{"id":"https://openalex.org/W2167010218","doi":"https://doi.org/10.1093/bioinformatics/bts502","title":"FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment","display_name":"FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment","publication_year":2012,"publication_date":"2012-08-24","ids":{"openalex":"https://openalex.org/W2167010218","doi":"https://doi.org/10.1093/bioinformatics/bts502","mag":"2167010218","pmid":"https://pubmed.ncbi.nlm.nih.gov/22923307"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts502","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts502","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/20/2662/16908958/bts502.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/28/20/2662/16908958/bts502.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043651523","display_name":"Haisu Ma","orcid":null},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Haisu Ma","raw_affiliation_strings":["1 Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511 and 2Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT 06520, USA"],"affiliations":[{"raw_affiliation_string":"1 Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511 and 2Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT 06520, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074828414","display_name":"Hongyu Zhao","orcid":"https://orcid.org/0000-0003-1195-9607"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hongyu Zhao","raw_affiliation_strings":["1 Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511 and 2Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT 06520, USA"],"affiliations":[{"raw_affiliation_string":"1 Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511 and 2Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT 06520, USA","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5074828414"],"corresponding_institution_ids":["https://openalex.org/I32971472"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.4188,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.89611731,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"28","issue":"20","first_page":"2662","last_page":"2670"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","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/T10885","display_name":"Gene expression and cancer classification","score":0.9891999959945679,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6944024562835693},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6532545685768127},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5468449592590332},{"id":"https://openalex.org/keywords/snapshot","display_name":"Snapshot (computer storage)","score":0.5123773813247681},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.5033029913902283},{"id":"https://openalex.org/keywords/bayesian-inference","display_name":"Bayesian inference","score":0.4759126305580139},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.47199371457099915},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4708644449710846},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4354391396045685},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.37059593200683594},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3306792974472046},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.31017768383026123},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21397149562835693}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6944024562835693},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6532545685768127},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5468449592590332},{"id":"https://openalex.org/C55282118","wikidata":"https://www.wikidata.org/wiki/Q252683","display_name":"Snapshot (computer storage)","level":2,"score":0.5123773813247681},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.5033029913902283},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.4759126305580139},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.47199371457099915},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4708644449710846},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4354391396045685},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.37059593200683594},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3306792974472046},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.31017768383026123},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21397149562835693},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"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":"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":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bts502","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts502","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/20/2662/16908958/bts502.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:22923307","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22923307","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:europepmc.org:2787192","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3467747","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts502","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts502","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/20/2662/16908958/bts502.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/3","score":0.6499999761581421,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G630330811","display_name":null,"funder_award_id":"GM59507","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7217317707","display_name":null,"funder_award_id":"DMS 1106738","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2167010218.pdf","grobid_xml":"https://content.openalex.org/works/W2167010218.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W180513472","https://openalex.org/W1874573848","https://openalex.org/W1976526581","https://openalex.org/W1986008049","https://openalex.org/W1986087295","https://openalex.org/W1986240377","https://openalex.org/W1998202992","https://openalex.org/W1998767819","https://openalex.org/W2022357980","https://openalex.org/W2023947478","https://openalex.org/W2025577942","https://openalex.org/W2029980980","https://openalex.org/W2035751541","https://openalex.org/W2044758109","https://openalex.org/W2051068375","https://openalex.org/W2072041551","https://openalex.org/W2087312216","https://openalex.org/W2088320215","https://openalex.org/W2094791588","https://openalex.org/W2096218546","https://openalex.org/W2111094216","https://openalex.org/W2121604817","https://openalex.org/W2122440289","https://openalex.org/W2123106337","https://openalex.org/W2125577585","https://openalex.org/W2126254909","https://openalex.org/W2128601422","https://openalex.org/W2130410032","https://openalex.org/W2133465414","https://openalex.org/W2133807576","https://openalex.org/W2139516171","https://openalex.org/W2143969914","https://openalex.org/W2152991541","https://openalex.org/W2153838454","https://openalex.org/W2154896031","https://openalex.org/W2158217645","https://openalex.org/W2158293950","https://openalex.org/W2169815691","https://openalex.org/W2918064359","https://openalex.org/W4237293127","https://openalex.org/W4388319965","https://openalex.org/W6639353686","https://openalex.org/W6644307160","https://openalex.org/W6678700986","https://openalex.org/W6858214765"],"related_works":["https://openalex.org/W2542847180","https://openalex.org/W3034994054","https://openalex.org/W2805712290","https://openalex.org/W2909129499","https://openalex.org/W2392087771","https://openalex.org/W2761598930","https://openalex.org/W2356600124","https://openalex.org/W4245782888","https://openalex.org/W3181327668","https://openalex.org/W2374624607"],"abstract_inverted_index":{"The":[0],"R":[1],"package":[2],"'FacPad'":[3],"is":[4],"publically":[5],"available":[6],"at:":[7],"http://cran.open-source-solution.org/web/packages/FacPad/.":[8]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}