{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,18]],"date-time":"2025-10-18T20:49:49Z","timestamp":1760820589424},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: The most common RNA-Seq strategy consists of random shearing, amplification and high-throughput sequencing of the RNA fraction. Methods to analyze transcription level variations along the genome from the read count profiles generated by the RNA-Seq protocol are needed.<\/jats:p><jats:p>Results: We developed a statistical approach to estimate the local transcription levels and to identify transcript borders. This transcriptional landscape reconstruction relies on a state-space model to describe transcription level variations in terms of abrupt shifts and more progressive drifts. A new emission model is introduced to capture not only the read count variance inside a transcript but also its short-range autocorrelation and the fraction of positions with zero counts. The estimation relies on a particle Gibbs algorithm whose running time makes it more suited to microbial genomes. The approach outperformed read-overlapping strategies on synthetic and real microbial datasets.<\/jats:p><jats:p>Availability: A program named Parseq is available at: http:\/\/www.lgm.upmc.fr\/parseq\/.<\/jats:p><jats:p>Contact: \u00a0bodgan.mirauta@upmc.fr<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu042","type":"journal-article","created":{"date-parts":[[2014,1,28]],"date-time":"2014-01-28T01:56:48Z","timestamp":1390874208000},"page":"1409-1416","source":"Crossref","is-referenced-by-count":13,"title":["Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models"],"prefix":"10.1093","volume":"30","author":[{"given":"Bogdan","family":"Mirauta","sequence":"first","affiliation":[{"name":"1 Biologie Computationnelle et Quantitative, UPMC and CNRS UMR7238, Paris, France and 2Math\u00e9matique Informatique et G\u00e9nome, INRA UR1077, Jouy-en-Josas, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre","family":"Nicolas","sequence":"additional","affiliation":[{"name":"1 Biologie Computationnelle et Quantitative, UPMC and CNRS UMR7238, Paris, France and 2Math\u00e9matique Informatique et G\u00e9nome, INRA UR1077, Jouy-en-Josas, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hugues","family":"Richard","sequence":"additional","affiliation":[{"name":"1 Biologie Computationnelle et Quantitative, UPMC and CNRS UMR7238, Paris, France and 2Math\u00e9matique Informatique et G\u00e9nome, INRA UR1077, Jouy-en-Josas, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,1,27]]},"reference":[{"key":"2023041302471787000_","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":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1111\/j.1467-9868.2009.00736.x","article-title":"Particle markov chain monte carlo methods","volume":"72","author":"Andrieu","year":"2010","journal-title":"J. R. Stat. Soc. Ser. B Stat. Methodol."},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"D700","DOI":"10.1093\/nar\/gkr1029","article-title":"Saccharomyces genome database: the genomics resource of budding yeast","volume":"40","author":"Cherry","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"Consortium","year":"2012","journal-title":"Nature"},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1016\/S0022-2836(99)80005-9","article-title":"Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their rna stem-loop structures","volume":"216","author":"d\u2019Aubenton Carafa","year":"1990","journal-title":"J. Mol. Biol."},{"key":"2023041302471787000_","article-title":"A tutorial on particle filtering and smoothing: fifteen years later","author":"Doucet","year":"2008","journal-title":"Technical report, Department of Statistics, University of British Columbia"},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1093\/gbe\/evt028","article-title":"On the immortality of television sets: \u201cfunction\u201d in the human genome according to the evolution-free gospel of ENCODE","volume":"5","author":"Graur","year":"2013","journal-title":"Genome. Biol. Evol."},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"10073","DOI":"10.1093\/nar\/gks666","article-title":"Modelling and simulating generic RNA-Seq experiments with the flux simulator","volume":"40","author":"Griebel","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1038\/nbt.1633","article-title":"Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs","volume":"28","author":"Guttman","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1101\/gr.073262.107","article-title":"The new paradigm of flow cell sequencing","volume":"18","author":"Holt","year":"2008","journal-title":"Genome res."},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"1963","DOI":"10.1093\/bioinformatics\/btl289","article-title":"Transcript mapping with high-density oligonucleotide tiling arrays","volume":"22","author":"Huber","year":"2006","journal-title":"Bioinformatics"},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1093\/bioinformatics\/btp113","article-title":"Statistical inferences for isoform expression in RNA-Seq","volume":"25","author":"Jiang","year":"2009","journal-title":"Bioinformatics"},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1111\/j.1751-5823.2005.tb00250.x","article-title":"Mixed poisson distributions","volume":"73","author":"Karlis","year":"2005","journal-title":"Int. Stat. Rev."},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1038\/nmeth.1491","article-title":"Comprehensive comparative analysis of strand-specific RNA sequencing methods","volume":"7","author":"Levin","year":"2010","journal-title":"Nat. Methods"},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2010-11-5-r50","article-title":"Modeling non-uniformity in short-read rates in RNA-Seq data","volume":"11","author":"Li","year":"2010","journal-title":"Genome Biol."},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1186\/1471-2164-14-620","article-title":"A combination of improved differential and global rna-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional rnas in propionibacterium acnes, a major contributor to wide-spread human disease","volume":"14","author":"Lin","year":"2013","journal-title":"BMC Genomics"},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"1509","DOI":"10.1101\/gr.079558.108","article-title":"RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays","volume":"18","author":"Marioni","year":"2008","journal-title":"Genome Res."},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1038\/nrg3068","article-title":"Next-generation transcriptome assembly","volume":"12","author":"Martin","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"e140","DOI":"10.1093\/nar\/gkt444","article-title":"Computational analysis of bacterial RNA-Seq data","volume":"41","author":"McClure","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nat. Methods"},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"1344","DOI":"10.1126\/science.1158441","article-title":"The transcriptional landscape of the yeast genome defined by RNA sequencing","volume":"320","author":"Nagalakshmi","year":"2008","journal-title":"Science"},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"2341","DOI":"10.1093\/bioinformatics\/btp395","article-title":"Transcriptional landscape estimation from tiling array data using a model of signal shift and drift","volume":"25","author":"Nicolas","year":"2009","journal-title":"Bioinformatics"},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1126\/science.1206848","article-title":"Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis","volume":"335","author":"Nicolas","year":"2012","journal-title":"Science"},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.1016\/j.cell.2010.11.020","article-title":"Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation","volume":"143","author":"Ozsolak","year":"2010","journal-title":"Cell"},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1038\/nature12121","article-title":"Extensive transcriptional heterogeneity revealed by isoform profiling","volume":"497","author":"Pelechano","year":"2013","journal-title":"Nature"},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1186\/1471-2105-6-27","article-title":"A statistical approach for array CGH data analysis","volume":"6","author":"Picard","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"e00156","DOI":"10.1128\/mBio.00156-12","article-title":"Antisense transcription is pervasive but rarely conserved in enteric bacteria","volume":"3","author":"Raghavan","year":"2012","journal-title":"MBio"},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"e112","DOI":"10.1093\/nar\/gkq041","article-title":"Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments","volume":"38","author":"Richard","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"D203","DOI":"10.1093\/nar\/gks1201","article-title":"RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more","volume":"41","author":"Salgado","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1146\/annurev-genet-102209-163523","article-title":"Bacterial antisense RNAs: how many are there, and what are they doing?","volume":"44","author":"Thomason","year":"2010","journal-title":"Annu. Rev. Genet."},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","article-title":"Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation","volume":"28","author":"Trapnell","year":"2010","journal-title":"Nat. Biotech."},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"e1000371","DOI":"10.1371\/journal.pbio.1000371","article-title":"Most Dark matter transcripts are associated with known genes","volume":"8","author":"van Bakel","year":"2010","journal-title":"PLoS Biol."},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1038\/nature10118","article-title":"XUTs are a class of xrn1-sensitive antisense regulatory non-coding RNA in yeast","volume":"475","author":"van Dijk","year":"2011","journal-title":"Nature"},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"e178","DOI":"10.1093\/nar\/gkq622","article-title":"Mapsplice: accurate mapping of RNA-seq reads for splice junction discovery","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1093\/bioinformatics\/btq696","article-title":"Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq","volume":"27","author":"Wu","year":"2010","journal-title":"Bioinformatics"},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"3264","DOI":"10.1073\/pnas.0812841106","article-title":"Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing","volume":"106","author":"Yassour","year":"2009","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023041302471787000_","doi-asserted-by":"crossref","first-page":"2838","DOI":"10.1093\/nar\/gki583","article-title":"Mapping of transcription start sites in saccharomyces cerevisiae using 5\u2032 SAGE","volume":"33","author":"Zhang","year":"2005","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/10\/1409\/49860492\/bioinformatics_30_10_1409.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/10\/1409\/49860492\/bioinformatics_30_10_1409.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,10]],"date-time":"2023-07-10T02:48:57Z","timestamp":1688957337000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/10\/1409\/267021"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,1,27]]},"references-count":39,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2014,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu042","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,5,15]]},"published":{"date-parts":[[2014,1,27]]}}}