{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,5]],"date-time":"2024-09-05T22:23:22Z","timestamp":1725575002738},"publisher-location":"Berlin, Heidelberg","reference-count":27,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540332954"},{"type":"electronic","value":"9783540332961"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006]]},"DOI":"10.1007\/11732990_48","type":"book-chapter","created":{"date-parts":[[2006,3,28]],"date-time":"2006-03-28T12:59:27Z","timestamp":1143550767000},"page":"595-609","source":"Crossref","is-referenced-by-count":1,"title":["Detecting the Dependent Evolution of Biosequences"],"prefix":"10.1007","author":[{"given":"Jeremy","family":"Darot","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chen-Hsiang","family":"Yeang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Haussler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"48_CR1","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-642-86659-3","volume-title":"Evolution by gene duplication","author":"S. Ohno","year":"1970","unstructured":"Ohno, S.: Evolution by gene duplication. Springer, Heidelberg (1970)"},{"key":"48_CR2","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1126\/science.290.5494.1151","volume":"290","author":"M. Lynch","year":"2000","unstructured":"Lynch, M., Conery, J.S.: The evolutionary fate and consequences of duplicated genes. Science\u00a0290, 1151\u20131155 (2000)","journal-title":"Science"},{"key":"48_CR3","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1006\/jmbi.2000.3732","volume":"299","author":"C.S. Goh","year":"2000","unstructured":"Goh, C.S., Bogan, A.A., Joachmiak, M., Walther, D., Cohen, F.E.: Co-evolution of proteins with their interaction partners. J. Mol. Biol.\u00a0299, 283\u2013293 (2000)","journal-title":"J. Mol. Biol."},{"key":"48_CR4","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1016\/S0022-2836(03)00114-1","volume":"327","author":"A.K. Ramani","year":"2003","unstructured":"Ramani, A.K., Marcotte, E.M.: Exploiting the co-evolution of interacting proteins to discover interaction specificity. J. Mol. Biol.\u00a0327, 273\u2013284 (2003)","journal-title":"J. Mol. Biol."},{"key":"48_CR5","doi-asserted-by":"publisher","first-page":"750","DOI":"10.1126\/science.1068696","volume":"296","author":"H.B. Fraser","year":"2002","unstructured":"Fraser, H.B., Hirsh, A.E., Steinmetz, L.M., Scharfe, C., Feldman, M.W.: Evolutionary fate in the protein interaction network. Science\u00a0296, 750\u2013752 (2002)","journal-title":"Science"},{"key":"48_CR6","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1006\/jmbi.1998.2601","volume":"287","author":"D.D. Pollock","year":"1999","unstructured":"Pollock, D.D., Taylor, W.R., Goldman, N.: Coevolving protein residues: maximum likelihood identification and relationship to structure. J. Mol. Biol.\u00a0287, 187\u2013198 (1999)","journal-title":"J. Mol. Biol."},{"key":"48_CR7","doi-asserted-by":"publisher","first-page":"2454","DOI":"10.1073\/pnas.0409169102","volume":"102","author":"S. Washietl","year":"2005","unstructured":"Washietl, S., Hofacker, I.L., Stadler, P.F.: Fast and reliable prediction of noncoding RNAs. PNAS\u00a0102, 2454\u20132459 (2005)","journal-title":"PNAS"},{"key":"48_CR8","doi-asserted-by":"publisher","first-page":"5483","DOI":"10.1073\/pnas.0501761102","volume":"102","author":"D.P. Wall","year":"2005","unstructured":"Wall, D.P., Hirsh, A.E., Fraser, H.B., Kumm, J., Giaver, G., Eisen, M., Feldman, M.W.: Functional genomic analysis of the rates of protein evolution. PNAS\u00a0102, 5483\u20135488 (2005)","journal-title":"PNAS"},{"key":"48_CR9","doi-asserted-by":"publisher","first-page":"2058","DOI":"10.1093\/molbev\/msh222","volume":"21","author":"I.K. Jordan","year":"2004","unstructured":"Jordan, I.K., Marino-Ramfrez, L., Wolf, Y.I., Koonin, E.V.: Conservation and coevolution in the scale-free human gene coexpression network. Mol.\u00a0Biol.\u00a0Evol.\u00a021, 2058\u20132070 (2004)","journal-title":"Mol.\u00a0Biol.\u00a0Evol."},{"key":"48_CR10","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1126\/science.6163215","volume":"212","author":"H.F. Noller","year":"1981","unstructured":"Noller, H.F., Woese, C.R.: Secondary structure of 16S ribosomal RNA. Science\u00a0212, 403\u2013411 (1981)","journal-title":"Science"},{"key":"48_CR11","doi-asserted-by":"publisher","first-page":"3825","DOI":"10.1093\/nar\/26.16.3825","volume":"26","author":"I.L. Hofacker","year":"1998","unstructured":"Hofacker, I.L., Fekete, M., Flamm, C., Huynen, M.A., Rauscher, S., Stolorz, P.E., Stadler, P.F.: Automatic detection of conserved RNA structure elements in complete RNA virus genomes. Nucleic Acids Res.\u00a026, 3825\u20133836 (1998)","journal-title":"Nucleic Acids Res."},{"key":"48_CR12","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1038\/35103511","volume":"2","author":"S.R. Eddy","year":"2001","unstructured":"Eddy, S.R.: Non-coding RNA genes and the modern RNA world. Nat.\u00a0Rev.\u00a0Genet.\u00a02, 919\u2013929 (2001)","journal-title":"Nat.\u00a0Rev.\u00a0Genet."},{"key":"48_CR13","doi-asserted-by":"publisher","first-page":"1369","DOI":"10.1016\/S0960-9822(01)00401-8","volume":"11","author":"E. Rivas","year":"2001","unstructured":"Rivas, E., Klein, R.J., Jones, T.A., Eddy, S.R.: Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr.\u00a0Biol.\u00a011, 1369\u20131373 (2001)","journal-title":"Curr.\u00a0Biol."},{"key":"48_CR14","doi-asserted-by":"publisher","first-page":"1606","DOI":"10.1093\/bioinformatics\/btg229","volume":"19","author":"D. Bernardo di","year":"2003","unstructured":"di Bernardo, D., Down, T., Hubbard, T.: ddbRNA: detection of conserved secondary structures in multiple alignments. Bioinformatics\u00a019, 1606\u20131611 (2003)","journal-title":"Bioinformatics"},{"key":"48_CR15","doi-asserted-by":"publisher","first-page":"12102","DOI":"10.1073\/pnas.0404193101","volume":"101","author":"A. Coventry","year":"2004","unstructured":"Coventry, A., Kleitman, D.J., Berger, B.: MSARI: multiple sequence alignments for statistical detection of RNA secondary structure. PNAS\u00a0101, 12102\u201312107 (2004)","journal-title":"PNAS"},{"key":"48_CR16","doi-asserted-by":"publisher","first-page":"4925","DOI":"10.1093\/nar\/gkh839","volume":"32","author":"J.S. Pedersen","year":"2004","unstructured":"Pedersen, J.S., Meyer, I.M., Forsberg, R., Simmonds, P., Hein, J.: A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res.\u00a032, 4925\u20134936 (2004)","journal-title":"Nucleic Acids Res."},{"key":"48_CR17","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1038\/nbt1144","volume":"23","author":"S. Washietl","year":"2005","unstructured":"Washietl, S., Hofacker, I.L., Lukasser, M., Huttenhofer, A., Stadler, P.F.: Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat.\u00a0Biotechnol.\u00a023, 1383\u20131390 (2005)","journal-title":"Nat.\u00a0Biotechnol."},{"key":"48_CR18","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1371\/journal.pcbi.0010024","volume":"1","author":"D. Barker","year":"2005","unstructured":"Barker, D., Pagel, M.: Predicting functional gene links from phylogenetic-statistical analyses of whole genomes. PLoS Comp.\u00a0Biol.\u00a01, 24\u201331 (2005)","journal-title":"PLoS Comp.\u00a0Biol."},{"key":"48_CR19","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1093\/genetics\/139.2.993","volume":"139","author":"Z. Yang","year":"1995","unstructured":"Yang, Z.: A space-time process model for the evolution of DNA sequences. Genetics\u00a0139, 993\u20131005 (1995)","journal-title":"Genetics"},{"key":"48_CR20","first-page":"93","volume":"13","author":"J. Felsenstein","year":"1996","unstructured":"Felsenstein, J., Churchill, G.: A hidden Markov model approach to variation among sites in rate of evolution. Mol.\u00a0Biol.\u00a0Evol.\u00a013, 93\u2013104 (1996)","journal-title":"Mol.\u00a0Biol.\u00a0Evol."},{"key":"48_CR21","first-page":"413","volume":"11","author":"A. Siepel","year":"2004","unstructured":"Siepel, A., Haussler, D.: Combining phylogenetic and hidden Markov models in biosequence analysis. JCB\u00a011, 413\u2013428 (2004)","journal-title":"JCB"},{"key":"48_CR22","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1007\/BF02101694","volume":"22","author":"M. Hasegawa","year":"1985","unstructured":"Hasegawa, M., Kishino, H., Yano, T.: Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J.\u00a0Mol.\u00a0Evol.\u00a022, 160\u2013174 (1985)","journal-title":"J.\u00a0Mol.\u00a0Evol."},{"key":"48_CR23","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1007\/BF01734359","volume":"17","author":"J. Felsenstein","year":"1981","unstructured":"Felsenstein, J.: Evolutionary trees from DNA sequences: a maximum likelihood approach. J.\u00a0Mol.\u00a0Evol.\u00a017, 368\u2013376 (1981)","journal-title":"J.\u00a0Mol.\u00a0Evol."},{"key":"48_CR24","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1098\/rspb.1994.0006","volume":"255","author":"M. Pagel","year":"1994","unstructured":"Pagel, M.: Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proceedings of the Royal Society in London, series B\u00a0255, 37\u201345 (1994)","journal-title":"Proceedings of the Royal Society in London, series B"},{"key":"48_CR25","unstructured":"RNA families database, http:\/\/www.sanger.ac.uk\/cgi-bin\/Rfam\/getacc?RF00005"},{"key":"48_CR26","unstructured":"MrBayes: Bayesian inference of phylogeny, http:\/\/mrbayes.csit.fsu.edu\/index.php"},{"key":"48_CR27","unstructured":"http:\/\/evolution.genetics.washington.edu\/phylip.html"}],"container-title":["Lecture Notes in Computer Science","Research in Computational Molecular Biology"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/11732990_48.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,7,25]],"date-time":"2021-07-25T06:33:49Z","timestamp":1627194829000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/11732990_48"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006]]},"ISBN":["9783540332954","9783540332961"],"references-count":27,"URL":"https:\/\/doi.org\/10.1007\/11732990_48","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2006]]}}}