{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T14:54:40Z","timestamp":1770908080553,"version":"3.50.1"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"suppl_2","license":[{"start":{"date-parts":[[2016,11,14]],"date-time":"2016-11-14T00:00:00Z","timestamp":1479081600000},"content-version":"vor","delay-in-days":3118,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,7,1]]},"DOI":"10.1093\/nar\/gkn195","type":"journal-article","created":{"date-parts":[[2008,5,4]],"date-time":"2008-05-04T00:46:56Z","timestamp":1209862016000},"page":"W128-W132","source":"Crossref","is-referenced-by-count":51,"title":["ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species"],"prefix":"10.1093","volume":"36","author":[{"given":"Bart","family":"Hooghe","sequence":"first","affiliation":[]},{"given":"Paco","family":"Hulpiau","sequence":"additional","affiliation":[]},{"given":"Frans","family":"van Roy","sequence":"additional","affiliation":[]},{"given":"Pieter","family":"De Bleser","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2008,5,2]]},"reference":[{"key":"key\n\t\t\t\t20170720104339_B1","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1093\/nar\/gkg108","article-title":"TRANSFAC: transcriptional regulation, from patterns to profiles","volume":"31","author":"Matys","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720104339_B2","doi-asserted-by":"crossref","first-page":"D102","DOI":"10.1093\/nar\/gkm955","article-title":"JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update","volume":"36","author":"Bryne","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720104339_B3","doi-asserted-by":"crossref","first-page":"2041","DOI":"10.1101\/gr.2584104","article-title":"An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression","volume":"14","author":"Messina","year":"2004","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20170720104339_B4","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1093\/bioinformatics\/btm055","article-title":"Position dependencies in transcription factor binding sites","volume":"23","author":"Tomovic","year":"2007","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170720104339_B5","doi-asserted-by":"crossref","first-page":"W617","DOI":"10.1093\/nar\/gkl123","article-title":"FootPrinter3: phylogenetic footprinting in partially alignable sequences","volume":"34","author":"Fang","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720104339_B6","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\t20170720104339_B7","doi-asserted-by":"crossref","first-page":"R563","DOI":"10.1186\/bcr1043","article-title":"Alternative initiation and splicing in dicer gene expression in human breast cells","volume":"7","author":"Irvin-Wilson","year":"2005","journal-title":"Breast Cancer Res."},{"key":"key\n\t\t\t\t20170720104339_B8","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/S0167-4781(99)00221-3","article-title":"Molecular cloning and characterization of a novel human gene (HERNA) which encodes a putative RNA-helicase","volume":"1490","author":"Matsuda","year":"2000","journal-title":"Biochim. Biophys. Acta"},{"key":"key\n\t\t\t\t20170720104339_B9","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":"Blanchette","year":"2004","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20170720104339_B10","doi-asserted-by":"crossref","first-page":"D773","DOI":"10.1093\/nar\/gkm966","article-title":"The UCSC Genome Browser Database: 2008 update","volume":"36","author":"Karolchik","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720104339_B11","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":"Miller","year":"2007","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20170720104339_B12","doi-asserted-by":"crossref","first-page":"760","DOI":"10.1101\/gr.6034307","article-title":"Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome","volume":"17","author":"Margulies","year":"2007","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20170720104339_B13","doi-asserted-by":"crossref","first-page":"11484","DOI":"10.1073\/pnas.1932072100","article-title":"Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes","volume":"100","author":"Kent","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20170720104339_B14","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1101\/gr.809403","article-title":"Human-mouse alignments with BLASTZ","volume":"13","author":"Schwartz","year":"2003","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20170720104339_B15","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1073\/pnas.231608898","article-title":"Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome","volume":"99","author":"Berman","year":"2002","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20170720104339_B16","doi-asserted-by":"crossref","first-page":"e807","DOI":"10.1371\/journal.pone.0000807","article-title":"Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site","volume":"2","author":"Tabach","year":"2007","journal-title":"PLoS ONE"},{"key":"key\n\t\t\t\t20170720104339_B17","doi-asserted-by":"crossref","first-page":"D107","DOI":"10.1093\/nar\/gkm967","article-title":"ORegAnno: an open-access community-driven resource for regulatory annotation","volume":"36","author":"Griffith","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720104339_B18","doi-asserted-by":"crossref","first-page":"R207","DOI":"10.1186\/gb-2007-8-10-r207","article-title":"PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation","volume":"8","author":"Portales-Casamar","year":"2007","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20170720104339_B19","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1093\/bioinformatics\/btg430","article-title":"The Jalview Java alignment editor","volume":"20","author":"Clamp","year":"2004","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170720104339_B20","doi-asserted-by":"crossref","first-page":"1267","DOI":"10.1016\/S1097-2765(01)00260-X","article-title":"The two-handed E box binding zinc finger protein SIP1 downregulates E-cadherin and induces invasion","volume":"7","author":"Comijn","year":"2001","journal-title":"Mol. Cell"},{"key":"key\n\t\t\t\t20170720104339_B21","doi-asserted-by":"crossref","first-page":"8433","DOI":"10.1158\/0008-5472.CAN-07-1585","article-title":"MicroRNA-34b and MicroRNA-34c are targets of p53 and cooperate in control of cell proliferation and adhesion-independent growth","volume":"67","author":"Corney","year":"2007","journal-title":"Cancer Res."},{"key":"key\n\t\t\t\t20170720104339_B22","doi-asserted-by":"crossref","first-page":"D319","DOI":"10.1093\/nar\/gkj147","article-title":"The HUGO Gene Nomenclature Database, 2006 updates","volume":"34","author":"Eyre","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720104339_B23","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":"Papatsenko","year":"2002","journal-title":"Genome Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/36\/suppl_2\/W128\/18780908\/gkn195.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,4,2]],"date-time":"2018-04-02T10:40:05Z","timestamp":1522665605000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article-lookup\/doi\/10.1093\/nar\/gkn195"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,5,2]]},"references-count":23,"journal-issue":{"issue":"suppl_2","published-online":{"date-parts":[[2008,5,2]]},"published-print":{"date-parts":[[2008,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkn195","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,5,2]]}}}