{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,8]],"date-time":"2024-09-08T18:15:41Z","timestamp":1725819341163},"publisher-location":"Cham","reference-count":20,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319164823"},{"type":"electronic","value":"9783319164830"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015]]},"DOI":"10.1007\/978-3-319-16483-0_37","type":"book-chapter","created":{"date-parts":[[2015,3,16]],"date-time":"2015-03-16T10:36:38Z","timestamp":1426502198000},"page":"368-378","source":"Crossref","is-referenced-by-count":0,"title":["Towards a More Efficient Discovery of Biologically Significant DNA Motifs"],"prefix":"10.1007","author":[{"given":"Abdulrakeeb M.","family":"Al-Ssulami","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aqil M.","family":"Azmi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"37_CR1","doi-asserted-by":"crossref","unstructured":"Azmi, A.M., Al-Ssulami, A.: A linear algorithm to discover exact string motifs. PLoS ONE 9(5), e95148 (2014)","DOI":"10.1371\/journal.pone.0095148"},{"key":"37_CR2","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. Mach. Learning\u00a021, 51\u201380 (1995)","journal-title":"Mach. Learning"},{"key":"37_CR3","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/1748-7188-2-13","volume":"2","author":"V. Boeva","year":"2007","unstructured":"Boeva, V., Clement, J., Regnier, M., Roytberg, M.A., Makeev, V.J.: Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules. Algo. Mol. Biol.\u00a02, 13 (2007)","journal-title":"Algo. Mol. Biol."},{"key":"37_CR4","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1006\/geno.1996.0298","volume":"34","author":"M. Burset","year":"1996","unstructured":"Burset, M., Gulg, R.: Evaluation of gene structure prediction programs. Genomics\u00a034, 353\u2013367 (1996)","journal-title":"Genomics"},{"key":"37_CR5","doi-asserted-by":"crossref","unstructured":"Buhler, J., Tompa, M.: Finding motifs using random projections. In: Proc. 5th Annual Int. Conf. on Comput. Biol. (RECOMB 2001), Montreal, Canada, pp. 69\u201376 (2001)","DOI":"10.1145\/369133.369172"},{"key":"37_CR6","doi-asserted-by":"crossref","unstructured":"Chin, F., Leung, H.: An efficient algorithm for string motif discovery. In: Proc. 4th Asia-Pacific Bioinfor. Conf (APBC 2006), Taipei, Taiwan, pp. 79\u201388 (2006)","DOI":"10.1142\/9781860947292_0011"},{"key":"37_CR7","unstructured":"Cormen, T.H., Leiserson, C.E., Rivest, R.L., Stein, C.: Introduction to Algorithms, 2nd edn. MIT Press (2001)"},{"key":"37_CR8","doi-asserted-by":"publisher","first-page":"2303","DOI":"10.1093\/bioinformatics\/btn444","volume":"24","author":"F. Fauteux","year":"2008","unstructured":"Fauteux, F., Blanchette, M., Strmvik, M.V.: Seeder: discriminative seeding DNA motif discovery. Bioinfor.\u00a024, 2303\u20132307 (2008)","journal-title":"Bioinfor."},{"key":"37_CR9","doi-asserted-by":"publisher","first-page":"3585","DOI":"10.1093\/nar\/gkl372","volume":"34","author":"D. GuhaThakurta","year":"2006","unstructured":"GuhaThakurta, D.: Computational identification of transcriptional regulatory elements in DNA sequence. Nucleic Acids Res.\u00a034, 3585\u20133598 (2006)","journal-title":"Nucleic Acids Res."},{"key":"37_CR10","doi-asserted-by":"publisher","first-page":"4899","DOI":"10.1093\/nar\/gki791","volume":"33","author":"J. Hu","year":"2006","unstructured":"Hu, J., Li, B., Kihara, D.: Limitations and potentials of current motif discovery algorithms. Nucleic Acids Res.\u00a033, 4899\u20134913 (2006)","journal-title":"Nucleic Acids Res."},{"key":"37_CR11","doi-asserted-by":"publisher","first-page":"7952","DOI":"10.1016\/j.eswa.2008.10.087","volume":"36","author":"A. Karci","year":"2009","unstructured":"Karci, A.: Efficient automatic exact motif discovery algorithms for biological sequences. Expert Sys. With App.\u00a036, 7952\u20137963 (2009)","journal-title":"Expert Sys. With App."},{"key":"37_CR12","doi-asserted-by":"publisher","first-page":"1039","DOI":"10.1016\/j.eswa.2007.11.008","volume":"36","author":"M. Kaya","year":"2009","unstructured":"Kaya, M.: MOGAMOD. Multi-objective genetic algorithm for motif discovery. Expert Sys. With App.\u00a036, 1039\u20131047 (2009)","journal-title":"Expert Sys. With App."},{"key":"37_CR13","doi-asserted-by":"crossref","unstructured":"Marschall, T., Rahmann, S.: Efficient exact motif discovery. Bioinfor. 29, i356\u2013i364 (2009)","DOI":"10.1093\/bioinformatics\/btp188"},{"key":"37_CR14","doi-asserted-by":"crossref","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. 32, W199\u2013W203 (2004)","DOI":"10.1093\/nar\/gkh465"},{"key":"37_CR15","unstructured":"Pevzner, P.A., Sze, S.H.: Combinatorial approaches to finding subtle signals in DNA sequences. In: Proc. Int. Conf. Intel. Sys. Mol. Biol., vol.\u00a08, pp. 269\u2013278 (2000)"},{"key":"37_CR16","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1186\/1471-2105-8-193","volume":"8","author":"G.K. Sandve","year":"2007","unstructured":"Sandve, G.K., Abul, O., Walseng, V., Drabls, F.: Improved benchmarks for computational motif discovery. BMC Bioinfor.\u00a08, 163 (2007)","journal-title":"BMC Bioinfor."},{"key":"37_CR17","series-title":"Lecture Notes in Bioinformatics","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1007\/978-3-540-48540-7_17","volume-title":"Systems Biology and Regulatory Genomics","author":"S.H. Sze","year":"2007","unstructured":"Sze, S.H., Zhao, X.: Improved Pattern-driven Algorithms for Motif Finding in DNA Sequences. In: Eskin, E., Ideker, T., Raphael, B., Workman, C. (eds.) RECOMB 2005. LNCS (LNBI), vol.\u00a04023, pp. 198\u2013211. Springer, Heidelberg (2007)"},{"key":"37_CR18","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1038\/nbt1053","volume":"23","author":"M. Tompa","year":"2005","unstructured":"Tompa, M., Li, N., Bailey, T.L., Church, G.M., Moor, B.D., Eskin, E., Favorov, A.V., Frith, M.C., Fu, Y., Kent, W.J., Makeev, V.J., Mironov, A.A., Noble, W.S., Pavesi, G., Pesole, G., Regnier, 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. Biotech.\u00a023, 137\u2013144 (2005)","journal-title":"Nat. Biotech."},{"key":"37_CR19","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., Knuppel, R.: TRANSFAC: A database on transcription factors and their DNA binding sites. Nucleic Acids Res.\u00a024, 238\u2013241 (1996)","journal-title":"Nucleic Acids Res."},{"key":"37_CR20","doi-asserted-by":"crossref","unstructured":"Yu, Q., Huo, H., Vitter, J.S., Huan, J., Nekrich, Y.: StemFinder: An efficient algorithm for searching large motif stems over large alphabets. In: Proc. IEEE Int. Conf. Bioinfor. and Biomed. (BIBM), Shanghai, China, pp. 473\u2013476 (2013)","DOI":"10.1109\/BIBM.2013.6732539"}],"container-title":["Lecture Notes in Computer Science","Bioinformatics and Biomedical Engineering"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-16483-0_37","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,29]],"date-time":"2019-05-29T16:43:57Z","timestamp":1559148237000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-319-16483-0_37"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015]]},"ISBN":["9783319164823","9783319164830"],"references-count":20,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-16483-0_37","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2015]]}}}