{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T00:19:25Z","timestamp":1767831565317,"version":"3.49.0"},"reference-count":44,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2008,6,6]],"date-time":"2008-06-06T00:00:00Z","timestamp":1212710400000},"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.1000090","type":"journal-article","created":{"date-parts":[[2008,6,5]],"date-time":"2008-06-05T21:20:54Z","timestamp":1212700854000},"page":"e1000090","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":14,"title":["CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing"],"prefix":"10.1371","volume":"4","author":[{"given":"Pradipta","family":"Ray","sequence":"first","affiliation":[]},{"given":"Suyash","family":"Shringarpure","sequence":"additional","affiliation":[]},{"given":"Mladen","family":"Kolar","sequence":"additional","affiliation":[]},{"given":"Eric P.","family":"Xing","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2008,6,6]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"1391","DOI":"10.1126\/science.1081331","article-title":"Phylogenetic shadowing of primate sequences to find functional regions of the human genome.","volume":"299","author":"D Boffelli","year":"2003","journal-title":"Science"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1101\/gr.6902","article-title":"Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting.","volume":"12","author":"M Blanchette","year":"2002","journal-title":"Genome Research"},{"key":"ref3","first-page":"277","article-title":"Combining phylogenetic and hidden Markov models in biosequence analysis.","author":"AC Siepel","year":"2003"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"2369","DOI":"10.1093\/bioinformatics\/btg329","article-title":"Combining phylogenetic data with co-regulated genes to identify regulatory motifs.","volume":"19","author":"T Wang","year":"2003","journal-title":"Bioinformatics"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1850","DOI":"10.1093\/bioinformatics\/bth153","article-title":"Multiple-sequence functional annotation and the generalized hidden markov phylogeny.","volume":"20","author":"JD McAuliffe","year":"2004","journal-title":"Bioinformatics"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1093\/bioinformatics\/19.2.219","article-title":"Gene finding with a hidden markov model of genome structure and evolution.","volume":"19","author":"J Pedersen","year":"2003","journal-title":"Bioinformatics"},{"key":"ref7","first-page":"177","article-title":"Computational identification of evolutionarily conserved exons. Proceedings of the eighth annual international conference on Research in computational molecular biology (RECOMB)","author":"AC Siepel","year":"2004"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"e93","DOI":"10.1371\/journal.pbio.0030093","article-title":"Functional evolution of a cisregulatory module.","volume":"3","author":"MZ Ludwig","year":"2005","journal-title":"PLoS Biol"},{"key":"ref9","first-page":"30","article-title":"Phylogibbs: A gibbs sampler incorporating phylogenetic information.","author":"R Siddharthan","year":"2004"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1186\/1471-2105-5-170","article-title":"PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences.","volume":"5","author":"S Sinha","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1242\/dev.125.5.949","article-title":"Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change.","volume":"12","author":"MZ Ludwig","year":"1998","journal-title":"Development"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"e130","DOI":"10.1371\/journal.pcbi.0020130","article-title":"Large-scale turnover of functional transcription factor binding sites in Drosophila.","volume":"2","author":"AM Moses","year":"2006","journal-title":"PLoS Comput Biol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1038\/35000615","article-title":"Evidence for stabilizing selection in a eukaryotic enhancer element.","volume":"403","author":"MZ Ludwig","year":"2000","journal-title":"Nature"},{"key":"ref14","first-page":"69","article-title":"An empirical comparison of tools for phylogenetic footprinting.","author":"M Blanchette","year":"2003"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"3840","DOI":"10.1093\/nar\/gkg606","article-title":"FootPrinter: A program designed for phylogenetic footprinting.","volume":"31","author":"M Blanchette","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"ref16","first-page":"69","article-title":"VISTA family of computational tools for comparative analysis of DNA sequences and whole genomes.","volume":"338","author":"I Dubchak","year":"2006","journal-title":"Methods Mol Biol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1093\/nar\/gkh372","article-title":"ConSite: web-based prediction of regulatory elements using cross-species comparison.","volume":"32","author":"A Sandelin","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1007\/978-1-59745-514-5_26","article-title":"Web-Based Identification of Evolutionary Conserved DNA cis-Regulatory Elements.","volume":"395","author":"PV Benos","year":"2007","journal-title":"Methods Mol Biol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"i249","DOI":"10.1093\/bioinformatics\/btm211","article-title":"A statistical method for alignment-free comparison of regulatory sequences.","volume":"23","author":"MR Kantorovitz","year":"2007","journal-title":"Bioinformatics"},{"key":"ref20","first-page":"324","article-title":"Phylogenetic motif detection by expectation-maximization on evolutionary mixtures.","author":"AM Moses","year":"2004","journal-title":"Pac Symp Biocomput"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"R98","DOI":"10.1186\/gb-2004-5-12-r98","article-title":"Monkey: Identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model.","volume":"5","author":"AM Moses","year":"2004","journal-title":"Genome Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"R225","DOI":"10.1186\/gb-2007-8-10-r225","article-title":"Phylogenetic Simulation of Promoter Evolution: Estimation and Modeling of Binding Site Turnover Events and Assessing Their Impact on Alignment Tools.","volume":"8","author":"W Huang","year":"2007","journal-title":"Genome Biol"},{"key":"ref23","doi-asserted-by":"crossref","DOI":"10.1007\/11732990_17","article-title":"New methods for detecting lineage-specific selection.","volume":"3909","author":"A Siepel","year":"2006","journal-title":"Lecture Notes in Computer Science"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"2507","DOI":"10.1101\/gr.1602203","article-title":"Identification and characterization of multi-species conserved sequences.","volume":"13","author":"EH Margulies","year":"2003","journal-title":"Genome Res"},{"key":"ref25","first-page":"297","article-title":"A graphical model for predicting protein molecular function.","author":"BE Engelhardt","year":"2006"},{"key":"ref26","first-page":"21","article-title":"Evolution of protein molecules.","author":"TH Jukes","year":"1969"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1007\/BF01734359","article-title":"Evolutionary trees from DNA sequences: a maximum likelihood approach.","volume":"17","author":"J Felsenstein","year":"1981","journal-title":"J Mol Evol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1093\/bioinformatics\/btg1040","article-title":"A probabilistic method to detect regulatory modules.","volume":"19","author":"S Sinha","year":"2003","journal-title":"Bioinformatics"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1093\/oxfordjournals.molbev.a025575","article-title":"A Hidden Markov Model approach to variation among sites in rate of evolution.","volume":"13","author":"J Felsenstein","year":"1996","journal-title":"Mol Biol Evol"},{"key":"ref30","article-title":"Inferring Phylogenies","author":"J Felsenstein","year":"2001"},{"key":"ref31","article-title":"Probabilistic Networks and Expert Systems","author":"RG Cowell","year":"2005"},{"key":"ref32","article-title":"A generalized mean field algorithm for variational inference in exponential families.","author":"EP Xing","year":"2003"},{"key":"ref33","first-page":"266","article-title":"LOGOS: a modular Bayesian model for de novo motif detection.","volume":"2","author":"EP Xing","year":"2003","journal-title":"Proc IEEE Comput Soc Bioinform Conf"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"3214","DOI":"10.1093\/nar\/gkf438","article-title":"Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences.","volume":"30","author":"MC Frith","year":"2002","journal-title":"Nucleic Acids Research"},{"key":"ref35","first-page":"115","article-title":"Context-specific independence in Bayesian networks.","author":"C Boutilier","year":"1996"},{"key":"ref36","first-page":"41","article-title":"fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood.","volume":"10","author":"GJ Olsen","year":"1994","journal-title":"Comput Appl Biosci"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1038\/nbt1053","article-title":"Assessing computational tools for the discovery of transcription factor binding sites.","volume":"23","author":"M Tompa","year":"2005","journal-title":"Nat Biotechnol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1101\/gr.212502","article-title":"Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers.","volume":"12","author":"DA Papatsenko","year":"2002","journal-title":"Genome Res"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1747","DOI":"10.1093\/bioinformatics\/bti173","article-title":"Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster.","volume":"21","author":"C Bergman","year":"2005","journal-title":"Bioinformatics"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1093\/nar\/gkg094","article-title":"The FlyBase Database of the Drosophila Genome Projects and community literature.","volume":"31","year":"2003","journal-title":"Nucleic Acids Research"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1093\/bioinformatics\/btk027","article-title":"Oreganno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation.","volume":"22","author":"SB Montgomery","year":"2006","journal-title":"Bioinformatics"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1747","DOI":"10.1093\/bioinformatics\/bti173","article-title":"Drosophila dnase i footprint database:a systematic genome annotation of transcription factor binding sites in the fruitfly, drosophila melanogaster.","volume":"21","author":"CM Bergman","year":"2005","journal-title":"Bioinformatics"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: A Sequence Logo Generator.","volume":"14","author":"GE Crooks","year":"2004","journal-title":"Genome Res"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1007\/BF02101694","article-title":"Dating of the human-ape splitting by a molecular clock of mitochondrial DNA.","volume":"22","author":"M Hasegawa","year":"1985","journal-title":"J Mol Evol"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000090","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,11]],"date-time":"2021-09-11T20:15:26Z","timestamp":1631391326000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000090"}},"subtitle":[],"editor":[{"given":"Uwe","family":"Ohler","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2008,6,6]]},"references-count":44,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2008,6,6]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000090","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,6,6]]}}}