{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T10:26:05Z","timestamp":1790504765068,"version":"4.1.0"},"reference-count":71,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Syst Biol"],"published-print":{"date-parts":[[2016,11]]},"DOI":"10.1093\/sysbio\/syw050","type":"journal-article","created":{"date-parts":[[2016,7,2]],"date-time":"2016-07-02T01:45:02Z","timestamp":1467423902000},"page":"1041-1056","source":"Crossref","is-referenced-by-count":68,"title":["Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates"],"prefix":"10.1093","volume":"65","author":[{"given":"Mandev S.","family":"Gill","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippe","family":"Lemey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shannon N.","family":"Bennett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roman","family":"Biek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc A.","family":"Suchard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,7,1]]},"reference":[{"key":"2016101700073901000_65.6.1041.1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0602768103"},{"key":"2016101700073901000_65.6.1041.2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msm277"},{"key":"2016101700073901000_65.6.1041.3","doi-asserted-by":"publisher","DOI":"10.1126\/science.1101476"},{"key":"2016101700073901000_65.6.1041.4","doi-asserted-by":"publisher","DOI":"10.1126\/science.1122033"},{"key":"2016101700073901000_65.6.1041.5","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msp285"},{"key":"2016101700073901000_65.6.1041.6","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msg182"},{"key":"2016101700073901000_65.6.1041.7","doi-asserted-by":"publisher","DOI":"10.1038\/nature12060"},{"key":"2016101700073901000_65.6.1041.8","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0700741104"},{"key":"2016101700073901000_65.6.1041.9","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2010.08.010"},{"key":"2016101700073901000_65.6.1041.10","doi-asserted-by":"publisher","DOI":"10.1097\/QAI.0b013e31818a6561"},{"key":"2016101700073901000_65.6.1041.11","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0907189107"},{"key":"2016101700073901000_65.6.1041.12","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.79.23.14680-14687.2005"},{"key":"2016101700073901000_65.6.1041.13","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.240326697"},{"key":"2016101700073901000_65.6.1041.14","unstructured":"Chipman H., George E., McCulloch R. 2001. The practical implementation of Bayesian model selection. (IMS Lecture Notes - Monograph Series; vol. 38). Beachwood, Ohio: Institute of Mathematical Statistics. p. 67\u2013134."},{"key":"2016101700073901000_65.6.1041.15","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-1795.1999.tb00078.x"},{"key":"2016101700073901000_65.6.1041.16","doi-asserted-by":"publisher","DOI":"10.1038\/nature02225"},{"key":"2016101700073901000_65.6.1041.17","doi-asserted-by":"publisher","DOI":"10.1038\/364218a0"},{"key":"2016101700073901000_65.6.1041.18","doi-asserted-by":"publisher","DOI":"10.1038\/339532a0"},{"key":"2016101700073901000_65.6.1041.19","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.ge.29.120195.002153"},{"key":"2016101700073901000_65.6.1041.20","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mss075"},{"key":"2016101700073901000_65.6.1041.21","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1093\/genetics\/161.3.1307","article-title":"Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data.","volume":"161","author":"Drummond","year":"2002.","journal-title":"Genetics"},{"key":"2016101700073901000_65.6.1041.22","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msi103"},{"key":"2016101700073901000_65.6.1041.23","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msq326"},{"key":"2016101700073901000_65.6.1041.24","doi-asserted-by":"publisher","DOI":"10.1126\/science.1256739"},{"key":"2016101700073901000_65.6.1041.25","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2011.04.028"},{"key":"2016101700073901000_65.6.1041.26","doi-asserted-by":"publisher","DOI":"10.1098\/rsbl.2007.0146"},{"key":"2016101700073901000_65.6.1041.27","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2010.0060"},{"key":"2016101700073901000_65.6.1041.28","doi-asserted-by":"publisher","DOI":"10.2307\/2290777"},{"key":"2016101700073901000_65.6.1041.29","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mss265"},{"key":"2016101700073901000_65.6.1041.30","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.1994.0079"},{"key":"2016101700073901000_65.6.1041.31","doi-asserted-by":"publisher","DOI":"10.1038\/364203a0"},{"key":"2016101700073901000_65.6.1041.32","doi-asserted-by":"publisher","DOI":"10.1038\/366552a0"},{"key":"2016101700073901000_65.6.1041.33","doi-asserted-by":"publisher","DOI":"10.1093\/biomet\/57.1.97"},{"key":"2016101700073901000_65.6.1041.34","doi-asserted-by":"crossref","unstructured":"Heled J., Drummond A. 2008. Bayesian inference of population size history from multiple loci. BMC Evol. Biol. 8:289.","DOI":"10.1186\/1471-2148-8-289"},{"key":"2016101700073901000_65.6.1041.35","first-page":"679","article-title":"WHO-UNAIDS Network for HIV Isolation and Characterisation.","volume":"25","author":"Hemelaar","year":"2011.","journal-title":"Global trends in molecular epidemiology of HIV-1 during 2000-2007."},{"key":"2016101700073901000_65.6.1041.36","doi-asserted-by":"publisher","DOI":"10.1111\/j.1755-0998.2011.02988.x"},{"key":"2016101700073901000_65.6.1041.37","doi-asserted-by":"publisher","DOI":"10.1016\/0040-5809(83)90013-8"},{"key":"2016101700073901000_65.6.1041.38","doi-asserted-by":"publisher","DOI":"10.1017\/S030500410001330X"},{"key":"2016101700073901000_65.6.1041.39","unstructured":"Jeffreys H. 1961. Theory of probability. Oxford University Press."},{"key":"2016101700073901000_65.6.1041.40","doi-asserted-by":"publisher","DOI":"10.1029\/97JC00167"},{"key":"2016101700073901000_65.6.1041.41","doi-asserted-by":"publisher","DOI":"10.7589\/0090-3558-6.4.507"},{"key":"2016101700073901000_65.6.1041.42","doi-asserted-by":"publisher","DOI":"10.1016\/0304-4149(82)90011-4"},{"key":"2016101700073901000_65.6.1041.43","doi-asserted-by":"publisher","DOI":"10.2307\/3213548"},{"key":"2016101700073901000_65.6.1041.44","doi-asserted-by":"publisher","DOI":"10.1111\/1467-9469.00308"},{"key":"2016101700073901000_65.6.1041.45","doi-asserted-by":"publisher","DOI":"10.1006\/tpbi.1997.1299"},{"key":"2016101700073901000_65.6.1041.46","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1093\/genetics\/149.1.429","article-title":"Maximum likelihood estimation of population growth rates based on the coalescent.","volume":"149","author":"Kuhner","year":"1998.","journal-title":"Genetics"},{"key":"2016101700073901000_65.6.1041.47","first-page":"65","article-title":"Variable selection for regression models.","volume":"60","author":"Kuo","year":"1998.","journal-title":"Sankhya B"},{"key":"2016101700073901000_65.6.1041.48","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0936469100"},{"key":"2016101700073901000_65.6.1041.49","doi-asserted-by":"crossref","unstructured":"Liu Y., Mittler J. 2008. Selection dramatically reduces effective population size in HIV-1 infection. BMC Evol. Biol. 8:133.","DOI":"10.1186\/1471-2148-8-133"},{"key":"2016101700073901000_65.6.1041.50","doi-asserted-by":"publisher","DOI":"10.1038\/nature10574"},{"key":"2016101700073901000_65.6.1041.51","doi-asserted-by":"publisher","DOI":"10.1063\/1.1699114"},{"key":"2016101700073901000_65.6.1041.52","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msn090"},{"key":"2016101700073901000_65.6.1041.53","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1007\/BF00173909","article-title":"The coalescent and the genealogical process in geographically structured population.","volume":"29","author":"Notohara","year":"1990.","journal-title":"J. Math. Biol."},{"key":"2016101700073901000_65.6.1041.54","doi-asserted-by":"crossref","unstructured":"Opgen- Rhein R., Fahrmeir L., Strimmer K. 2005. Inference of demographic history from genealogical trees using reversible jump Markov chain Monte Carlo. BMC Evol. Biol. 5:6.","DOI":"10.1186\/1471-2148-5-6"},{"key":"2016101700073901000_65.6.1041.55","doi-asserted-by":"publisher","DOI":"10.1111\/biom.12003"},{"key":"2016101700073901000_65.6.1041.56","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.329"},{"key":"2016101700073901000_65.6.1041.57","doi-asserted-by":"publisher","DOI":"10.3390\/v2020639"},{"key":"2016101700073901000_65.6.1041.58","doi-asserted-by":"crossref","first-page":"1429","DOI":"10.1093\/genetics\/155.3.1429","article-title":"An integrated framework for the inference of viral population history from reconstructed genealogies.","volume":"155","author":"Pybus","year":"2000.","journal-title":"Genetics"},{"key":"2016101700073901000_65.6.1041.59","unstructured":"Rodrigo A., Felsenstein J. 1999. Coalescent approaches to HIV population genetics. Baltimore, (MD): Johns Hopkins Universtiy Press. p. 233\u2013274."},{"key":"2016101700073901000_65.6.1041.60","doi-asserted-by":"publisher","DOI":"10.1126\/science.1101074"},{"key":"2016101700073901000_65.6.1041.61","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1093\/genetics\/129.2.555","article-title":"Pairwise comparison of mitochondrial DNA sequences in stable and exponentially growing populations.","volume":"129","author":"Slatkin,","year":"1991.","journal-title":"Genetics"},{"key":"2016101700073901000_65.6.1041.62","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msq083"},{"key":"2016101700073901000_65.6.1041.63","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a003776"},{"key":"2016101700073901000_65.6.1041.64","doi-asserted-by":"publisher","DOI":"10.1038\/nature02890"},{"key":"2016101700073901000_65.6.1041.65","doi-asserted-by":"publisher","DOI":"10.1080\/10635150390238879"},{"key":"2016101700073901000_65.6.1041.66","unstructured":"Tener J. 1965. Muskoxen in Canada: a biological and taxonomic review. (Monograph Series No. 2). Ottawa: Canadian Wildlife Service."},{"key":"2016101700073901000_65.6.1041.67","unstructured":"UNAIDS. 2015. AIDSinfo. http:\/\/aidsinfo.unaids.org\/ ."},{"key":"2016101700073901000_65.6.1041.68","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.109.106021"},{"key":"2016101700073901000_65.6.1041.69","unstructured":"WHO. 2015a. World Health Organization, Dengue. http:\/\/www.who.int\/topics\/dengue\/en\/ ."},{"key":"2016101700073901000_65.6.1041.70","unstructured":"WHO. 2015b. World Health Organization, Rabies. http:\/\/www.who.int\/rabies\/en\/ ."},{"key":"2016101700073901000_65.6.1041.71","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1093\/genetics\/16.2.97","article-title":"Evolution in Mendelian populations.","volume":"16","author":"Wright","year":"1931.","journal-title":"Genetics"}],"container-title":["Systematic Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/sysbio\/article-pdf\/65\/6\/1041\/17841030\/syw050.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,2]],"date-time":"2022-07-02T15:20:48Z","timestamp":1656775248000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/sysbio\/article-lookup\/doi\/10.1093\/sysbio\/syw050"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,7,1]]},"references-count":71,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2016,10,16]]},"published-print":{"date-parts":[[2016,11]]}},"alternative-id":["10.1093\/sysbio\/syw050"],"URL":"https:\/\/doi.org\/10.1093\/sysbio\/syw050","relation":{},"ISSN":["1063-5157","1076-836X"],"issn-type":[{"value":"1063-5157","type":"print"},{"value":"1076-836X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,7,1]]}}}