{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:22:20Z","timestamp":1767961340587,"version":"3.49.0"},"reference-count":38,"publisher":"Public Library of Science (PLoS)","issue":"1","content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000257","type":"journal-article","created":{"date-parts":[[2009,1,2]],"date-time":"2009-01-02T21:59:28Z","timestamp":1230933568000},"page":"e1000257","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":103,"title":["Predicting Cellular Growth from Gene Expression Signatures"],"prefix":"10.1371","volume":"5","author":[{"given":"Edoardo M.","family":"Airoldi","sequence":"first","affiliation":[]},{"given":"Curtis","family":"Huttenhower","sequence":"additional","affiliation":[]},{"given":"David","family":"Gresham","sequence":"additional","affiliation":[]},{"given":"Charles","family":"Lu","sequence":"additional","affiliation":[]},{"given":"Amy A.","family":"Caudy","sequence":"additional","affiliation":[]},{"given":"Maitreya J.","family":"Dunham","sequence":"additional","affiliation":[]},{"given":"James R.","family":"Broach","sequence":"additional","affiliation":[]},{"given":"David","family":"Botstein","sequence":"additional","affiliation":[]},{"given":"Olga G.","family":"Troyanskaya","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2009,1,2]]},"reference":[{"key":"ref1","article-title":"Methods in Yeast Genetics: A Cold Spring Harbor Laboratory Course Manual","author":"DC Amberg","year":"2005"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/S1046-2023(02)00032-4","article-title":"Hybridization array technology coupled with chemostat culture: tools to interrogate gene expression in Saccharomyces cerevisiae.","volume":"26","author":"A Hayes","year":"2002","journal-title":"Methods"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1038\/nrg929","article-title":"The origin and evolution of model organisms.","volume":"3","author":"SB Hedges","year":"2002","journal-title":"Nat Rev Genet"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1091\/mbc.E07-08-0779","article-title":"Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast.","volume":"19","author":"MJ Brauer","year":"2008","journal-title":"Mol Biol Cell"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/S0968-0004(99)01460-7","article-title":"The economics of ribosome biosynthesis in yeast.","volume":"24","author":"JR Warner","year":"1999","journal-title":"Trends Biochem Sci"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"4241","DOI":"10.1091\/mbc.11.12.4241","article-title":"Genomic expression programs in the response of yeast cells to environmental changes.","volume":"11","author":"AP Gasch","year":"2000","journal-title":"Mol Biol Cell"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1200","DOI":"10.1073\/pnas.0306490101","article-title":"A genomewide oscillation in transcription gates DNA replication and cell cycle.","volume":"101","author":"RR Klevecz","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref8","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":"ref9","doi-asserted-by":"crossref","first-page":"e128","DOI":"10.1371\/journal.pbio.0020128","article-title":"Ras and Gpa2 mediate one branch of a redundant glucose signaling pathway in yeast.","volume":"2","author":"Y Wang","year":"2004","journal-title":"PLoS Biol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/S0092-8674(00)00015-5","article-title":"Functional discovery via a compendium of expression profiles.","volume":"102","author":"TR Hughes","year":"2000","journal-title":"Cell"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1146\/annurev.genet.41.110306.130206","article-title":"How Saccharomyces responds to nutrients.","volume":"42","author":"S Zaman","year":"2008","journal-title":"Annu Rev Genet"},{"key":"ref12","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":"BP Tu","year":"2005","journal-title":"Science"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"3273","DOI":"10.1091\/mbc.9.12.3273","article-title":"Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.","volume":"9","author":"PT Spellman","year":"1998","journal-title":"Mol Biol Cell"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1126\/science.112.2920.715","article-title":"Description of the chemostat.","volume":"112","author":"A Novick","year":"1950","journal-title":"Science"},{"key":"ref15","first-page":"390","article-title":"La technique de culture continue, theorie et applications.","volume":"79","author":"J Monod","year":"1950","journal-title":"Ann Inst Pasteur"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"2890","DOI":"10.1093\/bioinformatics\/btl492","article-title":"A scalable method for integration and functional analysis of multiple microarray datasets.","volume":"22","author":"C Huttenhower","year":"2006","journal-title":"Bioinformatics"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing.","volume":"57","author":"Y Benjamini","year":"1995","journal-title":"J R Stat Soc Ser B"},{"key":"ref18","article-title":"Introduction to the Practice of Statistics","author":"DS Moore","year":"2005"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1038\/nature01644","article-title":"Sequencing and comparison of yeast species to identify genes and regulatory elements.","volume":"423","author":"M Kellis","year":"2003","journal-title":"Nature"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"W330","DOI":"10.1093\/nar\/gkl311","article-title":"YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms.","volume":"34","author":"CJ Penkett","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1038\/nbt1297-1351","article-title":"Stress tolerance: the key to effective strains of industrial baker&apos;s yeast.","volume":"15","author":"PV Attfield","year":"1997","journal-title":"Nat Biotechnol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1002\/yea.320090503","article-title":"Carbon source induces growth of stationary phase yeast cells, independent of carbon source metabolism.","volume":"9","author":"D Granot","year":"1993","journal-title":"Yeast"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1002\/yea.931","article-title":"Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae.","volume":"20","author":"J Warringer","year":"2003","journal-title":"Yeast"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1038\/ng1986","article-title":"Epistatic buffering of fitness loss in yeast double deletion strains.","volume":"39","author":"L Jasnos","year":"2007","journal-title":"Nat Genet"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1016\/j.pep.2006.02.006","article-title":"Purification and characterization of the chaperone-like Hsp26 from Saccharomyces cerevisiae.","volume":"47","author":"RM Ferreira","year":"2006","journal-title":"Protein Expr Purif"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"6304","DOI":"10.1128\/MCB.13.10.6304","article-title":"HSP78 encodes a yeast mitochondrial heat shock protein in the Clp family of ATP-dependent proteases.","volume":"13","author":"SA Leonhardt","year":"1993","journal-title":"Mol Cell Biol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1126\/science.1102033","article-title":"Very low gene duplication rate in the yeast genome.","volume":"306","author":"LZ Gao","year":"2004","journal-title":"Science"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"239","DOI":"10.2323\/jgam.41.239","article-title":"Growth temperatures and electrophoretic karyotyping as tools for practical discrimination of Saccharomyces bayanus and Saccharomyces cerevisiae.","volume":"41","author":"M Kishimoto","year":"1995","journal-title":"J Gen Appl Microbiol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"1756","DOI":"10.1091\/mbc.E06-10-0928","article-title":"Modulation of cell cycle-specific gene expressions at the onset of S phase arrest contributes to the robust DNA replication checkpoint response in fission yeast.","volume":"18","author":"Z Chu","year":"2007","journal-title":"Mol Biol Cell"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"10273","DOI":"10.1128\/MCB.25.23.10273-10285.2005","article-title":"Loss of SOD1 and LYS7 sensitizes Saccharomyces cerevisiae to hydroxyurea and DNA damage agents and downregulates MEC1 pathway effectors.","volume":"25","author":"CD Carter","year":"2005","journal-title":"Mol Cell Biol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"2431","DOI":"10.1101\/gad.1256704","article-title":"What better measure than ribosome synthesis?","volume":"18","author":"D Rudra","year":"2004","journal-title":"Genes Dev"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1916","DOI":"10.1126\/science.1140958","article-title":"Restriction of DNA replication to the reductive phase of the metabolic cycle protects genome integrity.","volume":"316","author":"Z Chen","year":"2007","journal-title":"Science"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/0092-8674(90)90813-T","article-title":"SRV2, a gene required for RAS activation of adenylate cyclase in yeast.","volume":"61","author":"M Fedor-Chaiken","year":"1990","journal-title":"Cell"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.molcel.2007.09.027","article-title":"A universal framework for regulatory element discovery across all genomes and data types.","volume":"28","author":"O Elemento","year":"2007","journal-title":"Mol Cell"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"38723","DOI":"10.1074\/jbc.M303008200","article-title":"Genome expression analysis in yeast reveals novel transcriptional regulation by inositol and choline and new regulatory functions for Opi1p, Ino2p, and Ino4p.","volume":"278","author":"TC Santiago","year":"2003","journal-title":"J Biol Chem"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"e79","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":"AP Gerber","year":"2004","journal-title":"PLoS Biol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"6602","DOI":"10.1093\/emboj\/19.23.6602","article-title":"The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast.","volume":"19","author":"W Olivas","year":"2000","journal-title":"EMBO J"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"2364","DOI":"10.1111\/j.1742-4658.2008.06398.x","article-title":"Collective behavior in gene regulation: post-transcriptional regulation and the temporal compartmentalization of cellular cycles.","volume":"275","author":"MC Palumbo","year":"2008","journal-title":"FEBS J"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000257","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,6]],"date-time":"2025-02-06T18:21:34Z","timestamp":1738866094000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000257"}},"subtitle":[],"editor":[{"given":"Andrey","family":"Rzhetsky","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2009,1,2]]},"references-count":38,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2009,1,2]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000257","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,1,2]]}}}