{"id":"https://openalex.org/W2159906806","doi":"https://doi.org/10.1186/1471-2105-7-s1-s5","title":"A classification-based framework for predicting and analyzing gene regulatory response","display_name":"A classification-based framework for predicting and analyzing gene regulatory response","publication_year":2006,"publication_date":"2006-03-01","ids":{"openalex":"https://openalex.org/W2159906806","doi":"https://doi.org/10.1186/1471-2105-7-s1-s5","mag":"2159906806","pmid":"https://pubmed.ncbi.nlm.nih.gov/16723008"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-s1-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-s1-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-S1-S5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-S1-S5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083952534","display_name":"Anshul Kundaje","orcid":"https://orcid.org/0000-0003-3084-2287"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anshul Kundaje","raw_affiliation_strings":["Department of Computer Science, Columbia University, New York, NY 10027, USA. abk2001@cs.columbia.edu","Department of Computer Science, Columbia University, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Columbia University, New York, NY 10027, USA. abk2001@cs.columbia.edu","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Computer Science, Columbia University, New York, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060328938","display_name":"Manuel Middendorf","orcid":null},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Manuel Middendorf","raw_affiliation_strings":["Department of Physics, Columbia University, New York, NY, 10027, USA","Department of Physics, Columbia University, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, Columbia University, New York, NY, 10027, USA","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Physics, Columbia University, New York, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071214455","display_name":"Mihir Shah","orcid":"https://orcid.org/0000-0003-0854-2384"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mihir Shah","raw_affiliation_strings":["Department of Computer Science, Columbia University, New York, NY, 10027, USA","Department of Computer Science, Columbia University, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Columbia University, New York, NY, 10027, USA","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Computer Science, Columbia University, New York, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085649470","display_name":"Chris H. Wiggins","orcid":null},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chris H Wiggins","raw_affiliation_strings":["Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, 10027, USA","Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, 10027, USA","Department of Applied Physics and Applied Mathematics, Columbia University, New York, USA","Center for Computational Biology and Bioinformatics, Columbia University, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, 10027, USA","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, 10027, USA","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Applied Physics and Applied Mathematics, Columbia University, New York, USA","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, Columbia University, New York, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072341135","display_name":"Yoav Freund","orcid":"https://orcid.org/0000-0002-3850-6184"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yoav Freund","raw_affiliation_strings":["Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, 10027, USA","Center for Computational Learning Systems, Columbia University, New York, NY, 10027, USA","Department of Computer Science, Columbia University, New York, NY, 10027, USA","Center for Computational Learning Systems, Columbia University, New York, USA","Department of Computer Science, Columbia University, New York, USA","Center for Computational Biology and Bioinformatics, Columbia University, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, 10027, USA","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Center for Computational Learning Systems, Columbia University, New York, NY, 10027, USA","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Computer Science, Columbia University, New York, NY, 10027, USA","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Center for Computational Learning Systems, Columbia University, New York, USA","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Computer Science, Columbia University, New York, USA","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, Columbia University, New York, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085231879","display_name":"Christina S. Leslie","orcid":"https://orcid.org/0000-0002-4571-5910"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Christina Leslie","raw_affiliation_strings":["Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, 10027, USA","Center for Computational Learning Systems, Columbia University, New York, NY, 10027, USA","Department of Computer Science, Columbia University, New York, NY, 10027, USA","Center for Computational Biology and Bioinformatics, Columbia University, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, 10027, USA","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Center for Computational Learning Systems, Columbia University, New York, NY, 10027, USA","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Computer Science, Columbia University, New York, NY, 10027, USA","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, Columbia University, New York, USA","institution_ids":["https://openalex.org/I78577930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5085231879"],"corresponding_institution_ids":["https://openalex.org/I78577930"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.227,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.77956422,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"7","issue":"S1","first_page":"S5","last_page":"S5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.6183000206947327,"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":0.6183000206947327,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.18889999389648438,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.08489999920129776,"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/decision-tree","display_name":"Decision tree","score":0.6614471673965454},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6369176506996155},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.611676037311554},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6009206771850586},{"id":"https://openalex.org/keywords/boosting","display_name":"Boosting (machine learning)","score":0.5711876153945923},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5496051907539368},{"id":"https://openalex.org/keywords/adaboost","display_name":"AdaBoost","score":0.49560415744781494},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.46283841133117676},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.4307589828968048},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.4263670742511749},{"id":"https://openalex.org/keywords/decision-rule","display_name":"Decision rule","score":0.4137311279773712},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39654093980789185},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.25073307752609253},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2377755343914032},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.23656514286994934},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1694737672805786},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16683530807495117},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1625293791294098}],"concepts":[{"id":"https://openalex.org/C84525736","wikidata":"https://www.wikidata.org/wiki/Q831366","display_name":"Decision tree","level":2,"score":0.6614471673965454},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6369176506996155},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.611676037311554},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6009206771850586},{"id":"https://openalex.org/C46686674","wikidata":"https://www.wikidata.org/wiki/Q466303","display_name":"Boosting (machine learning)","level":2,"score":0.5711876153945923},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5496051907539368},{"id":"https://openalex.org/C141404830","wikidata":"https://www.wikidata.org/wiki/Q2823869","display_name":"AdaBoost","level":3,"score":0.49560415744781494},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.46283841133117676},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.4307589828968048},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.4263670742511749},{"id":"https://openalex.org/C84839998","wikidata":"https://www.wikidata.org/wiki/Q5249245","display_name":"Decision rule","level":2,"score":0.4137311279773712},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39654093980789185},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.25073307752609253},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2377755343914032},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23656514286994934},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1694737672805786},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16683530807495117},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1625293791294098},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006360","descriptor_name":"Heat-Shock Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006360","descriptor_name":"Heat-Shock Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006360","descriptor_name":"Heat-Shock Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006360","descriptor_name":"Heat-Shock Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018832","descriptor_name":"Molecular Chaperones","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018832","descriptor_name":"Molecular Chaperones","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018832","descriptor_name":"Molecular Chaperones","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018832","descriptor_name":"Molecular Chaperones","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":"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":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-7-s1-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-s1-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-S1-S5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16723008","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16723008","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:academiccommons.columbia.edu:10.7916/D82V2DNH","is_oa":false,"landing_page_url":"https://doi.org/10.7916/D82V2DNH","pdf_url":null,"source":{"id":"https://openalex.org/S4306402601","display_name":"Columbia Academic Commons (Columbia University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I78577930","host_organization_name":"Columbia University","host_organization_lineage":["https://openalex.org/I78577930"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:1810316","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1810316","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"doi:10.7916/d82v2dnh","is_oa":true,"landing_page_url":"https://doi.org/10.7916/d82v2dnh","pdf_url":null,"source":{"id":"https://openalex.org/S4306402601","display_name":"Columbia Academic Commons (Columbia University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I78577930","host_organization_name":"Columbia University","host_organization_lineage":["https://openalex.org/I78577930"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-7-s1-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-s1-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-S1-S5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.47999998927116394,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G4077323095","display_name":"QSB: Optimal Information Processing in Biological Networks","funder_award_id":"0425850","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4916684654","display_name":"SGER: Developing Learning Theory for Genetic Network Inference","funder_award_id":"0332479","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"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":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2159906806.pdf","grobid_xml":"https://content.openalex.org/works/W2159906806.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W181622860","https://openalex.org/W1650502025","https://openalex.org/W1969264035","https://openalex.org/W1985467760","https://openalex.org/W2001914359","https://openalex.org/W2010029425","https://openalex.org/W2032210760","https://openalex.org/W2034873647","https://openalex.org/W2059085198","https://openalex.org/W2061280979","https://openalex.org/W2073727170","https://openalex.org/W2100603120","https://openalex.org/W2103012681","https://openalex.org/W2108420379","https://openalex.org/W2116690411","https://openalex.org/W2124491835","https://openalex.org/W2125508747","https://openalex.org/W2126602684","https://openalex.org/W2129065437","https://openalex.org/W2137683543","https://openalex.org/W2144710927","https://openalex.org/W2146578381","https://openalex.org/W2154733002","https://openalex.org/W2158128075","https://openalex.org/W2162735386","https://openalex.org/W2164893466","https://openalex.org/W2167190345","https://openalex.org/W2168157737","https://openalex.org/W4233413206","https://openalex.org/W4238387639","https://openalex.org/W4244952642","https://openalex.org/W4292025355"],"related_works":["https://openalex.org/W2327035729","https://openalex.org/W2348748958","https://openalex.org/W3039673966","https://openalex.org/W1538046993","https://openalex.org/W2884325279","https://openalex.org/W1570592793","https://openalex.org/W1525436954","https://openalex.org/W2385662756","https://openalex.org/W2585372724","https://openalex.org/W2241444561"],"abstract_inverted_index":{"BACKGROUND:":[0],"We":[1,293,355],"have":[2],"recently":[3],"introduced":[4],"a":[5,17,41,47,54,92,121,132,136,146,161,179,206,214,287,336,349,388],"predictive":[6,166],"framework":[7,182,376],"for":[8,44,183,269,318,418],"studying":[9],"gene":[10,48,191,319],"transcriptional":[11,405],"regulation":[12,196],"in":[13,31,53,67,82,112,124,231,252,286,363,383],"simpler":[14],"organisms":[15,33],"using":[16,348],"novel":[18,207,401],"supervised":[19],"learning":[20,89],"algorithm":[21,153],"called":[22],"GeneClass.":[23],"GeneClass":[24,86,119,152,204,309,413],"is":[25,49,416],"motivated":[26],"by":[27,377],"the":[28,60,68,73,83,88,105,116,125,141,151,172,229,241,253,266,278,308,324,357,361,364,371,374,394],"hypothesis":[29],"that":[30,154,212,237],"model":[32,317],"such":[34,78],"as":[35,79,91],"Saccharomyces":[36],"cerevisiae,":[37],"we":[38,144,312,330,369],"can":[39],"learn":[40],"decision":[42,130,137],"rule":[43],"predicting":[45],"whether":[46],"up-":[50,101],"or":[51],"down-regulated":[52],"particular":[55],"microarray":[56,113],"experiment":[57,84],"based":[58],"on":[59,335,344],"presence":[61],"of":[62,76,107,127,135,150,171,210,216,228,256,265,280,327,352,360,373,381,390,393],"binding":[63,301],"site":[64],"subsequences":[65],"(\"motifs\")":[66],"gene's":[69],"regulatory":[70],"region":[71],"and":[72,96,102,109,157,164,188,198,250,277,290,311,342,347,368,387,396,406,411],"expression":[74,320],"levels":[75,106],"regulators":[77],"transcription":[80,398],"factors":[81],"(\"parents\").":[85],"formulates":[87],"task":[90],"classification":[93],"problem--predicting":[94],"+1":[95],"-1":[97],"labels":[98],"corresponding":[99],"to":[100,177,193,199,223,274,297],"down-regulation":[103],"beyond":[104],"biological":[108,184],"measurement":[110],"noise":[111,316],"measurements.":[114],"Using":[115,323],"Adaboost":[117],"algorithm,":[118,310],"learns":[120],"prediction":[122,173,366],"function":[123,268],"form":[126],"an":[128,314],"alternating":[129],"tree,":[131,367],"margin-based":[133],"generalization":[134],"tree.":[138,292],"METHODS:":[139],"In":[140],"current":[142],"work,":[143],"introduce":[145,178],"new,":[147],"robust":[148],"version":[149],"increases":[155],"stability":[156,170,359],"computational":[158,259],"efficiency,":[159],"yielding":[160],"more":[162,288],"scalable":[163],"reliable":[165],"model.":[167],"The":[168],"improved":[169,315,325,358],"tree":[174],"enables":[175],"us":[176],"detailed":[180],"post-processing":[181,375],"interpretation,":[185],"including":[186],"individual":[187],"group":[189],"target":[190],"analysis":[192],"reveal":[194],"condition-specific":[195],"programs":[197],"suggest":[200],"signaling":[201],"pathways.":[202],"Robust":[203,328,412],"uses":[205],"stabilized":[208],"variant":[209],"boosting":[211],"allows":[213],"set":[215,351,389],"correlated":[217,239],"features,":[218,222,271],"rather":[219,247],"than":[220,248],"single":[221,242],"be":[224],"included":[225],"at":[226],"nodes":[227],"tree;":[230],"this":[232],"way,":[233],"biologically":[234],"important":[235],"features":[236,362],"are":[238,245],"with":[240],"best":[243],"feature":[244],"retained":[246],"decorrelated":[249],"lost":[251],"next":[254],"round":[255],"boosting.":[257],"Other":[258],"developments":[260],"include":[261],"fast":[262],"matrix":[263],"computation":[264],"loss":[267],"all":[270,345],"allowing":[272],"scalability":[273,326],"large":[275],"datasets,":[276],"use":[279,313],"abstaining":[281],"weak":[282],"rules,":[283],"which":[284],"results":[285,410],"shallow":[289],"interpretable":[291],"also":[294],"show":[295,370],"how":[296],"incorporate":[298],"genome-wide":[299],"protein-DNA":[300],"data":[302],"from":[303,420],"ChIP":[304],"chip":[305],"experiments":[306,334],"into":[307],"data.":[321],"RESULTS:":[322],"GeneClass,":[329],"present":[331],"larger":[332],"scale":[333],"yeast":[337],"environmental":[338],"stress":[339],"dataset,":[340],"training":[341],"testing":[343],"genes":[346,382],"comprehensive":[350],"potential":[353],"regulators.":[354],"demonstrate":[356],"learned":[365],"utility":[372],"analyzing":[378],"two":[379],"groups":[380],"yeast--the":[384],"protein":[385],"chaperones":[386],"putative":[391],"targets":[392],"Nrg1":[395],"Nrg2":[397],"factors--and":[399],"suggesting":[400],"hypotheses":[402],"about":[403],"their":[404],"post-transcriptional":[407],"regulation.":[408],"Detailed":[409],"source":[414],"code":[415],"available":[417],"download":[419],"http://www.cs.columbia.edu/compbio/robust-geneclass.":[421]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
