{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T05:29:05Z","timestamp":1782883745155,"version":"3.54.5"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: RNA-seq has been widely used in transcriptome analysis to effectively measure gene expression levels. Although sequencing costs are rapidly decreasing, almost 70% of all the human RNA-seq samples in the gene expression omnibus do not have biological replicates and more unreplicated RNA-seq data were published than replicated RNA-seq data in 2011. Despite the large amount of single replicate studies, there is currently no satisfactory method for detecting differentially expressed genes when only a single biological replicate is available.<\/jats:p>\n               <jats:p>Results: We present the GFOLD (generalized fold change) algorithm to produce biologically meaningful rankings of differentially expressed genes from RNA-seq data. GFOLD assigns reliable statistics for expression changes based on the posterior distribution of log fold change. In this way, GFOLD overcomes the shortcomings of P-value and fold change calculated by existing RNA-seq analysis methods and gives more stable and biological meaningful gene rankings when only a single biological replicate is available.<\/jats:p>\n               <jats:p>Availability: The open source C\/C++ program is available at http:\/\/www.tongji.edu.cn\/\u223czhanglab\/GFOLD\/index.html<\/jats:p>\n               <jats:p>Contact: xsliu@jimmy.harvard.edu or yzhang@tongji.edu.cn<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts515","type":"journal-article","created":{"date-parts":[[2012,8,25]],"date-time":"2012-08-25T02:27:06Z","timestamp":1345861626000},"page":"2782-2788","source":"Crossref","is-referenced-by-count":388,"title":["GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data"],"prefix":"10.1093","volume":"28","author":[{"given":"Jianxing","family":"Feng","sequence":"first","affiliation":[{"name":"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"},{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clifford A.","family":"Meyer","sequence":"additional","affiliation":[{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qian","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, School of Life sciences 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