{"id":"https://openalex.org/W2170968232","doi":"https://doi.org/10.1093/bioinformatics/btp009","title":"Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools","display_name":"Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools","publication_year":2009,"publication_date":"2009-01-08","ids":{"openalex":"https://openalex.org/W2170968232","doi":"https://doi.org/10.1093/bioinformatics/btp009","mag":"2170968232","pmid":"https://pubmed.ncbi.nlm.nih.gov/19131367"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp009","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp009","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/4/545/48983771/bioinformatics_25_4_545.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/25/4/545/48983771/bioinformatics_25_4_545.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020817486","display_name":"Qihao Qi","orcid":null},"institutions":[{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qihao Qi","raw_affiliation_strings":["1 Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, 3900 Reservoir Rd. NW, Washington, DC 20057-1455, 2Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892-7434 and 3The EMMES Corporation, Rockville, MD 20850, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, 3900 Reservoir Rd. NW, Washington, DC 20057-1455, 2Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892-7434 and 3The EMMES Corporation, Rockville, MD 20850, USA","institution_ids":["https://openalex.org/I184565670","https://openalex.org/I4210140884"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063843258","display_name":"Yingdong Zhao","orcid":"https://orcid.org/0000-0002-8514-0293"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yingdong Zhao","raw_affiliation_strings":["1 Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, 3900 Reservoir Rd. NW, Washington, DC 20057-1455, 2Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892-7434 and 3The EMMES Corporation, Rockville, MD 20850, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, 3900 Reservoir Rd. NW, Washington, DC 20057-1455, 2Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892-7434 and 3The EMMES Corporation, Rockville, MD 20850, USA","institution_ids":["https://openalex.org/I184565670","https://openalex.org/I4210140884"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011156691","display_name":"Ming\u2010Chung Li","orcid":null},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"MingChung Li","raw_affiliation_strings":["1 Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, 3900 Reservoir Rd. NW, Washington, DC 20057-1455, 2Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892-7434 and 3The EMMES Corporation, Rockville, MD 20850, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, 3900 Reservoir Rd. NW, Washington, DC 20057-1455, 2Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892-7434 and 3The EMMES Corporation, Rockville, MD 20850, USA","institution_ids":["https://openalex.org/I184565670","https://openalex.org/I4210140884"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101715307","display_name":"Richard Simon","orcid":"https://orcid.org/0000-0003-3558-4598"},"institutions":[{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Richard Simon","raw_affiliation_strings":["1 Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, 3900 Reservoir Rd. NW, Washington, DC 20057-1455, 2Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892-7434 and 3The EMMES Corporation, Rockville, MD 20850, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biochemistry and Molecular Biology, Georgetown University School of Medicine, 3900 Reservoir Rd. NW, Washington, DC 20057-1455, 2Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892-7434 and 3The EMMES Corporation, Rockville, MD 20850, USA","institution_ids":["https://openalex.org/I184565670","https://openalex.org/I4210140884"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101715307"],"corresponding_institution_ids":["https://openalex.org/I184565670","https://openalex.org/I4210140884"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.887,"has_fulltext":false,"cited_by_count":50,"citation_normalized_percentile":{"value":0.85648584,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"25","issue":"4","first_page":"545","last_page":"547"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9926000237464905,"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/T11269","display_name":"Algorithms and Data Compression","score":0.975600004196167,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/non-negative-matrix-factorization","display_name":"Non-negative matrix factorization","score":0.9406445026397705},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6759135723114014},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.641242504119873},{"id":"https://openalex.org/keywords/matrix-decomposition","display_name":"Matrix decomposition","score":0.5905423760414124},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5028459429740906},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4665486514568329},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.4172891080379486},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.40458303689956665},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37167656421661377},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3552517890930176},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18868622183799744}],"concepts":[{"id":"https://openalex.org/C152671427","wikidata":"https://www.wikidata.org/wiki/Q10843505","display_name":"Non-negative matrix factorization","level":4,"score":0.9406445026397705},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6759135723114014},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.641242504119873},{"id":"https://openalex.org/C42355184","wikidata":"https://www.wikidata.org/wiki/Q1361088","display_name":"Matrix decomposition","level":3,"score":0.5905423760414124},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5028459429740906},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4665486514568329},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.4172891080379486},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.40458303689956665},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37167656421661377},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3552517890930176},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18868622183799744},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C158693339","wikidata":"https://www.wikidata.org/wiki/Q190524","display_name":"Eigenvalues and eigenvectors","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":"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":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","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},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btp009","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp009","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/4/545/48983771/bioinformatics_25_4_545.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:19131367","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19131367","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp009","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp009","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/4/545/48983771/bioinformatics_25_4_545.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":[{"id":"https://metadata.un.org/sdg/17","score":0.41999998688697815,"display_name":"Partnerships for the goals"},{"id":"https://metadata.un.org/sdg/9","score":0.4000000059604645,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2170968232.pdf","grobid_xml":"https://content.openalex.org/works/W2170968232.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1814100322","https://openalex.org/W1886306325","https://openalex.org/W1902027874","https://openalex.org/W1975152892","https://openalex.org/W1991596242","https://openalex.org/W2064690543","https://openalex.org/W2071949631","https://openalex.org/W2099738271","https://openalex.org/W2102330962","https://openalex.org/W2124890708","https://openalex.org/W2132692097","https://openalex.org/W2136787567","https://openalex.org/W2137784044","https://openalex.org/W2154097321","https://openalex.org/W2496585406","https://openalex.org/W4233287056","https://openalex.org/W4242743062","https://openalex.org/W6682845024"],"related_works":["https://openalex.org/W2127243424","https://openalex.org/W4390394189","https://openalex.org/W2037504162","https://openalex.org/W2539013788","https://openalex.org/W2792706544","https://openalex.org/W1568451138","https://openalex.org/W2156699640","https://openalex.org/W2045265907","https://openalex.org/W2972997031","https://openalex.org/W2075222291"],"abstract_inverted_index":{"The":[0,18],"NMF":[1,22],"analysis":[2],"plug-in":[3],"is":[4],"freely":[5],"available":[6,26],"in":[7],"BRB-ArrayTools":[8,12],"for":[9,21],"non-commercial":[10],"users.":[11],"can":[13],"be":[14],"downloaded":[15],"at":[16,27],"http://linus.nci.nih.gov/BRB-ArrayTools.html.":[17],"algorithms":[19],"used":[20],"and":[23],"Semi-NMF":[24],"are":[25],"ftp://linus.nci.nih.gov/pub/NMF.":[28]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":11},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":3}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
