Joel O. Wertheim, Ph.D. - Publications

Affiliations: 
2009 Ecology & Evolutionary Biology University of Arizona, Tucson, AZ 
Area:
Virology Biology, Evolution and Development Biology

92 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Wertheim JO, Steel M, Sanderson MJ. Accuracy in near-perfect virus phylogenies. Systematic Biology. PMID 34398231 DOI: 10.1093/sysbio/syab069  1
2021 Skaathun B, Ragonnet-Cronin M, Poortinga K, Sheng Z, Hu YW, Wertheim JO. Interplay Between Geography and HIV Transmission Clusters in Los Angeles County. Open Forum Infectious Diseases. 8: ofab211. PMID 34159215 DOI: 10.1093/ofid/ofab211  1
2021 Wilbourn B, Saafir-Callaway B, Jair K, Wertheim JO, Laeyendecker O, Jordan JA, Kharfen M, Castel A. Characterization of HIV Risk Behaviors and Clusters Using HIV-TRACE among a Cohort of Persons Living with HIV in Washington, DC. Aids Research and Human Retroviruses. PMID 34157853 DOI: 10.1089/AID.2021.0031  0.01
2021 Fujimoto K, Bahl J, Wertheim JO, Del Vecchio N, Hicks JT, Damodaran L, Hallmark CJ, Lavingia R, Mora R, Carr M, Yang B, Schneider JA, Hwang LY, McNeese M. Author Correction: Methodological synthesis of Bayesian phylodynamics, HIV-TRACE, and GEE: HIV-1 transmission epidemiology in a racially/ethnically diverse Southern U.S. context. Scientific Reports. 11: 10336. PMID 33976320 DOI: 10.1038/s41598-021-89879-w  0.01
2021 West AP, Wertheim JO, Wang JC, Vasylyeva TI, Havens JL, Chowdhury MA, Gonzalez E, Fang CE, Di Lonardo SS, Hughes S, Rakeman JL, Lee HH, Barnes CO, Gnanapragasam PNP, Yang Z, et al. Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Biorxiv : the Preprint Server For Biology. PMID 33907745 DOI: 10.1101/2021.02.14.431043  0.01
2021 Oster AM, Panneer N, Lyss SB, McClung RP, Watson M, Saduvala N, Ocfemia MCB, Linley L, Switzer WM, Wertheim JO, Campbell E, Hernandez AL, France AM. Increasing Capacity to Detect Clusters of Rapid HIV Transmission in Varied Populations-United States. Viruses. 13. PMID 33808053 DOI: 10.3390/v13040577  1
2021 Pekar J, Worobey M, Moshiri N, Scheffler K, Wertheim JO. Timing the SARS-CoV-2 index case in Hubei province. Science (New York, N.Y.). PMID 33737402 DOI: 10.1126/science.abf8003  1
2021 Wertheim JO, Hostager R, Ryu D, Merkel K, Angedakin S, Arandjelovic M, Ayimisin EA, Babweteera F, Bessone M, Brun-Jeffery KJ, Dieguez P, Eckardt W, Fruth B, Herbinger I, Jones S, et al. Discovery of novel herpes simplexviruses in wild gorillas, bonobos, and chimpanzees supports zoonotic origin of HSV-2. Molecular Biology and Evolution. PMID 33720357 DOI: 10.1093/molbev/msab072  0.01
2021 Martin DP, Weaver S, Tegally H, San EJ, Shank SD, Wilkinson E, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ, Gupta RK, Wertheim JO, et al. The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. Medrxiv : the Preprint Server For Health Sciences. PMID 33688681 DOI: 10.1101/2021.02.23.21252268  1
2021 Fujimoto K, Bahl J, Wertheim JO, Del Vecchio N, Hicks JT, Damodaran L, Hallmark CJ, Lavingia R, Mora R, Carr M, Yang B, Schneider JA, Hwang LY, McNeese M. Methodological synthesis of Bayesian phylodynamics, HIV-TRACE, and GEE: HIV-1 transmission epidemiology in a racially/ethnically diverse Southern U.S. context. Scientific Reports. 11: 3325. PMID 33558579 DOI: 10.1038/s41598-021-82673-8  0.01
2020 de Bernardi Schneider A, Osiowy C, Hostager R, Krarup H, Børresen M, Tanaka Y, Morriseau T, Wertheim JO. Analysis of Hepatitis B Virus Genotype D in Greenland Suggests the Presence of a Novel Quasi-Subgenotype. Frontiers in Microbiology. 11: 602296. PMID 33519744 DOI: 10.3389/fmicb.2020.602296  0.01
2020 Ragonnet-Cronin M, Benbow N, Hayford C, Poortinga K, Ma F, Forgione LA, Sheng Z, Hu Y, Torian L, Wertheim JO. Sorting by race/ethnicity across HIV genetic transmission networks in three major metropolitan areas in the United States. Aids Research and Human Retroviruses. PMID 33349132 DOI: 10.1089/AID.2020.0145  1
2020 Pekar J, Worobey M, Moshiri N, Scheffler K, Wertheim JO. Timing the SARS-CoV-2 Index Case in Hubei Province. Biorxiv : the Preprint Server For Biology. PMID 33269353 DOI: 10.1101/2020.11.20.392126  1
2020 Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO, Lemey P. The emergence of SARS-CoV-2 in Europe and North America. Science (New York, N.Y.). PMID 32912998 DOI: 10.1126/Science.Abc8169  1
2020 Dawson L, Benbow N, Fletcher FE, Kassaye S, Killelea A, Latham SR, Lee LM, Leitner T, Little SJ, Mehta SR, Martinez O, Minalga B, Poon A, Rennie S, Sugarman J, ... ... Wertheim JO, et al. Addressing ethical challenges in US-based HIV phylogenetic research. The Journal of Infectious Diseases. PMID 32525980 DOI: 10.1093/Infdis/Jiaa107  1
2020 Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO, Lemey P. The emergence of SARS-CoV-2 in Europe and the US. Biorxiv : the Preprint Server For Biology. PMID 32511416 DOI: 10.1101/2020.05.21.109322  1
2020 Wertheim JO, Panneer N, France AM, Saduvala N, Oster AM. Incident infection in high-priority HIV molecular transmission clusters in the united states. Aids (London, England). PMID 32287065 DOI: 10.1097/Qad.0000000000002531  1
2020 Wertheim JO. A glimpse into the origins of genetic diversity in SARS-CoV-2. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 32129842 DOI: 10.1093/Cid/Ciaa213  0.01
2020 Hassan A, De Gruttola V, Hu YW, Sheng Z, Poortinga K, Wertheim JO. The relationship between the HIV-1 transmission network and the HIV care continuum in Los Angeles County. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 32020172 DOI: 10.1093/Cid/Ciaa114  1
2020 Panneer N, France AM, Whiteside YO, Zhang T, Wertheim JO, Oster AM. Temporal Changes in HIV Transmission Patterns among Young Men Who Have Sex with Men, United States, 2009-2016. Journal of Acquired Immune Deficiency Syndromes (1999). PMID 31977598 DOI: 10.1097/Qai.0000000000002305  1
2019 Wertheim JO, Oster AM, Switzer WM, Zhang C, Panneer N, Campbell E, Saduvala N, Johnson JA, Heneine W. Natural selection favoring more transmissible HIV detected in United States molecular transmission network. Nature Communications. 10: 5788. PMID 31857582 DOI: 10.1038/S41467-019-13723-Z  1
2019 Hassan A, Wertheim JO, Blumenthal JS, Ellorin E, Dube MP, Corado K, Moore DJ, Morris SR. Characteristics of a cohort of high-risk men who have sex with men on pre-exposure prophylaxis reporting transgender sexual partners. Medicine. 98: e18232. PMID 31852085 DOI: 10.1097/Md.0000000000018232  0.01
2019 Xia Q, Wertheim JO, Braunstein SL, Misra K, Udeagu CC, Torian LV. Use of molecular HIV surveillance data and predictive modeling to prioritize persons for transmission-reduction interventions. Aids (London, England). PMID 31794522 DOI: 10.1097/Qad.0000000000002452  1
2019 Hostager R, Ragonnet-Cronin M, Murrell B, Hedskog C, Osinusi A, Susser S, Sarrazin C, Svarovskaia E, Wertheim JO. Hepatitis C virus genotype 1 and 2 recombinant genomes and the phylogeographic history of the 2k/1b lineage. Virus Evolution. 5: vez041. PMID 31616569 DOI: 10.1093/Ve/Vez041  1
2019 de Bernardi Schneider A, Ford CT, Hostager R, Williams J, Cioce M, Çatalyürek ÜV, Wertheim JO, Janies D. StrainHub: A phylogenetic tool to construct pathogen transmission networks. Bioinformatics (Oxford, England). PMID 31418766 DOI: 10.1093/Bioinformatics/Btz646  0.01
2019 Wertheim JO, Morris S, Ragonnet-Cronin M. Consent and criminalisation concerns over phylogenetic analysis of surveillance data - Authors' reply. The Lancet. Hiv. 6: e420-e421. PMID 31272659 DOI: 10.1016/S2352-3018(19)30142-0  1
2019 Ragonnet-Cronin M, Hostager R, Hedskog C, Osinusi A, Svarovskaia E, Wertheim JO. HIV co-infection is associated with increased transmission risk in patients with chronic hepatitis C virus. Journal of Viral Hepatitis. PMID 31194901 DOI: 10.1111/Jvh.13160  1
2019 Ragonnet-Cronin M, Hodcroft EB, Wertheim JO. Understanding disclosed and cryptic HIV transmission risk via genetic analysis: what are we missing and when does it matter? Current Opinion in Hiv and Aids. 14: 205-212. PMID 30946142 DOI: 10.1097/Coh.0000000000000537  1
2019 Wertheim JO, Chato C, Poon AFY. Comparative analysis of HIV sequences in real time for public health. Current Opinion in Hiv and Aids. PMID 30882486 DOI: 10.1097/Coh.0000000000000539  0.01
2019 Ragonnet-Cronin M, Hu YW, Morris SR, Sheng Z, Poortinga K, Wertheim JO. HIV transmission networks among transgender women in Los Angeles County, CA, USA: a phylogenetic analysis of surveillance data. The Lancet. Hiv. PMID 30765313 DOI: 10.1016/S2352-3018(18)30359-X  1
2019 Grande KM, Schumann CL, Bañez Ocfemia MC, Vergeront JM, Wertheim JO, Oster AM. Transmission Patterns in a Low HIV-Morbidity State - Wisconsin, 2014-2017. Mmwr. Morbidity and Mortality Weekly Report. 68: 149-152. PMID 30763299 DOI: 10.15585/Mmwr.Mm6806A5  1
2018 Wertheim JO, Oster AM, Murrell B, Saduvala N, Heneine W, Switzer WM, Johnson JA. Maintenance and reappearance of extremely divergent intra-host HIV-1 variants. Virus Evolution. 4: vey030. PMID 30538823 DOI: 10.1093/Ve/Vey030  1
2018 Moshiri N, Ragonnet-Cronin M, Wertheim JO, Mirarab S. FAVITES: simultaneous simulation of transmission networks, phylogenetic trees, and sequences. Bioinformatics (Oxford, England). PMID 30395173 DOI: 10.1093/Bioinformatics/Bty921  1
2018 Oster AM, France AM, Panneer N, Bañez Ocfemia MC, Campbell E, Dasgupta S, Switzer WM, Wertheim JO, Hernandez AL. Identifying Clusters of Recent and Rapid HIV Transmission Through Analysis of Molecular Surveillance Data. Journal of Acquired Immune Deficiency Syndromes (1999). PMID 30222659 DOI: 10.1097/Qai.0000000000001856  1
2018 Singh R, Stoneham C, Lim C, Jia X, Guenaga J, Wyatt R, Wertheim JO, Xiong Y, Guatelli J. Phosphoserine acidic cluster motifs bind distinct basic regions on the µ subunits of clathrin adaptor protein complexes. The Journal of Biological Chemistry. PMID 30135209 DOI: 10.1074/Jbc.Ra118.003080  0.01
2018 Wertheim JO, Murrell B, Mehta SR, Forgione LA, Kosakovsky Pond SL, Smith DM, Torian LV. Growth of HIV-1 Molecular Transmission Clusters in New York City. The Journal of Infectious Diseases. PMID 30010850 DOI: 10.1093/Infdis/Jiy431  1
2018 Kosakovsky Pond SL, Weaver S, Leigh Brown AJ, Wertheim JO. HIV-TRACE (Transmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens. Molecular Biology and Evolution. PMID 29401317 DOI: 10.1093/Molbev/Msy016  1
2017 Temereanca A, Oprea C, Wertheim JO, Ianache I, Ceausu E, Cernescu C, Mehta SR, Ruta S. HIV transmission clusters among injecting drug users in Romania. Romanian Biotechnological Letters. 22: 12307-12315. PMID 29213206  1
2017 Chaillon A, Gianella S, Lada SM, Perez-Santiago J, Jordan P, Ignacio C, Karris M, Richman D, Mehta SR, Little SJ, Wertheim JO, Smith DM. Size, Composition, and Evolution of HIV DNA Populations during Early Antiretroviral Therapy and Intensification with Maraviroc. Journal of Virology. PMID 29142136 DOI: 10.1128/Jvi.01589-17  1
2017 Bhardwaj N, Ragonnet-Cronin M, Murrell B, Chodavarapu K, Martin R, Chang S, Miller MD, Feld JJ, Sulkowski M, Mangia A, Wertheim JO, Osinusi A, McNally J, Brainard D, Mo H, et al. Intrapatient viral diversity and treatment outcome in patients with genotype 3a hepatitis C virus infection on sofosbuvir-containing regimens. Journal of Viral Hepatitis. PMID 29112331 DOI: 10.1111/Jvh.12825  1
2017 Valverde EE, Oster AM, Xu S, Wertheim JO, Hernandez AL. HIV Transmission Dynamics among Foreign-born Persons in the United States. Journal of Acquired Immune Deficiency Syndromes (1999). PMID 28902072 DOI: 10.1097/Qai.0000000000001541  1
2017 Chaillon A, Nakazawa M, Wertheim JO, Little SJ, Smith DM, Mehta SR, Gianella S. No Substantial Evidence for Sexual Transmission of Minority HIV Drug Resistance Mutations in Men Who Have Sex with Men. Journal of Virology. PMID 28794047 DOI: 10.1128/Jvi.00769-17  1
2017 Forrester NL, Wertheim JO, Dugan VG, Auguste AJ, Lin D, Adams AP, Chen R, Gorchakov R, Leal G, Estrada-Franco JG, Pandya J, Halpin RA, Hari K, Jain R, Stockwell TB, et al. Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas. Plos Neglected Tropical Diseases. 11: e0005693. PMID 28771475 DOI: 10.1371/Journal.Pntd.0005693  1
2017 Chaillon A, Avila-Ríos S, Wertheim JO, Dennis A, García-Morales C, Tapia-Trejo D, Mejía-Villatoro C, Pascale JM, Porras-Cortés G, Quant-Durán CJ, Lorenzana I, Meza RI, Palou EY, Manzanero M, Cedillos RA, et al. Identification of major routes of HIV transmission throughout Mesoamerica. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. PMID 28645708 DOI: 10.1016/J.Meegid.2017.06.021  1
2017 Wertheim JO, Oster AM, Johnson JA, Switzer WM, Saduvala N, Hernandez AL, Hall HI, Heneine W. Transmission fitness of drug-resistant HIV revealed in a surveillance system transmission network. Virus Evolution. 3: vex008. PMID 28458918 DOI: 10.1093/Ve/Vex008  1
2017 Ahn MY, Wertheim JO, Kim WJ, Kim SW, Lee JS, Ann HW, Jeon Y, Ahn JY, Song JE, Oh DH, Kim YC, Kim EJ, Jung IY, Kim MH, Jeong W, et al. HIV-1 Transmission Networks Across South Korea. Aids Research and Human Retroviruses. PMID 28346838 DOI: 10.1089/Aid.2016.0212  1
2017 Oster AM, Switzer WM, Hernandez AL, Saduvala N, Wertheim JO, Nwangwu-Ike N, Ocfemia MC, Campbell E, Hall HI. Increasing HIV-1 subtype diversity in seven states, United States, 2006-2013. Annals of Epidemiology. PMID 28318764 DOI: 10.1016/J.Annepidem.2017.02.002  1
2017 Wertheim JO. Viral Evolution: Mummy Virus Challenges Presumed History of Smallpox. Current Biology : Cb. 27: R119-R120. PMID 28171759 DOI: 10.1016/J.Cub.2016.12.008  0.01
2017 Wertheim JO, Kosakovsky Pond SL, Forgione LA, Mehta SR, Murrell B, Shah S, Smith DM, Scheffler K, Torian LV. Social and Genetic Networks of HIV-1 Transmission in New York City. Plos Pathogens. 13: e1006000. PMID 28068413 DOI: 10.1371/Journal.Ppat.1006000  1
2016 Bartlett SR, Wertheim JO, Bull RA, Matthews GV, Lamoury FM, Scheffler K, Hellard M, Maher L, Dore GJ, Lloyd AR, Applegate TL, Grebely J. A molecular transmission network of recent hepatitis C infection in people with and without HIV: Implications for targeted treatment strategies. Journal of Viral Hepatitis. PMID 27882678 DOI: 10.1111/Jvh.12652  1
2016 Rose R, Lamers SL, Dollar JJ, Grabowski M, Hodcroft EB, Ragonnet-Cronin M, Wertheim JO, Redd AD, German D, Laeyendecker O. Identifying transmission clusters with Cluster Picker and HIV-TRACE. Aids Research and Human Retroviruses. PMID 27824249 DOI: 10.1089/Aid.2016.0205  1
2016 Pines HA, Wertheim JO, Liu L, Garfein RS, Little SJ, Karris MY. Concurrency and HIV transmission network characteristics among men who have sex with men with recent HIV infection. Aids (London, England). PMID 27662550 DOI: 10.1097/Qad.0000000000001256  1
2016 Madinda NF, Ehlers B, Wertheim JO, Akoua-Koffi C, Bergl RA, Boesch C, Boji Mungu Akonkwa D, Eckardt W, Fruth B, Gillespie TR, Gray M, Hohmann G, Karhemere S, Kujirakwinja D, Langergraber K, et al. Assessing host-virus co-divergence for close relatives of Merkel cell polyomavirus infecting African great apes. Journal of Virology. PMID 27440885 DOI: 10.1128/Jvi.00247-16  0.01
2016 Murrell B, Vollbrecht T, Guatelli J, Wertheim JO. The Evolutionary Histories of Antiretroviral Proteins SERINC3 and SERINC5 Do Not Support an Evolutionary Arms Race in Primates. Journal of Virology. PMID 27356902 DOI: 10.1128/Jvi.00972-16  1
2016 Mehta SR, Murrell B, Anderson CM, Kosakovsky Pond SL, Wertheim JO, Young JA, Freitas L, Richman DD, Mathews WC, Scheffler K, Little SJ, Smith DM. Using HIV Sequence and Epidemiologic Data to Assess the Effect of Self-referral Testing for Acute HIV Infection on Incident Diagnoses in San Diego, California. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 27174704 DOI: 10.1093/Cid/Ciw161  1
2016 Wertheim JO, Oster AM, Hernandez AL, Saduvala N, Bañez Ocfemia MC, Hall I. The International Dimension of the U.S. HIV Transmission Network and Onward Transmission of HIV Recently Imported into the United States. Aids Research and Human Retroviruses. PMID 27105549 DOI: 10.1089/AID.2015.0272  1
2016 Chin BS, Chaillon A, Mehta SR, Wertheim JO, Kim G, Shin HS, Smith DM. Molecular epidemiology identifies HIV transmission networks associated with younger age and heterosexual exposure among Korean individuals. Journal of Medical Virology. PMID 26990771 DOI: 10.1002/Jmv.24523  1
2016 Yebra G, Ragonnet-Cronin M, Ssemwanga D, Parry CM, Logue C, Wertheim JO, Cane PA, Kaleebu P, Brown AL. Inclusion of old sequences improves the estimation of evolutionary parameters from deep-rooted HIV epidemics F1000research. 5. DOI: 10.7490/F1000Research.1111351.1  1
2015 Mehta SR, Wertheim JO, Brouwer KC, Wagner KD, Chaillon A, Strathdee S, Patterson TL, Rangel MG, Vargas M, Murrell B, Garfein R, Little SJ, Smith DM. HIV Transmission Networks in the San Diego-Tijuana Border Region. Ebiomedicine. 2: 1456-63. PMID 26629540 DOI: 10.1016/J.Ebiom.2015.07.024  1
2015 Whiteside YO, Song R, Wertheim JO, Oster AM. Molecular analysis allows inference into HIV transmission among young men who have sex with men in the United States. Aids (London, England). 29: 2517-22. PMID 26558547 DOI: 10.1097/Qad.0000000000000852  1
2015 Panichsillapakit T, Smith DM, Wertheim JO, Richman DD, Little SJ, Mehta SR. Prevalence of transmitted HIV drug resistance among recently infected persons in San Diego, California 1996-2013. Journal of Acquired Immune Deficiency Syndromes (1999). PMID 26413846 DOI: 10.1097/Qai.0000000000000831  1
2015 Oster AM, Wertheim JO, Hernandez AL, Ocfemia MC, Saduvala N, Hall HI. Using Molecular HIV Surveillance Data to Understand Transmission Between Subpopulations in the United States. Journal of Acquired Immune Deficiency Syndromes (1999). 70: 444-51. PMID 26302431 DOI: 10.1097/QAI.0000000000000809  1
2015 Wang X, Wu Y, Mao L, Xia W, Zhang W, Dai L, Mehta SR, Wertheim JO, Dong X, Zhang T, Wu H, Smith DM. Targeting Prevention based on Molecular Epidemiology among Deeply Sampled Sub-Networks of Men Have who Sex with Men. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 26129754 DOI: 10.1093/Cid/Civ526  1
2015 Gianella S, Massanella M, Wertheim JO, Smith DM. The Sordid Affair Between Human Herpesvirus and HIV. The Journal of Infectious Diseases. PMID 25748324 DOI: 10.1093/Infdis/Jiv148  1
2015 Murrell B, Weaver S, Smith MD, Wertheim JO, Murrell S, Aylward A, Eren K, Pollner T, Martin DP, Smith DM, Scheffler K, Kosakovsky Pond SL. Gene-wide identification of episodic selection. Molecular Biology and Evolution. 32: 1365-71. PMID 25701167 DOI: 10.1093/Molbev/Msv035  1
2015 Smith MD, Wertheim JO, Weaver S, Murrell B, Scheffler K, Kosakovsky Pond SL. Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection. Molecular Biology and Evolution. 32: 1342-53. PMID 25697341 DOI: 10.1093/Molbev/Msv022  1
2015 Wertheim JO, Murrell B, Smith MD, Kosakovsky Pond SL, Scheffler K. RELAX: detecting relaxed selection in a phylogenetic framework. Molecular Biology and Evolution. 32: 820-32. PMID 25540451 DOI: 10.1093/Molbev/Msu400  1
2015 Mehta SR, Wertheim JO, Brouwer KC, Wagner KD, Chaillon A, Strathdee S, Patterson TL, Rangel MG, Vargas M, Murrell B, Garfein R, Little SJ, Smith DM. HIV Transmission Networks in the San Diego-Tijuana Border Region Ebiomedicine. DOI: 10.1016/j.ebiom.2015.07.024  1
2014 Wertheim JO, Smith MD, Smith DM, Scheffler K, Kosakovsky Pond SL. Evolutionary origins of human herpes simplex viruses 1 and 2. Molecular Biology and Evolution. 31: 2356-64. PMID 24916030 DOI: 10.1093/Molbev/Msu185  1
2014 Little SJ, Kosakovsky Pond SL, Anderson CM, Young JA, Wertheim JO, Mehta SR, May S, Smith DM. Using HIV networks to inform real time prevention interventions. Plos One. 9: e98443. PMID 24901437 DOI: 10.1371/Journal.Pone.0098443  1
2014 Benndorf R, Martin JL, Kosakovsky Pond SL, Wertheim JO. Neuropathy- and myopathy-associated mutations in human small heat shock proteins: Characteristics and evolutionary history of the mutation sites. Mutation Research. Reviews in Mutation Research. PMID 24607769 DOI: 10.1016/J.Mrrev.2014.02.004  1
2014 Chaillon A, Gianella S, Wertheim JO, Richman DD, Mehta SR, Smith DM. HIV migration between blood and cerebrospinal fluid or semen over time. The Journal of Infectious Diseases. 209: 1642-52. PMID 24302756 DOI: 10.1093/Infdis/Jit678  1
2014 Wertheim JO, Leigh Brown AJ, Hepler NL, Mehta SR, Richman DD, Smith DM, Kosakovsky Pond SL. The global transmission network of HIV-1. The Journal of Infectious Diseases. 209: 304-13. PMID 24151309 DOI: 10.1093/Infdis/Jit524  1
2013 Chaillon A, Wagner GA, Hepler NL, Little SJ, Kosakovsky Pond SL, Caballero G, Pacold ME, Phung P, Wrin T, Richman DD, Wertheim JO, Smith DM. Dynamics of viral evolution and neutralizing antibody response after HIV-1 superinfection. Journal of Virology. 87: 12737-44. PMID 24049166 DOI: 10.1128/Jvi.02260-13  1
2013 Wertheim JO, Chu DK, Peiris JS, Kosakovsky Pond SL, Poon LL. A case for the ancient origin of coronaviruses. Journal of Virology. 87: 7039-45. PMID 23596293 DOI: 10.1128/Jvi.03273-12  1
2013 Koeppel AF, Wertheim JO, Barone L, Gentile N, Krizanc D, Cohan FM. Speedy speciation in a bacterial microcosm: new species can arise as frequently as adaptations within a species. The Isme Journal. 7: 1080-91. PMID 23364353 DOI: 10.1038/Ismej.2013.3  1
2013 Wertheim JO, Scheffler K, Choi JY, Smith DM, Kosakovsky Pond SL. Phylogenetic relatedness of HIV-1 donor and recipient populations. The Journal of Infectious Diseases. 207: 1181-2. PMID 23315327 DOI: 10.1093/Infdis/Jit021  1
2012 Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, Kosakovsky Pond SL. Detecting individual sites subject to episodic diversifying selection. Plos Genetics. 8: e1002764. PMID 22807683 DOI: 10.1371/Journal.Pgen.1002764  1
2012 Wertheim JO, Fourment M, Kosakovsky Pond SL. Inconsistencies in estimating the age of HIV-1 subtypes due to heterotachy. Molecular Biology and Evolution. 29: 451-6. PMID 22045998 DOI: 10.1093/Molbev/Msr266  1
2011 Wertheim JO, Kosakovsky Pond SL, Little SJ, De Gruttola V. Using HIV transmission networks to investigate community effects in HIV prevention trials. Plos One. 6: e27775. PMID 22114692 DOI: 10.1371/Journal.Pone.0027775  1
2011 Wertheim JO, Kosakovsky Pond SL. Purifying selection can obscure the ancient age of viral lineages. Molecular Biology and Evolution. 28: 3355-65. PMID 21705379 DOI: 10.1093/Molbev/Msr170  1
2011 Mehta SR, Wertheim JO, Delport W, Ene L, Tardei G, Duiculescu D, Pond SL, Smith DM. Using phylogeography to characterize the origins of the HIV-1 subtype F epidemic in Romania. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 11: 975-9. PMID 21439403 DOI: 10.1016/J.Meegid.2011.03.009  1
2011 Wertheim JO, Sanderson MJ. Estimating diversification rates: how useful are divergence times? Evolution; International Journal of Organic Evolution. 65: 309-20. PMID 21044059 DOI: 10.1111/J.1558-5646.2010.01159.X  1
2011 Bjork A, Liu W, Wertheim JO, Hahn BH, Worobey M. Evolutionary history of chimpanzees inferred from complete mitochondrial genomes. Molecular Biology and Evolution. 28: 615-23. PMID 20802239 DOI: 10.1093/Molbev/Msq227  1
2010 Wertheim JO. The re-emergence of H1N1 influenza virus in 1977: a cautionary tale for estimating divergence times using biologically unrealistic sampling dates. Plos One. 5: e11184. PMID 20567599 DOI: 10.1371/Journal.Pone.0011184  1
2010 Wertheim JO, Sanderson MJ, Worobey M, Bjork A. Relaxed molecular clocks, the bias-variance trade-off, and the quality of phylogenetic inference. Systematic Biology. 59: 1-8. PMID 20525616 DOI: 10.1093/Sysbio/Syp072  1
2009 Wertheim JO. When pigs fly: the avian origin of a 'swine flu'. Environmental Microbiology. 11: 2191-2. PMID 19737300 DOI: 10.1111/J.1462-2920.2009.02039.X  1
2009 Wertheim JO, Tang KF, Navarro SA, Lightner DV. A quick fuse and the emergence of Taura syndrome virus. Virology. 390: 324-9. PMID 19524995 DOI: 10.1016/J.Virol.2009.05.010  1
2009 Wertheim JO, Worobey M. Dating the age of the SIV lineages that gave rise to HIV-1 and HIV-2. Plos Computational Biology. 5: e1000377. PMID 19412344 DOI: 10.1371/Journal.Pcbi.1000377  1
2009 Wertheim JO, Worobey M. Relaxed selection and the evolution of RNA virus mucin-like pathogenicity factors. Journal of Virology. 83: 4690-4. PMID 19224988 DOI: 10.1128/Jvi.02358-08  1
2007 Wertheim JO, Worobey M. A challenge to the ancient origin of SIVagm based on African green monkey mitochondrial genomes. Plos Pathogens. 3: e95. PMID 17616975 DOI: 10.1371/Journal.Ppat.0030095  1
2007 Worobey M, Bjork A, Wertheim JO. Point, counterpoint: The evolution of pathogenic viruses and their human hosts Annual Review of Ecology, Evolution, and Systematics. 38: 515-540. DOI: 10.1146/Annurev.Ecolsys.38.091206.095722  1
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