{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T04:55:31Z","timestamp":1771995331320,"version":"3.50.1"},"reference-count":110,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,3]]},"DOI":"10.1093\/bib\/bbs016","type":"journal-article","created":{"date-parts":[[2012,4,20]],"date-time":"2012-04-20T02:15:34Z","timestamp":1334888134000},"page":"225-237","source":"Crossref","is-referenced-by-count":120,"title":["Motif discovery and transcription factor binding sites before and after the next-generation sequencing era"],"prefix":"10.1093","volume":"14","author":[{"given":"Federico","family":"Zambelli","sequence":"first","affiliation":[]},{"given":"Graziano","family":"Pesole","sequence":"additional","affiliation":[]},{"given":"Giulio","family":"Pavesi","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2012,4,19]]},"reference":[{"key":"key\n\t\t\t\t20170523192509_bbs016-B1","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1093\/bib\/5.3.217","article-title":"In silico representation and discovery of transcription factor binding sites","volume":"5","author":"Pavesi","year":"2004","journal-title":"Brief Bioinform"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B2","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1745-6150-1-11","article-title":"A survey of motif discovery methods in an integrated framework","volume":"1","author":"Sandve","year":"2006","journal-title":"Biol Direct"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B3","doi-asserted-by":"crossref","first-page":"2551","DOI":"10.1101\/gad.831000","article-title":"Orchestrated response: a symphony of transcription factors for gene control","volume":"14","author":"Lemon","year":"2000","journal-title":"Genes Dev"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B4","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1038\/nature01763","article-title":"Transcription regulation and animal diversity","volume":"424","author":"Levine","year":"2003","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B5","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1038\/ng1031","article-title":"Fundamentals of experimental design for cDNA microarrays","volume":"32","author":"Churchill","year":"2002","journal-title":"Nat Genet"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B6","doi-asserted-by":"crossref","first-page":"E190","DOI":"10.1038\/35087138","article-title":"Navigating gene expression using microarrays\u2014a technology review","volume":"3","author":"Schulze","year":"2001","journal-title":"Nat Cell Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B7","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/S0014-5793(00)01772-5","article-title":"Gene expression data analysis","volume":"480","author":"Brazma","year":"2000","journal-title":"FEBS Lett"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B8","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1093\/bfgp\/elm034","article-title":"Microarray data analysis and mining approaches","volume":"6","author":"Cordero","year":"2007","journal-title":"Brief Funct Genomic Proteomic"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B9","doi-asserted-by":"crossref","first-page":"929","DOI":"10.2741\/2733","article-title":"Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation","volume":"13","author":"Collas","year":"2008","journal-title":"Front Biosci"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B10","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1007\/978-1-59745-190-1_23","article-title":"ChIP on chip assays: genome-wide analysis of transcription factor binding and histone modifications","volume":"523","author":"Pillai","year":"2009","journal-title":"Methods Mol Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B11","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1038\/nmeth0807-613","article-title":"ChIP-seq: welcome to the new frontier","volume":"4","author":"Mardis","year":"2007","journal-title":"Nat Methods"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B12","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1073\/pnas.83.1.4","article-title":"Nomenclature for incompletely specified bases in nucleic acid sequences. Recommendations 1984","volume":"83","author":"Nomenclature Committee of the International Union of Biochemistry (NC-IUB).","year":"1986","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B13","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B14","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1093\/bioinformatics\/16.1.16","article-title":"DNA binding sites: representation and discovery","volume":"16","author":"Stormo","year":"2000","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B15","doi-asserted-by":"crossref","first-page":"W253","DOI":"10.1093\/nar\/gkm272","article-title":"STAMP: a web tool for exploring DNA-binding motif similarities","volume":"35","author":"Mahony","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B16","doi-asserted-by":"crossref","first-page":"R24","DOI":"10.1186\/gb-2007-8-2-r24","article-title":"Quantifying similarity between motifs","volume":"8","author":"Gupta","year":"2007","journal-title":"Genome Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B17","article-title":"On approximation algorithms for local multiple alignment, RECOMB 2000","author":"Akutsu"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B18","first-page":"81","article-title":"Identification of consensus patterns in unaligned DNA sequences known to be functionally related","volume":"6","author":"Hertz","year":"1990","journal-title":"Comput Appl Biosci"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B19","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1093\/bioinformatics\/15.7.563","article-title":"Identifying DNA and protein patterns with statistically significant alignments of multiple sequences","volume":"15","author":"Hertz","year":"1999","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B20","first-page":"28","article-title":"Fitting a mixture model by expectation maximization to discover motifs in biopolymers","volume":"2","author":"Bailey","year":"1994","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B21","first-page":"21","article-title":"The value of prior knowledge in discovering motifs with MEME","volume":"3","author":"Bailey","year":"1995","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B22","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1126\/science.8211139","article-title":"Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment","volume":"262","author":"Lawrence","year":"1993","journal-title":"Science"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B23","doi-asserted-by":"crossref","first-page":"1618","DOI":"10.1002\/pro.5560040820","article-title":"Gibbs motif sampling: detection of bacterial outer membrane protein repeats","volume":"4","author":"Neuwald","year":"1995","journal-title":"Protein Sci"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B24","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1002\/prot.340070105","article-title":"An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences","volume":"7","author":"Lawrence","year":"1990","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B25","doi-asserted-by":"crossref","first-page":"1205","DOI":"10.1006\/jmbi.2000.3519","article-title":"Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae","volume":"296","author":"Hughes","year":"2000","journal-title":"J Mol Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B26","first-page":"467","article-title":"ANN-Spec: a method for discovering transcription factor binding sites with improved specificity","author":"Workman","year":"2000","journal-title":"Pac Symp Biocomput"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B27","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1093\/bioinformatics\/17.12.1113","article-title":"A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling","volume":"17","author":"Thijs","year":"2001","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B28","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/S0966-842X(02)00030-6","article-title":"Genome-specific higher-order background models to improve motif detection","volume":"11","author":"Marchal","year":"2003","journal-title":"Trends Microbiol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B29","doi-asserted-by":"crossref","first-page":"1952","DOI":"10.1093\/bioinformatics\/btg266","article-title":"Background rareness-based iterative multiple sequence alignment algorithm for regulatory element detection","volume":"19","author":"Narasimhan","year":"2003","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B30","doi-asserted-by":"crossref","first-page":"W369","DOI":"10.1093\/nar\/gkl198","article-title":"MEME: discovering and analyzing DNA and protein sequence motifs","volume":"34","author":"Bailey","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B31","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1089\/10665270252935566","article-title":"A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes","volume":"9","author":"Thijs","year":"2002","journal-title":"J Comput Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B32","first-page":"127","article-title":"BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes","author":"Liu","year":"2001","journal-title":"Pac Symp Biocomput"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B33","doi-asserted-by":"crossref","first-page":"1753","DOI":"10.1093\/nar\/gkg268","article-title":"Toucan: deciphering the cis-regulatory logic of coregulated genes","volume":"31","author":"Aerts","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B34","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1093\/nar\/gkh169","article-title":"Finding functional sequence elements by multiple local alignment","volume":"32","author":"Frith","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B35","doi-asserted-by":"crossref","first-page":"3580","DOI":"10.1093\/nar\/gkg608","article-title":"Gibbs Recursive sampler: finding transcription factor binding sites","volume":"31","author":"Thompson","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B36","doi-asserted-by":"crossref","first-page":"1445","DOI":"10.1093\/nar\/gki282","article-title":"NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence","volume":"33","author":"Down","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B37","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1089\/cmb.2008.16TT","article-title":"GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery","volume":"16","author":"Li","year":"2009","journal-title":"J Comput Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B38","doi-asserted-by":"crossref","first-page":"3826","DOI":"10.1093\/nar\/gkh713","article-title":"Discovery of sequence motifs related to coexpression of genes using evolutionary computation","volume":"32","author":"Fogel","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B39","doi-asserted-by":"crossref","first-page":"2715","DOI":"10.1093\/bioinformatics\/btp490","article-title":"info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling","volume":"25","author":"Defrance","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B40","doi-asserted-by":"crossref","first-page":"2221","DOI":"10.1093\/nar\/11.7.2221","article-title":"Regulatory pattern identification in nucleic acid sequences","volume":"11","author":"Sadler","year":"1983","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B41","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1007\/BF02459500","article-title":"Pattern recognition in several sequences: consensus and alignment","volume":"46","author":"Waterman","year":"1984","journal-title":"Bull Math Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B42","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/0022-2836(85)90262-1","article-title":"Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli","volume":"186","author":"Galas","year":"1985","journal-title":"J Mol Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B43","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1089\/106652700750050826","article-title":"Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification","volume":"7","author":"Marsan","year":"2000","journal-title":"J Comput Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B44","doi-asserted-by":"crossref","first-page":"S207","DOI":"10.1093\/bioinformatics\/17.suppl_1.S207","article-title":"An algorithm for finding signals of unknown length in DNA sequences","volume":"17","author":"Pavesi","year":"2001","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B45","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1471-2105-3-7","article-title":"Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes","volume":"3","author":"Caselle","year":"2002","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B46","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1186\/1471-2105-5-57","article-title":"Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrepresented upstream motifs","volume":"5","author":"Cora","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B47","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1006\/jmbi.1998.1947","article-title":"Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies","volume":"281","author":"van Helden","year":"1998","journal-title":"J Mol Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B48","doi-asserted-by":"crossref","first-page":"II206","DOI":"10.1093\/bioinformatics\/btg1079","article-title":"Finding optimal degenerate patterns in DNA sequences","volume":"19","author":"Shinozaki","year":"2003","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B49","doi-asserted-by":"crossref","first-page":"3586","DOI":"10.1093\/nar\/gkg618","article-title":"YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation","volume":"31","author":"Sinha","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B50","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1093\/bioinformatics\/btl681","article-title":"Compressed suffix tree\u2014a basis for genome-scale sequence analysis","volume":"23","author":"Valimaki","year":"2007","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B51","doi-asserted-by":"crossref","first-page":"W199","DOI":"10.1093\/nar\/gkh465","article-title":"Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes","volume":"32","author":"Pavesi","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B52","doi-asserted-by":"crossref","first-page":"i356","DOI":"10.1093\/bioinformatics\/btp188","article-title":"Efficient exact motif discovery","volume":"25","author":"Marschall","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B53","first-page":"269","article-title":"Combinatorial approaches to finding subtle signals in DNA sequences","volume":"8","author":"Pevzner","year":"2000","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B54","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/1471-2105-12-238","article-title":"MotifClick: prediction of cis-regulatory binding sites via merging cliques","volume":"12","author":"Zhang","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B55","doi-asserted-by":"crossref","first-page":"e150","DOI":"10.1093\/bioinformatics\/btl243","article-title":"MotifCut: regulatory motifs finding with maximum density subgraphs","volume":"22","author":"Fratkin","year":"2006","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B56","doi-asserted-by":"crossref","first-page":"S16","DOI":"10.1186\/1471-2105-12-S1-S16","article-title":"SOMEA: self-organizing map based extraction algorithm for DNA motif identification with heterogeneous model","volume":"12","author":"Lee","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B57","doi-asserted-by":"crossref","first-page":"1807","DOI":"10.1093\/bioinformatics\/bti256","article-title":"Transcription factor binding site identification using the self-organizing map","volume":"21","author":"Mahony","year":"2005","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B58","first-page":"235","article-title":"Finding weak motifs in DNA sequences","author":"Sze","year":"2002","journal-title":"Pac Symp Biocomput"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B59","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1089\/10665270252935430","article-title":"Finding motifs using random projections","volume":"9","author":"Buhler","year":"2002","journal-title":"J Comput Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B60","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":"Tompa","year":"2005","journal-title":"Nat Biotechnol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B61","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1748-7188-1-8","article-title":"Analysis of computational approaches for motif discovery","volume":"1","author":"Li","year":"2006","journal-title":"Algorithms Mol Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B62","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1186\/1471-2105-8-193","article-title":"Improved benchmarks for computational motif discovery","volume":"8","author":"Sandve","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B63","doi-asserted-by":"crossref","first-page":"W217","DOI":"10.1093\/nar\/gkm376","article-title":"WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches","volume":"35","author":"Romer","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B64","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1093\/bioinformatics\/btq636","article-title":"GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments","volume":"27","author":"van Heeringen","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B65","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1093\/bioinformatics\/btq707","article-title":"CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments","volume":"27","author":"Kuttippurathu","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B66","doi-asserted-by":"crossref","first-page":"W247","DOI":"10.1093\/nar\/gkp464","article-title":"Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes","volume":"37","author":"Zambelli","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B67","doi-asserted-by":"crossref","first-page":"R43","DOI":"10.1186\/gb-2003-4-7-r43","article-title":"Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts","volume":"4","author":"Chiang","year":"2003","journal-title":"Genome Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B68","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1093\/bioinformatics\/bti819","article-title":"Evaluating phylogenetic footprinting for human-rodent comparisons","volume":"22","author":"Sauer","year":"2006","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B69","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":"Dermitzakis","year":"2002","journal-title":"Mol Biol Evol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B70","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1126\/science.1098119","article-title":"Ultraconserved elements in the human genome","volume":"304","author":"Bejerano","year":"2004","journal-title":"Science"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B71","doi-asserted-by":"crossref","first-page":"e67","DOI":"10.1371\/journal.pcbi.0010067","article-title":"PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny","volume":"1","author":"Siddharthan","year":"2005","journal-title":"PLoS Comput Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B72","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":"Sinha","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B73","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":"Odom","year":"2007","journal-title":"Nat Genet"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B74","doi-asserted-by":"crossref","first-page":"e215","DOI":"10.1371\/journal.pcbi.0030215","article-title":"A nucleosome-guided map of transcription factor binding sites in yeast","volume":"3","author":"Narlikar","year":"2007","journal-title":"PLoS Comput Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B75","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1186\/1471-2105-11-179","article-title":"The value of position-specific priors in motif discovery using MEME","volume":"11","author":"Bailey","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B76","doi-asserted-by":"crossref","first-page":"1347","DOI":"10.1089\/cmb.2007.0176","article-title":"BayesMD: flexible biological modeling for motif discovery","volume":"15","author":"Tang","year":"2008","journal-title":"J Comput Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B77","doi-asserted-by":"crossref","first-page":"2195","DOI":"10.1093\/bioinformatics\/btq357","article-title":"PriorsEditor: a tool for the creation and use of positional priors in motif discovery","volume":"26","author":"Klepper","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B78","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.tig.2007.12.007","article-title":"The impact of next-generation sequencing technology on genetics","volume":"24","author":"Mardis","year":"2008","journal-title":"Trends Genet"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B79","doi-asserted-by":"crossref","first-page":"S22","DOI":"10.1038\/nmeth.1371","article-title":"Computation for ChIP-seq and RNA-seq studies","volume":"6","author":"Pepke","year":"2009","journal-title":"Nat Methods"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B80","doi-asserted-by":"crossref","first-page":"9703","DOI":"10.1074\/jbc.M611752200","article-title":"Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays","volume":"282","author":"Krig","year":"2007","journal-title":"J Biol Chem"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B81","doi-asserted-by":"crossref","first-page":"17834","DOI":"10.1073\/pnas.0604129103","article-title":"Global mapping of c-Myc binding sites and target gene networks in human B cells","volume":"103","author":"Zeller","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B82","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/ng1760","article-title":"The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells","volume":"38","author":"Loh","year":"2006","journal-title":"Nat Genet"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B83","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":"Chen","year":"2008","journal-title":"Cell"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B84","doi-asserted-by":"crossref","first-page":"1696","DOI":"10.1093\/bioinformatics\/btr189","article-title":"MEME-ChIP: motif analysis of large DNA datasets","volume":"27","author":"Machanick","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B85","doi-asserted-by":"crossref","first-page":"2154","DOI":"10.1093\/nar\/gkp1180","article-title":"On the detection and refinement of transcription factor binding sites using ChIP-Seq data","volume":"38","author":"Hu","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B86","doi-asserted-by":"crossref","first-page":"e126","DOI":"10.1093\/nar\/gkr574","article-title":"STEME: efficient EM to find motifs in large data sets","volume":"39","author":"Reid","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B87","doi-asserted-by":"crossref","first-page":"2622","DOI":"10.1093\/bioinformatics\/btq488","article-title":"Deep and wide digging for binding motifs in ChIP-Seq data","volume":"26","author":"Kulakovskiy","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B88","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1038\/nbt717","article-title":"An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments","volume":"20","author":"Liu","year":"2002","journal-title":"Nat Biotechnol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B89","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1038\/nmeth1061","article-title":"Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation","volume":"4","author":"Ettwiller","year":"2007","journal-title":"Nat Methods"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B90","doi-asserted-by":"crossref","first-page":"1180","DOI":"10.1101\/gr.076117.108","article-title":"Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets","volume":"18","author":"Linhart","year":"2008","journal-title":"Genome Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B91","doi-asserted-by":"crossref","first-page":"1653","DOI":"10.1093\/bioinformatics\/btr261","article-title":"DREME: motif discovery in transcription factor ChIP-seq data","volume":"27","author":"Bailey","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B92","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1093\/dnares\/dsp014","article-title":"Exhaustive search for over-represented DNA sequence motifs with CisFinder","volume":"16","author":"Sharov","year":"2009","journal-title":"DNA Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B93","doi-asserted-by":"crossref","first-page":"R19","DOI":"10.1186\/gb-2010-11-2-r19","article-title":"Evidence-ranked motif identification","volume":"11","author":"Georgiev","year":"2010","journal-title":"Genome Biol"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B94","article-title":"RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets","author":"Thomas-Chollier","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B95","doi-asserted-by":"crossref","first-page":"5221","DOI":"10.1093\/nar\/gkn488","article-title":"Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data","volume":"36","author":"Jothi","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B96","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1038\/84792","article-title":"Regulatory element detection using correlation with expression","volume":"27","author":"Bussemaker","year":"2001","journal-title":"Nat Genet"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B97","doi-asserted-by":"crossref","first-page":"3487","DOI":"10.1093\/nar\/gkg630","article-title":"REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data","volume":"31","author":"Roven","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B98","doi-asserted-by":"crossref","first-page":"1757","DOI":"10.1101\/gr.121541.111","article-title":"Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity","volume":"21","author":"Song","year":"2011","journal-title":"Genome Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B99","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1186\/1471-2164-12-134","article-title":"ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis","volume":"12","author":"Ho","year":"2011","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B100","doi-asserted-by":"crossref","first-page":"1152","DOI":"10.1093\/bioinformatics\/btq106","article-title":"Localized motif discovery in gene regulatory sequences","volume":"26","author":"Narang","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B101","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1093\/bioinformatics\/btr614","article-title":"Epigenetic priors for identifying active transcription factor binding sites","volume":"28","author":"Cuellar-Partida","year":"2012","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B102","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1101\/gr.112623.110","article-title":"Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data","volume":"21","author":"Pique-Regi","year":"2011","journal-title":"Genome Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B103","doi-asserted-by":"crossref","first-page":"D912","DOI":"10.1093\/nar\/gkr1012","article-title":"ENCODE whole-genome data in the UCSC Genome Browser: update 2012","volume":"40","author":"Rosenbloom","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B104","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1038\/nature02800","article-title":"Transcriptional regulatory code of a eukaryotic genome","volume":"431","author":"Harbison","year":"2004","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B105","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1186\/1471-2105-8-189","article-title":"MATLIGN: a motif clustering, comparison and matching tool","volume":"8","author":"Kankainen","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B106","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1016\/j.cell.2011.11.013","article-title":"Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution","volume":"147","author":"Rhee","year":"2011","journal-title":"Cell"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B107","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1016\/j.molcel.2011.01.015","article-title":"A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces","volume":"41","author":"Venters","year":"2011","journal-title":"Mol Cell"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B108","doi-asserted-by":"crossref","first-page":"i403","DOI":"10.1093\/bioinformatics\/bti1043","article-title":"Mining ChIP-chip data for transcription factor and cofactor binding sites","volume":"21","author":"Smith","year":"2005","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B109","doi-asserted-by":"crossref","first-page":"e16432","DOI":"10.1371\/journal.pone.0016432","article-title":"An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq","volume":"6","author":"Mercier","year":"2011","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20170523192509_bbs016-B110","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1093\/bib\/bbq068","article-title":"Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts","volume":"12","author":"Szalkowski","year":"2011","journal-title":"Brief Bioinform"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/14\/2\/225\/17485553\/bbs016.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,6,27]],"date-time":"2019-06-27T15:52:06Z","timestamp":1561650726000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article-lookup\/doi\/10.1093\/bib\/bbs016"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,4,19]]},"references-count":110,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2012,4,19]]},"published-print":{"date-parts":[[2013,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbs016","relation":{},"ISSN":["1477-4054","1467-5463"],"issn-type":[{"value":"1477-4054","type":"electronic"},{"value":"1467-5463","type":"print"}],"subject":[],"published":{"date-parts":[[2012,4,19]]}}}