{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T00:05:13Z","timestamp":1740096313324,"version":"3.37.3"},"publisher-location":"Berlin, Heidelberg","reference-count":19,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642411892"},{"type":"electronic","value":"9783642411908"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013]]},"DOI":"10.1007\/978-3-642-41190-8_45","type":"book-chapter","created":{"date-parts":[[2013,9,3]],"date-time":"2013-09-03T00:13:58Z","timestamp":1378167238000},"page":"418-427","source":"Crossref","is-referenced-by-count":0,"title":["Pardiff: Inference of Differential Expression at Base-Pair Level from RNA-Seq Experiments"],"prefix":"10.1007","author":[{"given":"Bogdan","family":"Mirauta","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre","family":"Nicolas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hugues","family":"Richard","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"issue":"10","key":"45_CR1","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1186\/gb-2010-11-10-r106","volume":"11","author":"S. Anders","year":"2010","unstructured":"Anders, S., Huber, W.: Differential expression analysis for sequence count data. Genome Biology\u00a011(10), R106 (2010), \n                    \n                      http:\/\/genomebiology.com\/2010\/11\/10\/R106","journal-title":"Genome Biology"},{"issue":"3","key":"45_CR2","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1111\/j.1467-9868.2009.00736.x","volume":"72","author":"C. Andrieu","year":"2010","unstructured":"Andrieu, C., Doucet, A., Holenstein, R.: Particle markov chain monte carlo methods. Journal of the Royal Statistical Society: Series B (Statistical Methodology)\u00a072(3), 269\u2013342 (2010)","journal-title":"Journal of the Royal Statistical Society: Series B (Statistical Methodology)"},{"issue":"2","key":"45_CR3","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1093\/bioinformatics\/19.2.185","volume":"19","author":"B. Bolstad","year":"2003","unstructured":"Bolstad, B., Irizarry, R., \u00c5strand, M., Speed, T.: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics\u00a019(2), 185\u2013193 (2003)","journal-title":"Bioinformatics"},{"issue":"1","key":"45_CR4","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1186\/1471-2105-11-94","volume":"11","author":"J. Bullard","year":"2010","unstructured":"Bullard, J., Purdom, E., Hansen, K., Dudoit, S.: Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics\u00a011(1), 94 (2010), \n                    \n                      http:\/\/www.biomedcentral.com\/1471-2105\/11\/94","journal-title":"BMC Bioinformatics"},{"key":"45_CR5","doi-asserted-by":"crossref","first-page":"D700","DOI":"10.1093\/nar\/gkr1029","volume":"40","author":"J.M. Cherry","year":"2012","unstructured":"Cherry, J.M., Hong, E.L., et al.: Saccharomyces genome database: the genomics resource of budding yeast. Nucleic Acids Res\u00a040(Database issue), D700\u2013D705 (2012), \n                    \n                      http:\/\/dx.doi.org\/10.1093\/nar\/gkr1029","journal-title":"Nucleic Acids Res"},{"key":"45_CR6","doi-asserted-by":"crossref","unstructured":"Clark, T., Schweitzer, A., et al.: Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biology\u00a08(4), R64 (2007)","DOI":"10.1186\/gb-2007-8-4-r64"},{"issue":"4","key":"45_CR7","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1038\/ng1296-457","volume":"14","author":"J. DeRisi","year":"1996","unstructured":"DeRisi, J., Bittner, M.: Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat. Genet.\u00a014(4), 457\u2013460 (1996)","journal-title":"Nat. Genet."},{"issue":"7354","key":"45_CR8","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1038\/nature10118","volume":"475","author":"E.L. Dijk van","year":"2011","unstructured":"van Dijk, E.L., Chen, C.L., et al.: Xuts are a class of xrn1-sensitive antisense regulatory non-coding rna in yeast. Nature\u00a0475(7354), 114\u2013117 (2011), \n                    \n                      http:\/\/dx.doi.org\/10.1038\/nature10118","journal-title":"Nature"},{"issue":"2","key":"45_CR9","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1111\/j.2517-6161.1954.tb00159.x","volume":"16","author":"E.C. Fieller","year":"1954","unstructured":"Fieller, E.C.: Some problems in interval estimation. Journal of the Royal Statistical Society. Series B (Methodological)\u00a016(2), 175\u2013185 (1954)","journal-title":"Journal of the Royal Statistical Society. Series B (Methodological)"},{"key":"45_CR10","unstructured":"Frazee, A., Jaffe, A., Sabunciyan, S., Leek, J.: Differential expression analysis of rna-seq data at base-pair resolution in multiple biological replicates. Biostatistics (under revision)"},{"issue":"5","key":"45_CR11","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1038\/nbt.1633","volume":"28","author":"M. Guttman","year":"2010","unstructured":"Guttman, M., Garber, M., Levin, J.Z., Donaghey, J., Robinson, J., Adiconis, X., Fan, L., Koziol, M.J., Gnirke, A., Nusbaum, C., Rinn, J.L., Lander, E.S., Regev, A.: Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature Biotechnology\u00a028(5), 503\u2013510 (2010), \n                    \n                      http:\/\/www.nature.com\/doifinder\/10.1038\/nbt.1633","journal-title":"Nature Biotechnology"},{"key":"45_CR12","doi-asserted-by":"crossref","unstructured":"Li, J., Jiang, H., Wong, W.H.: Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol. 11(5), R25 (2010)","DOI":"10.1186\/gb-2010-11-5-r50"},{"issue":"6","key":"45_CR13","doi-asserted-by":"publisher","first-page":"765","DOI":"10.1093\/bioinformatics\/btp053","volume":"25","author":"D.J. McCarthy","year":"2009","unstructured":"McCarthy, D.J., Smyth, G.K.: Testing significance relative to a fold-change threshold is a TREAT. Bioinformatics\u00a025(6), 765\u2013771 (2009)","journal-title":"Bioinformatics"},{"key":"45_CR14","unstructured":"Mirauta, B., Nicolas, P., Richard, H.: Parseq: transcriptional landscape reconstruction from rna-seq data based on state-space models (submitted, 2013)"},{"issue":"7","key":"45_CR15","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1038\/nmeth.1226","volume":"5","author":"A. Mortazavi","year":"2008","unstructured":"Mortazavi, A., Williams, B.A., et al.: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods\u00a05(7), 621\u2013628 (2008), \n                    \n                      http:\/\/www.nature.com\/doifinder\/10.1038\/nmeth.1226","journal-title":"Nature Methods"},{"issue":"18","key":"45_CR16","doi-asserted-by":"publisher","first-page":"2341","DOI":"10.1093\/bioinformatics\/btp395","volume":"25","author":"P. Nicolas","year":"2009","unstructured":"Nicolas, P., Leduc, A., et al.: Transcriptional landscape estimation from tiling array data using a model of signal shift and drift. Bioinformatics\u00a025(18), 2341\u20132347 (2009)","journal-title":"Bioinformatics"},{"issue":"1","key":"45_CR17","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","volume":"26","author":"M.D. Robinson","year":"2010","unstructured":"Robinson, M.D., McCarthy, D.J., Smyth, G.K.: edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics\u00a026(1), 139\u2013140 (2010), \n                    \n                      http:\/\/bioinformatics.oxfordjournals.org\/content\/26\/1\/139.abstract","journal-title":"Bioinformatics"},{"issue":"1","key":"45_CR18","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1038\/nbt.2450","volume":"31","author":"C. Trapnell","year":"2013","unstructured":"Trapnell, C., Hendrickson, D.G., Sauvageau, M., Goff, L., Rinn, J.L., Pachter, L.: Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotech.\u00a031(1), 46\u201353 (2013), \n                    \n                      http:\/\/dx.doi.org\/10.1038\/nbt.2450","journal-title":"Nat. Biotech."},{"issue":"5","key":"45_CR19","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1038\/nbt.1621","volume":"28","author":"C. Trapnell","year":"2010","unstructured":"Trapnell, C., Williams, B.A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M.J., Salzberg, S.L., Wold, B.J., Pachter, L.: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotech.\u00a028(5), 511\u2013515 (2010), \n                    \n                      http:\/\/dx.doi.org\/10.1038\/nbt.1621","journal-title":"Nat. Biotech."}],"container-title":["Lecture Notes in Computer Science","New Trends in Image Analysis and Processing \u2013 ICIAP 2013"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-41190-8_45","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,16]],"date-time":"2019-05-16T21:24:48Z","timestamp":1558041888000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-41190-8_45"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013]]},"ISBN":["9783642411892","9783642411908"],"references-count":19,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-41190-8_45","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2013]]}}}