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    Joel Wertheim

    TitleAssistant Adjunct Professor
    SchoolUniversity of California, San Diego
    DepartmentMedicine
    Address200 W. Arbor Drive #8208
    CA San Diego 92103
    Phone619-543-5065
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      Collapse Research 
      Collapse Research Activities and Funding
      Inferring physico-chemical constraints at individual sites in protein evolution
      NIH/NIAID R21AI115701Jul 15, 2015 - Jun 30, 2017
      Role: Principal Investigator
      Public Health Implications of HIV Transmission Networks
      NIH/NIAID K01AI110181Jun 4, 2014 - May 31, 2019
      Role: Principal Investigator

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Valverde EE, Oster AM, Xu S, Wertheim J, Hernandez AL. HIV Transmission Dynamics among Foreign-born Persons in the United States. J Acquir Immune Defic Syndr. 2017 Sep 07. PMID: 28902072.
        View in: PubMed
      2. Chaillon A, Nakazawa M, Wertheim J, 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. J Virol. 2017 Aug 09. PMID: 28794047.
        View in: PubMed
      3. Forrester NL, Wertheim J, 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, Das SR, Wentworth DE, Smith MD, Kosakovsky Pond SL, Weaver SC. Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas. PLoS Negl Trop Dis. 2017 Aug; 11(8):e0005693. PMID: 28771475.
        View in: PubMed
      4. Chaillon A, Avila-Ríos S, Wertheim J, 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, Reyes-Terán G, Mehta SR. Identification of major routes of HIV transmission throughout Mesoamerica. Infect Genet Evol. 2017 Oct; 54:98-107. PMID: 28645708.
        View in: PubMed
      5. Wertheim J, 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 Evol. 2017 Jan; 3(1):vex008. PMID: 28458918.
        View in: PubMed
      6. Ahn MY, Wertheim J, 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, Jeong SJ, Ku NS, Kim JM, Smith DM, Choi JY. Short Communication: HIV-1 Transmission Networks Across South Korea. AIDS Res Hum Retroviruses. 2017 Aug; 33(8):827-831. PMID: 28346838.
        View in: PubMed
      7. Oster AM, Switzer WM, Hernandez AL, Saduvala N, Wertheim J, Nwangwu-Ike N, Ocfemia MC, Campbell E, Hall HI. Increasing HIV-1 subtype diversity in seven states, United States, 2006-2013. Ann Epidemiol. 2017 Apr; 27(4):244-251.e1. PMID: 28318764.
        View in: PubMed
      8. Wertheim J. Viral Evolution: Mummy Virus Challenges Presumed History of Smallpox. Curr Biol. 2017 Feb 06; 27(3):R119-R120. PMID: 28171759.
        View in: PubMed
      9. Wertheim J, 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 Pathog. 2017 Jan; 13(1):e1006000. PMID: 28068413.
        View in: PubMed
      10. Rose R, Lamers SL, Dollar JJ, Grabowski MK, Hodcroft EB, Ragonnet-Cronin M, Wertheim J, Redd AD, German D, Laeyendecker O. Identifying Transmission Clusters with Cluster Picker and HIV-TRACE. AIDS Res Hum Retroviruses. 2017 Mar; 33(3):211-218. PMID: 27824249.
        View in: PubMed
      11. Pines HA, Wertheim J, Liu L, Garfein RS, Little SJ, Karris MY. Concurrency and HIV transmission network characteristics among MSM with recent HIV infection. AIDS. 2016 Nov 28; 30(18):2875-2883. PMID: 27662550.
        View in: PubMed
      12. Madinda NF, Ehlers B, Wertheim J, Akoua-Koffi C, Bergl RA, Boesch C, Akonkwa DB, Eckardt W, Fruth B, Gillespie TR, Gray M, Hohmann G, Karhemere S, Kujirakwinja D, Langergraber K, Muyembe JJ, Nishuli R, Pauly M, Petrzelkova KJ, Robbins MM, Todd A, Schubert G, Stoinski TS, Wittig RM, Zuberbühler K, Peeters M, Leendertz FH, Calvignac-Spencer S. Assessing Host-Virus Codivergence for Close Relatives of Merkel Cell Polyomavirus Infecting African Great Apes. J Virol. 2016 Oct 01; 90(19):8531-41. PMID: 27440885; PMCID: PMC5021428 [Available on 03/12/17].
      13. Murrell B, Vollbrecht T, Guatelli J, Wertheim J. The Evolutionary Histories of Antiretroviral Proteins SERINC3 and SERINC5 Do Not Support an Evolutionary Arms Race in Primates. J Virol. 2016 Sep 15; 90(18):8085-9. PMID: 27356902; PMCID: PMC5008085 [Available on 02/26/17].
      14. Wertheim J, Oster AM, Hernandez AL, Saduvala N, Bañez Ocfemia MC, Hall HI. The International Dimension of the U.S. HIV Transmission Network and Onward Transmission of HIV Recently Imported into the United States. AIDS Res Hum Retroviruses. 2016 Oct/Nov; 32(10-11):1046-1053. PMID: 27105549.
        View in: PubMed
      15. Mehta SR, Murrell B, Anderson CM, Kosakovsky Pond SL, Wertheim J, 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. Clin Infect Dis. 2016 Jul 01; 63(1):101-107. PMID: 27174704; PMCID: PMC4901863 [Available on 07/01/17].
      16. Chin BS, Chaillon A, Mehta SR, Wertheim J, Kim G, Shin HS, Smith DM. Molecular epidemiology identifies HIV transmission networks associated with younger age and heterosexual exposure among Korean individuals. J Med Virol. 2016 Oct; 88(10):1832-5. PMID: 26990771.
        View in: PubMed
      17. Panichsillapakit T, Smith DM, Wertheim J, Richman DD, Little SJ, Mehta SR. Prevalence of Transmitted HIV Drug Resistance Among Recently Infected Persons in San Diego, CA 1996-2013. J Acquir Immune Defic Syndr. 2016 Feb 01; 71(2):228-36. PMID: 26413846; PMCID: PMC4712087 [Available on 02/01/17].
      18. Oster AM, Wertheim J, Hernandez AL, Ocfemia MC, Saduvala N, Hall HI. Using Molecular HIV Surveillance Data to Understand Transmission Between Subpopulations in the United States. J Acquir Immune Defic Syndr. 2015 Dec 01; 70(4):444-51. PMID: 26302431; PMCID: PMC4878401 [Available on 12/01/16].
      19. Whiteside YO, Song R, Wertheim J, Oster AM. Molecular analysis allows inference into HIV transmission among young men who have sex with men in the United States. AIDS. 2015 Nov 28; 29(18):2517-22. PMID: 26558547; PMCID: PMC4862399.
      20. Mehta SR, Wertheim J, 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. 2015 Oct; 2(10):1456-63. PMID: 26629540; PMCID: PMC4634195.
      21. Wang X, Wu Y, Mao L, Xia W, Zhang W, Dai L, Mehta SR, Wertheim J, Dong X, Zhang T, Wu H, Smith DM. Targeting HIV Prevention Based on Molecular Epidemiology Among Deeply Sampled Subnetworks of Men Who Have Sex With Men. Clin Infect Dis. 2015 Nov 01; 61(9):1462-8. PMID: 26129754; PMCID: PMC4599390 [Available on 11/01/16].
      22. Gianella S, Massanella M, Wertheim J, Smith DM. The Sordid Affair Between Human Herpesvirus and HIV. J Infect Dis. 2015 Sep 15; 212(6):845-52. PMID: 25748324; PMCID: PMC4548466.
      23. Murrell B, Weaver S, Smith MD, Wertheim J, Murrell S, Aylward A, Eren K, Pollner T, Martin DP, Smith DM, Scheffler K, Kosakovsky Pond SL. Gene-wide identification of episodic selection. Mol Biol Evol. 2015 May; 32(5):1365-71. PMID: 25701167; PMCID: PMC4408417.
      24. Smith MD, Wertheim J, 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. Mol Biol Evol. 2015 May; 32(5):1342-53. PMID: 25697341; PMCID: PMC4408413.
      25. Wertheim J, Murrell B, Smith MD, Kosakovsky Pond SL, Scheffler K. RELAX: detecting relaxed selection in a phylogenetic framework. Mol Biol Evol. 2015 Mar; 32(3):820-32. PMID: 25540451; PMCID: PMC4327161.
      26. Wertheim J, Smith MD, Smith DM, Scheffler K, Kosakovsky Pond SL. Evolutionary origins of human herpes simplex viruses 1 and 2. Mol Biol Evol. 2014 Sep; 31(9):2356-64. PMID: 24916030; PMCID: PMC4137711.
      27. Little SJ, Kosakovsky Pond SL, Anderson CM, Young JA, Wertheim J, Mehta SR, May S, Smith DM. Using HIV networks to inform real time prevention interventions. PLoS One. 2014; 9(6):e98443. PMID: 24901437; PMCID: PMC4047027.
      28. Benndorf R, Martin JL, Kosakovsky Pond SL, Wertheim J. Neuropathy- and myopathy-associated mutations in human small heat shock proteins: Characteristics and evolutionary history of the mutation sites. Mutat Res Rev Mutat Res. 2014 Mar 06. PMID: 24607769.
        View in: PubMed
      29. Chaillon A, Gianella S, Wertheim J, Richman DD, Mehta SR, Smith DM. HIV migration between blood and cerebrospinal fluid or semen over time. J Infect Dis. 2014 May 15; 209(10):1642-52. PMID: 24302756; PMCID: PMC3997580.
      30. Wertheim J, Leigh Brown AJ, Hepler NL, Mehta SR, Richman DD, Smith DM, Kosakovsky Pond SL. The global transmission network of HIV-1. J Infect Dis. 2014 Jan 15; 209(2):304-13. PMID: 24151309; PMCID: PMC3873788.
      31. Chaillon A, Wagner GA, Hepler NL, Little SJ, Kosakovsky Pond SL, Caballero G, Pacold ME, Phung P, Wrin T, Richman DD, Wertheim J, Smith DM. Dynamics of viral evolution and neutralizing antibody response after HIV-1 superinfection. J Virol. 2013 Dec; 87(23):12737-44. PMID: 24049166; PMCID: PMC3838120.
      32. Wertheim J, Chu DK, Peiris JS, Kosakovsky Pond SL, Poon LL. A case for the ancient origin of coronaviruses. J Virol. 2013 Jun; 87(12):7039-45. PMID: 23596293; PMCID: PMC3676139.
      33. Koeppel AF, Wertheim J, 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. ISME J. 2013 Jun; 7(6):1080-91. PMID: 23364353; PMCID: PMC3660680.
      34. Wertheim J, Scheffler K, Choi JY, Smith DM, Kosakovsky Pond SL. Phylogenetic relatedness of HIV-1 donor and recipient populations. J Infect Dis. 2013 Apr; 207(7):1181-2. PMID: 23315327; PMCID: PMC3583277.
      35. Murrell B, Wertheim J, Moola S, Weighill T, Scheffler K, Kosakovsky Pond SL. Detecting individual sites subject to episodic diversifying selection. PLoS Genet. 2012; 8(7):e1002764. PMID: 22807683; PMCID: PMC3395634.
      36. Wertheim J, Kosakovsky Pond SL, Little SJ, De Gruttola V. Using HIV transmission networks to investigate community effects in HIV prevention trials. PLoS One. 2011; 6(11):e27775. PMID: 22114692; PMCID: PMC3218056.
      37. Wertheim J, Fourment M, Kosakovsky Pond SL. Inconsistencies in estimating the age of HIV-1 subtypes due to heterotachy. Mol Biol Evol. 2012 Feb; 29(2):451-6. PMID: 22045998; PMCID: PMC3258043.
      38. Wertheim J, Kosakovsky Pond SL. Purifying selection can obscure the ancient age of viral lineages. Mol Biol Evol. 2011 Dec; 28(12):3355-65. PMID: 21705379; PMCID: PMC3247791.
      39. Mehta SR, Wertheim J, 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. Infect Genet Evol. 2011 Jul; 11(5):975-9. PMID: 21439403; PMCID: PMC3104099.
      40. Wertheim J, Sanderson MJ. Estimating diversification rates: how useful are divergence times? Evolution. 2011 Feb; 65(2):309-20. PMID: 21044059; PMCID: PMC3057369.
      41. Bjork A, Liu W, Wertheim J, Hahn BH, Worobey M. Evolutionary history of chimpanzees inferred from complete mitochondrial genomes. Mol Biol Evol. 2011 Jan; 28(1):615-23. PMID: 20802239; PMCID: PMC3108604.
      42. Wertheim J. The re-emergence of H1N1 influenza virus in 1977: a cautionary tale for estimating divergence times using biologically unrealistic sampling dates. PLoS One. 2010 Jun 17; 5(6):e11184. PMID: 20567599; PMCID: PMC2887442.
      43. Wertheim J, Sanderson MJ, Worobey M, Bjork A. Relaxed molecular clocks, the bias-variance trade-off, and the quality of phylogenetic inference. Syst Biol. 2010 Jan; 59(1):1-8. PMID: 20525616; PMCID: PMC2909785.
      44. Wertheim J. When pigs fly: the avian origin of a 'swine flu'. Environ Microbiol. 2009 Sep; 11(9):2191-2. PMID: 19737300.
        View in: PubMed
      45. Wertheim J, Tang KF, Navarro SA, Lightner DV. A quick fuse and the emergence of Taura syndrome virus. Virology. 2009 Aug 01; 390(2):324-9. PMID: 19524995.
        View in: PubMed
      46. Wertheim J, Worobey M. Dating the age of the SIV lineages that gave rise to HIV-1 and HIV-2. PLoS Comput Biol. 2009 May; 5(5):e1000377. PMID: 19412344; PMCID: PMC2669881.
      47. Wertheim J, Worobey M. Relaxed selection and the evolution of RNA virus mucin-like pathogenicity factors. J Virol. 2009 May; 83(9):4690-4. PMID: 19224988; PMCID: PMC2668480.
      48. Wertheim J, Worobey M. A challenge to the ancient origin of SIVagm based on African green monkey mitochondrial genomes. PLoS Pathog. 2007 Jul; 3(7):e95. PMID: 17616975; PMCID: PMC1904472.
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