sets":[70],"(GWCoGAPS),":[71],"first":[73],"robust":[74],"whole":[75],"genome":[76],"Bayesian":[77],"using":[79],"sparse,":[81],"MCMC":[82],"algorithm,":[83,116],"CoGAPS.":[84],"Additionally,":[85],"manual":[87,108],"version":[88],"GWCoGAPS":[91,141,156],"algorithm":[92],"contains":[93],"analytic":[94],"tools":[97],"including":[98],"patternMatcher,":[99],"Shiny":[101],"web":[102],"application.":[103],"The":[104],"decomposition":[105],"pipeline":[109],"be":[111],"replaced":[112],"any":[114],"further":[118],"generalization":[119],"software.":[122],"Using":[123],"these":[124],"tools,":[125],"find":[127],"granular":[128],"brain-region":[129],"cell-type":[131],"specific":[132],"signatures":[133],"corresponding":[135],"biomarkers":[136,147],"GTEx":[138],"data,":[139],"illustrating":[140],"ascertainment":[144],"data-driven":[146],"from":[148],"AVAILABILITY":[151],"AND":[152],"IMPLEMENTATION:":[153],"PatternMarkers":[154],"&":[155],"are":[157,178],"Bioconductor":[161],"package":[162],"(3.5)":[163],"under":[164],"GPL":[166],"license.":[167],"CONTACT:":[168],"gsteinobrien@jhmi.edu":[169],"ccolantu@jhmi.edu":[171],"ejfertig@jhmi.edu.":[173],"SUPPLEMENTARY":[174],"INFORMATION:":[175],"Supplementary":[176],"data":[177],"available":[179],"at":[180],"Bioinformatics":[181],"online.":[182]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2017-02-17T00:00:00"}
