{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T06:33:01Z","timestamp":1767853981353,"version":"3.49.0"},"reference-count":48,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2012,6,27]],"date-time":"2012-06-27T00:00:00Z","timestamp":1340755200000},"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\/1471-2105-13-151","type":"journal-article","created":{"date-parts":[[2012,6,27]],"date-time":"2012-06-27T17:21:16Z","timestamp":1340817676000},"source":"Crossref","is-referenced-by-count":25,"title":["Towards a theoretical understanding of false positives in DNA motif finding"],"prefix":"10.1186","volume":"13","author":[{"given":"Amin","family":"Zia","sequence":"first","affiliation":[]},{"given":"Alan M","family":"Moses","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,6,27]]},"reference":[{"key":"5322_CR1","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1038\/nrg1315","volume":"5","author":"WW Wasserman","year":"2004","unstructured":"Wasserman WW, Sandelin A: Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 2004, 5: 276\u2013287. 10.1038\/nrg1315","journal-title":"Nat Rev Genet"},{"issue":"Suppl. 7","key":"5322_CR2","doi-asserted-by":"publisher","first-page":"S21","DOI":"10.1186\/1471-2105-8-S7-S21","volume":"8","author":"MK Das","year":"2007","unstructured":"Das MK, Dai HK: A survey of DNA motif finding algorithms. BMC Bioinforma 2007, 8(Suppl. 7):S21.","journal-title":"BMC Bioinforma"},{"key":"5322_CR3","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1007\/978-0-387-92738-1_7","volume-title":"Bioinformatics: Tools and Applications","author":"AM Moses","year":"2009","unstructured":"Moses AM, Sinha S, et al.: Regulatory Motif Analysis. In Bioinformatics: Tools and Applications. Edited by: Edwards D. Springer Science\u2009+\u2009Business Media LLC, ; 2009:137\u2013163."},{"issue":"1","key":"5322_CR4","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1038\/nbt1053","volume":"23","author":"M Tompa","year":"2005","unstructured":"Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, R\u00e9gnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z: Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 2005, 23(1):137\u2013144. 10.1038\/nbt1053","journal-title":"Nat Biotechnol"},{"key":"5322_CR5","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1186\/1471-2105-8-193","volume":"8","author":"GK Sandve","year":"2007","unstructured":"Sandve GK, Abul O, Walseng V, Drabl\u00f8s F: Improved benchmarks for computational motif discovery. BMC Bioinforma 2007, 8: 193. 10.1186\/1471-2105-8-193","journal-title":"BMC Bioinforma"},{"issue":"15","key":"5322_CR6","doi-asserted-by":"publisher","first-page":"4899","DOI":"10.1093\/nar\/gki791","volume":"33","author":"J Hu","year":"2005","unstructured":"Hu J, Li B, Kihara D: Limitations and potentials of current motif discovery algorithms. Nucleic Acids Res 2005, 33(15):4899\u20134913. 10.1093\/nar\/gki791","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"5322_CR7","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1038\/84792","volume":"27","author":"H Bussemaker","year":"2001","unstructured":"Bussemaker H, Li H, Siggia E: Regulatory element detection using correlation with expression. Nat Genet 2001, 27(2):167\u2013171. 10.1038\/84792","journal-title":"Nat Genet"},{"issue":"8","key":"5322_CR8","doi-asserted-by":"publisher","first-page":"962","DOI":"10.1101\/gr.5113606","volume":"16","author":"A Tanay","year":"2006","unstructured":"Tanay A: Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res 2006, 16(8):962\u2013972. 10.1101\/gr.5113606","journal-title":"Genome Res"},{"issue":"14","key":"5322_CR9","doi-asserted-by":"publisher","first-page":"e141","DOI":"10.1093\/bioinformatics\/btl223","volume":"22","author":"BC Foat","year":"2006","unstructured":"Foat BC, Morozov AV, Bussemaker HJ: Statistical mechanical modelling of genome-wide transcription factor occupancy data by matrix reduce. Bioinformatics 2006, 22(14):e141-e149. 10.1093\/bioinformatics\/btl223","journal-title":"Bioinformatics"},{"issue":"3","key":"5322_CR10","doi-asserted-by":"publisher","first-page":"e39","DOI":"10.1371\/journal.pcbi.0030039","volume":"3","author":"E Eden","year":"2007","unstructured":"Eden E, Lipson D, Yogev S, Yakhini Z: Discovering motifs in ranked lists of DNA sequences. PLoS Comput Biol 2007, 3(3):e39. 10.1371\/journal.pcbi.0030039","journal-title":"PLoS Comput Biol"},{"issue":"6937","key":"5322_CR11","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 ES: Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423(6937):241\u2013254. 10.1038\/nature01644","journal-title":"Nature"},{"issue":"18","key":"5322_CR12","doi-asserted-by":"publisher","first-page":"2369","DOI":"10.1093\/bioinformatics\/btg329","volume":"19","author":"T Wang","year":"2003","unstructured":"Wang T, Stormo GD: Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics 2003, 19(18):2369\u20132380. 10.1093\/bioinformatics\/btg329","journal-title":"Bioinformatics"},{"issue":"7","key":"5322_CR13","doi-asserted-by":"publisher","first-page":"e67","DOI":"10.1371\/journal.pcbi.0010067","volume":"1","author":"S Siddharthan","year":"2005","unstructured":"Siddharthan S, Siggia ED, Nimwegen EV: PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Computat Biol 2005, 1(7):e67. 10.1371\/journal.pcbi.0010067","journal-title":"PLoS Computat Biol"},{"key":"5322_CR14","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1186\/1471-2105-7-113","volume":"7","author":"KD Macisaac","year":"2006","unstructured":"Macisaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Frankel E: An improved map of conserved regulatory sites for saccharomyces cerevisiae. BMC Bioinforma 2006, 7: 113. 10.1186\/1471-2105-7-113","journal-title":"BMC Bioinforma"},{"key":"5322_CR15","first-page":"384","volume-title":"ISMB (Supplement of Bioinformatics)","author":"L Narlikar","year":"2006","unstructured":"Narlikar L, Gordan R, Ohler U, Hartemink AJ: ISMB (Supplement of Bioinformatics). 2006, 384\u2013392."},{"issue":"17","key":"5322_CR16","doi-asserted-by":"publisher","first-page":"7068","DOI":"10.1073\/pnas.0701356104","volume":"104","author":"AV Morozov","year":"2007","unstructured":"Morozov AV, Siggia ED: Connecting protein structure with predictions of regulatory sites. Proc Nat Acad Sci USA 2007, 104(17):7068\u20137073. 10.1073\/pnas.0701356104","journal-title":"Proc Nat Acad Sci USA"},{"key":"5322_CR17","first-page":"107","volume-title":"Proceedings of RECOMB","author":"L Narlikar","year":"2007","unstructured":"Narlikar L, Gordan R, Hartemink AJ: Nucleotide occupancy information improves de novo motif discovery. Proceedings of RECOMB 2007, 107\u2013121."},{"key":"5322_CR18","first-page":"15","volume":"21","author":"P Ng","year":"2008","unstructured":"Ng P, Keich U: Factoring local sequence composition in motif significance analysis. Genome informatics 2008, 21: 15\u201326.","journal-title":"Genome informatics"},{"key":"5322_CR19","doi-asserted-by":"publisher","first-page":"1743","DOI":"10.1126\/science.1102216","volume":"305","author":"W Ao","year":"2004","unstructured":"Ao W, Gaudet J, Kent WJ, Muttumu S, Mango SE: Environmentally induced foregut remodelling by PHA-4\/FoxA and DAF-12\/NHR. Science 2004, 305: 1743\u20131746. 10.1126\/science.1102216","journal-title":"Science"},{"key":"5322_CR20","first-page":"191","volume":"6","author":"M R\u00e9gnier","year":"2004","unstructured":"R\u00e9gnier M, Denise A: Rare events and conditional events on random strings. Discrete Math Theor Comput Sci 2004, 6: 191\u2013214.","journal-title":"Discrete Math Theor Comput Sci"},{"key":"5322_CR21","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1038\/nature02800","volume":"431","author":"CT Harbison","year":"2004","unstructured":"Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA: Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431: 99\u2013104. 10.1038\/nature02800","journal-title":"Nature"},{"issue":"10","key":"5322_CR22","doi-asserted-by":"publisher","first-page":"1382","DOI":"10.1093\/bioinformatics\/18.10.1382","volume":"18","author":"U Keich","year":"2002","unstructured":"Keich U, Pevzner PA: Subtle motifs: defining the limits of motif finding algorithms. Bioinformatics 2002, 18(10):1382\u20131390. 10.1093\/bioinformatics\/18.10.1382","journal-title":"Bioinformatics"},{"issue":"2","key":"5322_CR23","first-page":"89","volume":"5","author":"R Staden","year":"1989","unstructured":"Staden R: Methods for calculating the probabilities of finding patterns in sequences. Computat Appl Biosci 1989, 5(2):89\u201396.","journal-title":"Computat Appl Biosci"},{"issue":"5","key":"5322_CR24","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1093\/bioinformatics\/btl662","volume":"23","author":"J Zhang","year":"2007","unstructured":"Zhang J, Jiang B, Li M, Tromp J, Zhang X, Zhang MQ: Computing exact p-values for DNA motifs. Bioinformatics 2007, 23(5):531\u2013537. 10.1093\/bioinformatics\/btl662","journal-title":"Bioinformatics"},{"issue":"Supplement","key":"5322_CR25","doi-asserted-by":"publisher","first-page":"i311","DOI":"10.1093\/bioinformatics\/bti1044","volume":"21","author":"N Nagarajan","year":"2005","unstructured":"Nagarajan N, Jones N, Keich U: Computing the P-value of the information content from an alignment of multiple sequences. Bioinformatics 2005, 21(Supplement):i311-i318.","journal-title":"Bioinformatics"},{"issue":"4","key":"5322_CR26","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1093\/bioinformatics\/btm594","volume":"24","author":"N Nagarajan","year":"2008","unstructured":"Nagarajan N, Keich U: FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments. Bioinformatics 2008, 24(4):577\u2013578. 10.1093\/bioinformatics\/btm594","journal-title":"Bioinformatics"},{"issue":"7\u20138","key":"5322_CR27","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(7\u20138):563\u2013577.","journal-title":"Bioinformatics"},{"issue":"14","key":"5322_CR28","doi-asserted-by":"publisher","first-page":"e393","DOI":"10.1093\/bioinformatics\/btl245","volume":"22","author":"P Ng","year":"2006","unstructured":"Ng P, Nagarajan N, Jones N, Keich U: Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone. Bioinformatics 2006, 22(14):e393-e401. 10.1093\/bioinformatics\/btl245","journal-title":"Bioinformatics"},{"issue":"1","key":"5322_CR29","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(1):189\u2013200. 10.1093\/nar\/gkh169","journal-title":"Nucleic Acids Res"},{"key":"5322_CR30","first-page":"61","volume":"19","author":"U Keich","year":"2007","unstructured":"Keich U, Ng P: A conservative parametric approach to motif significance analysis. Genome Inform 2007, 19: 61\u201372.","journal-title":"Genome Inform"},{"key":"5322_CR31","doi-asserted-by":"publisher","DOI":"10.1002\/0471200611","volume-title":"Elements of information theory","author":"TM Cover","year":"1991","unstructured":"Cover TM, Thomas JA: Elements of information theory. Wiley Interscience, New York; 1991."},{"issue":"Web Server issu","key":"5322_CR32","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1093\/nar\/gkl198","volume":"34","author":"TL Bailey","year":"2006","unstructured":"Bailey TL, Williams N, Misleh C, Li WW: Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 2006, 34(Web Server issue):369\u2013373.","journal-title":"Nucleic Acids Res"},{"key":"5322_CR33","unstructured":"The MEME Suite. , ; \n                    http:\/\/meme.sdsc.edu"},{"issue":"19","key":"5322_CR34","doi-asserted-by":"publisher","first-page":"2256","DOI":"10.1093\/bioinformatics\/btn408","volume":"24","author":"P Ng","year":"2008","unstructured":"Ng P, Keich U: GIMSAN: a Gibbs motif finder with significant analysis. Bioinformatics 2008, 24(19):2256\u20132257. 10.1093\/bioinformatics\/btn408","journal-title":"Bioinformatics"},{"key":"5322_CR35","unstructured":"GIMSAN. , ; \n                    http:\/\/www.cs.cornell.edu\/~ppn3\/gimsan"},{"issue":"5131","key":"5322_CR36","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(5131):208\u2013214. 10.1126\/science.8211139","journal-title":"Science"},{"issue":"432","key":"5322_CR37","doi-asserted-by":"publisher","first-page":"1156","DOI":"10.1080\/01621459.1995.10476622","volume":"90","author":"JS Liu","year":"1995","unstructured":"Liu JS, Neuwald AF, Lawrence CE: Bayesian models for multiple local sequence alignment and Gibbs sampling strategies. J Am Stat Assoc 1995, 90(432):1156\u20131170. 10.1080\/01621459.1995.10476622","journal-title":"J Am Stat Assoc"},{"key":"5322_CR38","unstructured":"The Gibbs Sampler. , ; \n                    http:\/\/bayesweb.wadsworth.org\/gibbs"},{"issue":"Suppl. 1","key":"5322_CR39","doi-asserted-by":"publisher","first-page":"S207","DOI":"10.1093\/bioinformatics\/17.suppl_1.S207","volume":"17","author":"G Pavesi","year":"2001","unstructured":"Pavesi G, Mauri G, Pesole G: An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics 2001, 17(Suppl. 1):S207-S214.","journal-title":"Bioinformatics"},{"issue":"32, Web Server","key":"5322_CR40","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1093\/nar\/gkh465","volume":"1","author":"G Pavesi","year":"2004","unstructured":"Pavesi G, Mereghetti P, Mauri G, Pesole G: Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Res 2004, 1(32, Web Server issue):199\u2013203.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"5322_CR41","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(1):16\u201323. 10.1093\/bioinformatics\/16.1.16","journal-title":"Bioinformatics"},{"issue":"4","key":"5322_CR42","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1006\/jtbi.1997.0540","volume":"189","author":"TD Schnider","year":"1997","unstructured":"Schnider TD: Information content of individual genetic sequences. J Theor Biol 1997, 189(4):427\u2013441. 10.1006\/jtbi.1997.0540","journal-title":"J Theor Biol"},{"issue":"12","key":"5322_CR43","doi-asserted-by":"publisher","first-page":"1113","DOI":"10.1093\/bioinformatics\/17.12.1113","volume":"17","author":"G Thijs","year":"2001","unstructured":"Thijs G, Lescot M, Marchal K, Rombauts S, De Moor B, Rouz\u00e9 P, Moreau Y: A higher order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics 2001, 17(12):1113\u20131122. 10.1093\/bioinformatics\/17.12.1113","journal-title":"Bioinformatics"},{"issue":"2","key":"5322_CR44","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1089\/10665270252935566","volume":"9","author":"G Thijs","year":"2002","unstructured":"Thijs G, Marchal K, Lescot M, Rombauts S, De Moor B, Rouz\u00e9 P, Moreau Y: A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes. J Comput Biol 2002, 9(2):447\u2013464. 10.1089\/10665270252935566","journal-title":"J Comput Biol"},{"key":"5322_CR45","first-page":"464","volume":"5","author":"CT Workman","year":"2000","unstructured":"Workman CT, Stormo GD: ANN-SPEC: A method for discovering transcription binding sites with improved specificity. Proc Pacific Symp Biocomput 2000, 5: 464\u2013475.","journal-title":"Proc Pacific Symp Biocomput"},{"key":"5322_CR46","first-page":"8","volume-title":"Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology","author":"S Sinha","year":"2000","unstructured":"Sinha S, Tompa M: A statistical method for finding transcription factor binding sites. In Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology. AAAI Press, c1993, Menlo Park, Calif. United States; 2000:8\u201337."},{"key":"5322_CR47","volume-title":"Nucleic Acids Res","author":"JC Bryne","year":"2008","unstructured":"Bryne JC, Valen E, Tang MHE, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A: JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res 2008. Database issue Database issue"},{"key":"5322_CR48","doi-asserted-by":"publisher","first-page":"2505","DOI":"10.1109\/18.720546","volume":"44","author":"I Csiszar","year":"1998","unstructured":"Csiszar I: Method of types. IEEE Trans Inf Theory 1998, 44: 2505\u20132523. 10.1109\/18.720546","journal-title":"IEEE Trans Inf Theory"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-151.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-13-151\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-151.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T10:54:25Z","timestamp":1548240865000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-13-151"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,6,27]]},"references-count":48,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,12]]}},"alternative-id":["5322"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-13-151","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,6,27]]},"article-number":"151"}}