{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,5]],"date-time":"2022-04-05T08:47:19Z","timestamp":1649148439060},"reference-count":48,"publisher":"Springer Science and Business Media LLC","issue":"S19","license":[{"start":{"date-parts":[[2012,12,1]],"date-time":"2012-12-01T00:00:00Z","timestamp":1354320000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2012,12]]},"DOI":"10.1186\/1471-2105-13-s19-s2","type":"journal-article","created":{"date-parts":[[2012,12,19]],"date-time":"2012-12-19T17:17:10Z","timestamp":1355937430000},"source":"Crossref","is-referenced-by-count":0,"title":["Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites"],"prefix":"10.1186","volume":"13","author":[{"given":"Mathieu","family":"Blanchette","sequence":"first","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,12,19]]},"reference":[{"key":"5511_CR1","doi-asserted-by":"crossref","unstructured":"Genome 10K Community of Scientists: A proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered. 2009, 659-674. 100","DOI":"10.1093\/jhered\/esp086"},{"issue":"6","key":"5511_CR2","doi-asserted-by":"publisher","first-page":"760","DOI":"10.1101\/gr.6034307","volume":"17","author":"E Margulies","year":"2007","unstructured":"Margulies E, Cooper G: Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 2007, 17 (6): 760-74. 10.1101\/gr.6034307.","journal-title":"Genome Res"},{"issue":"7167","key":"5511_CR3","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1038\/nature06340","volume":"450","author":"A Stark","year":"2007","unstructured":"Stark A, Lin M, Kheradpour P, Pedersen J, Parts L, Carlson J: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 2007, 450 (7167): 219-32. 10.1038\/nature06340.","journal-title":"Nature"},{"issue":"6937","key":"5511_CR4","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1038\/nature01644","volume":"423","author":"M Kellis","year":"2003","unstructured":"Kellis M, Patterson N, Endrizzi M, Birren B, Lander E: Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 2003, 423 (6937): 241-54. 10.1038\/nature01644.","journal-title":"Nature"},{"key":"5511_CR5","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1146\/annurev.genom.8.080706.092300","volume":"8","author":"M Blanchette","year":"2007","unstructured":"Blanchette M: Computation and analysis of genomic multi-sequence alignments. Annual Reviews on Genomics Human Genetics. 2007, 8: 193-213. 10.1146\/annurev.genom.8.080706.092300.","journal-title":"Annual Reviews on Genomics Human Genetics"},{"key":"5511_CR6","first-page":"26","volume":"12","author":"G Bourque","year":"2002","unstructured":"Bourque G, Pevzner PA: Genome-Scale Evolution: Reconstructing Gene Orders in the Ancestral Species. Genome Res. 2002, 12: 26-36.","journal-title":"Genome Res"},{"key":"5511_CR7","volume-title":"Genome Research","author":"J Ma","year":"2006","unstructured":"Ma J, Zhang L, Suh B, Raney BJ, Kent WJ, Blanchette M, Haussler D, Miller W: Reconstructing Contiguous Regions of an Ancestral Genome. Genome Research. 2006,"},{"issue":"19","key":"5511_CR8","doi-asserted-by":"publisher","first-page":"2664","DOI":"10.1093\/bioinformatics\/btr461","volume":"27","author":"A Ouangraoua","year":"2011","unstructured":"Ouangraoua A, Tannier E, Chauve C: Reconstructing the architecture of the ancestral amniote genome. Bioinformatics. 2011, 27 (19): 2664-71. 10.1093\/bioinformatics\/btr461.","journal-title":"Bioinformatics"},{"issue":"7","key":"5511_CR9","doi-asserted-by":"publisher","first-page":"879","DOI":"10.1089\/cmb.2010.0189","volume":"18","author":"J Ma","year":"2011","unstructured":"Ma J: Reconstructing the history of large-scale genomic changes: biological questions and computational challenges. J Comput Biol. 2011, 18 (7): 879-93. 10.1089\/cmb.2010.0189.","journal-title":"J Comput Biol"},{"key":"5511_CR10","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1007\/978-1-61779-582-4_15","volume":"855","author":"N El-Mabrouk","year":"2012","unstructured":"El-Mabrouk N, Sankoff D: Analysis of gene order evolution beyond single-copy genes. Methods Mol Biol. 2012, 855: 397-429. 10.1007\/978-1-61779-582-4_15.","journal-title":"Methods Mol Biol"},{"issue":"4","key":"5511_CR11","doi-asserted-by":"publisher","first-page":"708","DOI":"10.1101\/gr.1933104","volume":"14","author":"M Blanchette","year":"2004","unstructured":"Blanchette M: Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004, 14 (4): 708-715. 10.1101\/gr.1933104.","journal-title":"Genome Res"},{"issue":"4","key":"5511_CR12","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1101\/gr.926603","volume":"13","author":"M Brudno","year":"2003","unstructured":"Brudno M, Do CB: LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Research. 2003, 13 (4): 721-731. 10.1101\/gr.926603.","journal-title":"Genome Research"},{"issue":"3","key":"5511_CR13","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1093\/bioinformatics\/btn630","volume":"25","author":"B Paten","year":"2009","unstructured":"Paten B, Herrero J, Beal K, Birney E: Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Bioinformatics. 2009, 25 (3): 295-301. 10.1093\/bioinformatics\/btn630.","journal-title":"Bioinformatics"},{"issue":"11","key":"5511_CR14","doi-asserted-by":"publisher","first-page":"1829","DOI":"10.1101\/gr.076521.108","volume":"18","author":"B Paten","year":"2008","unstructured":"Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, Holmes I, Birney E: Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Res. 2008, 18 (11): 1829-43. 10.1101\/gr.076521.108.","journal-title":"Genome Res"},{"issue":"4","key":"5511_CR15","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1089\/cmb.2007.A006","volume":"14","author":"A Diallo","year":"2007","unstructured":"Diallo A, Makarenkov V, Blanchette M: Exact and heuristic algorithms for the Indel Maximum Likelihood Problem. J Comput Biol. 2007, 14 (4): 446-61. 10.1089\/cmb.2007.A006.","journal-title":"J Comput Biol"},{"issue":"1","key":"5511_CR16","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1093\/bioinformatics\/btp600","volume":"26","author":"A Diallo","year":"2010","unstructured":"Diallo A, Makarenkov V, Blanchette M: Ancestors 1.0: a web server for ancestral sequence reconstruction. Bioinformatics. 2010, 26 (1): 130-1. 10.1093\/bioinformatics\/btp600.","journal-title":"Bioinformatics"},{"key":"5511_CR17","doi-asserted-by":"crossref","unstructured":"Kim J, Sinha S: Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment. Bioinformatics. 2007, 23 (3):","DOI":"10.1093\/bioinformatics\/btl578"},{"issue":"4","key":"5511_CR18","doi-asserted-by":"publisher","first-page":"e34572","DOI":"10.1371\/journal.pone.0034572","volume":"7","author":"O Westesson","year":"2012","unstructured":"Westesson O, Lunter G, Paten B, Holmes I: Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. PLoS One. 2012, 7 (4): e34572-10.1371\/journal.pone.0034572.","journal-title":"PLoS One"},{"key":"5511_CR19","doi-asserted-by":"publisher","first-page":"614","DOI":"10.1038\/35054550","volume":"409","author":"W Murphy","year":"2001","unstructured":"Murphy W, Eizirik E, Johnson W, Zhang Y, Ryder OA, O'Brien SJ: Molecular phylogenetics and the origins of placental mammals. Nature. 2001, 409: 614-618. 10.1038\/35054550.","journal-title":"Nature"},{"issue":"12","key":"5511_CR20","doi-asserted-by":"publisher","first-page":"2412","DOI":"10.1101\/gr.2800104","volume":"14","author":"M Blanchette","year":"2004","unstructured":"Blanchette M, Green ED, Miller W, Haussler D: Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res. 2004, 14 (12): 2412-2423. 10.1101\/gr.2800104.","journal-title":"Genome Res"},{"issue":"1","key":"5511_CR21","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1186\/gb-2003-5-1-201","volume":"5","author":"M Bulyk","year":"2003","unstructured":"Bulyk M: Computational prediction of transcription-factor binding site locations. Genome Biol. 2003, 5 (1): 201-10.1186\/gb-2003-5-1-201.","journal-title":"Genome Biol"},{"key":"5511_CR22","first-page":"61","volume":"349","author":"G Natoli","year":"2011","unstructured":"Natoli G: Specialized chromatin patterns in the control of inflammatory gene expression. Curr Top Microbiol Immunol. 2011, 349: 61-72.","journal-title":"Curr Top Microbiol Immunol"},{"issue":"21","key":"5511_CR23","doi-asserted-by":"publisher","first-page":"2227","DOI":"10.1101\/gad.176826.111","volume":"25","author":"K Zaret","year":"2011","unstructured":"Zaret K, Carroll J: Pioneer transcription factors: establishing competence for gene expression. Genes Dev. 2011, 25 (21): 2227-41. 10.1101\/gad.176826.111.","journal-title":"Genes Dev"},{"issue":"2","key":"5511_CR24","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1016\/j.sbi.2007.12.002","volume":"18","author":"D Panne","year":"2008","unstructured":"Panne D: The enhanceosome. Curr Opin Struct Biol. 2008, 18 (2): 236-42. 10.1016\/j.sbi.2007.12.002.","journal-title":"Curr Opin Struct Biol"},{"key":"5511_CR25","doi-asserted-by":"publisher","first-page":"2306","DOI":"10.1126\/science.290.5500.2306","volume":"290","author":"B Ren","year":"2000","unstructured":"Ren B, Robert F: Genome-wide location and function of DNA binding proteins. Science. 2000, 290: 2306-2309. 10.1126\/science.290.5500.2306.","journal-title":"Science"},{"key":"5511_CR26","doi-asserted-by":"publisher","first-page":"1497","DOI":"10.1126\/science.1141319","volume":"316","author":"D Johnson","year":"2007","unstructured":"Johnson D, Mortazavi A, Myers R, Wold B: Genome-wide mapping of in vivo protein-DNA interactions. Science. 2007, 316: 1497-1502. 10.1126\/science.1141319.","journal-title":"Science"},{"issue":"7146","key":"5511_CR27","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1038\/nature05874","volume":"447","author":"E Birney","year":"2007","unstructured":"Birney E, Stamatoyannopoulos J: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007, 447 (7146): 799-816. 10.1038\/nature05874.","journal-title":"Nature"},{"key":"5511_CR28","volume-title":"Nat Meth","author":"Y Chen","year":"2012","unstructured":"Chen Y, Negre N: Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Meth. 2012"},{"key":"5511_CR29","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1101\/gr.6902","volume":"12","author":"M Blanchette","year":"2002","unstructured":"Blanchette M, Tompa M: Discovery of Regulatory elements by a computational method for phylogenetic footprinting. Genome Research. 2002, 12: 739-748. 10.1101\/gr.6902.","journal-title":"Genome Research"},{"key":"5511_CR30","doi-asserted-by":"publisher","first-page":"R9","DOI":"10.1186\/gb-2004-5-12-r98","volume":"5","author":"A Moses","year":"2004","unstructured":"Moses A, Chiang D, Pollard D, Iyer V, Eisen M: MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol. 2004, 5: R9-10.1186\/gb-2004-5-2-r9.","journal-title":"Genome Biol"},{"issue":"Web Server issu","key":"5511_CR31","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1093\/nar\/gkh383","volume":"32","author":"GG Loots","year":"2004","unstructured":"Loots GG, Ovcharenko I: rVISTA 2.0: evolutionary analysis of transcription factor binding sites. Nucleic Acids Res. 2004, 32 (Web Server issue): 217-221.","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"5511_CR32","doi-asserted-by":"publisher","first-page":"e130","DOI":"10.1371\/journal.pcbi.0020130","volume":"2","author":"A Moses","year":"2006","unstructured":"Moses A, Pollard D, Nix D, Iyer V, Li X, Biggin M, Eisen M: Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput Biol. 2006, 2 (10): e130-10.1371\/journal.pcbi.0020130.","journal-title":"PLoS Comput Biol"},{"issue":"4","key":"5511_CR33","doi-asserted-by":"publisher","first-page":"874","DOI":"10.1093\/molbev\/msi090","volume":"22","author":"S Sinha","year":"2005","unstructured":"Sinha S, Siggia E: Sequence turnover and tandem repeats in cis-regulatory modules in drosophila. Mol Biol Evol. 2005, 22 (4): 874-85. 10.1093\/molbev\/msi090.","journal-title":"Mol Biol Evol"},{"issue":"12","key":"5511_CR34","doi-asserted-by":"publisher","first-page":"1797","DOI":"10.1101\/gr.6761107","volume":"17","author":"W Miller","year":"2007","unstructured":"Miller W, Rosenbloom K, Hardison R, Hou M: 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res. 2007, 17 (12): 1797-808. 10.1101\/gr.6761107.","journal-title":"Genome Res"},{"issue":"4","key":"5511_CR35","doi-asserted-by":"publisher","first-page":"708","DOI":"10.1101\/gr.1933104","volume":"14","author":"M Blanchette","year":"2004","unstructured":"Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W: Aligning multiple genomic sequences with the threaded blockset aligner. Genome Research. 2004, 14 (4): 708-715. 10.1101\/gr.1933104.","journal-title":"Genome Research"},{"issue":"1","key":"5511_CR36","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1101\/gr.809403","volume":"13","author":"S Schwartz","year":"2003","unstructured":"Schwartz S, Kent W, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler D, Miller W: Human-mouse alignments with BLASTZ. Genome Research. 2003, 13 (1): 103-7. 10.1101\/gr.809403.","journal-title":"Genome Research"},{"key":"5511_CR37","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1093\/nar\/24.1.238","volume":"24","author":"E Wingender","year":"1996","unstructured":"Wingender E, Dietze P, Karas H, Kn\u00fcppel R: TRANSFAC: a Database on Transcription Factors and their DNA Binding Sites. Nucleic Acids Research. 1996, 24: 238-241. 10.1093\/nar\/24.1.238.","journal-title":"Nucleic Acids Research"},{"issue":"Database issue","key":"5511_CR38","doi-asserted-by":"publisher","first-page":"D105","DOI":"10.1093\/nar\/gkp950","volume":"38","author":"E Portales-Casamar","year":"2010","unstructured":"Portales-Casamar E, Thongjuea S: JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 2010, 38 (Database issue): D105-10.","journal-title":"Nucleic Acids Res"},{"key":"5511_CR39","doi-asserted-by":"publisher","first-page":"2079","DOI":"10.1093\/nar\/22.11.2079","volume":"22","author":"S Eddy","year":"1994","unstructured":"Eddy S, Durbin R: RNA sequence analysis using covariance models. Nucleic Acids Research. 1994, 22: 2079-2088. 10.1093\/nar\/22.11.2079. 11","journal-title":"Nucleic Acids Research"},{"issue":"8","key":"5511_CR40","doi-asserted-by":"publisher","first-page":"1034","DOI":"10.1101\/gr.3715005","volume":"15","author":"A Siepel","year":"2005","unstructured":"Siepel A, Bejerano G, Pedersen J, Hinrichs A: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005, 15 (8): 1034-1050. 10.1101\/gr.3715005.","journal-title":"Genome Res"},{"issue":"Database issue","key":"5511_CR41","doi-asserted-by":"publisher","first-page":"D871","DOI":"10.1093\/nar\/gkq1017","volume":"39","author":"B Raney","year":"2011","unstructured":"Raney B, Cline M: ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res. 2011, 39 (Database issue): D871-5.","journal-title":"Nucleic Acids Res"},{"key":"5511_CR42","volume-title":"The Regulatory Genome: Gene Regulatory Networks In Development And Evolution","author":"E Davidson","year":"2006","unstructured":"Davidson E: The Regulatory Genome: Gene Regulatory Networks In Development And Evolution. 2006, Elsevier"},{"issue":"5","key":"5511_CR43","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1101\/gr.4866006","volume":"16","author":"M Blanchette","year":"2006","unstructured":"Blanchette M, Bataille A: Genome-wide computation prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Research. 2006, 16 (5): 656-68. 10.1101\/gr.4866006.","journal-title":"Genome Research"},{"issue":"7118","key":"5511_CR44","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1038\/nature05295","volume":"444","author":"L Pennacchio","year":"2006","unstructured":"Pennacchio L, Ahituv N, Moses A: In vivo enhancer analysis of human conserved non-coding sequences. Nature. 2006, 444 (7118): 499-502. 10.1038\/nature05295.","journal-title":"Nature"},{"issue":"5675","key":"5511_CR45","doi-asserted-by":"publisher","first-page":"1321","DOI":"10.1126\/science.1098119","volume":"304","author":"G Bejerano","year":"2004","unstructured":"Bejerano G, Pheasant M, Makunin I: Ultraconserved elements in the human genome. Science. 2004, 304 (5675): 1321-5. 10.1126\/science.1098119.","journal-title":"Science"},{"issue":"5","key":"5511_CR46","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1101\/gr.4866006","volume":"16","author":"M Blanchette","year":"2006","unstructured":"Blanchette M, Bataille A, Chen X, Poitras C, Laganiere J, Lefebvre C, Deblois G, Giguere V, Ferretti V, Bergeron D, Coulombe B, Robert F: Genome-wide computation prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Research. 2006, 16 (5): 656-68. 10.1101\/gr.4866006.","journal-title":"Genome Research"},{"key":"5511_CR47","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1126\/science.1073774","volume":"297","author":"W Fairbrother","year":"2002","unstructured":"Fairbrother W, Yeh R, Sharp P, Burge C: Predictive identification of exonic splicing enhancers in human genes. Science. 2002, 297: 1007-1013. 10.1126\/science.1073774.","journal-title":"Science"},{"issue":"7104","key":"5511_CR48","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1038\/nature04979","volume":"442","author":"E Segal","year":"2006","unstructured":"Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, Moore I, Wang J, Widom J: A genomic code for nucleosome positioning. Nature. 2006, 442 (7104): 772-8. 10.1038\/nature04979.","journal-title":"Nature"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-S19-S2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-13-S19-S2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-S19-S2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,7,7]],"date-time":"2019-07-07T07:31:32Z","timestamp":1562484692000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-13-S19-S2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,12]]},"references-count":48,"journal-issue":{"issue":"S19","published-print":{"date-parts":[[2012,12]]}},"alternative-id":["5511"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-13-s19-s2","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,12]]},"article-number":"S2"}}