{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,13]],"date-time":"2025-02-13T05:05:29Z","timestamp":1739423129105,"version":"3.37.0"},"publisher-location":"Berlin, Heidelberg","reference-count":29,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642040191"},{"type":"electronic","value":"9783642040207"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009]]},"DOI":"10.1007\/978-3-642-04020-7_42","type":"book-chapter","created":{"date-parts":[[2009,9,14]],"date-time":"2009-09-14T18:43:19Z","timestamp":1252953799000},"page":"397-406","source":"Crossref","is-referenced-by-count":0,"title":["MotifMiner: A Table Driven Greedy Algorithm for DNA Motif Mining"],"prefix":"10.1007","author":[{"given":"K. R.","family":"Seeja","sequence":"first","affiliation":[]},{"given":"M. A.","family":"Alam","sequence":"additional","affiliation":[]},{"given":"S. K.","family":"Jain","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"issue":"5","key":"42_CR1","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1006\/jmbi.1998.1947","volume":"281","author":"J.V. Helden","year":"1998","unstructured":"Helden, J.V., Andre, B., Collado-Vides, J.: Extracting Regulatory Sites from the Upstream Region of Yeast Genes by Computational Analysis of Oligonucleotide Frequencies. J. Mol. Biol.\u00a0281(5), 827\u2013842 (1998)","journal-title":"J. Mol. Biol."},{"issue":"24","key":"42_CR2","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 Rranscription Factor Binding Sites by Statistical Overrepresentation. Nucleic Acids Res.\u00a030(24), 5549\u20135560 (2002)","journal-title":"Nucleic Acids Res."},{"key":"42_CR3","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1007\/BFb0054337","volume-title":"Proceedings of the Third Latin American Symposium on Theoretical Informatics","author":"M.F. Sagot","year":"1998","unstructured":"Sagot, M.F.: Spelling Approximate Repeated or Common Motifs Using a Sufix Tree. In: Proceedings of the Third Latin American Symposium on Theoretical Informatics, pp. 374\u2013390. Springer, Heidelberg (1998)"},{"issue":"suppl. 1","key":"42_CR4","doi-asserted-by":"crossref","first-page":"207","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\u00a017(suppl. 1), S207\u2013S214 (2001)","journal-title":"Bioinformatics"},{"issue":"suppl.1","key":"42_CR5","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1093\/bioinformatics\/18.suppl_1.S354","volume":"18","author":"E. Eskin","year":"2002","unstructured":"Eskin, E., Pevzner, P.A.: Finding Composite Regulatory Patterns in DNA Sequences. Bioinformatics\u00a018(suppl.1), 354\u2013363 (2002)","journal-title":"Bioinformatics"},{"key":"42_CR6","unstructured":"Pevzner, P., Sze, S.: Combinatorial Approaches to Finding Subtle Signals in DNA Sequences. In: Proc. Int. Conf. Intell. Syst. Mol. Biol., vol.\u00a08, pp. 269\u2013278 (2000)"},{"key":"42_CR7","first-page":"81","volume":"6","author":"G.Z. Hertz","year":"1990","unstructured":"Hertz, G.Z., Hartzell, G.W., Stormo, G.D.: Identification of Consensus Patterns in Unaligned DNA Sequences Known to be Functionally Related. Comput. Appl. Biosci.\u00a06, 81\u201392 (1990)","journal-title":"Comput. Appl. Biosci."},{"key":"42_CR8","first-page":"51","volume":"21","author":"T.L. Bailey","year":"1995","unstructured":"Bailey, T.L., Elkan, C.: Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization. Machine Learning\u00a021, 51\u201380 (1995)","journal-title":"Machine Learning"},{"key":"42_CR9","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1126\/science.8211139","volume":"262","author":"C.E. Lawrence","year":"1993","unstructured":"Lawrence, C.E., Altschul, S.F., Boguski, M.S., Liu, J.S., Neuwald, A.F., Wootton, J.C.: Detecting Subtle Sequence Signals: a Gibbs Sampling Strategy for Multiple Alignment. Science\u00a0262, 208\u2013214 (1993)","journal-title":"Science"},{"key":"42_CR10","doi-asserted-by":"publisher","first-page":"939","DOI":"10.1038\/nbt1098-939","volume":"16","author":"F.P. Roth","year":"1998","unstructured":"Roth, F.P., Hughes, J.D., Estep, P.W., Church, G.M.: Finding DNA Regulatory Motifs within Unaligned Noncoding Sequences Clustered by Whole-genome mRNA Quantitation. Nature Biotechnology\u00a016, 939\u2013945 (1998)","journal-title":"Nature Biotechnology"},{"key":"42_CR11","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1145\/369133.369253","volume":"5","author":"G. Thijs","year":"2001","unstructured":"Thijs, G., Marchal, K., Moreau, Y.: A Gibbs Sampling Method to Detect Over-represented Motifs in Upstream Regions of Co-expressed Genes. RECOMB\u00a05, 305\u2013312 (2001)","journal-title":"RECOMB"},{"key":"42_CR12","doi-asserted-by":"crossref","unstructured":"Liu, X., Brutlag, D.L., Liu, J.S.: BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-expressed Genes. In: Proceedings of the Sixth Pacific Symposium on Biocomputing, pp. 127\u2013138 (2001)","DOI":"10.1142\/9789814447362_0014"},{"key":"42_CR13","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1186\/1471-2105-7-486","volume":"7","author":"K. Shida","year":"2006","unstructured":"Shida, K., Gibbs, S.T.: A Gibbs Sampling Method for Motif Discovery with Enhanced Resistance to Local Optima. BMC Bioinformatics\u00a07, 486 (2006)","journal-title":"BMC Bioinformatics"},{"key":"42_CR14","doi-asserted-by":"crossref","unstructured":"Liu, F.F.M., Tsai, J.J.P., Chen, R.M., Chen, S.N., Shih, S.H.: Finding Motifs by Genetic Algorithm. In: Fourth IEEE Symposium on Bioinformatics and Bioengineering, p. 459 (2004)","DOI":"10.1109\/BIBE.2004.1317378"},{"issue":"3","key":"42_CR15","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1109\/tcbb.2007.1044","volume":"4","author":"A. Michael","year":"2007","unstructured":"Michael, A., Andy, M.: Tyrrell, Regulatory Motif Discovery Using a Population Clustering Evolutionary Algorithm. IEEE\/ACM Transactions on Computational Biology and Bioinformatics\u00a04(3), 403\u2013414 (2007)","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics"},{"key":"42_CR16","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1109\/TNN.2006.875987","volume":"17","author":"D. Liu","year":"2006","unstructured":"Liu, D., Xiong, X., Das Gupta, B., Zhang, H.: Motif Discoveries in Unaligned Molecular Sequences Using Self-organizing Neural Network. IEEE Transactions on Neural Networks\u00a017, 919\u2013928 (2006)","journal-title":"IEEE Transactions on Neural Networks"},{"key":"42_CR17","doi-asserted-by":"publisher","first-page":"774","DOI":"10.1093\/nar\/29.3.774","volume":"29","author":"L. McCue","year":"2001","unstructured":"McCue, L., Thompson, W., Carmack, C., Ryan, M., Liu, J., Derbyshire, V., Lawrence, C.: Phylogenetic Footprinting of Transcription Factor Binding Sites in Proteobacterial Genomes. Nucleic Acids Res.\u00a029, 774\u2013782 (2001)","journal-title":"Nucleic Acids Res."},{"key":"42_CR18","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1101\/gr.1642804","volume":"14","author":"E. Berezikov","year":"2004","unstructured":"Berezikov, E., Guryev, V., Plasterk, R.H.A., Cuppen, E.: CONREAL: Conserved Regulatory Elements Anchored Alignment Algorithm for Identification of Transcription Factor Binding Sites by Phylogenetic Footprinting. Genome Res.\u00a014, 170\u2013178 (2004)","journal-title":"Genome Res."},{"key":"42_CR19","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1126\/science.1084337","volume":"301","author":"P. Cliften","year":"2003","unstructured":"Cliften, P., Sudarsanam, P., Desikan, A., Fulton, L., Fulton, B., Majors, J., Waterston, R., Cohen, B.A., Johnston, M.: Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting. Science\u00a0301, 71\u201376 (2003)","journal-title":"Science"},{"key":"42_CR20","doi-asserted-by":"publisher","first-page":"2369","DOI":"10.1093\/bioinformatics\/btg329","volume":"19","author":"T. Wang","year":"2003","unstructured":"Wang, T., Stormo, G.D.: Combining Phylogenetic Data with Coregulated Genes to Identify Regulatory Motifs. Bioinformatics\u00a019, 2369\u20132380 (2003)","journal-title":"Bioinformatics"},{"key":"42_CR21","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1186\/1471-2105-5-170","volume":"5","author":"S. Sinha","year":"2004","unstructured":"Sinha, S., Blanchette, M., Tompa, M.: PhyME: A probabilistic Algorithm for Finding Motifs in Sets of Orthologous Sequences. BMC Bioinformatics\u00a05, 170 (2004)","journal-title":"BMC Bioinformatics"},{"key":"42_CR22","doi-asserted-by":"crossref","unstructured":"Moses, A., Chiang, D., Eisen, M.: Phylogenetic Motif Detection by Expectation-maximization on Evolutionary Mixtures. In: Proceedings of the Ninth Pacific Symposium on Biocomputing, pp. 324\u2013335 (2004)","DOI":"10.1142\/9789812704856_0031"},{"key":"42_CR23","doi-asserted-by":"publisher","first-page":"534","DOI":"10.1371\/journal.pcbi.0010067","volume":"1","author":"R. Siddharthan","year":"2005","unstructured":"Siddharthan, R., Siggia, E.D., Van, N.E.: PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny. PLoS Comput. Biol.\u00a01, 534\u2013556 (2005)","journal-title":"PLoS Comput. Biol."},{"key":"42_CR24","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1186\/1748-7188-1-23","volume":"1","author":"K.R. Chandan","year":"2006","unstructured":"Chandan, K.R., Weng, Y.C., Chiang, H.D.: Refining Motifs by Improving Information Content Scores Using Neighborhood Profile Search. Algorithms for Molecular Biology\u00a01, 23 (2006)","journal-title":"Algorithms for Molecular Biology"},{"key":"42_CR25","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1006\/jmbi.1998.1700","volume":"278","author":"W.W. Wasserman","year":"1998","unstructured":"Wasserman, W.W., Fickett, J.W.: Identification of Regulatory Regions Which Confer Muscle-specific Gene Expression. Journal of Molecular Biology\u00a0278, 167\u2013181 (1998)","journal-title":"Journal of Molecular Biology"},{"issue":"5","key":"42_CR26","doi-asserted-by":"publisher","first-page":"1560","DOI":"10.1073\/pnas.0406123102","volume":"102","author":"D.S. Andrew","year":"2005","unstructured":"Andrew, D.S., Pavel, S., Zhang, M.Q.: Identifying Tissue-selective Transcription Factor Binding Sites in Vertebrate Promoters. PNAS\u00a0102(5), 1560\u20131565 (2005)","journal-title":"PNAS"},{"key":"42_CR27","unstructured":"TOMTOM motif comparison tool, http:\/\/meme.sdsc.edu\/meme4_1\/cgi-bin\/tomtom.cgi"},{"key":"42_CR28","unstructured":"JASPAR, http:\/\/jaspar.cgb.ki.se\/"},{"key":"42_CR29","unstructured":"CRP Motif sequences, http:\/\/dragon.bio.purdue.edu\/pmotif\/"}],"container-title":["Lecture Notes in Computer Science","Emerging Intelligent Computing Technology and Applications. With Aspects of Artificial Intelligence"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-04020-7_42.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,12]],"date-time":"2025-02-12T04:18:43Z","timestamp":1739333923000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-04020-7_42"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009]]},"ISBN":["9783642040191","9783642040207"],"references-count":29,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-04020-7_42","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2009]]}}}