{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T13:01:31Z","timestamp":1762866091479},"reference-count":30,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2012,11,8]],"date-time":"2012-11-08T00:00:00Z","timestamp":1352332800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1002772","type":"journal-article","created":{"date-parts":[[2012,11,8]],"date-time":"2012-11-08T21:58:38Z","timestamp":1352411918000},"page":"e1002772","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":12,"title":["Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay"],"prefix":"10.1371","volume":"8","author":[{"given":"Filippo","family":"Cacace","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paola","family":"Paci","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Valerio","family":"Cusimano","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alfredo","family":"Germani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lorenzo","family":"Farina","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2012,11,8]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1038\/nrm2104","article-title":"The highways and byways of mrna decay","volume":"8","author":"N Garneau","year":"2007","journal-title":"Nat Rev Mol Cell Bio"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"2787","DOI":"10.1091\/mbc.E11-01-0028","article-title":"Dynamic profiling of mrna turnover reveals gene-specific and system-wide regulation of mrna decay","volume":"22","author":"S Munchel","year":"2011","journal-title":"Mol Biol Cell"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1186\/1741-7007-8-95","article-title":"The global dynamics of rna stability orchestrates responses to cellular activation","volume":"8","author":"J Keene","year":"2010","journal-title":"BMC Biol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1371\/journal.pbio.0020079","article-title":"Extensive association of functionally and cytotopically related mrnas with puf family rna-binding proteins in yeast","volume":"2","author":"A Gerber","year":"2004","journal-title":"PLoS Biol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"e255","DOI":"10.1371\/journal.pbio.0060255","article-title":"Diverse rna-binding proteins interact with functionally related sets of rnas, suggesting extensive regulatory system","volume":"6","author":"D Hogan","year":"2008","journal-title":"PLoS Biol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1016\/j.cell.2009.01.019","article-title":"The many pathways of rna degradation","volume":"136","author":"J Houseley","year":"2009","journal-title":"Cell"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1177\/1087057110365897","article-title":"A review of methods to monitor the modulation of mrna stability: a novel approach to drug discovery and therapeutic intervention","volume":"15","author":"D Cheneval","year":"2010","journal-title":"J Biomol Screen"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"3418","DOI":"10.1105\/tpc.107.055046","article-title":"Genome-wide analysis of mrna decay rates and their determinants in arabidopsis thaliana","volume":"19","author":"R Narsai","year":"2007","journal-title":"Plant Cell"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1093\/dnares\/dsn030","article-title":"Database for mrna half-life of 19977 genes obtained by dna microarray analysis of pluripotent and differentiating mouse embryonic cells","volume":"16","author":"L Sharova","year":"2009","journal-title":"DNA Res"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1038\/msb.2008.59","article-title":"Transient transcriptional re- sponses to stress are generated by opposing effects of mrna production and degradation","volume":"4","author":"O Shalem","year":"2008","journal-title":"Mol Syst Biol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"5860","DOI":"10.1073\/pnas.092538799","article-title":"Precision and functional specificity in mrna decay","volume":"99","author":"Y Wang","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"5534","DOI":"10.1128\/MCB.24.12.5534-5547.2004","article-title":"Genome-wide analysis of mrna stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors","volume":"25","author":"J Grigull","year":"2004","journal-title":"Mol Cell Biol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1016\/S0076-6879(08)02614-1","article-title":"Methods to determine mrna half-life in saccharomyces cerevisiae","volume":"448","author":"J Coller","year":"2008","journal-title":"Methods Enzymol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1038\/nbt.1861","article-title":"Metabolic labeling of rna uncovers principles of rna production and degradation dynamics in mammalian cells","volume":"29","author":"M Rabani","year":"2011","journal-title":"Nature Biotechnol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1016\/j.molcel.2004.06.004","article-title":"Genomic run-on evaluates transcription rates for all yeasts genes and identifies gene regulatory mechanisms","volume":"15","author":"J Garcia-Martinez","year":"2004","journal-title":"Mol Cell"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"E5","DOI":"10.1371\/journal.pbio.0000005","article-title":"The transcriptome of the intraery- throcytic developmental cycle of <italic>Plasmodium falciparum<\/italic>","volume":"I","author":"Z Bozdech","year":"2003","journal-title":"PLoS Biol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"R134","DOI":"10.1186\/gb-2007-8-7-r134","article-title":"Whole-genome analysis of mrna decay in <italic>Plasmodium falci- parum<\/italic> reveals a global lengthening of mrna half-life during the intra-erythrocytic developmental cycle","volume":"8","author":"J Shock","year":"2007","journal-title":"Genome Biol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"2266","DOI":"10.1101\/gad.1450606","article-title":"The forkhead transcription factor hcm1 regulates chromosome segregation genes and fills the s-phase gap in the transcriptional circuitry of the cell cycle","volume":"20","author":"T Pramila","year":"2006","journal-title":"Genes Dev"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"944","DOI":"10.1038\/nature06955","article-title":"Global control of cell-cycle tran- scription by coupled cdk and network oscillators","volume":"453","author":"D Orlando","year":"2008","journal-title":"Nature"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1152","DOI":"10.1126\/science.1120499","article-title":"Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes","volume":"310","author":"B Tu","year":"2005","journal-title":"Science"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1128\/MMBR.59.3.423-450.1995","article-title":"mrna stability in mammalian cells","volume":"59","author":"J Ross","year":"1995","journal-title":"Microbiol Rev"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1186\/1471-2164-11-259","article-title":"Major role for mrna stability in shaping the kinetics of gene induction","volume":"11","author":"R Elkon","year":"2010","journal-title":"BMC Genomics"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"e1000141","DOI":"10.1371\/journal.pcbi.1000141","article-title":"Embedding mrna stability in corre-lation analysis of time-series gene expression data","volume":"4","author":"L Farina","year":"2008","journal-title":"PLoS Comput Biol"},{"key":"ref24","unstructured":"Kailath T (1980) Linear systems. Prentice-Hall. 682 p."},{"key":"ref25","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1115\/1.3662552","article-title":"A new approach to linear filtering and prediction problems","volume":"82","author":"R Kalman","year":"1960","journal-title":"Transactions of the ASME\u2013Journal of Basic Engineering"},{"key":"ref26","first-page":"10","article-title":"Gorilla: A tool for discovery and visualization of enriched go terms in ranked gene lists","volume":"2009","author":"E Eden","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1016\/0092-8674(91)90182-X","article-title":"Progression of the cell cycle through mitosis leads to abortion of nascent transcripts","volume":"67","author":"A Shermoen","year":"1991","journal-title":"Cell"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1016\/j.tig.2011.05.008","article-title":"Regulatory mechanisms and networks couple the different phases of gene expression","volume":"27","author":"O Dahan","year":"2011","journal-title":"Trends Genet"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1093\/bioinformatics\/bti093","article-title":"Comparison of computa-tional methods for the identification of cell cycle-regulated genes","volume":"21","author":"U de Lichtenberg","year":"2004","journal-title":"Bioinformatics"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1089\/10665270360688057","article-title":"Continuous representations of time-series gene expression data","volume":"10","author":"Z Bar-Joseph","year":"2003","journal-title":"J Comput Biol"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002772","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,7,15]],"date-time":"2020-07-15T21:00:27Z","timestamp":1594846827000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002772"}},"subtitle":[],"editor":[{"given":"Teresa M.","family":"Przytycka","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2012,11,8]]},"references-count":30,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2012,11,8]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1002772","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,11,8]]}}}