{"id":"https://openalex.org/W2155839154","doi":"https://doi.org/10.1093/bioinformatics/bts515","title":"GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data","display_name":"GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data","publication_year":2012,"publication_date":"2012-08-24","ids":{"openalex":"https://openalex.org/W2155839154","doi":"https://doi.org/10.1093/bioinformatics/bts515","mag":"2155839154","pmid":"https://pubmed.ncbi.nlm.nih.gov/22923299"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts515","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts515","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/21/2782/48875974/bioinformatics_28_21_2782.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/28/21/2782/48875974/bioinformatics_28_21_2782.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101945559","display_name":"Jianxing Feng","orcid":"https://orcid.org/0000-0002-4180-3323"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Jianxing Feng","raw_affiliation_strings":["1 Department of Bioinformatics, School of Life sciences and Technology, Tongji University, 1239 Siping Road, Shanghai 20092, China, 2Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, 220 Handan Road, Shanghai, 200433, China, 3Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Harvard University and 4Department of Statistics, Harvard University, Science Center 715, 1 Oxford Street, Cambridge, MA 02138, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Bioinformatics, School of Life sciences and Technology, Tongji University, 1239 Siping Road, Shanghai 20092, China, 2Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, 220 Handan Road, Shanghai, 200433, China, 3Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Harvard University and 4Department of Statistics, Harvard University, Science Center 715, 1 Oxford Street, Cambridge, MA 02138, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I116953780","https://openalex.org/I4210117453","https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021521447","display_name":"Clifford A. Meyer","orcid":"https://orcid.org/0000-0002-8321-2839"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Clifford A. Meyer","raw_affiliation_strings":["1 Department of Bioinformatics, School of Life sciences and Technology, Tongji University, 1239 Siping Road, Shanghai 20092, China, 2Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, 220 Handan Road, Shanghai, 200433, China, 3Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Harvard University and 4Department of Statistics, Harvard University, Science Center 715, 1 Oxford Street, Cambridge, MA 02138, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Bioinformatics, School of Life sciences and Technology, Tongji University, 1239 Siping Road, Shanghai 20092, China, 2Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, 220 Handan Road, Shanghai, 200433, China, 3Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Harvard University and 4Department of Statistics, Harvard University, Science Center 715, 1 Oxford Street, Cambridge, MA 02138, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I116953780","https://openalex.org/I4210117453","https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115695507","display_name":"Qian Wang","orcid":"https://orcid.org/0000-0002-6052-9665"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Qian Wang","raw_affiliation_strings":["1 Department of Bioinformatics, School of Life sciences and Technology, Tongji University, 1239 Siping Road, Shanghai 20092, China, 2Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, 220 Handan Road, Shanghai, 200433, China, 3Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Harvard University and 4Department of Statistics, Harvard University, Science Center 715, 1 Oxford Street, Cambridge, MA 02138, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Bioinformatics, School of Life sciences and Technology, Tongji University, 1239 Siping Road, Shanghai 20092, China, 2Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, 220 Handan Road, Shanghai, 200433, China, 3Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Harvard University and 4Department of Statistics, Harvard University, Science Center 715, 1 Oxford Street, Cambridge, MA 02138, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I116953780","https://openalex.org/I4210117453","https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012820890","display_name":"Jun S. Liu","orcid":"https://orcid.org/0000-0002-4450-7239"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Jun S. Liu","raw_affiliation_strings":["1 Department of Bioinformatics, School of Life sciences and Technology, Tongji University, 1239 Siping Road, Shanghai 20092, China, 2Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, 220 Handan Road, Shanghai, 200433, China, 3Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Harvard University and 4Department of Statistics, Harvard University, Science Center 715, 1 Oxford Street, Cambridge, MA 02138, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Bioinformatics, School of Life sciences and Technology, Tongji University, 1239 Siping Road, Shanghai 20092, China, 2Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, 220 Handan Road, Shanghai, 200433, China, 3Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Harvard University and 4Department of Statistics, Harvard University, Science Center 715, 1 Oxford Street, Cambridge, MA 02138, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I116953780","https://openalex.org/I4210117453","https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045575546","display_name":"X. Shirley Liu","orcid":"https://orcid.org/0000-0003-4736-7339"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"X. Shirley Liu","raw_affiliation_strings":["1 Department of Bioinformatics, School of Life sciences and Technology, Tongji University, 1239 Siping Road, Shanghai 20092, China, 2Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, 220 Handan Road, Shanghai, 200433, China, 3Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Harvard University and 4Department of Statistics, Harvard University, Science Center 715, 1 Oxford Street, Cambridge, MA 02138, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Bioinformatics, School of Life sciences and Technology, Tongji University, 1239 Siping Road, Shanghai 20092, China, 2Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, 220 Handan Road, Shanghai, 200433, China, 3Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Harvard University and 4Department of Statistics, Harvard University, Science Center 715, 1 Oxford Street, Cambridge, MA 02138, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I116953780","https://openalex.org/I4210117453","https://openalex.org/I24943067"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007650371","display_name":"Yong Zhang","orcid":"https://orcid.org/0000-0001-6316-2734"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Yong Zhang","raw_affiliation_strings":["1 Department of Bioinformatics, School of Life sciences and Technology, Tongji University, 1239 Siping Road, Shanghai 20092, China, 2Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, 220 Handan Road, Shanghai, 200433, China, 3Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Harvard University and 4Department of Statistics, Harvard University, Science Center 715, 1 Oxford Street, Cambridge, MA 02138, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Bioinformatics, School of Life sciences and Technology, Tongji University, 1239 Siping Road, Shanghai 20092, China, 2Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, 220 Handan Road, Shanghai, 200433, China, 3Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Harvard University and 4Department of Statistics, Harvard University, Science Center 715, 1 Oxford Street, Cambridge, MA 02138, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I116953780","https://openalex.org/I4210117453","https://openalex.org/I24943067"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5007650371","https://openalex.org/A5045575546"],"corresponding_institution_ids":["https://openalex.org/I116953780","https://openalex.org/I136199984","https://openalex.org/I24943067","https://openalex.org/I4210117453"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":8.21,"has_fulltext":true,"cited_by_count":466,"citation_normalized_percentile":{"value":0.98446154,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"28","issue":"21","first_page":"2782","last_page":"2788"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.4293000102043152,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.4293000102043152,"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":0.11999999731779099,"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":0.09319999814033508,"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/replicate","display_name":"Replicate","score":0.8101620078086853},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.7948681116104126},{"id":"https://openalex.org/keywords/fold-change","display_name":"Fold change","score":0.6336896419525146},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6248389482498169},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5843163132667542},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5336760878562927},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.514370322227478},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.49485963582992554},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4857233166694641},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.42846834659576416},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32421597838401794},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.31056469678878784},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.10599315166473389},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.105284184217453},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.0964033305644989}],"concepts":[{"id":"https://openalex.org/C2781162219","wikidata":"https://www.wikidata.org/wiki/Q26250693","display_name":"Replicate","level":2,"score":0.8101620078086853},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.7948681116104126},{"id":"https://openalex.org/C2779018089","wikidata":"https://www.wikidata.org/wiki/Q17014303","display_name":"Fold change","level":4,"score":0.6336896419525146},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6248389482498169},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5843163132667542},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5336760878562927},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.514370322227478},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49485963582992554},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4857233166694641},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.42846834659576416},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32421597838401794},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.31056469678878784},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.10599315166473389},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.105284184217453},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0964033305644989}],"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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000191","qualifier_name":"economics","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000191","qualifier_name":"economics","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000191","qualifier_name":"economics","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":"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":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bts515","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts515","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/21/2782/48875974/bioinformatics_28_21_2782.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:22923299","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22923299","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/bts515","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts515","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/21/2782/48875974/bioinformatics_28_21_2782.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":[],"awards":[{"id":"https://openalex.org/G1690469056","display_name":null,"funder_award_id":"31028011","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1704137926","display_name":null,"funder_award_id":"NCET-11-","funder_id":"https://openalex.org/F4320334924","funder_display_name":"Program for New Century Excellent Talents in University"},{"id":"https://openalex.org/G2203569063","display_name":null,"funder_award_id":"31071114","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5389176904","display_name":null,"funder_award_id":"10QA1407300","funder_id":"https://openalex.org/F4320327803","funder_display_name":"Shanghai Rising-Star Program"},{"id":"https://openalex.org/G698902282","display_name":null,"funder_award_id":"IRT1168","funder_id":"https://openalex.org/F4320321106","funder_display_name":"Ministry of Education of the People's Republic of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321106","display_name":"Ministry of Education of the People's Republic of China","ror":"https://ror.org/01mv9t934"},{"id":"https://openalex.org/F4320322449","display_name":"Tongji University","ror":"https://ror.org/03rc6as71"},{"id":"https://openalex.org/F4320327803","display_name":"Shanghai Rising-Star Program","ror":null},{"id":"https://openalex.org/F4320332588","display_name":"Shanghai Key Laboratory of Intelligent Information Processing","ror":"https://ror.org/013q1eq08"},{"id":"https://openalex.org/F4320334924","display_name":"Program for New Century Excellent Talents in University","ror":"https://ror.org/01mv9t934"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2155839154.pdf","grobid_xml":"https://content.openalex.org/works/W2155839154.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1948145985","https://openalex.org/W1981509058","https://openalex.org/W1984708728","https://openalex.org/W1989367702","https://openalex.org/W1992133876","https://openalex.org/W1992550017","https://openalex.org/W2015553373","https://openalex.org/W2042372709","https://openalex.org/W2047765648","https://openalex.org/W2067151470","https://openalex.org/W2070929669","https://openalex.org/W2071837646","https://openalex.org/W2072349313","https://openalex.org/W2075610412","https://openalex.org/W2094678200","https://openalex.org/W2100448568","https://openalex.org/W2101042581","https://openalex.org/W2102304447","https://openalex.org/W2105776281","https://openalex.org/W2107060225","https://openalex.org/W2114104545","https://openalex.org/W2117089877","https://openalex.org/W2118532317","https://openalex.org/W2119034410","https://openalex.org/W2121211805","https://openalex.org/W2122683221","https://openalex.org/W2128016314","https://openalex.org/W2130410032","https://openalex.org/W2133166282","https://openalex.org/W2133210805","https://openalex.org/W2137839234","https://openalex.org/W2141458291","https://openalex.org/W2144141220","https://openalex.org/W2146614932","https://openalex.org/W2151081606","https://openalex.org/W2152239989","https://openalex.org/W2154431984","https://openalex.org/W2156631105","https://openalex.org/W2164216268"],"related_works":["https://openalex.org/W4362511917","https://openalex.org/W2904597490","https://openalex.org/W4362530199","https://openalex.org/W4362511560","https://openalex.org/W4377231761","https://openalex.org/W4285162488","https://openalex.org/W4362512073","https://openalex.org/W4362485908","https://openalex.org/W2268123450","https://openalex.org/W2093288248"],"abstract_inverted_index":{"MOTIVATION:":[0],"RNA-seq":[1,27,42,48,98,131],"has":[2],"been":[3],"widely":[4],"used":[5],"in":[6,29,50],"transcriptome":[7],"analysis":[8,132],"to":[9,88],"effectively":[10],"measure":[11],"gene":[12,31,141],"expression":[13,32,105],"levels.":[14],"Although":[15],"sequencing":[16],"costs":[17],"are":[18],"rapidly":[19],"decreasing,":[20],"almost":[21],"70%":[22],"of":[23,56,93,112,123],"all":[24],"the":[25,30,53,82,109,121],"human":[26],"samples":[28],"omnibus":[33],"do":[34],"not":[35],"have":[36],"biological":[37,75,139,147],"replicates":[38],"and":[39,125,134,138],"more":[40,136],"unreplicated":[41],"data":[43,49],"were":[44],"published":[45],"than":[46],"replicated":[47],"2011.":[51],"Despite":[52],"large":[54],"amount":[55],"single":[57,74,146],"replicate":[58,76,148],"studies,":[59],"there":[60],"is":[61,77,149,157],"currently":[62],"no":[63],"satisfactory":[64],"method":[65],"for":[66,104],"detecting":[67],"differentially":[68,94],"expressed":[69,95],"genes":[70,96],"when":[71,143],"only":[72,144],"a":[73,145],"available.":[78,150],"RESULTS:":[79],"We":[80],"present":[81],"GFOLD":[83,100,119],"(generalized":[84],"fold":[85,114,126],"change)":[86],"algorithm":[87],"produce":[89],"biologically":[90],"meaningful":[91,140],"rankings":[92,142],"from":[97],"data.":[99],"assigns":[101],"reliable":[102],"statistics":[103],"changes":[106],"based":[107],"on":[108],"posterior":[110],"distribution":[111],"log":[113],"change.":[115],"In":[116],"this":[117],"way,":[118],"overcomes":[120],"shortcomings":[122],"P-value":[124],"change":[127],"calculated":[128],"by":[129],"existing":[130],"methods":[133],"gives":[135],"stable":[137],"AVAILABILITY:":[151],"The":[152],"open":[153],"source":[154],"C/C++":[155],"program":[156],"available":[158],"at":[159],"http://www.tongji.edu.cn/\u223czhanglab/GFOLD/index.html":[160]},"counts_by_year":[{"year":2026,"cited_by_count":12},{"year":2025,"cited_by_count":27},{"year":2024,"cited_by_count":27},{"year":2023,"cited_by_count":34},{"year":2022,"cited_by_count":34},{"year":2021,"cited_by_count":56},{"year":2020,"cited_by_count":63},{"year":2019,"cited_by_count":34},{"year":2018,"cited_by_count":46},{"year":2017,"cited_by_count":30},{"year":2016,"cited_by_count":40},{"year":2015,"cited_by_count":31},{"year":2014,"cited_by_count":19},{"year":2013,"cited_by_count":11},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-04T07:58:01.006859","created_date":"2025-10-10T00:00:00"}