{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,11]],"date-time":"2024-09-11T05:58:05Z","timestamp":1726034285421},"publisher-location":"Berlin, Heidelberg","reference-count":26,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540457671"},{"type":"electronic","value":"9783540457688"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006]]},"DOI":"10.1007\/11875741_3","type":"book-chapter","created":{"date-parts":[[2006,11,21]],"date-time":"2006-11-21T13:13:09Z","timestamp":1164114789000},"page":"21-31","source":"Crossref","is-referenced-by-count":3,"title":["Promoter Prediction Using Physico-Chemical Properties of DNA"],"prefix":"10.1007","author":[{"given":"Philip","family":"Uren","sequence":"first","affiliation":[]},{"given":"R. Michael","family":"Cameron-Jones","sequence":"additional","affiliation":[]},{"given":"Arthur","family":"Sale","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"key":"3_CR1","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1101\/gr.7.9.861","volume":"7","author":"J.W. Fickett","year":"1997","unstructured":"Fickett, J.W., Hatzigeorgiou, A.G.: Eukaryotic Promoter Recognition. Genome Research\u00a07, 861\u2013878 (1997)","journal-title":"Genome Research"},{"key":"3_CR2","doi-asserted-by":"publisher","first-page":"1467","DOI":"10.1038\/nbt1032","volume":"22","author":"V.B. Bajic","year":"2004","unstructured":"Bajic, V.B., Tan, S.L., Suzuki, Y., Sugano, S.: Promoter prediction analysis on the whole human genome. Nature Biotechnology\u00a022, 1467\u20131473 (2004)","journal-title":"Nature Biotechnology"},{"key":"3_CR3","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1006\/jmbi.1998.1972","volume":"281","author":"A.G. Pedersen","year":"1998","unstructured":"Pedersen, A.G., Baldi, P., Chauvin, Y., Brunak, S.: DNA Structure in Human RNA Polymerase II Promoters. J. Mol. Biol.\u00a0281, 663\u2013673 (1998)","journal-title":"J. Mol. Biol."},{"key":"3_CR4","doi-asserted-by":"publisher","first-page":"4255","DOI":"10.1093\/nar\/gki737","volume":"33","author":"K. Florquin","year":"2005","unstructured":"Florquin, K., Saeys, Y., Degroeve, S., Rouze, P., Van de Peer, Y.: Large-scale structural analysis of the core promoter in mammalian and plant genomes. Nucl. Acids Res.\u00a033, 4255\u20134264 (2005)","journal-title":"Nucl. Acids Res."},{"key":"3_CR5","doi-asserted-by":"publisher","first-page":"5834","DOI":"10.1093\/nar\/gkh905","volume":"32","author":"Y. Fukue","year":"2004","unstructured":"Fukue, Y., Sumida, N., Nishikawa, J.-i., Ohyama, T.: Core promoter elements of eukaryotic genes have a highly distinctive mechanical property. Nuc. Acids Res.\u00a032, 5834\u20135840 (2004)","journal-title":"Nuc. Acids Res."},{"key":"3_CR6","doi-asserted-by":"publisher","first-page":"3821","DOI":"10.1093\/nar\/gki700","volume":"33","author":"Y. Fukue","year":"2005","unstructured":"Fukue, Y., Sumida, N., Tanase, J.-i., Ohyama, T.: A highly distinctive mechanical property found in the majority of human promoters and its transcriptional relevance. Nuc. Acids Res.\u00a033, 3821\u20133827 (2005)","journal-title":"Nuc. Acids Res."},{"key":"3_CR7","doi-asserted-by":"publisher","first-page":"3165","DOI":"10.1093\/nar\/gki627","volume":"33","author":"A. Kanhere","year":"2005","unstructured":"Kanhere, A., Bansal, M.: Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes. Nucleic Acids Research\u00a033, 3165\u20133175 (2005)","journal-title":"Nucleic Acids Research"},{"key":"3_CR8","doi-asserted-by":"publisher","first-page":"1584","DOI":"10.1093\/nar\/gkh335","volume":"32","author":"C.H. Choi","year":"2004","unstructured":"Choi, C.H., Kalosakas, G., Rasmussen, K., Hiromura, M., Bishop, A.R., Usheva, A.: DNA dynamically directs its own transcription initiation. Nucleic Acids Res.\u00a032, 1584\u20131590 (2004)","journal-title":"Nucleic Acids Res."},{"key":"3_CR9","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1080\/07391102.2002.10506828","volume":"20","author":"L. Tsai","year":"2002","unstructured":"Tsai, L., Luo, L., Sun, Z.: Sequence-dependent flexibility in promoter sequences. J. Biomol. Struct. Dyn.\u00a020, 127\u2013134 (2002)","journal-title":"J. Biomol. Struct. Dyn."},{"key":"3_CR10","first-page":"183","volume":"1","author":"A. Gabrielian","year":"1999","unstructured":"Gabrielian, A., Landsman, D., Bolshoy, A.: Curved DNA in promoter sequences. In Silico Biol.\u00a01, 183\u2013196 (1999-2000)","journal-title":"In Silico Biol."},{"key":"3_CR11","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1111\/j.1432-1033.1994.tb19058.x","volume":"223","author":"S. Lisser","year":"1994","unstructured":"Lisser, S., Margalit, H.: Determination of common structural features in Escherichia coli promoters by computer analysis. Eur. J. Biochem.\u00a0223, 823\u2013830 (1994)","journal-title":"Eur. J. Biochem."},{"key":"3_CR12","doi-asserted-by":"publisher","first-page":"1575","DOI":"10.1101\/gr.2080004","volume":"14","author":"H. Wang","year":"2004","unstructured":"Wang, H., Noordeweier, M., Benham, C.J.: Stress-Induced DNA Duplex Destabilization (SIDD) in the E. coli Genome: SIDD Sites Are Closely Associated With Promoters. Genome Research\u00a014, 1575\u20131584 (2004)","journal-title":"Genome Research"},{"key":"3_CR13","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1093\/bioinformatics\/17.suppl_1.S199","volume":"17","author":"U. Ohler","year":"2001","unstructured":"Ohler, U., Niemann, H., Liao, G., Rubin, G.: Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. Bioinformatics\u00a017, S199\u2013S206 (2001)","journal-title":"Bioinformatics"},{"key":"3_CR14","unstructured":"Baldi, P., Chauvin, Y., Brunak, S., Anders, J.G., Pedersen, G.: Computational Applications of DNA Structural Scales. In: Int. Conf. Intell. Syst. Mol. Biol., pp. 35\u201342 (1998)"},{"key":"3_CR15","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1038\/ng1285","volume":"36","author":"T. Ota","year":"2004","unstructured":"Ota, T., Suzuki, Y., Nishikawa, T., Otsuki, T., Sugiyama, T., Irie, R., Wakamatsu, A., Hayashi, K., Sato, H., Nagai, K., Kimura, K., Makita, H., Sekine, M., Obayashi, M., Nishi, T., Shibahara, T.: Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat. Genet.\u00a036, 40\u201345 (2004)","journal-title":"Nat. Genet."},{"key":"3_CR16","first-page":"73","volume":"221","author":"Y. Suzuki","year":"2003","unstructured":"Suzuki, Y., Sugano, S.: Construction of a full-length enriched and a 5\u2019-end enriched cDNA library using the oligo-capping method. Methods Mol. Biol.\u00a0221, 73\u201391 (2003)","journal-title":"Methods Mol. Biol."},{"issue":"Database issue","key":"3_CR17","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1093\/nar\/gkh076","volume":"32","author":"Y. Suzuki","year":"2004","unstructured":"Suzuki, Y., Yamashita, R., Sugano, S., Nakai, K.: DBTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res.\u00a032 (Database issue), 78\u201381 (2004)","journal-title":"Nucleic Acids Res."},{"key":"3_CR18","first-page":"1258","volume":"28","author":"V.I. Ivanov","year":"1994","unstructured":"Ivanov, V.I., Minchenkova, L.E.: The A-form of DNA: in search of the biological role. Mol. Biol. (Mosk)\u00a028, 1258\u20131271 (1994)","journal-title":"Mol. Biol. (Mosk)"},{"key":"3_CR19","doi-asserted-by":"publisher","first-page":"918","DOI":"10.1006\/jmbi.1994.0190","volume":"247","author":"A.V. Sivolob","year":"1995","unstructured":"Sivolob, A.V., Khrapunov, S.N.: Translational positioning of nucleosomes on DNA: the role of sequence-dependent isotropic DNA bending stiffness. J. Mol. Biol.\u00a0247, 918\u2013931 (1995)","journal-title":"J. Mol. Biol."},{"key":"3_CR20","doi-asserted-by":"publisher","first-page":"3323","DOI":"10.1093\/nar\/26.14.3323","volume":"26","author":"R.D. Blake","year":"1998","unstructured":"Blake, R.D., Delcourt, S.G.: Thermal stability of DNA. Nucleic Acids Res.\u00a026, 3323\u20133332 (1998)","journal-title":"Nucleic Acids Res."},{"key":"3_CR21","doi-asserted-by":"publisher","first-page":"3746","DOI":"10.1073\/pnas.83.11.3746","volume":"83","author":"K. Breslauer","year":"1986","unstructured":"Breslauer, K., Frank, R., Blocker, H., Marky, L.: Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA\u00a083, 3746\u20133750 (1986)","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"3_CR22","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1016\/0022-2836(86)90452-3","volume":"191","author":"S.C. Satchwell","year":"1986","unstructured":"Satchwell, S.C., Drew, H.R., Travers, A.A.: Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol.\u00a0191, 659\u2013675 (1986)","journal-title":"J. Mol. Biol."},{"key":"3_CR23","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1006\/jmbi.1996.0304","volume":"259","author":"M. Hassan el","year":"1996","unstructured":"el Hassan, M., Calladine, C.: Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA. J. Mol. Biol.\u00a0259, 95\u2013103 (1996)","journal-title":"J. Mol. Biol."},{"key":"3_CR24","volume-title":"Data Mining: Practical machine learning tools and techniques","author":"I.H. Witten","year":"2005","unstructured":"Witten, I.H., Frank, E.: Data Mining: Practical machine learning tools and techniques. Morgan Kaufmann, San Francisco (2005)"},{"key":"3_CR25","volume-title":"Advances in Kernel Methods - Support Vector Learning","author":"J. Platt","year":"1998","unstructured":"Platt, J.: Fast Training of Support Vector Machines using Sequential Minimal Optimization. In: Schoelkopf, B., Burges, C., Smola, A. (eds.) Advances in Kernel Methods - Support Vector Learning. MIT Press, Cambridge (1998)"},{"key":"3_CR26","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1162\/089976601300014493","volume":"13","author":"S.S. Keerthi","year":"2001","unstructured":"Keerthi, S.S., Shevade, S.K., Bhattacharyya, C., Murthy, K.R.K.: Improvements to Platt\u2019s SMO Algorithm for SVM Classifier Design. Neural Computation\u00a013, 637\u2013649 (2001)","journal-title":"Neural Computation"}],"container-title":["Lecture Notes in Computer Science","Computational Life Sciences II"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/11875741_3.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,4,27]],"date-time":"2021-04-27T07:26:09Z","timestamp":1619508369000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/11875741_3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006]]},"ISBN":["9783540457671","9783540457688"],"references-count":26,"URL":"https:\/\/doi.org\/10.1007\/11875741_3","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2006]]}}}