{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,2]],"date-time":"2025-11-02T10:08:14Z","timestamp":1762078094420},"reference-count":33,"publisher":"Proceedings of the National Academy of Sciences","issue":"25","content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2001,12,4]]},"abstract":"<jats:p>Changes in protein function can lead to changes in the selection\n acting on specific residues. This can often be detected as\n evolutionary rate changes at the sites in question. A\n maximum-likelihood method for detecting evolutionary rate shifts at\n specific protein positions is presented. The method determines\n significance values of the rate differences to give a sound statistical\n foundation for the conclusions drawn from the analyses. A statistical\n test for detecting slowly evolving sites is also described. The methods\n are applied to a set of Myc proteins for the identification of both\n conserved sites and those with changing evolutionary rates. Those\n positions with conserved and changing rates are related to the\n structures and functions of their proteins. The results are compared\n with an earlier Bayesian method, thereby highlighting the advantages of\n the new likelihood ratio tests.<\/jats:p>","DOI":"10.1073\/pnas.251526398","type":"journal-article","created":{"date-parts":[[2002,7,26]],"date-time":"2002-07-26T14:35:07Z","timestamp":1027694107000},"page":"14512-14517","update-policy":"http:\/\/dx.doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":88,"title":["A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins"],"prefix":"10.1073","volume":"98","author":[{"given":"Bjarne","family":"Knudsen","sequence":"first","affiliation":[{"name":"Bioinformatics Research Center, University of Aarhus, H\u00f8egh\r Guldbergsgade 10, Building 090, DK-8000 \u212brhus C, Denmark; and\r Department of Zoology, Box 118525, University of\r Florida, Gainesville, FL 32611-8525"}]},{"given":"Michael M.","family":"Miyamoto","sequence":"additional","affiliation":[{"name":"Bioinformatics Research Center, University of Aarhus, H\u00f8egh\r Guldbergsgade 10, Building 090, DK-8000 \u212brhus C, Denmark; and\r Department of Zoology, Box 118525, University of\r Florida, Gainesville, FL 32611-8525"}]}],"member":"341","published-online":{"date-parts":[[2001,12,4]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng0498-313"},{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a003824"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.292.5524.2095"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0169-5347(00)01994-7"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/17.7.660"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511623486"},{"key":"e_1_3_4_7_2","volume-title":"Fundamentals of Molecular Evolution","author":"Graur D","year":"2000","unstructured":"D Graur, W-H Li Fundamentals of Molecular Evolution (Sinauer, 2nd Ed., Sunderland, MA, 2000).","edition":"2"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.98.2.548"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/158.3.1311"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00486096"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1998.2601"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0025-5564(97)00081-3"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a003868"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a026105"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a026080"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.276.5310.227"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF01734359"},{"key":"e_1_3_4_18_2","first-page":"275","volume":"8","author":"Jones D T","year":"1992","unstructured":"D T Jones, W R Taylor, J M Thornton Comput Appl Biosci 8, 275\u2013282 (1992).","journal-title":"Comput Appl Biosci"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2001.4540"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1006\/mpev.2000.0783"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1080\/10635159950127367"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/22.22.4673"},{"key":"e_1_3_4_23_2","volume-title":"The Oncogene and Tumor Supressor Gene Factsbook","author":"Hesketh R","year":"1997","unstructured":"R Hesketh The Oncogene and Tumor Supressor Gene Factsbook (Academic, 2nd Ed., San Diego, 1997).","edition":"2"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1056346"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/35054544"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1038\/35054550"},{"key":"e_1_3_4_27_2","first-page":"555","volume":"13","author":"Yang Z","year":"1997","unstructured":"Z Yang Comput Appl Biosci 13, 555\u2013556 (1997).","journal-title":"Comput Appl Biosci"},{"key":"e_1_3_4_28_2","first-page":"1","volume-title":"Oncogenes as Transcriptional Regulators: Volume 1, Retroviral Oncogenes","author":"Prendergast G C","year":"1997","unstructured":"G C Prendergast Oncogenes as Transcriptional Regulators: Volume 1, Retroviral Oncogenes, eds M Yaniv, J Ghysdael (Birkh\u00e4user, Basel), pp. 1\u201328 (1997)."},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1096\/fasebj.12.9.633"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1038\/sj.onc.1202746"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a003835"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a025932"},{"key":"e_1_3_4_33_2","volume-title":"PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods)","author":"Swofford D L","year":"1998","unstructured":"D L Swofford PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods) (Sinauer, Sunderland, MA, , Version 4.0. (1998)."}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.251526398","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,13]],"date-time":"2022-04-13T13:52:22Z","timestamp":1649857942000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/full\/10.1073\/pnas.251526398"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2001,12,4]]},"references-count":33,"journal-issue":{"issue":"25","published-print":{"date-parts":[[2001,12,4]]}},"alternative-id":["10.1073\/pnas.251526398"],"URL":"https:\/\/doi.org\/10.1073\/pnas.251526398","relation":{},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2001,12,4]]},"assertion":[{"value":"2001-07-09","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2001-09-28","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2001-12-04","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}