{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T14:48:39Z","timestamp":1776178119157,"version":"3.50.1"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,11,14]],"date-time":"2016-11-14T00:00:00Z","timestamp":1479081600000},"content-version":"vor","delay-in-days":895,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The widespread adoption of RNA-seq to quantitatively measure gene expression has increased the scope of sequencing experimental designs to include time-course experiments. maSigPro is an R package specifically suited for the analysis of time-course gene expression data, which was developed originally for microarrays and hence was limited in its application to count data.<\/jats:p>\n               <jats:p>Results: We have updated maSigPro to support RNA-seq time series analysis by introducing generalized linear models in the algorithm to support the modeling of count data while maintaining the traditional functionalities of the package. We show a good performance of the maSigPro-GLM method in several simulated time-course scenarios and in a real experimental dataset.<\/jats:p>\n               <jats:p>Availability and implementation: The package is freely available under the LGPL license from the Bioconductor Web site ( http:\/\/bioconductor.org ).<\/jats:p>\n               <jats:p>Contact: \u00a0mj.nueda@ua.es or aconesa@cipf.es<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu333","type":"journal-article","created":{"date-parts":[[2014,6,4]],"date-time":"2014-06-04T05:56:45Z","timestamp":1401861405000},"page":"2598-2602","source":"Crossref","is-referenced-by-count":333,"title":["Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series"],"prefix":"10.1093","volume":"30","author":[{"given":"Mar\u00eda Jos\u00e9","family":"Nueda","sequence":"first","affiliation":[{"name":"1 Statistics and Operational Research Department, University of Alicante, 03690, Alicante, Spain, 2 Genomics of Gene Expression Laboratory, Prince Felipe Research Centre, 46012 Valencia, Spain and 3 Applied Statistics, Operational Research and Quality Department, Polytechnic University of Valencia, 46020 Valencia, Spain"}]},{"given":"Sonia","family":"Tarazona","sequence":"additional","affiliation":[{"name":"1 Statistics and Operational Research Department, University of Alicante, 03690, Alicante, Spain, 2 Genomics of Gene Expression Laboratory, Prince Felipe Research Centre, 46012 Valencia, Spain and 3 Applied Statistics, Operational Research and Quality Department, Polytechnic University of Valencia, 46020 Valencia, Spain"},{"name":"1 Statistics and Operational Research Department, University of Alicante, 03690, Alicante, Spain, 2 Genomics of Gene Expression Laboratory, Prince Felipe Research Centre, 46012 Valencia, Spain and 3 Applied Statistics, Operational Research and Quality Department, Polytechnic University of Valencia, 46020 Valencia, Spain"}]},{"given":"Ana","family":"Conesa","sequence":"additional","affiliation":[{"name":"1 Statistics and Operational Research Department, University of Alicante, 03690, Alicante, Spain, 2 Genomics of Gene Expression Laboratory, Prince Felipe Research Centre, 46012 Valencia, Spain and 3 Applied Statistics, Operational Research and Quality Department, Polytechnic University of Valencia, 46020 Valencia, Spain"}]}],"member":"286","published-online":{"date-parts":[[2014,6,3]]},"reference":[{"key":"2023012711553929700_btu333-B1","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol."},{"key":"2023012711553929700_btu333-B2","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/1471-2105-11-94","article-title":"Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments","volume":"11","author":"Bullard","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012711553929700_btu333-B3","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1093\/bioinformatics\/btl056","article-title":"maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments","volume":"22","author":"Conesa","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012711553929700_btu333-B4","volume-title":"An Introduction to Generalized Linear Models","author":"Dobson","year":"2002","edition":"2nd edn"},{"key":"2023012711553929700_btu333-B5","doi-asserted-by":"crossref","first-page":"2219","DOI":"10.1073\/pnas.1306807110","article-title":"Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts","volume":"110","author":"Hacquard","year":"2013","journal-title":"Proc. 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