Joel Wertheim

TitleAssistant Adjunct Professor
InstitutionUniversity of California San Diego
Address200 W. Arbor Drive #8208
San Diego CA 92103
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    Collapse Research 
    Collapse Research Activities and Funding
    Automation and Evaluation of Real-Time Transmission Network-Based HIV Prevention Services in New York City
    NIH/NIAID R01AI135992Jan 24, 2018 - Dec 31, 2022
    Role: Principal Investigator
    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 
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    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. 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. J Biol Chem. 2018 Aug 22. PMID: 30135209.
      View in: PubMed
    2. 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. J Infect Dis. 2018 Jul 14. PMID: 30010850.
      View in: PubMed
    3. 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. Mol Biol Evol. 2018 Jan 31. PMID: 29401317.
      View in: PubMed
    4. Chaillon A, Gianella S, Lada SM, Perez-Santiago J, Jordan P, Ignacio C, Karris M, Richman DD, Mehta SR, Little SJ, Wertheim JO, Smith DM. Size, Composition, and Evolution of HIV DNA Populations during Early Antiretroviral Therapy and Intensification with Maraviroc. J Virol. 2018 Feb 01; 92(3). PMID: 29142136.
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    5. Valverde EE, Oster AM, Xu S, Wertheim JO, Hernandez AL. HIV Transmission Dynamics Among Foreign-Born Persons in the United States. J Acquir Immune Defic Syndr. 2017 12 15; 76(5):445-452. PMID: 28902072.
      View in: PubMed
    6. 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. J Virol. 2017 11 01; 91(21). PMID: 28794047.
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    7. 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, 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.
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    8. 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, Reyes-Terán G, Mehta SR. Identification of major routes of HIV transmission throughout Mesoamerica. Infect Genet Evol. 2017 10; 54:98-107. PMID: 28645708.
      View in: PubMed
    9. 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 Evol. 2017 Jan; 3(1):vex008. PMID: 28458918.
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    10. 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, 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.
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    11. 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. Ann Epidemiol. 2017 Apr; 27(4):244-251.e1. PMID: 28318764.
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    12. Wertheim JO. Viral Evolution: Mummy Virus Challenges Presumed History of Smallpox. Curr Biol. 2017 Feb 06; 27(3):R119-R120. PMID: 28171759.
      View in: PubMed
    13. 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 Pathog. 2017 Jan; 13(1):e1006000. PMID: 28068413.
      View in: PubMed
    14. 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. Rom Biotechnol Lett. 2017 Jan-Feb; 22(1):12307-12315. PMID: 29213206.
      View in: PubMed
    15. Rose R, Lamers SL, Dollar JJ, Grabowski MK, Hodcroft EB, Ragonnet-Cronin M, Wertheim JO, Redd AD, German D, Laeyendecker O. Identifying Transmission Clusters with Cluster Picker and HIV-TRACE. AIDS Res Hum Retroviruses. 2017 03; 33(3):211-218. PMID: 27824249.
      View in: PubMed
    16. Pines HA, Wertheim JO, 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
    17. 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. J Viral Hepat. 2017 May; 24(5):404-411. PMID: 27882678.
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    18. Madinda NF, Ehlers B, Wertheim JO, 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 10 01; 90(19):8531-41. PMID: 27440885; PMCID: PMC5021428 [Available on 03/12/17].
    19. 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. J Virol. 2016 09 15; 90(18):8085-9. PMID: 27356902; PMCID: PMC5008085 [Available on 02/26/17].
    20. Wertheim JO, 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.
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    21. 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. Clin Infect Dis. 2016 Jul 01; 63(1):101-107. PMID: 27174704; PMCID: PMC4901863 [Available on 07/01/17].
    22. 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. J Med Virol. 2016 10; 88(10):1832-5. PMID: 26990771; PMCID: PMC4969179 [Available on 10/01/17].
    23. 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, CA 1996-2013. J Acquir Immune Defic Syndr. 2016 Feb 01; 71(2):228-36. PMID: 26413846; PMCID: PMC4712087 [Available on 02/01/17].
    24. 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. J Acquir Immune Defic Syndr. 2015 Dec 01; 70(4):444-51. PMID: 26302431; PMCID: PMC4878401 [Available on 12/01/16].
    25. 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. 2015 Nov 28; 29(18):2517-22. PMID: 26558547; PMCID: PMC4862399.
    26. 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. 2015 Oct; 2(10):1456-63. PMID: 26629540; PMCID: PMC4634195.
    27. 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 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].
    28. Gianella S, Massanella M, Wertheim JO, Smith DM. The Sordid Affair Between Human Herpesvirus and HIV. J Infect Dis. 2015 Sep 15; 212(6):845-52. PMID: 25748324; PMCID: PMC4548466.
    29. 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. Mol Biol Evol. 2015 May; 32(5):1342-53. PMID: 25697341; PMCID: PMC4408413.
    30. 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. Mol Biol Evol. 2015 May; 32(5):1365-71. PMID: 25701167; PMCID: PMC4408417.
    31. Wertheim JO, 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.
    32. Wertheim JO, 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.
    33. 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. 2014; 9(6):e98443. PMID: 24901437; PMCID: PMC4047027.
    34. 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. Mutat Res Rev Mutat Res. 2014 Mar 06. PMID: 24607769.
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    35. Chaillon A, Gianella S, Wertheim JO, 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.
    36. Wertheim JO, 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.
      View in: PubMed
    37. 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. J Virol. 2013 Dec; 87(23):12737-44. PMID: 24049166; PMCID: PMC3838120.
    38. Wertheim JO, 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.
    39. 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. ISME J. 2013 Jun; 7(6):1080-91. PMID: 23364353; PMCID: PMC3660680.
    40. Wertheim JO, 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.
    41. Murrell B, Wertheim JO, 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.
    42. Wertheim JO, 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.
    43. Wertheim JO, 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.
    44. Wertheim JO, 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.
    45. 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. Infect Genet Evol. 2011 Jul; 11(5):975-9. PMID: 21439403; PMCID: PMC3104099.
    46. Wertheim JO, Sanderson MJ. Estimating diversification rates: how useful are divergence times? Evolution. 2011 Feb; 65(2):309-20. PMID: 21044059; PMCID: PMC3057369.
    47. Bjork A, Liu W, Wertheim JO, 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.
    48. 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. 2010 Jun 17; 5(6):e11184. PMID: 20567599; PMCID: PMC2887442.
    49. Wertheim JO, 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.
    50. Wertheim JO. When pigs fly: the avian origin of a 'swine flu'. Environ Microbiol. 2009 Sep; 11(9):2191-2. PMID: 19737300.
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    51. Wertheim JO, 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
    52. Wertheim JO, 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.
    53. Wertheim JO, 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.
    54. Wertheim JO, 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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