{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,15]],"date-time":"2025-04-15T06:13:12Z","timestamp":1744697592694,"version":"3.37.3"},"reference-count":31,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2016,10,19]],"date-time":"2016-10-19T00:00:00Z","timestamp":1476835200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"ALW professorship funds"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1005146","type":"journal-article","created":{"date-parts":[[2016,10,19]],"date-time":"2016-10-19T13:39:43Z","timestamp":1476884383000},"page":"e1005146","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":7,"title":["DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks"],"prefix":"10.1371","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9190-3704","authenticated-orcid":true,"given":"Daifeng","family":"Wang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1165-3248","authenticated-orcid":true,"given":"Fei","family":"He","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3701-492X","authenticated-orcid":true,"given":"Sergei","family":"Maslov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark","family":"Gerstein","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2016,10,19]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"1706","DOI":"10.1101\/gr.903503","article-title":"Subsystem identification through dimensionality reduction of large-scale gene expression data","volume":"13","author":"PM Kim","year":"2003","journal-title":"Genome Res"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"2006","DOI":"10.1038\/msb4100058","article-title":"Modularizing gene regulation","volume":"2","author":"JM Vilar","year":"2006","journal-title":"Mol Syst Biol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1016\/j.cell.2011.02.017","article-title":"Evolution of gene regulatory networks controlling body plan development","volume":"144","author":"IS Peter","year":"2011","journal-title":"Cell"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1038\/nrg1990","article-title":"The evolution of gene regulation by transcription factors and microRNAs","volume":"8","author":"K Chen","year":"2007","journal-title":"Nat Rev Genet"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1016\/j.devcel.2012.04.004","article-title":"Developmental milestones punctuate gene expression in the Caenorhabditis embryo","volume":"22","author":"M Levin","year":"2012","journal-title":"Dev Cell"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1038\/nature09634","article-title":"Gene expression divergence recapitulates the developmental hourglass model","volume":"468","author":"AT Kalinka","year":"2010","journal-title":"Nature"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1016\/j.devcel.2011.03.015","article-title":"Mapping gene expression in two Xenopus species: evolutionary constraints and developmental flexibility","volume":"20","author":"I Yanai","year":"2011","journal-title":"Dev Cell"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/ncomms1248","article-title":"Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis","volume":"2","author":"N Irie","year":"2011","journal-title":"Nat Commun"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1038\/nrg2940","article-title":"Development: Hourglass theory gets molecular approval","volume":"12","author":"T Casci","year":"2011","journal-title":"Nat Rev Genet"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1038\/nature13424","article-title":"Comparative analysis of the transcriptome across distant species","volume":"512","author":"MB Gerstein","year":"2014","journal-title":"Nature"},{"first-page":"xviii","year":"1991","author":"WL Brogan","key":"ref11"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1361","DOI":"10.1093\/bioinformatics\/bth093","article-title":"Modeling T-cell activation using gene expression profiling and state-space models","volume":"20","author":"C Rangel","year":"2004","journal-title":"Bioinformatics"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1093\/bioinformatics\/btl003","article-title":"Inference of gene regulatory networks and compound mode of action from time course gene expression profiles","volume":"22","author":"M Bansal","year":"2006","journal-title":"Bioinformatics"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"27","DOI":"10.3233\/BD-2007-26104","article-title":"A non-genetic basis for cancer progression and metastasis: self-organizing attractors in cell regulatory networks","volume":"26","author":"S Huang","year":"2006","journal-title":"Breast Dis"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"2507","DOI":"10.1093\/bioinformatics\/btm344","article-title":"A review of feature selection techniques in bioinformatics","volume":"23","author":"Y Saeys","year":"2007","journal-title":"Bioinformatics"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1126\/science.282.5389.699","article-title":"The transcriptional program of sporulation in budding yeast","volume":"282","author":"S Chu","year":"1998","journal-title":"Science"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"e28805","DOI":"10.1371\/journal.pone.0028805","article-title":"Principal-oscillation-pattern analysis of gene expression","volume":"7","author":"D Wang","year":"2012","journal-title":"PLoS One"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1109\/TCBB.2011.150","article-title":"Eigen-genomic system dynamic-pattern analysis (ESDA): modeling mRNA degradation and self-regulation","volume":"9","author":"D Wang","year":"2012","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"first-page":"xxvii","year":"1996","author":"GH Golub","key":"ref19"},{"first-page":"xiii","year":"2005","author":"P Cull","key":"ref20"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"R110","DOI":"10.1186\/gb-2005-6-13-r110","article-title":"A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks","volume":"6","author":"JS Reece-Hoyes","year":"2005","journal-title":"Genome Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"D167","DOI":"10.1093\/nar\/gkt1165","article-title":"OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites","volume":"42","author":"S Shazman","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"W Huang da","year":"2009","journal-title":"Nat Protoc"},{"year":"1993","author":"M Bate","key":"ref24"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1242\/dev.00302","article-title":"Composition and dynamics of the Caenorhabditis elegans early embryonic transcriptome","volume":"130","author":"LR Baugh","year":"2003","journal-title":"Development"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1016\/j.tcb.2004.07.005","article-title":"A clean start: degradation of maternal proteins at the oocyte-to-embryo transition","volume":"14","author":"C DeRenzo","year":"2004","journal-title":"Trends Cell Biol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1016\/j.ydbio.2014.12.009","article-title":"E3 ubiquitin ligases promote progression of differentiation during C. elegans embryogenesis","volume":"398","author":"Z Du","year":"2015","journal-title":"Dev Biol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"R58","DOI":"10.1186\/gb-2010-11-6-r58","article-title":"Composition and regulation of maternal and zygotic transcriptomes reflects species-specific reproductive mode","volume":"11","author":"SS Shen-Orr","year":"2010","journal-title":"Genome Biol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1534\/g3.114.010652","article-title":"Coordinated metabolic transitions during Drosophila embryogenesis and the onset of aerobic glycolysis","volume":"4","author":"JM Tennessen","year":"2014","journal-title":"G3 (Bethesda)"},{"issue":"Suppl 2","key":"ref30","doi-asserted-by":"crossref","first-page":"S12","DOI":"10.1186\/1471-2105-9-S2-S12","article-title":"Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells","volume":"9","author":"M Mutarelli","year":"2008","journal-title":"BMC Bioinformatics"},{"first-page":"xi","year":"2000","author":"AJvd Schaft","key":"ref31"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005146","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T17:16:16Z","timestamp":1540314976000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005146"}},"subtitle":[],"editor":[{"given":"Teresa M.","family":"Przytycka","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,10,19]]},"references-count":31,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2016,10,19]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005146","relation":{},"ISSN":["1553-7358"],"issn-type":[{"type":"electronic","value":"1553-7358"}],"subject":[],"published":{"date-parts":[[2016,10,19]]}}}