{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,26]],"date-time":"2025-03-26T02:16:19Z","timestamp":1742955379859,"version":"3.40.3"},"publisher-location":"Berlin, Heidelberg","reference-count":20,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642167492"},{"type":"electronic","value":"9783642167508"}],"license":[{"start":{"date-parts":[[2010,1,1]],"date-time":"2010-01-01T00:00:00Z","timestamp":1262304000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010]]},"DOI":"10.1007\/978-3-642-16750-8_9","type":"book-chapter","created":{"date-parts":[[2010,11,8]],"date-time":"2010-11-08T15:26:09Z","timestamp":1289229969000},"page":"94-105","source":"Crossref","is-referenced-by-count":0,"title":["Mining Regulatory Elements in Non-coding Regions of Arabidopsis thaliana"],"prefix":"10.1007","author":[{"given":"Xi","family":"Li","sequence":"first","affiliation":[]},{"given":"Dianhui","family":"Wang","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"key":"9_CR1","doi-asserted-by":"publisher","first-page":"3157","DOI":"10.1093\/nar\/5.9.3157","volume":"5","author":"D.J. Galas","year":"1978","unstructured":"Galas, D.J., Schmitz, A.: DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res.\u00a05, 3157\u20133170 (1978)","journal-title":"Nucleic Acids Res."},{"key":"9_CR2","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1006\/jmbi.1998.1947","volume":"281","author":"J. Helden van","year":"1998","unstructured":"van Helden, J., Andr\u00e9, B., Collado-Vides, J.: Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol.\u00a0281, 827\u2013842 (1998)","journal-title":"J. Mol. Biol."},{"key":"9_CR3","first-page":"28","volume-title":"Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology","author":"T.L. Bailey","year":"1994","unstructured":"Bailey, T.L., Elkan, C.: Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In: Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28\u201336. AAAI Press, Menlo Park (1994)"},{"key":"9_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, T.L., et al.: Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology\u00a023, 137\u2013144 (2005)","journal-title":"Nature Biotechnology"},{"key":"9_CR5","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.\u00a033, 4899\u20134913 (2005)","journal-title":"Nucleic Acids Res."},{"key":"9_CR6","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1093\/bioinformatics\/btm606","volume":"24","author":"T.-M. Chan","year":"2008","unstructured":"Chan, T.-M., Leung, K.-S., Lee, K.-H.: TFBS identification based on genetic algorithm with combined representations and adaptive post-processing. Bioinformatics\u00a024, 341\u2013349 (2008)","journal-title":"Bioinformatics"},{"key":"9_CR7","doi-asserted-by":"publisher","first-page":"1188","DOI":"10.1093\/bioinformatics\/btm080","volume":"23","author":"L.P. Li","year":"2007","unstructured":"Li, L.P., Liang, Y., Bass, R.L.L.: GAPWM: a genetic algorithm method for optimizing a position weight matrix. Bioinformatics\u00a023, 1188\u20131194 (2007)","journal-title":"Bioinformatics"},{"key":"9_CR8","doi-asserted-by":"publisher","first-page":"1577","DOI":"10.1093\/bioinformatics\/btl147","volume":"22","author":"Z. Wei","year":"2006","unstructured":"Wei, Z., Jensen, S.T.: GAME: detecting cis-regulatory elements using a genetic algorithm. Bioinformatics\u00a022, 1577\u20131584 (2006)","journal-title":"Bioinformatics"},{"key":"9_CR9","doi-asserted-by":"crossref","unstructured":"Li, X., Wang, D.H.: Computational Discovery of Regulatory DNA Motifs Using Evolutionary Computation. In: CEC-IEEE 2010: IEEE Congress on Evolutionary Computation (accepted 2010)","DOI":"10.1109\/CEC.2010.5586380"},{"key":"9_CR10","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1007\/s00425-003-1150-0","volume":"218","author":"E. Fiume","year":"2004","unstructured":"Fiume, E., Christou, P., Giani, S., Breviario, D.: Introns are key regulatory elements of rice tubulin expression. Planta\u00a0218, 693\u2013704 (2004)","journal-title":"Planta"},{"key":"9_CR11","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1038\/nature03441","volume":"434","author":"X. Xie","year":"2005","unstructured":"Xie, X., Lu, J., Kulbokas, E.J., Golub, T.R., Mootha, V., Lindblad-Toh, K., Lander, E.S., Kellis, M.: Systematic discovery of regulatory motifs in human promoters and 3\u2019 UTRs by comparison of several mammals. Nature\u00a0434, 338\u2013345 (2005)","journal-title":"Nature"},{"key":"9_CR12","doi-asserted-by":"publisher","first-page":"662","DOI":"10.1126\/science.282.5389.662","volume":"282","author":"D.W. Meinke","year":"1998","unstructured":"Meinke, D.W., Cherry, J.M., Dean, C., Rounsley, S.D., Koornneef, M.: Arabidopsis thaliana: a model plant for genome analysis. Science\u00a0282, 662\u2013682 (1998)","journal-title":"Science"},{"key":"9_CR13","doi-asserted-by":"publisher","first-page":"1009","DOI":"10.1093\/nar\/gkm965","volume":"36","author":"D. Swarbreck","year":"2008","unstructured":"Swarbreck, D., Wilks, C., Lamesch, P., Berardini, T.Z., Garcia-Hernandez, M., Foerster, H., Li, D., Meyer, T., Muller, R., Ploetz, L., et al.: The arabidopsis information resource (TAIR): gene structure and function annotation. Nucleic Acids Res.\u00a036, D1009\u2013D1014 (2008)","journal-title":"Nucleic Acids Res."},{"key":"9_CR14","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1104\/pp.109.136028","volume":"150","author":"K. Vandepoele","year":"2009","unstructured":"Vandepoele, K., Quimbaya, M., Casneuf, T., De Veylder, L., Van de Peer, Y.: Unraveling transcriptional control in arabidopsis using cis-regulatory elements and coexpression networks. Plant Physiol.\u00a0150, 535\u2013546 (2009)","journal-title":"Plant Physiol."},{"key":"9_CR15","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1007\/978-3-642-02490-0_59","volume-title":"Advances in Neuro-Information Processing","author":"D.H. Wang","year":"2008","unstructured":"Wang, D.H., Lee, N.K.: MISCORE: mismatch-based matrix similarity scores for DNA motif detection. In: K\u00f6ppen, M., Kasabov, N., Coghill, G. (eds.) ICONIP 2008. LNCS, vol.\u00a05506, pp. 478\u2013485. Springer, Heidelberg (2008)"},{"key":"9_CR16","doi-asserted-by":"publisher","first-page":"4442","DOI":"10.1093\/nar\/gkf578","volume":"30","author":"P.V. Benos","year":"2002","unstructured":"Benos, P.V., Bulyk, M.L., Stormo, G.D.: Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res.\u00a030, 4442\u20134451 (2002)","journal-title":"Nucleic Acids Res."},{"key":"9_CR17","unstructured":"Wang, D.H.: Characterization of regulatory motif models. Technical Report, La Trobe University, Australia (October 2009)"},{"key":"9_CR18","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\u00a017, 1113\u20131122 (2001)","journal-title":"Bioinformatics"},{"key":"9_CR19","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1093\/genetics\/159.2.907","volume":"159","author":"N. Galtier","year":"2001","unstructured":"Galtier, N., Piganeau, G., Mouchiroud, D., Duret, L.: GC content evolution in mammalian genomes, the biased gene conversion hypothesis. Genetics\u00a0159, 907\u2013911 (2001)","journal-title":"Genetics"},{"key":"9_CR20","doi-asserted-by":"publisher","first-page":"1807","DOI":"10.1093\/bioinformatics\/bti256","volume":"21","author":"S. Mahony","year":"2005","unstructured":"Mahony, S., Hendrix, D., Golden, A., Smith, T.J., Rokhsar, D.S.: Transcription factor binding site identification using the Self-Organizing Map. Bioinformatics\u00a021, 1807\u20131814 (2005)","journal-title":"Bioinformatics"}],"container-title":["Communications in Computer and Information Science","Computational Systems-Biology and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-16750-8_9","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,11,13]],"date-time":"2021-11-13T06:54:04Z","timestamp":1636786444000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-16750-8_9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010]]},"ISBN":["9783642167492","9783642167508"],"references-count":20,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-16750-8_9","relation":{},"ISSN":["1865-0929","1865-0937"],"issn-type":[{"type":"print","value":"1865-0929"},{"type":"electronic","value":"1865-0937"}],"subject":[],"published":{"date-parts":[[2010]]}}}