{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T02:02:16Z","timestamp":1781056936722,"version":"3.54.1"},"reference-count":107,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2005,3,30]],"date-time":"2005-03-30T00:00:00Z","timestamp":1112140800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"},{"start":{"date-parts":[[2005,3,30]],"date-time":"2005-03-30T00:00:00Z","timestamp":1112140800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                        <jats:title>Background<\/jats:title>\n                        <jats:p><jats:italic>Cis<\/jats:italic>-regulatory modules are combinations of regulatory elements occurring in close proximity to each other that control the spatial and temporal expression of genes. The ability to identify them in a genome-wide manner depends on the availability of accurate models and of search methods able to detect putative regulatory elements with enhanced sensitivity and specificity.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Results<\/jats:title>\n                        <jats:p>We describe the implementation of a search method for putative transcription factor binding sites (TFBSs) based on hidden Markov models built from alignments of known sites. We built 1,079 models of TFBSs using experimentally determined sequence alignments of sites provided by the TRANSFAC and JASPAR databases and used them to scan sequences of the human, mouse, fly, worm and yeast genomes. In several cases tested the method identified correctly experimentally characterized sites, with better specificity and sensitivity than other similar computational methods. Moreover, a large-scale comparison using synthetic data showed that in the majority of cases our method performed significantly better than a nucleotide weight matrix-based method.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Conclusion<\/jats:title>\n                        <jats:p>The search engine, available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/mapper.chip.org\">http:\/\/mapper.chip.org<\/jats:ext-link>, allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, fly, worm and yeast genomes. In addition it allows the user to upload a sequence to query and to build a model by supplying a multiple sequence alignment of binding sites for a transcription factor of interest. Due to its extensive database of models, powerful search engine and flexible interface, MAPPER represents an effective resource for the large-scale computational analysis of transcriptional regulation.<\/jats:p>\n                     <\/jats:sec>","DOI":"10.1186\/1471-2105-6-79","type":"journal-article","created":{"date-parts":[[2005,3,31]],"date-time":"2005-03-31T06:16:05Z","timestamp":1112249765000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":164,"title":["MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes"],"prefix":"10.1186","volume":"6","author":[{"given":"Voichita D","family":"Marinescu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isaac S","family":"Kohane","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alberto","family":"Riva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2005,3,30]]},"reference":[{"key":"404_CR1","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1038\/35044174","volume":"408","author":"A Ghazi","year":"2000","unstructured":"Ghazi A, VijayRaghavan KV: Developmental biology. Control by combinatorial codes. Nature 2000, 408: 419\u2013420. 10.1038\/35044174","journal-title":"Nature"},{"key":"404_CR2","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1186\/gb-2003-5-1-201","volume":"5","author":"ML Bulyk","year":"2003","unstructured":"Bulyk ML: Computational prediction of transcription-factor binding site locations. Genome Biol 2003, 5: 201. 10.1186\/gb-2003-5-1-201","journal-title":"Genome Biol"},{"key":"404_CR3","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1016\/j.bbrc.2003.08.052","volume":"309","author":"P Qiu","year":"2003","unstructured":"Qiu P: Recent advances in computational promoter analysis in understanding the transcriptional regulatory network. Biochem Biophys Res Commun 2003, 309: 495\u2013501. 10.1016\/j.bbrc.2003.08.052","journal-title":"Biochem Biophys Res Commun"},{"key":"404_CR4","doi-asserted-by":"publisher","first-page":"1099","DOI":"10.1172\/JCI200317842","volume":"111","author":"LA Pennacchio","year":"2003","unstructured":"Pennacchio LA, Rubin EM: Comparative genomic tools and databases: providing insights into the human genome. J Clin Invest 2003, 111: 1099\u20131106. 10.1172\/JCI200317842","journal-title":"J Clin Invest"},{"key":"404_CR5","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1038\/35052548","volume":"2","author":"LA Pennacchio","year":"2001","unstructured":"Pennacchio LA, Rubin EM: Genomic strategies to identify mammalian regulatory sequences. Nat Rev Genet 2001, 2: 100\u2013109. 10.1038\/35052548","journal-title":"Nat Rev Genet"},{"key":"404_CR6","doi-asserted-by":"publisher","first-page":"1205","DOI":"10.1006\/jmbi.2000.3519","volume":"296","author":"JD Hughes","year":"2000","unstructured":"Hughes JD, Estep PW, Tavazoie S, Church GM: Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 2000, 296: 1205\u20131214. 10.1006\/jmbi.2000.3519","journal-title":"J Mol Biol"},{"key":"404_CR7","first-page":"21","volume":"3","author":"TL Bailey","year":"1995","unstructured":"Bailey TL, Elkan C: The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol 1995, 3: 21\u201329.","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"404_CR8","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1126\/science.8211139","volume":"262","author":"CE Lawrence","year":"1993","unstructured":"Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC: Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 1993, 262: 208\u2013214.","journal-title":"Science"},{"key":"404_CR9","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1093\/bioinformatics\/15.7.563","volume":"15","author":"GZ Hertz","year":"1999","unstructured":"Hertz GZ, Stormo GD: Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 1999, 15: 563\u2013577. 10.1093\/bioinformatics\/15.7.563","journal-title":"Bioinformatics"},{"key":"404_CR10","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1089\/10665270252935430","volume":"9","author":"J Buhler","year":"2002","unstructured":"Buhler J, Tompa M: Finding motifs using random projections. J Comput Biol 2002, 9: 225\u2013242. 10.1089\/10665270252935430","journal-title":"J Comput Biol"},{"key":"404_CR11","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1101\/gr.8.11.1202","volume":"8","author":"A Brazma","year":"1998","unstructured":"Brazma A, Jonassen I, Vilo J, Ukkonen E: Predicting gene regulatory elements in silico on a genomic scale. Genome Res 1998, 8: 1202\u20131215.","journal-title":"Genome Res"},{"key":"404_CR12","doi-asserted-by":"publisher","first-page":"835","DOI":"10.1038\/nbt717","volume":"20","author":"XS Liu","year":"2002","unstructured":"Liu XS, Brutlag DL, Liu JS: An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol 2002, 20: 835\u2013839.","journal-title":"Nat Biotechnol"},{"key":"404_CR13","first-page":"467","volume-title":"Pac Symp Biocomput","author":"CT Workman","year":"2000","unstructured":"Workman CT, Stormo GD: ANN-Spec: a method for discovering transcription factor binding sites with improved specificity. Pac Symp Biocomput 2000, 467\u2013478."},{"key":"404_CR14","doi-asserted-by":"publisher","first-page":"10096","DOI":"10.1073\/pnas.180265397","volume":"97","author":"HJ Bussemaker","year":"2000","unstructured":"Bussemaker HJ, Li H, Siggia ED: Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Proc Natl Acad Sci U S A 2000, 97: 10096\u201310100. 10.1073\/pnas.180265397","journal-title":"Proc Natl Acad Sci U S A"},{"key":"404_CR15","doi-asserted-by":"publisher","first-page":"1372","DOI":"10.1093\/nar\/gkh299","volume":"32","author":"MC Frith","year":"2004","unstructured":"Frith MC, Fu Y, Yu L, Chen JF, Hansen U, Weng Z: Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res 2004, 32: 1372\u20131381. 10.1093\/nar\/gkh299","journal-title":"Nucleic Acids Res"},{"key":"404_CR16","doi-asserted-by":"publisher","first-page":"3580","DOI":"10.1093\/nar\/gkg608","volume":"31","author":"W Thompson","year":"2003","unstructured":"Thompson W, Rouchka EC, Lawrence CE: Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Res 2003, 31: 3580\u20133585. 10.1093\/nar\/gkg608","journal-title":"Nucleic Acids Res"},{"key":"404_CR17","doi-asserted-by":"publisher","first-page":"W204","DOI":"10.1093\/nar\/gkh461","volume":"32","author":"Y Liu","year":"2004","unstructured":"Liu Y, Wei L, Batzoglou S, Brutlag DL, Liu JS, Liu XS: A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Res 2004, 32: W204\u20137.","journal-title":"Nucleic Acids Res"},{"key":"404_CR18","doi-asserted-by":"publisher","first-page":"W235","DOI":"10.1093\/nar\/gkh483","volume":"32","author":"Z Hu","year":"2004","unstructured":"Hu Z, Fu Y, Halees AS, Kielbasa SM, Weng Z: SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation. Nucleic Acids Res 2004, 32: W235\u201341. 10.1093\/nar\/gkh117","journal-title":"Nucleic Acids Res"},{"key":"404_CR19","doi-asserted-by":"publisher","first-page":"3576","DOI":"10.1093\/nar\/gkg585","volume":"31","author":"AE Kel","year":"2003","unstructured":"Kel AE, Gossling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E: MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 2003, 31: 3576\u20133579. 10.1093\/nar\/gkg585","journal-title":"Nucleic Acids Res"},{"key":"404_CR20","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1093\/nar\/gkg108","volume":"31","author":"V Matys","year":"2003","unstructured":"Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Munch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E: TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 2003, 31: 374\u2013378. 10.1093\/nar\/gkg108","journal-title":"Nucleic Acids Res"},{"key":"404_CR21","doi-asserted-by":"publisher","first-page":"D91","DOI":"10.1093\/nar\/gkh012","volume":"32 Database iss","author":"A Sandelin","year":"2004","unstructured":"Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B: JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 2004, 32 Database issue: D91\u20134. 10.1093\/nar\/gkh012","journal-title":"Nucleic Acids Res"},{"key":"404_CR22","doi-asserted-by":"publisher","first-page":"D368","DOI":"10.1093\/nar\/gkh017","volume":"32 Database iss","author":"NO Steffens","year":"2004","unstructured":"Steffens NO, Galuschka C, Schindler M, Bulow L, Hehl R: AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome. Nucleic Acids Res 2004, 32 Database issue: D368\u201372. 10.1093\/nar\/gkh017","journal-title":"Nucleic Acids Res"},{"key":"404_CR23","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1093\/nar\/30.1.312","volume":"30","author":"NA Kolchanov","year":"2002","unstructured":"Kolchanov NA, Ignatieva EV, Ananko EA, Podkolodnaya OA, Stepanenko IL, Merkulova TI, Pozdnyakov MA, Podkolodny NL, Naumochkin AN, Romashchenko AG: Transcription Regulatory Regions Database (TRRD): its status in 2002. Nucleic Acids Res 2002, 30: 312\u2013317. 10.1093\/nar\/30.1.312","journal-title":"Nucleic Acids Res"},{"key":"404_CR24","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1093\/nar\/30.1.332","volume":"30","author":"OV Kel-Margoulis","year":"2002","unstructured":"Kel-Margoulis OV, Kel AE, Reuter I, Deineko IV, Wingender E: TRANSCompel: a database on composite regulatory elements in eukaryotic genes. Nucleic Acids Res 2002, 30: 332\u2013334. 10.1093\/nar\/30.1.332","journal-title":"Nucleic Acids Res"},{"key":"404_CR25","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1038\/nature01763","volume":"424","author":"M Levine","year":"2003","unstructured":"Levine M, Tjian R: Transcription regulation and animal diversity. Nature 2003, 424: 147\u2013151. 10.1038\/nature01763","journal-title":"Nature"},{"key":"404_CR26","doi-asserted-by":"crossref","first-page":"II16","DOI":"10.1093\/bioinformatics\/btg1054","volume":"19 Suppl 2","author":"TL Bailey","year":"2003","unstructured":"Bailey TL, Noble WS: Searching for statistically significant regulatory modules. Bioinformatics 2003, 19 Suppl 2: II16-II25.","journal-title":"Bioinformatics"},{"key":"404_CR27","doi-asserted-by":"publisher","first-page":"I292","DOI":"10.1093\/bioinformatics\/btg1040","volume":"19 Suppl 1","author":"S Sinha","year":"2003","unstructured":"Sinha S, Van Nimwegen E, Siggia ED: A probabilistic method to detect regulatory modules. Bioinformatics 2003, 19 Suppl 1: I292-I301. 10.1093\/bioinformatics\/btg1040","journal-title":"Bioinformatics"},{"key":"404_CR28","doi-asserted-by":"publisher","first-page":"878","DOI":"10.1093\/bioinformatics\/17.10.878","volume":"17","author":"MC Frith","year":"2001","unstructured":"Frith MC, Hansen U, Weng Z: Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics 2001, 17: 878\u2013889. 10.1093\/bioinformatics\/17.10.878","journal-title":"Bioinformatics"},{"key":"404_CR29","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1186\/1471-2105-3-30","volume":"3","author":"N Rajewsky","year":"2002","unstructured":"Rajewsky N, Vergassola M, Gaul U, Siggia ED: Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics 2002, 3: 30. 10.1186\/1471-2105-3-30","journal-title":"BMC Bioinformatics"},{"key":"404_CR30","doi-asserted-by":"publisher","first-page":"757","DOI":"10.1073\/pnas.231608898","volume":"99","author":"BP Berman","year":"2002","unstructured":"Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB: Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A 2002, 99: 757\u2013762. 10.1073\/pnas.231608898","journal-title":"Proc Natl Acad Sci U S A"},{"key":"404_CR31","doi-asserted-by":"publisher","first-page":"1753","DOI":"10.1093\/nar\/gkg268","volume":"31","author":"S Aerts","year":"2003","unstructured":"Aerts S, Thijs G, Coessens B, Staes M, Moreau Y, Moor BD: Toucan: deciphering the cis-regulatory logic of coregulated genes. Nucleic Acids Res 2003, 31: 1753\u20131764. 10.1093\/nar\/gkg268","journal-title":"Nucleic Acids Res"},{"key":"404_CR32","doi-asserted-by":"publisher","first-page":"3214","DOI":"10.1093\/nar\/gkf438","volume":"30","author":"MC Frith","year":"2002","unstructured":"Frith MC, Spouge JL, Hansen U, Weng Z: Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Res 2002, 30: 3214\u20133224. 10.1093\/nar\/gkf438","journal-title":"Nucleic Acids Res"},{"key":"404_CR33","doi-asserted-by":"publisher","first-page":"W253","DOI":"10.1093\/nar\/gkh385","volume":"32","author":"R Sharan","year":"2004","unstructured":"Sharan R, Ben-Hur A, Loots GG, Ovcharenko I: CREME: Cis-Regulatory Module Explorer for the human genome. Nucleic Acids Res 2004, 32: W253\u20136.","journal-title":"Nucleic Acids Res"},{"key":"404_CR34","doi-asserted-by":"publisher","first-page":"W195","DOI":"10.1093\/nar\/gkh387","volume":"32","author":"WB Alkema","year":"2004","unstructured":"Alkema WB, Johansson O, Lagergren J, Wasserman WW: MSCAN: identification of functional clusters of transcription factor binding sites. Nucleic Acids Res 2004, 32: W195\u20138.","journal-title":"Nucleic Acids Res"},{"key":"404_CR35","doi-asserted-by":"crossref","first-page":"II50","DOI":"10.1093\/bioinformatics\/btg1059","volume":"19 Suppl 2","author":"C Dieterich","year":"2003","unstructured":"Dieterich C, Herwig R, Vingron M: Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites. Bioinformatics 2003, 19 Suppl 2: II50-II56.","journal-title":"Bioinformatics"},{"key":"404_CR36","doi-asserted-by":"publisher","first-page":"W249","DOI":"10.1093\/nar\/gkh372","volume":"32","author":"A Sandelin","year":"2004","unstructured":"Sandelin A, Wasserman WW, Lenhard B: ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res 2004, 32: W249\u201352. 10.1093\/nar\/gkh012","journal-title":"Nucleic Acids Res"},{"key":"404_CR37","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1101\/gr.1327604","volume":"14","author":"Y Liu","year":"2004","unstructured":"Liu Y, Liu XS, Wei L, Altman RB, Batzoglou S: Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res 2004, 14: 451\u2013458. 10.1101\/gr.1327604","journal-title":"Genome Res"},{"key":"404_CR38","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1186\/1471-2105-5-27","volume":"5","author":"HR Bigelow","year":"2004","unstructured":"Bigelow HR, Wenick AS, Wong A, Hobert O: CisOrtho: a program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting. BMC Bioinformatics 2004, 5: 27. 10.1186\/1471-2105-5-27","journal-title":"BMC Bioinformatics"},{"key":"404_CR39","doi-asserted-by":"publisher","first-page":"W217","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: W217\u201321. 10.1093\/nar\/gkh095","journal-title":"Nucleic Acids Res"},{"key":"404_CR40","volume-title":"Bioinformatics","author":"YH Grad","year":"2004","unstructured":"Grad YH, Roth FP, Halfon MS, Church GM: Prediction of similarly-acting cis-regulatory modules by subsequence profiling and comparative genomics in D. melanogaster and D. pseudoobscura. Bioinformatics 2004."},{"key":"404_CR41","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 Res 2002, 12: 739\u2013748. 10.1101\/gr.6902","journal-title":"Genome Res"},{"key":"404_CR42","first-page":"348","volume-title":"Pac Symp Biocomput","author":"A Prakash","year":"2004","unstructured":"Prakash A, Blanchette M, Sinha S, Tompa M: Motif discovery in heterogeneous sequence data. Pac Symp Biocomput 2004, 348\u2013359."},{"key":"404_CR43","doi-asserted-by":"publisher","first-page":"1408","DOI":"10.1101\/gr.255002","volume":"12","author":"AG Jegga","year":"2002","unstructured":"Jegga AG, Sherwood SP, Carman JW, Pinski AT, Phillips JL, Pestian JP, Aronow BJ: Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes. Genome Res 2002, 12: 1408\u20131417. 10.1101\/gr.255002","journal-title":"Genome Res"},{"key":"404_CR44","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/1475-4924-2-13","volume":"2","author":"B Lenhard","year":"2003","unstructured":"Lenhard B, Sandelin A, Mendoza L, Engstrom P, Jareborg N, Wasserman WW: Identification of conserved regulatory elements by comparative genome analysis. J Biol 2003, 2: 13. 10.1186\/1475-4924-2-13","journal-title":"J Biol"},{"key":"404_CR45","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1038\/79965","volume":"26","author":"WW Wasserman","year":"2000","unstructured":"Wasserman WW, Palumbo M, Thompson W, Fickett JW, Lawrence CE: Human-mouse genome comparisons to locate regulatory sites. Nat Genet 2000, 26: 225\u2013228. 10.1038\/79965","journal-title":"Nat Genet"},{"key":"404_CR46","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1186\/1471-2105-4-57","volume":"4","author":"EG Emberly","year":"2003","unstructured":"Emberly EG, Rajewsky N, Siggia ED: Conservation of Regulatory Elements between two species of Drosophila. BMC Bioinformatics 2003, 4: 57. 10.1186\/1471-2105-4-57","journal-title":"BMC Bioinformatics"},{"key":"404_CR47","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1093\/bioinformatics\/16.1.16","volume":"16","author":"GD Stormo","year":"2000","unstructured":"Stormo GD: DNA binding sites: representation and discovery. Bioinformatics 2000, 16: 16\u201323. 10.1093\/bioinformatics\/16.1.16","journal-title":"Bioinformatics"},{"key":"404_CR48","doi-asserted-by":"publisher","first-page":"4442","DOI":"10.1093\/nar\/gkf578","volume":"30","author":"PV Benos","year":"2002","unstructured":"Benos PV, Bulyk ML, Stormo GD: Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res 2002, 30: 4442\u20134451. 10.1093\/nar\/gkf578","journal-title":"Nucleic Acids Res"},{"key":"404_CR49","doi-asserted-by":"publisher","first-page":"2471","DOI":"10.1093\/nar\/29.12.2471","volume":"29","author":"TK Man","year":"2001","unstructured":"Man TK, Stormo GD: Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res 2001, 29: 2471\u20132478. 10.1093\/nar\/29.12.2471","journal-title":"Nucleic Acids Res"},{"key":"404_CR50","doi-asserted-by":"publisher","first-page":"1255","DOI":"10.1093\/nar\/30.5.1255","volume":"30","author":"ML Bulyk","year":"2002","unstructured":"Bulyk ML, Johnson PL, Church GM: Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res 2002, 30: 1255\u20131261. 10.1093\/nar\/30.5.1255","journal-title":"Nucleic Acids Res"},{"key":"404_CR51","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","volume":"14","author":"SR Eddy","year":"1998","unstructured":"Eddy SR: Profile hidden Markov models. Bioinformatics 1998, 14: 755\u2013763. 10.1093\/bioinformatics\/14.9.755","journal-title":"Bioinformatics"},{"key":"404_CR52","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511790492","volume-title":"Biological sequence analysis: probabilistic models of proteins and nucleic acids","author":"R Durbin","year":"1998","unstructured":"Durbin R, Eddy S, Krogh A, G. M: Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge, UK, Cambridge University Press; 1998."},{"key":"404_CR53","first-page":"95","volume":"12","author":"R Hughey","year":"1996","unstructured":"Hughey R, Krogh A: Hidden Markov models for sequence analysis: extension and analysis of the basic method. Comput Appl Biosci 1996, 12: 95\u2013107.","journal-title":"Comput Appl Biosci"},{"key":"404_CR54","first-page":"397","volume":"13","author":"WN Grundy","year":"1997","unstructured":"Grundy WN, Bailey TL, Elkan CP, Baker ME: Meta-MEME: motif-based hidden Markov models of protein families. Comput Appl Biosci 1997, 13: 397\u2013406.","journal-title":"Comput Appl Biosci"},{"key":"404_CR55","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1093\/nar\/30.1.276","volume":"30","author":"A Bateman","year":"2002","unstructured":"Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL: The Pfam protein families database. Nucleic Acids Res 2002, 30: 276\u2013280. 10.1093\/nar\/30.1.276","journal-title":"Nucleic Acids Res"},{"key":"404_CR56","volume-title":"Proceedings of the 27th Hawaii International Conference on Systems Sciences","author":"R Raman","year":"1994","unstructured":"Raman R, Overton GC: Application of hidden Markov modeling to the characterization of transcription factor binding sites. Proceedings of the 27th Hawaii International Conference on Systems Sciences 1994."},{"key":"404_CR57","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1093\/bioinformatics\/14.4.317","volume":"14","author":"T Yada","year":"1998","unstructured":"Yada T, Totoki Y, Ishikawa M, Asai K, Nakai K: Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences. Bioinformatics 1998, 14: 317\u2013325. 10.1093\/bioinformatics\/14.4.317","journal-title":"Bioinformatics"},{"key":"404_CR58","doi-asserted-by":"publisher","first-page":"1101","DOI":"10.1016\/S1097-2765(03)00134-5","volume":"11","author":"MD Conkright","year":"2003","unstructured":"Conkright MD, Guzman E, Flechner L, Su AI, Hogenesch JB, Montminy M: Genome-wide analysis of CREB target genes reveals a core promoter requirement for cAMP responsiveness. Mol Cell 2003, 11: 1101\u20131108. 10.1016\/S1097-2765(03)00134-5","journal-title":"Mol Cell"},{"key":"404_CR59","doi-asserted-by":"publisher","first-page":"S100","DOI":"10.1093\/bioinformatics\/18.suppl_2.S100","volume":"18 Suppl 2","author":"K Ellrott","year":"2002","unstructured":"Ellrott K, Yang C, Sladek FM, Jiang T: Identifying transcription factor binding sites through Markov chain optimization. Bioinformatics 2002, 18 Suppl 2: S100-S109.","journal-title":"Bioinformatics"},{"key":"404_CR60","doi-asserted-by":"publisher","first-page":"757","DOI":"10.1046\/j.1365-2958.2001.02534.x","volume":"41","author":"CW Price","year":"2001","unstructured":"Price CW, Fawcett P, Ceremonie H, Su N, Murphy CK, Youngman P: Genome-wide analysis of the general stress response in Bacillus subtilis. Mol Microbiol 2001, 41: 757\u2013774. 10.1046\/j.1365-2958.2001.02534.x","journal-title":"Mol Microbiol"},{"key":"404_CR61","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1210\/me.2004-0101","volume":"19","author":"A Sandelin","year":"2005","unstructured":"Sandelin A, Wasserman WW: Prediction of nuclear hormone receptor response elements. Mol Endocrinol 2005, 19: 595\u2013606. 10.1210\/me.2004-0101","journal-title":"Mol Endocrinol"},{"key":"404_CR62","doi-asserted-by":"publisher","first-page":"1115","DOI":"10.1101\/gad.1067003","volume":"17","author":"PC Fernandez","year":"2003","unstructured":"Fernandez PC, Frank SR, Wang L, Schroeder M, Liu S, Greene J, Cocito A, Amati B: Genomic targets of the human c-Myc protein. Genes Dev 2003, 17: 1115\u20131129. 10.1101\/gad.1067003","journal-title":"Genes Dev"},{"key":"404_CR63","doi-asserted-by":"publisher","first-page":"1101","DOI":"10.1101\/gad.1066903","volume":"17","author":"A Orian","year":"2003","unstructured":"Orian A, van Steensel B, Delrow J, Bussemaker HJ, Li L, Sawado T, Williams E, Loo LW, Cowley SM, Yost C, Pierce S, Edgar BA, Parkhurst SM, Eisenman RN: Genomic binding by the Drosophila Myc, Max, Mad\/Mnt transcription factor network. Genes Dev 2003, 17: 1101\u20131114. 10.1101\/gad.1066903","journal-title":"Genes Dev"},{"key":"404_CR64","doi-asserted-by":"publisher","first-page":"3645","DOI":"10.1038\/sj.onc.1206477","volume":"22","author":"A Mirza","year":"2003","unstructured":"Mirza A, Wu Q, Wang L, McClanahan T, Bishop WR, Gheyas F, Ding W, Hutchins B, Hockenberry T, Kirschmeier P, Greene JR, Liu S: Global transcriptional program of p53 target genes during the process of apoptosis and cell cycle progression. Oncogene 2003, 22: 3645\u20133654. 10.1038\/sj.onc.1206477","journal-title":"Oncogene"},{"key":"404_CR65","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1016\/S0092-8674(04)00127-8","volume":"116","author":"S Cawley","year":"2004","unstructured":"Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ, Wheeler R, Wong B, Drenkow J, Yamanaka M, Patel S, Brubaker S, Tammana H, Helt G, Struhl K, Gingeras TR: Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs. Cell 2004, 116: 499\u2013509. 10.1016\/S0092-8674(04)00127-8","journal-title":"Cell"},{"key":"404_CR66","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1006\/jmbi.1998.1700","volume":"278","author":"WW Wasserman","year":"1998","unstructured":"Wasserman WW, Fickett JW: Identification of regulatory regions which confer muscle-specific gene expression. J Mol Biol 1998, 278: 167\u2013181. 10.1006\/jmbi.1998.1700","journal-title":"J Mol Biol"},{"key":"404_CR67","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1089\/106652704773416858","volume":"11","author":"H Huang","year":"2004","unstructured":"Huang H, Kao MC, Zhou X, Liu JS, Wong WH: Determination of local statistical significance of patterns in Markov sequences with application to promoter element identification. J Comput Biol 2004, 11: 1\u201314. 10.1089\/106652704773416858","journal-title":"J Comput Biol"},{"key":"404_CR68","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/S1097-2765(00)80002-7","volume":"1","author":"H Hermeking","year":"1997","unstructured":"Hermeking H, Lengauer C, Polyak K, He TC, Zhang L, Thiagalingam S, Kinzler KW, Vogelstein B: 14\u20133-3 sigma is a p53-regulated inhibitor of G2\/M progression. Mol Cell 1997, 1: 3\u201311. 10.1016\/S1097-2765(00)80002-7","journal-title":"Mol Cell"},{"key":"404_CR69","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1006\/geno.1997.4947","volume":"45","author":"MR Jensen","year":"1997","unstructured":"Jensen MR, Factor VM, Zimonjic DB, Miller MJ, Keck CL, Thorgeirsson SS: Chromosome localization and structure of the murine cyclin G1 gene promoter sequence. Genomics 1997, 45: 297\u2013303. 10.1006\/geno.1997.4947","journal-title":"Genomics"},{"key":"404_CR70","doi-asserted-by":"publisher","first-page":"5015","DOI":"10.1093\/emboj\/17.17.5015","volume":"17","author":"R Utrera","year":"1998","unstructured":"Utrera R, Collavin L, Lazarevic D, Delia D, Schneider C: A novel p53-inducible gene coding for a microtubule-localized protein with G2-phase-specific expression. Embo J 1998, 17: 5015\u20135025. 10.1093\/emboj\/17.17.5015","journal-title":"Embo J"},{"key":"404_CR71","doi-asserted-by":"publisher","first-page":"9888","DOI":"10.1073\/pnas.152320899","volume":"99","author":"M Rebeiz","year":"2002","unstructured":"Rebeiz M, Reeves NL, Posakony JW: SCORE: a computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. Site clustering over random expectation. Proc Natl Acad Sci U S A 2002, 99: 9888\u20139893. 10.1073\/pnas.152320899","journal-title":"Proc Natl Acad Sci U S A"},{"key":"404_CR72","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1016\/S0960-9822(02)00743-1","volume":"12","author":"M Rohrbaugh","year":"2002","unstructured":"Rohrbaugh M, Ramos E, Nguyen D, Price M, Wen Y, Lai ZC: Notch activation of yan expression is antagonized by RTK\/pointed signaling in the Drosophila eye. Curr Biol 2002, 12: 576\u2013581. 10.1016\/S0960-9822(02)00743-1","journal-title":"Curr Biol"},{"key":"404_CR73","doi-asserted-by":"publisher","first-page":"14110","DOI":"10.1074\/jbc.272.22.14110","volume":"272","author":"Y Chen","year":"1997","unstructured":"Chen Y, Fischer WH, Gill GN: Regulation of the ERBB-2 promoter by RBPJkappa and NOTCH. J Biol Chem 1997, 272: 14110\u201314114. 10.1074\/jbc.272.22.14110","journal-title":"J Biol Chem"},{"key":"404_CR74","volume-title":"HMMER User's Guide: Biological sequence analysis using profile hidden Markov models","author":"SR Eddy","year":"2003","unstructured":"Eddy SR: HMMER User's Guide: Biological sequence analysis using profile hidden Markov models.2003. [http:\/\/hmmer.wustl.edu]"},{"key":"404_CR75","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/S0925-4773(01)00586-X","volume":"110","author":"KK Kelly","year":"2002","unstructured":"Kelly KK, Meadows SM, Cripps RM: Drosophila MEF2 is a direct regulator of Actin57B transcription in cardiac, skeletal, and visceral muscle lineages. Mech Dev 2002, 110: 39\u201350. 10.1016\/S0925-4773(01)00586-X","journal-title":"Mech Dev"},{"key":"404_CR76","doi-asserted-by":"crossref","first-page":"4623","DOI":"10.1242\/dev.128.22.4623","volume":"128","author":"DZ Wang","year":"2001","unstructured":"Wang DZ, Valdez MR, McAnally J, Richardson J, Olson EN: The Mef2c gene is a direct transcriptional target of myogenic bHLH and MEF2 proteins during skeletal muscle development. Development 2001, 128: 4623\u20134633.","journal-title":"Development"},{"key":"404_CR77","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1016\/S0161-5890(99)00030-9","volume":"36","author":"HM Shin","year":"1999","unstructured":"Shin HM, Han TH: CD28-mediated regulation of the c-jun promoter involves the MEF2 transcription factor in Jurkat T cells. Mol Immunol 1999, 36: 197\u2013203. 10.1016\/S0161-5890(99)00030-9","journal-title":"Mol Immunol"},{"key":"404_CR78","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1093\/nar\/gkh169","volume":"32","author":"MC Frith","year":"2004","unstructured":"Frith MC, Hansen U, Spouge JL, Weng Z: Finding functional sequence elements by multiple local alignment. Nucleic Acids Res 2004, 32: 189\u2013200. 10.1093\/nar\/gkh169","journal-title":"Nucleic Acids Res"},{"key":"404_CR79","first-page":"89","volume":"13","author":"K Frech","year":"1997","unstructured":"Frech K, Quandt K, Werner T: Software for the analysis of DNA sequence elements of transcription. Comput Appl Biosci 1997, 13: 89\u201397.","journal-title":"Comput Appl Biosci"},{"key":"404_CR80","doi-asserted-by":"publisher","first-page":"1559","DOI":"10.1101\/gr.180601","volume":"11","author":"W Krivan","year":"2001","unstructured":"Krivan W, Wasserman WW: A predictive model for regulatory sequences directing liver-specific transcription. Genome Res 2001, 11: 1559\u20131566. 10.1101\/gr.180601","journal-title":"Genome Res"},{"key":"404_CR81","first-page":"28","volume-title":"Seventh annual international conference in computational molecular biology (RECOMB)","author":"Y Barash","year":"2003","unstructured":"Barash Y, Elidan G, Friedman N, Kaplan T: Modeling dependencies in protein-DNA binding sites: . In Seventh annual international conference in computational molecular biology (RECOMB). Berlin, Germany; 2003:28\u201337."},{"key":"404_CR82","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/S0097-8485(96)80004-0","volume":"20","author":"M Gribskov","year":"1996","unstructured":"Gribskov M, Robinson N: Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput Chem 1996, 20: 25\u201333. 10.1016\/S0097-8485(96)80004-0","journal-title":"Comput Chem"},{"key":"404_CR83","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1101\/SQB.1991.056.01.034","volume":"56","author":"KM Hennessy","year":"1991","unstructured":"Hennessy KM, Botstein D: Regulation of DNA replication during the yeast cell cycle. Cold Spring Harb Symp Quant Biol 1991, 56: 279\u2013284.","journal-title":"Cold Spring Harb Symp Quant Biol"},{"key":"404_CR84","doi-asserted-by":"publisher","first-page":"2245","DOI":"10.1101\/gad.12.15.2245","volume":"12","author":"N Dyson","year":"1998","unstructured":"Dyson N: The regulation of E2F by pRB-family proteins. Genes Dev 1998, 12: 2245\u20132262.","journal-title":"Genes Dev"},{"key":"404_CR85","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1038\/nrm714","volume":"3","author":"JM Trimarchi","year":"2002","unstructured":"Trimarchi JM, Lees JA: Sibling rivalry in the E2F family. Nat Rev Mol Cell Biol 2002, 3: 11\u201320. 10.1038\/nrm714","journal-title":"Nat Rev Mol Cell Biol"},{"key":"404_CR86","doi-asserted-by":"crossref","first-page":"804","DOI":"10.1101\/gad.14.7.804","volume":"14","author":"Y Takahashi","year":"2000","unstructured":"Takahashi Y, Rayman JB, Dynlacht BD: Analysis of promoter binding by the E2F and pRB families in vivo: distinct E2F proteins mediate activation and repression. Genes Dev 2000, 14: 804\u2013816.","journal-title":"Genes Dev"},{"key":"404_CR87","doi-asserted-by":"publisher","first-page":"5797","DOI":"10.1128\/MCB.20.16.5797-5807.2000","volume":"20","author":"J Wells","year":"2000","unstructured":"Wells J, Boyd KE, Fry CJ, Bartley SM, Farnham PJ: Target gene specificity of E2F and pocket protein family members in living cells. Mol Cell Biol 2000, 20: 5797\u20135807. 10.1128\/MCB.20.16.5797-5807.2000","journal-title":"Mol Cell Biol"},{"key":"404_CR88","doi-asserted-by":"publisher","first-page":"2299","DOI":"10.1038\/sj.onc.1202544","volume":"18","author":"K Ohtani","year":"1999","unstructured":"Ohtani K, Iwanaga R, Nakamura M, Ikeda M, Yabuta N, Tsuruga H, Nojima H: Cell growth-regulated expression of mammalian MCM5 and MCM6 genes mediated by the transcription factor E2F. Oncogene 1999, 18: 2299\u20132309. 10.1038\/sj.onc.1202544","journal-title":"Oncogene"},{"key":"404_CR89","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/1471-2105-5-7","volume":"5","author":"B Schuster-Bockler","year":"2004","unstructured":"Schuster-Bockler B, Schultz J, Rahmann S: HMM Logos for visualization of protein families. BMC Bioinformatics 2004, 5: 7. 10.1186\/1471-2105-5-7","journal-title":"BMC Bioinformatics"},{"key":"404_CR90","first-page":"28","volume":"2","author":"TL Bailey","year":"1994","unstructured":"Bailey TL, Elkan C: Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994, 2: 28\u201336.","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"404_CR91","doi-asserted-by":"publisher","first-page":"5549","DOI":"10.1093\/nar\/gkf669","volume":"30","author":"S Sinha","year":"2002","unstructured":"Sinha S, Tompa M: Discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res 2002, 30: 5549\u20135560. 10.1093\/nar\/gkf669","journal-title":"Nucleic Acids Res"},{"key":"404_CR92","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1006\/jmbi.1996.0760","volume":"266","author":"F Tronche","year":"1997","unstructured":"Tronche F, Ringeisen F, Blumenfeld M, Yaniv M, Pontoglio M: Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome. J Mol Biol 1997, 266: 231\u2013245. 10.1006\/jmbi.1996.0760","journal-title":"J Mol Biol"},{"key":"404_CR93","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1093\/nar\/gkg129","volume":"31","author":"D Karolchik","year":"2003","unstructured":"Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ: The UCSC Genome Browser Database. Nucleic Acids Res 2003, 31: 51\u201354. 10.1093\/nar\/gkg129","journal-title":"Nucleic Acids Res"},{"key":"404_CR94","unstructured":"UCSC Genome Bioinformatics Sequence and Annotation Downloads[http:\/\/hgdownload.cse.ucsc.edu\/downloads.html]"},{"key":"404_CR95","unstructured":"HomoloGene[ftp:\/\/ftp.ncbi.nih.gov\/pub\/HomoloGene\/]"},{"key":"404_CR96","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1093\/nar\/gkg033","volume":"31","author":"DL Wheeler","year":"2003","unstructured":"Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Tatusova TA, Wagner L: Database resources of the National Center for Biotechnology. Nucleic Acids Res 2003, 31: 28\u201333. 10.1093\/nar\/gkg033","journal-title":"Nucleic Acids Res"},{"key":"404_CR97","unstructured":"UCSC Genome Bioinformatics Table Browser[http:\/\/genome.ucsc.edu\/cgi-bin\/hgTables]"},{"key":"404_CR98","volume-title":"Statistical Methods in Molecular Evolution","author":"A Siepel","year":"2004","unstructured":"Siepel A, Haussler D: Phylogenetic hidden Markov models. In Statistical Methods in Molecular Evolution. Edited by: Nielsen R. , Springer; 2004."},{"key":"404_CR99","unstructured":"MEME\/MAST Download[http:\/\/meme.sdsc.edu\/meme\/website\/meme-download.html]"},{"key":"404_CR100","unstructured":"JASPAR Sites Download[http:\/\/jaspar.cgb.ki.se\/DOWNLOAD\/SITES\/]"},{"key":"404_CR101","unstructured":"GLAM Datasets[http:\/\/zlab.bu.edu\/glam\/sup\/]"},{"key":"404_CR102","unstructured":"Software for the Analysis of DNA Sequence Elements of Transcription[http:\/\/anthea.gsf.de\/biodv\/review\/definition_data.html]"},{"key":"404_CR103","unstructured":"A Predictive Model for Regulatory Sequences Directing Liver-specific Transcription, Supplementary Material[http:\/\/www.cgb.ki.se\/krivan\/liver\/liver.html]"},{"key":"404_CR104","unstructured":"RSA-tools - Patser[http:\/\/rsat.ulb.ac.be\/rsat\/patser_form.cgi]"},{"key":"404_CR105","unstructured":"Sequence Analysis: Local Markov Method[http:\/\/www-personal.umich.edu\/~mckao\/website\/index_files\/Projects.htm]"},{"key":"404_CR106","unstructured":"AlignACE Accessory Software[http:\/\/atlas.med.harvard.edu\/download\/extra.html]"},{"issue":"Database","key":"404_CR107","first-page":"D91","volume":"33","author":"VD Marinescu","year":"2005","unstructured":"Marinescu VD, Kohane IS, Riva A: The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. Nucleic Acids Res 2005, 33(Database):D91\u20137.","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-79.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/1471-2105-6-79\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-79.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T12:09:48Z","timestamp":1728302988000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-79"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,3,30]]},"references-count":107,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2005,12]]}},"alternative-id":["404"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-79","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,3,30]]},"assertion":[{"value":"6 August 2004","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 March 2005","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 March 2005","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"79"}}