{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T21:46:14Z","timestamp":1722721574619},"reference-count":64,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2013,6,20]],"date-time":"2013-06-20T00:00:00Z","timestamp":1371686400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1003105","type":"journal-article","created":{"date-parts":[[2013,6,20]],"date-time":"2013-06-20T21:17:31Z","timestamp":1371763051000},"page":"e1003105","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":45,"title":["How the Dynamics and Structure of Sexual Contact Networks Shape Pathogen Phylogenies"],"prefix":"10.1371","volume":"9","author":[{"given":"Katy","family":"Robinson","sequence":"first","affiliation":[]},{"given":"Nick","family":"Fyson","sequence":"additional","affiliation":[]},{"given":"Ted","family":"Cohen","sequence":"additional","affiliation":[]},{"given":"Christophe","family":"Fraser","sequence":"additional","affiliation":[]},{"given":"Caroline","family":"Colijn","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2013,6,20]]},"reference":[{"key":"ref1","article-title":"Infectious diseases of humans: dynamics and control, volume 26","author":"R Anderson","year":"1992","journal-title":"Wiley Online Library"},{"key":"ref2","doi-asserted-by":"crossref","unstructured":"Draief M, Ganesh A, Massouli\u00e9 L (2006) Thresholds for virus spread on networks. In: Proceedings of the 1st international conference on Performance evaluation methodolgies and tools. ACM, p. 51.","DOI":"10.1145\/1190095.1190160"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1098\/rspb.2002.2305","article-title":"Disease evolution on networks: the role of contact structure","volume":"270","author":"J Read","year":"2003","journal-title":"Proceedings of the Royal Society of London Series B: Biological Sciences"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1097\/00007435-199701000-00009","article-title":"The role of sexual partnership networks in the epidemiology of gonorrhea","volume":"24","author":"A Ghani","year":"1997","journal-title":"Sexually transmitted diseases"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.tpb.2011.12.009","article-title":"The dynamics of sexual contact networks: Effects on disease spread and control","volume":"81","author":"K Robinson","year":"2012","journal-title":"Theoretical Population Biology"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"e74","DOI":"10.1371\/journal.pmed.0050074","article-title":"Social contacts and mixing patterns relevant to the spread of infectious diseases","volume":"5","author":"J Mossong","year":"2008","journal-title":"PLoS medicine"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"i43","DOI":"10.1136\/sti.2006.023598","article-title":"Prevention strategies for sexually transmitted infections: importance of sexual network structure and epidemic phase","volume":"83","author":"H Ward","year":"2007","journal-title":"Sexually transmitted infections"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"22020","DOI":"10.1073\/pnas.1009094108","article-title":"A high-resolution human contact network for infectious disease transmission","volume":"107","author":"M Salath\u00e9","year":"2010","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1098\/rsif.2008.0218","article-title":"Epidemic thresholds in dynamic contact networks","volume":"6","author":"E Volz","year":"2009","journal-title":"Journal of the Royal Society Interface"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"174","DOI":"10.2307\/3096941","article-title":"Respondent-driven sampling: a new approach to the study of hidden populations","volume":"44","author":"D Heckathorn","year":"1997","journal-title":"Social problems"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1007\/s10461-005-9030-1","article-title":"Critical issues and further questions about respondent-driven sampling: comment on ramirez-valles, et al.(2005)","volume":"9","author":"R Heimer","year":"2005","journal-title":"AIDS and Behavior"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1214\/08-AOAS221","article-title":"Modeling social networks from sampled data","volume":"4","author":"M Handcock","year":"2010","journal-title":"The Annals of Applied Statistics"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1086\/427661","article-title":"Identification of networks of sexually transmitted infection: a molecular, geographic, and social network analysis","volume":"191","author":"J Wylie","year":"2005","journal-title":"Journal of Infectious Diseases"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1835","DOI":"10.1016\/S0140-6736(01)06883-0","article-title":"Sexual behaviour in britain: partnerships, practices, and hiv risk behaviours","volume":"358","author":"A Johnson","year":"2001","journal-title":"The Lancet"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/1742-7622-3-10","article-title":"Mixing patterns and the spread of closecontact infectious diseases","volume":"3","author":"W Edmunds","year":"2006","journal-title":"Emerging themes in epidemiology"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1177\/004912418101000205","article-title":"Snowball sampling: Problems and techniques of chain referral sampling","volume":"10","author":"P Biernacki","year":"1981","journal-title":"Sociological Methods & Research"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1136\/sti.2003.007187","article-title":"Sexual network analysis of a gonorrhoea outbreak","volume":"80","author":"P De","year":"2004","journal-title":"Sexually transmitted infections"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1214\/aoms\/1177705148","article-title":"Snowball sampling","volume":"32","author":"L Goodman","year":"1961","journal-title":"The Annals of Mathematical Statistics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1126\/science.1090727","article-title":"Unifying the epidemiological and evolutionary dynamics of pathogens","volume":"303","author":"B Grenfell","year":"2004","journal-title":"Science"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1098\/rsif.2009.0530","article-title":"Protocols for sampling viral sequences to study epidemic dynamics","volume":"7","author":"J Stack","year":"2010","journal-title":"Journal of The Royal Society Interface"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/nrg2583","article-title":"Evolutionary analysis of the dynamics of viral infectious disease","volume":"10","author":"O Pybus","year":"2009","journal-title":"Nature Reviews Genetics"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1016\/j.tim.2010.06.008","article-title":"Unlocking pathogen genotyping information for public health by mathematical modeling","volume":"18","author":"M Kretzschmar","year":"2010","journal-title":"Trends in microbiology"},{"key":"ref23","article-title":"Contact heterogeneity and phylodynamics: How contact networks shape parasite evolutionary trees","volume":"2011","author":"E O'Dea","year":"2010","journal-title":"Interdisciplinary perspectives on infectious diseases"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"e1002413","DOI":"10.1371\/journal.pcbi.1002413","article-title":"Inferring epidemic contact structure from phylogenetic trees","volume":"8","author":"G Leventhal","year":"2012","journal-title":"PLoS Computational Biology"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1534\/genetics.111.126466","article-title":"Inferring epidemiological parameters on the basis of allele frequencies","volume":"188","author":"T Stadler","year":"2011","journal-title":"Genetics"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1534\/genetics.111.134627","article-title":"Complex population dynamics and the coalescent under neutrality","volume":"190","author":"E Volz","year":"2012","journal-title":"Genetics"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"e1002552","DOI":"10.1371\/journal.pcbi.1002552","article-title":"Simple epidemiological dynamics explain phylogenetic clustering of hiv from patients with recent infection","volume":"8","author":"E Volz","year":"2012","journal-title":"PLoS Computational Biology"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1126\/science.1182395","article-title":"Evolution of mrsa during hospital transmission and intercontinental spread","volume":"327","author":"S Harris","year":"2010","journal-title":"Science"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1056\/NEJMoa1003176","article-title":"Whole-genome sequencing and socialnetwork analysis of a tuberculosis outbreak","volume":"364","author":"J Gardy","year":"2011","journal-title":"New England Journal of Medicine"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/S1473-3099(12)70295-5","article-title":"Investigation of disease outbreaks with genome sequencing","volume":"13","author":"JL Gardy","year":"2013","journal-title":"The Lancet infectious diseases"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1128\/JCM.02279-12","article-title":"Rapid whole-genome sequencing for investigation of a suspected tuberculosis outbreak","volume":"51","author":"ME T\u00f6r\u00f6k","year":"2013","journal-title":"Journal of clinical microbiology"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"3065","DOI":"10.1073\/pnas.1121491109","article-title":"Genomic epidemiology of the escherichia coli o104: H4 outbreaks in europe, 2011","volume":"109","author":"YH Grad","year":"2012","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/S1473-3099(12)70277-3","article-title":"Whole-genome sequencing to delineate mycobacterium tuberculosis outbreaks: a retrospective observational study","volume":"13","author":"TM Walker","year":"2012","journal-title":"The Lancet infectious diseases"},{"key":"ref34","doi-asserted-by":"crossref","DOI":"10.1098\/rstb.2012.0198","article-title":"Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods","volume":"368","author":"T Stadler","year":"2013","journal-title":"Philosophical Transactions of the Royal Society B: Biological Sciences"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"e1002947","DOI":"10.1371\/journal.pcbi.1002947","article-title":"Viral phylodynamics","volume":"9","author":"EM Volz","year":"2013","journal-title":"PLoS computational biology"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1098\/rsif.2005.0051","article-title":"Networks and epidemic models","volume":"2","author":"M Keeling","year":"2005","journal-title":"Journal of the Royal Society Interface"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"3200","DOI":"10.1103\/PhysRevLett.86.3200","article-title":"Epidemic spreading in scale-free networks","volume":"86","author":"R Pastor-Satorras","year":"2001","journal-title":"Physical review letters"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/0304-4149(82)90011-4","article-title":"The coalescent","volume":"13","author":"J Kingman","year":"1982","journal-title":"Stochastic processes and their applications"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1093\/molbev\/msi103","article-title":"Bayesian coalescent inference of past population dynamics from molecular sequences","volume":"22","author":"A Drummond","year":"2005","journal-title":"Molecular Biology and Evolution"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1534\/genetics.108.092460","article-title":"Extensions of the coalescent effective population size","volume":"181","author":"J Wakeley","year":"2009","journal-title":"Genetics"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1093\/molbev\/msr217","article-title":"Estimating the basic reproductive number from viral sequence data","volume":"29","author":"T Stadler","year":"2012","journal-title":"Molecular Biology and Evolution"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1797","DOI":"10.1098\/rsif.2011.0850","article-title":"Inferring pandemic growth rates from sequence data","volume":"9","author":"E de Silva","year":"2012","journal-title":"Journal of The Royal Society Interface"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"1404","DOI":"10.1093\/bioinformatics\/18.10.1404","article-title":"Genie: estimating demographic history from molecular phylogenies","volume":"18","author":"O Pybus","year":"2002","journal-title":"Bioinformatics"},{"key":"ref44","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":"O Pybus","year":"2000","journal-title":"Genetics"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/35082140","article-title":"The web of human sexual contacts","volume":"411","author":"L Fredrik","year":"2001","journal-title":"Nature"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"i145","DOI":"10.1136\/sti.78.suppl_1.i145","article-title":"Gonorrhoea and chlamydia core groups and sexual networks in manitoba","volume":"78","author":"A Jolly","year":"2002","journal-title":"Sexually transmitted infections"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.1098\/rsif.2010.0007","article-title":"A two-tiered model for simulating the ecological and evolutionary dynamics of rapidly evolving viruses, with an application to inuenza","volume":"7","author":"K Koelle","year":"2010","journal-title":"Journal of The Royal Society Interface"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"2141","DOI":"10.2307\/2410685","article-title":"Patterns in Phylogenetic Tree Balance with Variable and Evolving Speciation Rates","volume":"50","author":"SB Heard","year":"1996","journal-title":"Evolution"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"1292","DOI":"10.1111\/j.0014-3820.2002.tb01440.x","article-title":"Does imbalance in phylogenies reect only bias?","volume":"56","author":"E Stam","year":"2002","journal-title":"Evolution; international journal of organic evolution"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"866","DOI":"10.1080\/10635150290102564","article-title":"Power of eight tree shape statistics to detect nonrandom diversifi-cation: a comparison by simulation of two models of cladogenesis","volume":"51","author":"PMM Agapow","year":"2002","journal-title":"Systematic biology"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"1818","DOI":"10.2307\/2410033","article-title":"Patterns in Tree Balance among Cladistic, Phenetic, and Randomly Generated Phylogenetic Trees","volume":"46","author":"SB Heard","year":"1992","journal-title":"Evolution"},{"key":"ref52","first-page":"44","article-title":"Gene genealogies and the coalescent process","volume":"7","author":"R Hudson","year":"1990","journal-title":"Oxford surveys in evolutionary biology"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"e1000590","DOI":"10.1371\/journal.ppat.1000590","article-title":"Molecular phylodynamics of the heterosexual hiv epidemic in the united kingdom","volume":"5","author":"G Hughes","year":"2009","journal-title":"PLoS pathogens"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"e50","DOI":"10.1371\/journal.pmed.0050050","article-title":"Episodic sexual transmission of hiv revealed by molecular phylodynamics","volume":"5","author":"F Lewis","year":"2008","journal-title":"PLoS medicine"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1093\/infdis\/jir468","article-title":"Transmission clustering drives the onward spread of the hiv epidemic among men who have sex with men in quebec","volume":"204","author":"B Brenner","year":"2011","journal-title":"Journal of Infectious Diseases"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1093\/infdis\/jir550","article-title":"Transmission network parameters estimated from hiv sequences for a nationwide epidemic","volume":"204","author":"A Brown","year":"2011","journal-title":"Journal of Infectious Diseases"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1038\/hdy.2010.78","article-title":"Reconstructing disease outbreaks from genetic data: a graph approach","volume":"106","author":"T Jombart","year":"2010","journal-title":"Heredity"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1086\/590501","article-title":"Hiv-1 transmission, by stage of infection","volume":"198","author":"T Hollingsworth","year":"2008","journal-title":"Journal of Infectious Diseases"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1097\/00007435-197804000-00003","article-title":"Dynamics and control of the transmission of gonorrhea","volume":"5","author":"J Yorke","year":"1978","journal-title":"Sexually transmitted diseases"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1056\/NEJM197901183000305","article-title":"Fifteen-month followup study of women infected with chlamydia trachomatis","volume":"300","author":"W McCormack","year":"1979","journal-title":"New England Journal of Medicine"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1098\/rspb.2011.0913","article-title":"Unravelling transmission trees of infectious diseases by combining genetic and epidemiological data","volume":"279","author":"R Ypma","year":"2012","journal-title":"Proceedings of the Royal Society B: Biological Sciences"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"1488","DOI":"10.1086\/651951","article-title":"Molecular epidemiology reveals longterm changes in hiv type 1 subtype b transmission in switzerland","volume":"201","author":"R Kouyos","year":"2010","journal-title":"Journal of Infectious Diseases"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"1609","DOI":"10.1053\/j.gastro.2009.02.006","article-title":"Evidence of a large, international network of hcv transmission in hiv-positive men who have sex with men","volume":"136","author":"T van de Laar","year":"2009","journal-title":"Gastroenterology"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.virol.2009.05.023","article-title":"Phylodynamic analysis of the dissemination of hiv-1 crf01 ae in vietnam","volume":"391","author":"H Liao","year":"2009","journal-title":"Virology"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003105","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,2,25]],"date-time":"2022-02-25T23:37:42Z","timestamp":1645832262000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003105"}},"subtitle":[],"editor":[{"given":"Sergei L.","family":"Kosakovsky Pond","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2013,6,20]]},"references-count":64,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2013,6,20]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003105","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.718033478.793480446","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,6,20]]}}}