{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,5]],"date-time":"2024-09-05T05:32:16Z","timestamp":1725514336315},"publisher-location":"Berlin, Heidelberg","reference-count":23,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540782964"},{"type":"electronic","value":"9783540782971"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008]]},"DOI":"10.1007\/978-3-540-78297-1_10","type":"book-chapter","created":{"date-parts":[[2008,5,29]],"date-time":"2008-05-29T10:26:01Z","timestamp":1212056761000},"page":"213-230","source":"Crossref","is-referenced-by-count":1,"title":["Improving Neural Network Promoter Prediction by Exploiting the Lengths of Coding and Non-Coding Sequences"],"prefix":"10.1007","author":[{"given":"Rachel","family":"Caldwell","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yun","family":"Dai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sheenal","family":"Srivastava","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yan-Xia","family":"Lin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ren","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"10_CR1_1","doi-asserted-by":"publisher","first-page":"1467","DOI":"10.1038\/nbt1032","volume":"22","author":"VB Bajic","year":"2004","unstructured":"Bajic, V.B., Tan, S.L., Suzuki, Y. and Sugano, S. (2004) Promoter prediction analysis on the whole human genome, Nature Biotechnology, 22: 1467\u20131473.","journal-title":"Nature Biotechnology"},{"key":"10_CR2_1","doi-asserted-by":"crossref","unstructured":"Burden, S., Lin, Y.-X. and Zhang, R. (2005) Improving promoter prediction for the NNPP2.2 algorithm: a case study using Escherichia coli DNA sequences, Bioinformatics, 21: 601\u2013607.","DOI":"10.1093\/bioinformatics\/bti047"},{"key":"10_CR3_1","doi-asserted-by":"publisher","first-page":"2602","DOI":"10.1101\/gr.1169203","volume":"13","author":"F Chiaromonte","year":"2003","unstructured":"Chiaromonte, F., Miller, W. and Bouhassira, E.E. (2003) Gene length and proximity to neighbors affect genome-wide expression levels, Genome Research, 13: 2602\u20132608.","journal-title":"Genome Research"},{"key":"10_CR4_1","doi-asserted-by":"crossref","unstructured":"Dai, Y., Zhang, R. and Lin, Y.-X. (2006) The probability distribution of distance TSS-TLS is organism characteristic and can be used for promoter prediction. In: Ali, M. and Daposigny, R. (eds) Advances in Applied Artificial Intelligence \u2013 Lecture Notes in Artificial Intelligence (LNAI 4031). Springer, Heidelberg Berlin New York, pp. 927\u2013934.","DOI":"10.1007\/11779568_99"},{"key":"10_CR5_1","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1101\/gr.7.9.861","volume":"7","author":"JW Fickett","year":"1997","unstructured":"Fickett, J.W. and Hatzigeorgiou, A.G. (1997) Eukaryotic promoter recognition, Genome Research, 7: 861\u2013878.","journal-title":"Genome Research"},{"key":"10_CR6_1","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1007\/s10142-002-0077-z","volume":"2","author":"M. Garcia-Hernandez","year":"2002","unstructured":"Garcia-Hernandez, M., Berardini, T., Chen, G., Crist, D., Doyle, A., Huala, E., Knee, E., Lambrecht, M., Miller, N., Mueller, L.A., Mundodi, S., Reiser, L., Rhee, S.Y., School, R., Tacklind, J., Weems, D.C., Wu, Y., Xu, I., Yoo, D. Yoon J. and Zhang, P. (2002) TAIR: a resource of integrated Arabidopsis data, Functional & Intergrative Genomics, 2: 239\u2013253.","journal-title":"Functional & Intergrative Genomics"},{"key":"10_CR7_1","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1016\/S0097-8485(99)00015-7","volume":"23","author":"A Gorm Pedersen","year":"1999","unstructured":"Gorm Pedersen, A., Baldi, P., Chauvin, Y. and Brunak, S. (1999) The biology of eukaryotic promoter prediction \u2013 a review, Computers & Chemistry, 23: 191\u2013207.","journal-title":"Computers & Chemistry"},{"key":"10_CR8_1","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1016\/j.tig.2006.01.001","volume":"22","author":"TA Hughes","year":"2006","unstructured":"Hughes, T.A. (2006) Regulation of gene expression by alternative untranslated regions, Trends in Genetics, 22: 119\u2013122.","journal-title":"Trends in Genetics"},{"key":"10_CR9_1","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1093\/bioinformatics\/15.5.356","volume":"15","author":"S. Knudsen","year":"1999","unstructured":"Knudsen, S. (1999) Promoter2.0: for the recognition of PolII promoter sequences, Bioinformatics, 15: 356\u2013361.","journal-title":"Bioinformatics"},{"key":"10_CR10_1","doi-asserted-by":"publisher","first-page":"1345","DOI":"10.1093\/molbev\/msi122","volume":"22","author":"B Lemos","year":"2005","unstructured":"Lemos, B., Bettencourt, B.R., Meiklejohn, C.D. and Hartl, D.L. (2005) Evolution of proteins and gene expression levels are coupled in Drosophila and are independently assocated with mRNA abundance, protein length, and number of protein\u2013protein interactions, Molecular Biology and Evolution, 22: 1345\u20131354.","journal-title":"Molecular Biology and Evolution"},{"key":"10_CR11_1","doi-asserted-by":"publisher","first-page":"D75","DOI":"10.1093\/nar\/gkh074","volume":"32","author":"Y Makita","year":"2004","unstructured":"Makita, Y., Nakao, M., Ogasawara, N. and Nakai, K. (2004) DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics, Nucleic Acid Research, 32: D75\u2013D77.","journal-title":"Nucleic Acid Research"},{"key":"10_CR12_1","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1038\/nature05805","volume":"447","author":"T.S. Mikkelsen","year":"2007","unstructured":"Mikkelsen, T.S., Wakefield, M.J., Aken, B., Amemiya, C.T., Chang, J.L., Duke, D., Garber, M., Gentles, A.J., Goodstadt, L., Heger, A., Jurka, J., Kamal, M., Mauceli, E., Searle, S.M.J., Sharpe, T., Baker, M.L., Batzer, M.A., Benos, P.V., Belov, K., Clamp, M., Cook, A., Cuff, J., Das, R., Davidow, L., Deakin, J.E., Fazzari, M.J., Glass, J.L., Grabherr, M., Greally, J.M., Gu, W., Hore, T.A., Huttley, G.A., Kleber, M., Jirtle, R.L., Koina, E., Lee, J.T., Mahony, S., Marra, M.A., Miller, R.D., Nicholls, R.D., Oda, M., Papenfuss, A.T., Parra, Z.E., Pollock, D.D., Ray, D.A., Schein, J.E., Speed, T.P., Thompson, K., VandeBerg, J.L., Wade, C.M., Walker, J.A., Waters, P.D., Webber, C., Weidman, J.R., Xie, X., Zody, M.C., Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, Marshall Graves, J.A., Ponting, C.P., Breen, M., Samollow, P.B., Lander, E.S. and Lindblad-Toh, K. (2007) Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences, Nature, 447: 167\u2013178.","journal-title":"Nature"},{"key":"10_CR13_1","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1016\/S0168-9525(00)02174-0","volume":"17","author":"U Ohler","year":"2001","unstructured":"Ohler, U. and Niemann, H. (2001) Identification and analysis of eukaryotic promoters: recent computational approaches, Trends in Genetics, 17: 56\u201360.","journal-title":"Trends in Genetics"},{"key":"10_CR14_1","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1016\/j.biosystems.2005.09.001","volume":"83","author":"SP Pandey","year":"2006","unstructured":"Pandey, S.P. and Krishnamachari, A. (2006) Computational analysis of plant RNA Pol-II promoters, BioSystems, 83: 38\u201350.","journal-title":"BioSystems"},{"key":"10_CR15_1","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1016\/j.bbrc.2003.08.052","volume":"309","author":"P Qui","year":"2003","unstructured":"Qui, P. (2003a) Recent advances in computational promoter analysis in understanding the transcriptional regulatory network, Biochemical and Biophysical Research Communications, 309: 495\u2013501.","journal-title":"Biochemical and Biophysical Research Communications"},{"key":"10_CR16_1","first-page":"125","volume":"4","author":"P Qui","year":"2003","unstructured":"Qui, P. (2003b) Computational approaches for deciphering the transcriptional regulatory network by promoter analysis, Biosilico, 4: 125\u2013133.","journal-title":"Biosilico"},{"key":"10_CR17_1","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1016\/S0097-8485(01)00099-7","volume":"26","author":"MG Reese","year":"2001","unstructured":"Reese, M.G. (2001) Application of a time-delay neural network to promoter annotation in the Drosophila Melanogaster genome, Computers and Chemistry, 26: 51\u201356.","journal-title":"Computers and Chemistry"},{"key":"10_CR18_1","doi-asserted-by":"crossref","first-page":"D394","DOI":"10.1093\/nar\/gkj156","volume":"34","author":"H. Salgado","year":"2006","unstructured":"Salgado, H., Cama-Castro, S., Peralta-Gil, M., Daz-Peredo, E., Snchez-Solano, F., Santo-Zavaleta, A., Martnez-Flores, I., Jimnez-Jacinto, V., Bonavides-Martnez, C., Segura-Salazar, J., Martnez-Antonio, A., and Collado-Vides, J. (2006) RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions, Nucleic Acids Research, 34: D394\u2013D397.","journal-title":"Nucleic Acids Research"},{"key":"10_CR19_1","doi-asserted-by":"publisher","first-page":"D78","DOI":"10.1093\/nar\/gkh076","volume":"32","author":"Y Suzuki","year":"2004","unstructured":"Suzuki, Y., Yamashita, R., Sugano, S. and Nakai, K. (2004) DBTSS, DataBase of transcriptional start sites: progress report 2004, Nucleic Acids Research, 32: D78\u2013D81.","journal-title":"Nucleic Acids Research"},{"key":"10_CR20_1","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1016\/j.physa.2004.11.021","volume":"350","author":"T Tan","year":"2005","unstructured":"Tan, T., Frenkel, D., Gupta, V. and Deem, M.W. (2005) Length, protein\u2013protein interactions, and complexity, Physica A, 350: 52\u201362.","journal-title":"Physica A"},{"key":"10_CR21_1","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1093\/molbev\/msh263","volume":"22","author":"D Wang","year":"2005","unstructured":"Wang, D., Hsieh, M. and Li, W. (2005) A general tendency for conservation of protein length across eukaryotic kingdoms, Molecular Biology and Evolution, 22: 142\u2013147.","journal-title":"Molecular Biology and Evolution"},{"key":"10_CR22_1","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1016\/S0168-9525(99)01922-8","volume":"16","author":"J Zhang","year":"2000","unstructured":"Zhang, J. (2000) Protein-length distributions for the three domains of life, Trends in Genetics, 16: 107\u2013109.","journal-title":"Trends in Genetics"},{"key":"10_CR23_1","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1093\/bioinformatics\/15.7.607","volume":"15","author":"J. Zhu","year":"1998","unstructured":"Zhu, J. and Zhang, M.Q. (1998) SCPD: a promoter database of the yeast Saccharomyces cerevisiae, Bioinformatics, 15: 607\u2013611.","journal-title":"Saccharomyces cerevisiae, Bioinformatics"}],"container-title":["Studies in Computational Intelligence","Advances of Computational Intelligence in Industrial Systems"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-540-78297-1_10.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,4,27]],"date-time":"2021-04-27T07:04:37Z","timestamp":1619507077000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-540-78297-1_10"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008]]},"ISBN":["9783540782964","9783540782971"],"references-count":23,"URL":"https:\/\/doi.org\/10.1007\/978-3-540-78297-1_10","relation":{},"ISSN":["1860-949X"],"issn-type":[{"type":"print","value":"1860-949X"}],"subject":[],"published":{"date-parts":[[2008]]}}}