{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T16:03:58Z","timestamp":1767974638496,"version":"3.49.0"},"reference-count":72,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2014,8,21]],"date-time":"2014-08-21T00:00:00Z","timestamp":1408579200000},"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.1003771","type":"journal-article","created":{"date-parts":[[2014,8,21]],"date-time":"2014-08-21T17:58:05Z","timestamp":1408643885000},"page":"e1003771","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":27,"title":["Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework"],"prefix":"10.1371","volume":"10","author":[{"given":"Ken Daigoro","family":"Yokoyama","sequence":"first","affiliation":[]},{"given":"Yang","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Jian","family":"Ma","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2014,8,21]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1038\/nrg2063","article-title":"The evolutionary significance of cis-regulatory mutations","volume":"8","author":"GA Wray","year":"2007","journal-title":"Nat Rev Genet"},{"key":"ref2","unstructured":"Davidson EH (2001) Genomic regulatory systems : development and evolution. San Diego: Academic Press. xii, 261 p. p."},{"key":"ref3","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1126\/science.1090005","article-title":"Evolution at two levels in humans and chimpanzees","volume":"188","author":"MC King","year":"1975","journal-title":"Science"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1377","DOI":"10.1093\/molbev\/msg140","article-title":"The evolution of transcriptional regulation in eukaryotes","volume":"20","author":"GA Wray","year":"2003","journal-title":"Mol Biol Evol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1038\/ng2047","article-title":"Tissue-specific transcriptional regulation has diverged significantly between human and mouse","volume":"39","author":"DT Odom","year":"2007","journal-title":"Nat Genet"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1036","DOI":"10.1126\/science.1186176","article-title":"Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding","volume":"328","author":"D Schmidt","year":"2010","journal-title":"Science"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1752","DOI":"10.1101\/gr.080663.108","article-title":"Evolution of the mammalian transcription factor binding repertoire via transposable elements","volume":"18","author":"G Bourque","year":"2008","journal-title":"Genome Res"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1038\/nature10842","article-title":"Insights into hominid evolution from the gorilla genome sequence","volume":"483","author":"A Scally","year":"2012","journal-title":"Nature"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1126\/science.1183621","article-title":"Variation in transcription factor binding among humans","volume":"328","author":"M Kasowski","year":"2010","journal-title":"Science"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1101\/gr.3715005","article-title":"Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes","volume":"15","author":"A Siepel","year":"2005","journal-title":"Genome Research"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1101\/gr.7.10.959","article-title":"Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome","volume":"7","author":"RC Hardison","year":"1997","journal-title":"Genome research"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1101\/gr.4866006","article-title":"Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression","volume":"16","author":"M Blanchette","year":"2006","journal-title":"Genome Res"},{"key":"ref13","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":"ref14","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":"ref15","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1038\/nature10530","article-title":"A high-resolution map of human evolutionary constraint using 29 mammals","volume":"478","author":"K Lindblad-Toh","year":"2011","journal-title":"Nature"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1019","DOI":"10.1126\/science.1202702","article-title":"Three periods of regulatory innovation during vertebrate evolution","volume":"333","author":"CB Lowe","year":"2011","journal-title":"Science"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1016\/j.celrep.2012.08.032","article-title":"A \u201cForward Genomics\u201d Approach Links Genotype to Phenotype using Independent Phenotypic Losses among Related Species","volume":"2","author":"M Hiller","year":"2012","journal-title":"Cell Rep"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1038\/nature09774","article-title":"Human-specific loss of regulatory DNA and the evolution of human-specific traits","volume":"471","author":"CY McLean","year":"2011","journal-title":"Nature"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1038\/nbt.1637","article-title":"Comparative assessment of methods for aligning multiple genome sequences","volume":"28","author":"X Chen","year":"2010","journal-title":"Nat Biotechnol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"6359","DOI":"10.1093\/nar\/gkr334","article-title":"PSAR: measuring multiple sequence alignment reliability by probabilistic sampling","volume":"39","author":"J Kim","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"e1001037","DOI":"10.1371\/journal.pcbi.1001037","article-title":"Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs","volume":"6","author":"WH Majoros","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1101\/gr.6725608","article-title":"Uncertainty in homology inferences: assessing and improving genomic sequence alignment","volume":"18","author":"G Lunter","year":"2008","journal-title":"Genome Res"},{"key":"ref23","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":"ref24","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1101\/gr.1933104","article-title":"Aligning multiple genomic sequences with the threaded blockset aligner","volume":"14","author":"M Blanchette","year":"2004","journal-title":"Genome Res"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/nature09534","article-title":"A map of human genome variation from population-scale sequencing","volume":"467","journal-title":"Nature"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1675","DOI":"10.1126\/science.1225057","article-title":"Evidence of abundant purifying selection in humans for recently acquired regulatory functions","volume":"337","author":"LD Ward","year":"2012","journal-title":"Science"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1038\/nature03441","article-title":"Systematic discovery of regulatory motifs in human promoters and 3\u2032 UTRs by comparison of several mammals","volume":"434","author":"X Xie","year":"2005","journal-title":"Nature"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"e1000299","DOI":"10.1371\/journal.pcbi.1000299","article-title":"Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution","volume":"5","author":"X He","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"1102","DOI":"10.1093\/gbe\/evs085","article-title":"SP transcription factor paralogs and DNA-binding sites coevolve and adaptively converge in mammals and birds","volume":"4","author":"KD Yokoyama","year":"2012","journal-title":"Genome Biol Evol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"e1000330","DOI":"10.1371\/journal.pgen.1000330","article-title":"Evolution of regulatory sequences in 12 Drosophila species","volume":"5","author":"J Kim","year":"2009","journal-title":"PLoS Genet"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1126\/science.1141319","article-title":"Genome-wide mapping of in vivo protein-DNA interactions","volume":"316","author":"DS Johnson","year":"2007","journal-title":"Science"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1016\/j.cell.2008.04.043","article-title":"Integration of external signaling pathways with the core transcriptional network in embryonic stem cells","volume":"133","author":"X Chen","year":"2008","journal-title":"Cell"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1038\/nature08514","article-title":"Human DNA methylomes at base resolution show widespread epigenomic differences","volume":"462","author":"R Lister","year":"2009","journal-title":"Nature"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"e1001046","DOI":"10.1371\/journal.pbio.1001046","article-title":"A user&apos;s guide to the encyclopedia of DNA elements (ENCODE)","volume":"9","author":"RM Myers","year":"2011","journal-title":"PLoS biology"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1186\/gb-2012-13-8-418","article-title":"An encyclopedia of mouse DNA elements (Mouse ENCODE)","volume":"13","author":"EC Mouse","year":"2012","journal-title":"Genome Biol"},{"key":"ref36","doi-asserted-by":"crossref","unstructured":"Davison AC (2003) Statistical Models. New York: Cambridge University Press.","DOI":"10.1017\/CBO9780511815850"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"1797","DOI":"10.1101\/gr.6761107","article-title":"28-way vertebrate alignment and conservation track in the UCSC Genome Browser","volume":"17","author":"W Miller","year":"2007","journal-title":"Genome Res"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"W202","DOI":"10.1093\/nar\/gkp335","article-title":"MEME SUITE: tools for motif discovery and searching","volume":"37","author":"TL Bailey","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1016\/j.cell.2011.11.058","article-title":"Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages","volume":"148","author":"D Schmidt","year":"2012","journal-title":"Cell"},{"key":"ref40","article-title":"Latent Regulatory Potential of Human-Specific Repetitive Elements","author":"MC Ward","year":"2012","journal-title":"Mol Cell"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"18613","DOI":"10.1073\/pnas.0703637104","article-title":"Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53","volume":"104","author":"T Wang","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref42","unstructured":"Smit AF, Hubley R, Green P (1996\u20132010) RepeatMasker Open-3.0."},{"key":"ref43","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1038\/ng.600","article-title":"Transposable elements have rewired the core regulatory network of human embryonic stem cells","volume":"42","author":"G Kunarso","year":"2010","journal-title":"Nat Genet"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1101\/gr.097857.109","article-title":"Detection of nonneutral substitution rates on mammalian phylogenies","volume":"20","author":"KS Pollard","year":"2010","journal-title":"Genome Res"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1093\/bioinformatics\/btn605","article-title":"MotifMap: a human genome-wide map of candidate regulatory motif sites","volume":"25","author":"X Xie","year":"2009","journal-title":"Bioinformatics"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1038\/nature06340","article-title":"Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures","volume":"450","author":"A Stark","year":"2007","journal-title":"Nature"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"7145","DOI":"10.1073\/pnas.0701811104","article-title":"Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites","volume":"104","author":"X Xie","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"1919","DOI":"10.1101\/gr.7090407","article-title":"Reliable prediction of regulator targets using 12 Drosophila genomes","volume":"17","author":"P Kheradpour","year":"2007","journal-title":"Genome Res"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"12556","DOI":"10.1073\/pnas.1209523109","article-title":"Cord blood-derived neuronal cells by ectopic expression of Sox2 and c-Myc","volume":"109","author":"A Giorgetti","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1242\/dev.010801","article-title":"Impaired generation of mature neurons by neural stem cells from hypomorphic Sox2 mutants","volume":"135","author":"M Cavallaro","year":"2008","journal-title":"Development"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1242\/dev.121.1.163","article-title":"Development of hematopoietic cells lacking transcription factor GATA-1","volume":"121","author":"L Pevny","year":"1995","journal-title":"Development"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"e41374","DOI":"10.1371\/journal.pone.0041374","article-title":"Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome","volume":"7","author":"H Chen","year":"2012","journal-title":"PLoS ONE"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nmeth.1906","article-title":"ChromHMM: automating chromatin-state discovery and characterization","volume":"9","author":"J Ernst","year":"2012","journal-title":"Nat Methods"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"D88","DOI":"10.1093\/nar\/gkl822","article-title":"VISTA Enhancer Browser\u2013a database of tissue-specific human enhancers","volume":"35","author":"A Visel","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1038\/nature10530","article-title":"A high-resolution map of human evolutionary constraint using 29 mammals","volume":"478","author":"K Lindblad-Toh","year":"2011","journal-title":"Nature"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"e7","DOI":"10.1371\/journal.pbio.0030007","article-title":"Highly conserved non-coding sequences are associated with vertebrate development","volume":"3","author":"A Woolfe","year":"2005","journal-title":"PLoS Biol"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1186\/1471-2105-4-57","article-title":"Conservation of regulatory elements between two species of Drosophila","volume":"4","author":"E Emberly","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"2376","DOI":"10.1101\/gr.142281.112","article-title":"Extensive compensatory cis-trans regulation in the evolution of mouse gene expression","volume":"22","author":"A Goncalves","year":"2012","journal-title":"Genome Res"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"1114","DOI":"10.1093\/oxfordjournals.molbev.a004169","article-title":"Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover","volume":"19","author":"ET Dermitzakis","year":"2002","journal-title":"Mol Biol Evol"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"e1000343","DOI":"10.1371\/journal.pbio.1000343","article-title":"Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species","volume":"8","author":"RK Bradley","year":"2010","journal-title":"PLoS Biol"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"R50","DOI":"10.1186\/gb-2012-13-9-r50","article-title":"Functional analysis of transcription factor binding sites in human promoters","volume":"13","author":"TW Whitfield","year":"2012","journal-title":"Genome Biol"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/nrg1315","article-title":"Applied bioinformatics for the identification of regulatory elements","volume":"5","author":"WW Wasserman","year":"2004","journal-title":"Nat Rev Genet"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1038\/nrg2538","article-title":"A census of human transcription factors: function, expression and evolution","volume":"10","author":"JM Vaquerizas","year":"2009","journal-title":"Nat Rev Genet"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1126\/science.1184655","article-title":"Heritable individual-specific and allele-specific chromatin signatures in humans","volume":"328","author":"R McDaniell","year":"2010","journal-title":"Science"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1038\/msb.2011.60","article-title":"Inferring regulatory mechanisms from patterns of evolutionary divergence","volume":"7","author":"I Tirosh","year":"2011","journal-title":"Mol Syst Biol"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1038\/msb4100198","article-title":"On the relation between promoter divergence and gene expression evolution","volume":"4","author":"I Tirosh","year":"2008","journal-title":"Mol Syst Biol"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1038\/nrg3229","article-title":"Comparative studies of gene expression and the evolution of gene regulation","volume":"13","author":"IG Romero","year":"2012","journal-title":"Nat Rev Genet"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"e1004226","DOI":"10.1371\/journal.pgen.1004226","article-title":"The functional consequences of variation in transcription factor binding","volume":"10","author":"DA Cusanovich","year":"2014","journal-title":"PLoS Genet"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1017\/S0001867800031050","article-title":"Quasi-stationary distributions of birth-and-death processes","volume":"10","author":"JA Cavender","year":"1978","journal-title":"Adv Appl Prob"},{"key":"ref70","first-page":"471","article-title":"Maximum-likelihood estimation of evolutionary trees from continuous characters","volume":"25","author":"J Felsenstein","year":"1973","journal-title":"Am J Hum Genet"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.2517-6161.1977.tb01600.x","article-title":"Maximum Likelihood from Incomplete Data Via Em Algorithm","volume":"39","author":"AP Dempster","year":"1977","journal-title":"Journal of the Royal Statistical Society Series B-Methodological"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/nar\/29.1.308","article-title":"dbSNP: the NCBI database of genetic variation","volume":"29","author":"ST Sherry","year":"2001","journal-title":"Nucleic Acids Res"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003771","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,1]],"date-time":"2024-06-01T19:15:01Z","timestamp":1717269301000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003771"}},"subtitle":[],"editor":[{"given":"Sheng","family":"Zhong","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2014,8,21]]},"references-count":72,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2014,8,21]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003771","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,8,21]]}}}