{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,5]],"date-time":"2024-09-05T04:45:09Z","timestamp":1725511509174},"publisher-location":"Berlin, Heidelberg","reference-count":33,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540482932"},{"type":"electronic","value":"9783540485407"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"DOI":"10.1007\/978-3-540-48540-7_8","type":"book-chapter","created":{"date-parts":[[2007,5,15]],"date-time":"2007-05-15T20:28:49Z","timestamp":1179260929000},"page":"80-94","source":"Crossref","is-referenced-by-count":0,"title":["Build a Dictionary, Learn a Grammar, Decipher Stegoscripts, and Discover Genomic Regulatory Elements"],"prefix":"10.1007","author":[{"given":"Guandong","family":"Wang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weixiong","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"issue":"20","key":"8_CR1","doi-asserted-by":"publisher","first-page":"2551","DOI":"10.1101\/gad.831000","volume":"14","author":"B. Lemon","year":"2000","unstructured":"Lemon, B., Tjian, R.: Orchestrated response: A symphony of transcription factors for gene control. Genes Dev.\u00a014(20), 2551\u20132569 (2000)","journal-title":"Genes Dev."},{"key":"8_CR2","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., Bogouski, M.S., Liu, J.S., Neuwald, A.F., Wooten, J.C.: Detecting subtle sequence signals: A gibbs sampling strategy for multiple alignment. Science\u00a0262, 208\u2013214 (1993)","journal-title":"Science"},{"issue":"1-2","key":"8_CR3","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1007\/BF00993379","volume":"21","author":"T.L. Bailey","year":"1995","unstructured":"Bailey, T.L., Elkan, C.: Unsupervised learning of multiple motifs in biopolymers using EM. Machine Learning\u00a021(1-2), 51\u201380 (1995)","journal-title":"Machine Learning"},{"issue":"7-8","key":"8_CR4","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1093\/bioinformatics\/15.7.563","volume":"15","author":"G.Z. Hertz","year":"1999","unstructured":"Hertz, G.Z., Stormo, G.D.: Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics\u00a015(7-8), 563\u2013577 (1999)","journal-title":"Bioinformatics"},{"issue":"5","key":"8_CR5","doi-asserted-by":"publisher","first-page":"1205","DOI":"10.1006\/jmbi.2000.3519","volume":"296","author":"J.D. Hughes","year":"2000","unstructured":"Hughes, J.D., Estep, P.W., Tavazoie, S., Church, G.M.: Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Molecular Biology\u00a0296(5), 1205\u20131214 (2000)","journal-title":"J. Molecular Biology"},{"issue":"5","key":"8_CR6","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., Andre, B., Collado-Vides, J.: Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Molecular Biology\u00a0281(5), 827\u2013842 (1998)","journal-title":"J. Molecular Biology"},{"key":"8_CR7","unstructured":"Sinha, S., Tompa, M.: A statistical method for finding transcription factor binding sites. In: 8th Intern. Conf. on Intelligent Systems for Molecular Biology (2000)"},{"issue":"8","key":"8_CR8","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1101\/gr.9.8.681","volume":"9","author":"M.Q. Zhang","year":"1999","unstructured":"Zhang, M.Q.: Large scale gene expression data analysis: A new challenge to computational biologists. Genome Research\u00a09(8), 681\u2013688 (1999)","journal-title":"Genome Research"},{"key":"8_CR9","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1093\/bioinformatics\/btg1038","volume":"19","author":"E. Segal","year":"2003","unstructured":"Segal, E., Yelensky, R., Koller, D.: Genome-wide discovery of transcriptional modules from DNA sequence and gene expression. Bioinformatics\u00a019, 273\u2013282 (2003)","journal-title":"Bioinformatics"},{"key":"8_CR10","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1093\/bioinformatics\/btg1082","volume":"19","author":"Y. Tamada","year":"2003","unstructured":"Tamada, Y., et al.: Estimating gene networks from gene expression data by combining bayesian network model with promoter element detection. Bioinformatics\u00a019, 227\u2013236 (2003)","journal-title":"Bioinformatics"},{"key":"8_CR11","volume-title":"Disappearing Cryptography","author":"P. Wayner","year":"2002","unstructured":"Wayner, P.: Disappearing Cryptography, 2nd edn. Morgan Kaufmann, San Francisco (2002)","edition":"2"},{"issue":"18","key":"8_CR12","doi-asserted-by":"publisher","first-page":"10096","DOI":"10.1073\/pnas.180265397","volume":"97","author":"H.J. Bussemaker","year":"2002","unstructured":"Bussemaker, H.J., Li, H., Siggia, E.D.: Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis. Proc. Natl. Acad. Sci. USA.\u00a097(18), 10096\u201310100 (2002)","journal-title":"Proc. Natl. Acad. Sci. USA."},{"key":"8_CR13","volume-title":"Introduction to Automata Theory, Languages, and Computation","author":"J.E. Hopcroft","year":"2001","unstructured":"Hopcroft, J.E., Motwani, R., Ullman, J.D.: Introduction to Automata Theory, Languages, and Computation, 2nd edn. Addison-Wesley, Reading (2001)","edition":"2"},{"key":"8_CR14","doi-asserted-by":"crossref","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., Mitchison, G.: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge (1998)"},{"key":"8_CR15","doi-asserted-by":"crossref","unstructured":"Regnier, M.: unified approach to word statistics. In: RECOMB, pp. 207\u2013213 (1998)","DOI":"10.1145\/279069.279116"},{"issue":"1-2","key":"8_CR16","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1089\/10665270050081360","volume":"7","author":"G. Reinert","year":"2000","unstructured":"Reinert, G., Schbath, S., Waterman, M.S.: Probabilistic and statistical properties of words: An overview. J. Computational Biology\u00a07(1-2), 1\u201346 (2000)","journal-title":"J. Computational Biology"},{"issue":"2","key":"8_CR17","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1038\/ng724","volume":"29","author":"Y. Pilpel","year":"2001","unstructured":"Pilpel, Y., Sudarsanam, P., Church, G.M.: Identifying regulatory networks by combinatorial analysis of promoter elements. Nature Genetics\u00a029(2), 153\u2013159 (2001)","journal-title":"Nature Genetics"},{"key":"8_CR18","doi-asserted-by":"crossref","first-page":"3273","DOI":"10.1091\/mbc.9.12.3273","volume":"9","author":"P.T. Spellman","year":"1998","unstructured":"Spellman, P.T., et al.: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell\u00a09, 3273\u20133297 (1998)","journal-title":"Molecular Biology of the Cell"},{"issue":"4","key":"8_CR19","doi-asserted-by":"crossref","first-page":"1746","DOI":"10.1128\/MCB.16.4.1746","volume":"16","author":"P. Dohrmann","year":"1996","unstructured":"Dohrmann, P., Voth, W., Stillman, D.: Role of negative regulation in promoter specificity of the homologous transcriptional activators ace2p and swi5p. Mol. Cell Biol.\u00a016(4), 1746\u20131758 (1996)","journal-title":"Mol. Cell Biol."},{"key":"8_CR20","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1093\/bioinformatics\/15.7.607","volume":"15","author":"J. Zhu","year":"1999","unstructured":"Zhu, J., Zhang, M.Q.: SCPD: A Promoter Database of Yeast Saccharomyces cerevisiae. Bioinformatics\u00a015, 607\u2013611 (1999)","journal-title":"Bioinformatics"},{"key":"8_CR21","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1186\/gb-2004-5-8-r56","volume":"5","author":"M. Kato","year":"2004","unstructured":"Kato, M., Hata, N., Banerjee, N., Futcher, B., Zhang, M.Q.: Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biology\u00a05, R56 (2004)","journal-title":"Genome Biology"},{"issue":"15","key":"8_CR22","doi-asserted-by":"publisher","first-page":"5703","DOI":"10.1073\/pnas.86.15.5703","volume":"86","author":"J.W. Dolan","year":"1989","unstructured":"Dolan, J.W., Kirkman, C., Fields, S.: The yeast STE12 protein binds to the DNA sequence mediating pheromone induction. Proc. Natl. Acad. Sci. USA\u00a086(15), 5703\u20135707 (1989)","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"8_CR23","doi-asserted-by":"publisher","first-page":"6327","DOI":"10.1093\/emboj\/17.21.6327","volume":"17","author":"P.L. Blaiseau","year":"1998","unstructured":"Blaiseau, P.L., Thomas, D.: Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA. EMBO J.\u00a017, 6327\u20136336 (1998)","journal-title":"EMBO J."},{"issue":"2","key":"8_CR24","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1002\/(SICI)1097-0061(20000130)16:2<177::AID-YEA516>3.0.CO;2-9","volume":"16","author":"J. Helden van","year":"2000","unstructured":"van Helden, J., Andre, B., Collado-Vides, J.: A web site for the computational analysis of yeast regulatory sequences. Yeast\u00a016(2), 177\u2013187 (2000)","journal-title":"Yeast"},{"issue":"5643","key":"8_CR25","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1126\/science.1087447","volume":"302","author":"J.M. Stuart","year":"2003","unstructured":"Stuart, J.M., Segal, E., Koller, D., Kim, S.K.: A gene coexpression network for global discovery of conserved genetic modules. Science\u00a0302(5643), 249\u2013255 (2003)","journal-title":"Science"},{"key":"8_CR26","doi-asserted-by":"publisher","first-page":"1551","DOI":"10.1126\/science.8372350","volume":"261","author":"C. Koch","year":"1993","unstructured":"Koch, C., Moll, T., Neuberg, M., Ahorn, H., Nasmyth, K.: A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phas. Science\u00a0261, 1551\u20131557 (1993)","journal-title":"Science"},{"key":"8_CR27","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1093\/genetics\/154.4.1533","volume":"154","author":"P.C. Hollenhorst","year":"2000","unstructured":"Hollenhorst, P.C., Bose, M.E., Mielke, M.R., M\u00fcller, U., Fox, C.A.: Forkhead genes in transcriptional silencing, cell morphology and the cell cycle: Overlapping and distinct functions for FKH1 and FKH2 in Saccharomyces cerevisiae. Genetics\u00a0154, 1533\u20131548 (2000)","journal-title":"Genetics"},{"key":"8_CR28","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1126\/science.1075090","volume":"298","author":"T.I. Lee","year":"2002","unstructured":"Lee, T.I., et al.: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science\u00a0298, 799\u2013804 (2002)","journal-title":"Science"},{"key":"8_CR29","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1198\/016214503388619094","volume":"98","author":"M. Gupta","year":"2003","unstructured":"Gupta, M., Liu, J.: Discovery of conserved sequence patterns using a stochastic dictionary model. J. Amer. Statist. Assoc.\u00a098, 55\u201366 (2003)","journal-title":"J. Amer. Statist. Assoc."},{"key":"8_CR30","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1093\/bioinformatics\/btg1040","volume":"19","author":"S. Sinha","year":"2003","unstructured":"Sinha, S., Nimwegen, E.V., Siggia, E.D.: A probabilistic method to detect regulatory modules. Bioinformatics\u00a019, 292\u2013301 (2003)","journal-title":"Bioinformatics"},{"issue":"6937","key":"8_CR31","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, E.S.: Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature\u00a0423(6937), 241\u2013254 (2003)","journal-title":"Nature"},{"issue":"2","key":"8_CR32","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1038\/79965","volume":"26","author":"W.W. Wasserman","year":"2000","unstructured":"Wasserman, W.W., Palumbo, M., Thompson, W., Fickett, J.W., Lawrence, C.E.: Human-mouse genome comparisons to locate regulatory sites. Nature Genetics\u00a026(2), 225\u2013228 (2000)","journal-title":"Nature Genetics"},{"key":"8_CR33","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1016\/j.gde.2005.02.004","volume":"15","author":"E.D. Siggia","year":"2005","unstructured":"Siggia, E.D.: Computational methods for transcriptional regulation. Cur. Opin. Gene. and Deve.\u00a015, 214\u2013221 (2005)","journal-title":"Cur. Opin. Gene. and Deve."}],"container-title":["Lecture Notes in Computer Science","Systems Biology and Regulatory Genomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-540-48540-7_8.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,11]],"date-time":"2023-05-11T21:28:52Z","timestamp":1683840532000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-540-48540-7_8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[null]]},"ISBN":["9783540482932","9783540485407"],"references-count":33,"URL":"https:\/\/doi.org\/10.1007\/978-3-540-48540-7_8","relation":{},"subject":[]}}