Joel Wertheim

Title(s)Adjunct Professor, Medicine
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    Collapse Biography 
    Collapse Education and Training
    University of Arizona, Tucson, AZPhD2009Ecology and Evolutionary Biology
    Wesleyan University, Middletown, CTBA2004Biology

    Collapse Research 
    Collapse Research Activities and Funding
    Secure HIV-TRACE Operation and Maintenance (O&M), and Development, Modernization, and Enhancement (DME)
    CDC 75D30123C17580Sep 11, 2023 - Sep 10, 2026
    Role: Principal Investigator
    Secure HIV-TRACE Operation and Maintenance (O&M), and Development, Modernization, and Enhancement (DME)
    CDC 75D30119C04031Jun 15, 2019 - Sep 10, 2023
    Role: Principal Investigator
    Next-Generation Phylodynamics-targeted Partner Service Models for Combined HIV Prevention
    NIH R01AI136056Feb 6, 2018 - Jan 31, 2024
    Role: Site-Principal Investigator
    Automation and Evaluation of Real-Time Transmission Network-Based HIV Prevention Services in New York City
    NIH R01AI135992Jan 24, 2018 - Dec 31, 2022
    Role: Principal Investigator
    Inferring physico-chemical constraints at individual sites in protein evolution
    NIH R21AI115701Jul 15, 2015 - Jun 30, 2018
    Role: Principal Investigator
    Public Health Implications of HIV Transmission Networks
    NIH K01AI110181Jun 4, 2014 - May 31, 2020
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications

    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic. Cell. 2024 Sep 19; 187(19):5468-5482.e11. Crits-Christoph A, Levy JI, Pekar JE, Goldstein SA, Singh R, Hensel Z, Gangavarapu K, Rogers MB, Moshiri N, Garry RF, Holmes EC, Koopmans MPG, Lemey P, Peacock TP, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KG, Worobey M, Débarre F. PMID: 39303692; PMCID: PMC11427129.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    2. Random-Effects Substitution Models for Phylogenetics via Scalable Gradient Approximations. Syst Biol. 2024 Sep 05; 73(3):562-578. Magee AF, Holbrook AJ, Pekar JE, Caviedes-Solis IW, Matsen Iv FA, Baele G, Wertheim JO, Ji X, Lemey P, Suchard MA. PMID: 38712512; PMCID: PMC11498053.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    3. Genomic epidemiology reveals 2022 mpox epidemic in New York City governed by heavy-tailed sexual contact networks. medRxiv. 2024 Aug 01. Pekar JE, Wang Y, Wang JC, Shao Y, Taki F, Forgione LA, Amin H, Clabby T, Johnson K, Torian LV, Braunstein SL, Pathela P, Omoregie E, Hughes S, Suchard MA, Vasylyeva TI, Lemey P, Wertheim JO. PMID: 39132479; PMCID: PMC11312668.
      View in: PubMed   Mentions:
    4. AUTO-TUNE: selecting the distance threshold for inferring HIV transmission clusters. Front Bioinform. 2024; 4:1400003. Weaver S, Dávila Conn VM, Ji D, Verdonk H, Ávila-Ríos S, Leigh Brown AJ, Wertheim JO, Kosakovsky Pond SL. PMID: 39086842; PMCID: PMC11289888.
      View in: PubMed   Mentions:
    5. The role of socio-economic disparities in the relative success and persistence of SARS-CoV-2 variants in New York City in early 2021. PLoS Pathog. 2024 Jun; 20(6):e1012288. Vasylyeva TI, Havens JL, Wang JC, Luoma E, Hassler GW, Amin H, Di Lonardo S, Taki F, Omoregie E, Hughes S, Wertheim JO. PMID: 38900824; PMCID: PMC11218943.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    6. Integrated Genomic and Social Network Analyses of SARS-CoV-2 Transmission in the Healthcare Setting. Clin Infect Dis. 2024 May 15; 78(5):1204-1213. Keehner J, Abeles SR, Longhurst CA, Horton LE, Myers FE, Riggs-Rodriguez L, Ahmad M, Baxter S, Boussina A, Cantrell K, Cardenas P, De Hoff P, El-Kareh R, Holland J, Ikeda D, Kurashige K, Laurent LC, SEARCH Alliance , Lucas A, Pride D, Sathe S, Tran AR, Vasylyeva TI, Yeo G, Knight R, Wertheim JO, Torriani FJ. PMID: 38227643; PMCID: PMC11093679.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCellsPHPublic Health
    7. Unveiling ecological/evolutionary insights in HIV viral load dynamics: Allowing random slopes to observe correlational changes to CpG-contents and other molecular and clinical predictors. Epidemics. 2024 Jun; 47:100770. Carrasco-Hernández R, Valenzuela-Ponce H, Soto-Nava M, García-Morales C, Matías-Florentino M, Wertheim JO, Smith DM, Reyes-Terán G, Ávila-Ríos S. PMID: 38761432; PMCID: PMC11213286.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    8. AUTO-TUNE: SELECTING THE DISTANCE THRESHOLD FOR INFERRING HIV TRANSMISSION CLUSTERS. bioRxiv. 2024 Mar 14. Weaver S, Dávila-Conn V, Ji D, Verdonk H, Ávila-Ríos S, Leigh Brown AJ, Wertheim JO, Kosakovsky Pond SL. PMID: 38559140; PMCID: PMC10979987.
      View in: PubMed   Mentions:
    9. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics. Cell. 2023 12 21; 186(26):5690-5704.e20. Matteson NL, Hassler GW, Kurzban E, Schwab MA, Perkins SA, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A, Rivera A, Wauer C, Holmes J, Wilson J, Ngo SN, Plascencia A, Lawrence ES, Smoot EW, Eisner ER, Tsai R, Chacón M, Baer NA, Seaver P, Salido RA, Aigner S, Ngo TT, Barber T, Ostrander T, Fielding-Miller R, Simmons EH, Zazueta OE, Serafin-Higuera I, Sanchez-Alavez M, Moreno-Camacho JL, García-Gil A, Murphy Schafer AR, McDonald E, Corrigan J, Malone JD, Stous S, Shah S, Moshiri N, Weiss A, Anderson C, Aceves CM, Spencer EG, Hufbauer EC, Lee JJ, King AJ, Ramesh KS, Nguyen KN, Saucedo K, Robles-Sikisaka R, Fisch KM, Gonias SL, Birmingham A, McDonald D, Karthikeyan S, Martin NK, Schooley RT, Negrete AJ, Reyna HJ, Chavez JR, Garcia ML, Cornejo-Bravo JM, Becker D, Isaksson M, Washington NL, Lee W, Garfein RS, Luna-Ruiz Esparza MA, Alcántar-Fernández J, Henson B, Jepsen K, Olivares-Flores B, Barrera-Badillo G, Lopez-Martínez I, Ramírez-González JE, Flores-León R, Kingsmore SF, Sanders A, Pradenas A, White B, Matthews G, Hale M, McLawhon RW, Reed SL, Winbush T, McHardy IH, Fielding RA, Nicholson L, Quigley MM, Harding A, Mendoza A, Bakhtar O, Browne SH, Olivas Flores J, Rincon Rodríguez DG, Gonzalez Ibarra M, Robles Ibarra LC, Arellano Vera BJ, Gonzalez Garcia J, Harvey-Vera A, Knight R, Laurent LC, Yeo GW, Wertheim JO, Ji X, Worobey M, Suchard MA, Andersen KG, Campos-Romero A, Wohl S, Zeller M. PMID: 38101407; PMCID: PMC10795731.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCellsPHPublic Health
    10. Optimizing ancestral trait reconstruction of large HIV Subtype C datasets through multiple-trait subsampling. Virus Evol. 2023; 9(2):vead069. Li X, Trovão NS, Wertheim JO, Baele G, de Bernardi Schneider A. PMID: 38046219; PMCID: PMC10691791.
      View in: PubMed   Mentions:
    11. Leveraging social networks for identification of people with HIV who are virally unsuppressed. AIDS. 2024 02 01; 38(2):245-254. Cummins B, Johnson K, Schneider JA, Del Vecchio N, Moshiri N, Wertheim JO, Goyal R, Skaathun B. PMID: 37890471; PMCID: PMC10843229.
      View in: PubMed   Mentions:    Fields:    Translation:HumansPHPublic Health
    12. Random-effects substitution models for phylogenetics via scalable gradient approximations. ArXiv. 2023 Sep 25. Magee AF, Holbrook AJ, Pekar JE, Caviedes-Solis IW, Iv FAM, Baele G, Wertheim JO, Ji X, Lemey P, Suchard MA. PMID: 36994154; PMCID: PMC10055484.
      View in: PubMed   Mentions:
    13. Recommendations on data sharing in HIV drug resistance research. PLoS Med. 2023 Sep; 20(9):e1004293. Inzaule SC, Siedner MJ, Little SJ, Avila-Rios S, Ayitewala A, Bosch RJ, Calvez V, Ceccherini-Silberstein F, Charpentier C, Descamps D, Eshleman SH, Fokam J, Frenkel LM, Gupta RK, Ioannidis JPA, Kaleebu P, Kantor R, Kassaye SG, Kosakovsky Pond SL, Kouamou V, Kouyos RD, Kuritzkes DR, Lessells R, Marcelin AG, Mbuagbaw L, Minalga B, Ndembi N, Neher RA, Paredes R, Pillay D, Raizes EG, Rhee SY, Richman DD, Ruxrungtham K, Sabeti PC, Schapiro JM, Sirivichayakul S, Steegen K, Sugiura W, van Zyl GU, Vandamme AM, Wensing AMJ, Wertheim JO, Gunthard HF, Jordan MR, Shafer RW. PMID: 37738247; PMCID: PMC10558071.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    14. Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic. bioRxiv. 2023 Sep 14. Crits-Christoph A, Levy JI, Pekar JE, Goldstein SA, Singh R, Hensel Z, Gangavarapu K, Rogers MB, Moshiri N, Garry RF, Holmes EC, Koopmans MPG, Lemey P, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KG, Worobey M, Débarre F. PMID: 37745602; PMCID: PMC10515900.
      View in: PubMed   Mentions: 1  
    15. The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2. bioRxiv. 2023 Jul 12. Pekar JE, Lytras S, Ghafari M, Magee AF, Parker E, Havens JL, Katzourakis A, Vasylyeva TI, Suchard MA, Hughes AC, Hughes J, Robertson DL, Dellicour S, Worobey M, Wertheim JO, Lemey P. PMID: 37502985; PMCID: PMC10369958.
      View in: PubMed   Mentions: 1  
    16. Hepatitis C Virus in people with experience of injection drug use following their displacement to Southern Ukraine before 2020. BMC Infect Dis. 2023 Jul 03; 23(1):446. Yakovleva A, Kovalenko G, Redlinger M, Smyrnov P, Tymets O, Korobchuk A, Kotlyk L, Kolodiazieva A, Podolina A, Cherniavska S, Antonenko P, Strathdee SA, Friedman SR, Goodfellow I, Wertheim JO, Bortz E, Meredith L, Vasylyeva TI. PMID: 37400776; PMCID: PMC10316605.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    17. Predictors of HIV Molecular Cluster Membership and Implications for Partner Services. AIDS Res Hum Retroviruses. 2023 05; 39(5):241-252. Hallmark CJ, Luswata C, Del Vecchio N, Hayford C, Mora R, Carr M, McNeese M, Benbow N, Schneider JA, Wertheim JO, Fujimoto K. PMID: 36785940; PMCID: PMC10171944.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    18. Author Correction: Tracking SARS-COV-2 variants using Nanopore sequencing in Ukraine in 2021. Sci Rep. 2023 Feb 13; 13(1):2555. Yakovleva A, Kovalenko G, Redlinger M, Liulchuk MG, Bortz E, Zadorozhna VI, Scherbinska AM, Wertheim JO, Goodfellow I, Meredith L, Vasylyeva TI. PMID: 36781923; PMCID: PMC9924184.
      View in: PubMed   Mentions:    Fields:    
    19. Phylodynamics and migration data help describe HIV transmission dynamics in internally displaced people who inject drugs in Ukraine. PNAS Nexus. 2023 Mar; 2(3):pgad008. Kovalenko G, Yakovleva A, Smyrnov P, Redlinger M, Tymets O, Korobchuk A, Kolodiazieva A, Podolina A, Cherniavska S, Skaathun B, Smith LR, Strathdee SA, Wertheim JO, Friedman SR, Bortz E, Goodfellow I, Meredith L, Vasylyeva TI. PMID: 36896134; PMCID: PMC9991454.
      View in: PubMed   Mentions: 4  
    20. Introduction and Establishment of SARS-CoV-2 Gamma Variant in New York City in Early 2021. J Infect Dis. 2022 12 13; 226(12):2142-2149. Vasylyeva TI, Fang CE, Su M, Havens JL, Parker E, Wang JC, Zeller M, Yakovleva A, Hassler GW, Chowdhury MA, Andersen KG, Hughes S, Wertheim JO. PMID: 35771664; PMCID: PMC9278250.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    21. Impact of molecular sequence data completeness on HIV cluster detection and a network science approach to enhance detection. Sci Rep. 2022 11 10; 12(1):19230. Mazrouee S, Hallmark CJ, Mora R, Del Vecchio N, Carrasco Hernandez R, Carr M, McNeese M, Fujimoto K, Wertheim JO. PMID: 36357480; PMCID: PMC9648870.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansPHPublic Health
    22. Tracking SARS-COV-2 variants using Nanopore sequencing in Ukraine in 2021. Sci Rep. 2022 09 21; 12(1):15749. Yakovleva A, Kovalenko G, Redlinger M, Liulchuk MG, Bortz E, Zadorozhna VI, Scherbinska AM, Wertheim JO, Goodfellow I, Meredith L, Vasylyeva TI. PMID: 36131001; PMCID: PMC9491264.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    23. Phylogeographic analysis reveals an ancient East African origin of human herpes simplex virus 2 dispersal out-of-Africa. Nat Commun. 2022 09 17; 13(1):5477. Havens JL, Calvignac-Spencer S, Merkel K, Burrel S, Boutolleau D, Wertheim JO. PMID: 36115862; PMCID: PMC9482657.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    24. Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions. Nat Commun. 2022 08 15; 13(1):4784. Parker E, Anderson C, Zeller M, Tibi A, Havens JL, Laroche G, Benlarbi M, Ariana A, Robles-Sikisaka R, Latif AA, Watts A, Awidi A, Jaradat SA, Gangavarapu K, Ramesh K, Kurzban E, Matteson NL, Han AX, Hughes LD, McGraw M, Spencer E, Nicholson L, Khan K, Suchard MA, Wertheim JO, Wohl S, Côté M, Abdelnour A, Andersen KG, Abu-Dayyeh I. PMID: 35970983; PMCID: PMC9376901.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCellsPHPublic Health
    25. The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic. Science. 2022 08 26; 377(6609):951-959. Worobey M, Levy JI, Malpica Serrano L, Crits-Christoph A, Pekar JE, Goldstein SA, Rasmussen AL, Kraemer MUG, Newman C, Koopmans MPG, Suchard MA, Wertheim JO, Lemey P, Robertson DL, Garry RF, Holmes EC, Rambaut A, Andersen KG. PMID: 35881010; PMCID: PMC9348750.
      View in: PubMed   Mentions: 115     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    26. The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2. Science. 2022 08 26; 377(6609):960-966. Pekar JE, Magee A, Parker E, Moshiri N, Izhikevich K, Havens JL, Gangavarapu K, Malpica Serrano LM, Crits-Christoph A, Matteson NL, Zeller M, Levy JI, Wang JC, Hughes S, Lee J, Park H, Park MS, Ching Zi Yan K, Lin RTP, Mat Isa MN, Noor YM, Vasylyeva TI, Garry RF, Holmes EC, Rambaut A, Suchard MA, Andersen KG, Worobey M, Wertheim JO. PMID: 35881005; PMCID: PMC9348752.
      View in: PubMed   Mentions: 80     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    27. Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City. Nat Commun. 2022 06 25; 13(1):3645. Wertheim JO, Wang JC, Leelawong M, Martin DP, Havens JL, Chowdhury MA, Pekar JE, Amin H, Arroyo A, Awandare GA, Chow HY, Gonzalez E, Luoma E, Morang'a CM, Nekrutenko A, Shank SD, Silver S, Quashie PK, Rakeman JL, Ruiz V, Torian LV, Vasylyeva TI, Kosakovsky Pond SL, Hughes S. PMID: 35752633; PMCID: PMC9233664.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    28. Establishing a framework towards monitoring HCV microelimination among men who have sex with men living with HIV in Germany: A modeling analysis. PLoS One. 2022; 17(5):e0267853. Marquez LK, Ingiliz P, Boesecke C, Krznaric I, Schewe K, Lutz T, Mauss S, Christensen S, Rockstroh JK, Jain S, He F, Wertheim JO, Martin NK. PMID: 35551326; PMCID: PMC9098082.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCellsPHPublic Health
    29. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nat Methods. 2022 04; 19(4):374-380. Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TT, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. PMID: 35396471; PMCID: PMC9467803.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCellsPHPublic Health
    30. Using molecular epidemiology to trace the history of the injection-related HIV epidemic in New York City, 1985-2019. AIDS. 2022 05 01; 36(6):889-895. Torian LV, Forgione L, Wertheim JO. PMID: 35212668; PMCID: PMC9566884.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    31. Accuracy in Near-Perfect Virus Phylogenies. Syst Biol. 2022 02 10; 71(2):426-438. Wertheim JO, Steel M, Sanderson MJ. PMID: 34398231; PMCID: PMC8385947.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    32. When viruses become more virulent. Science. 2022 02 04; 375(6580):493-494. Wertheim JO. PMID: 35113688.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    33. Forecasting HIV-1 Genetic Cluster Growth in Illinois,United States. J Acquir Immune Defic Syndr. 2022 01 01; 89(1):49-55. Ragonnet-Cronin M, Hayford C, D'Aquila R, Ma F, Ward C, Benbow N, Wertheim JO. PMID: 34878434; PMCID: PMC8667185.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    34. Do partner services linked to molecular clusters yield people with viremia or new HIV? AIDS. 2022 05 01; 36(6):845-852. Schneider JA, Hayford C, Hotton A, Tabidze I, Wertheim JO, Ramani S, Hallmark C, Morgan E, Janulis P, Khanna A, Ozik J, Fujimoto K, Flores R, D'aquila R, Benbow N. PMID: 34873085; PMCID: PMC9397139.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    35. Tracking SARS-COV-2 Variants Using Nanopore Sequencing in Ukraine in Summer 2021. Res Sq. 2021 Nov 30. Yakovleva A, Kovalenko G, Redlinger M, Liulchuk MG, Bortz E, Zadorozhna VI, Scherbinska AM, Wertheim JO, Goodfellow I, Meredith L, Vasylyeva TI. PMID: 34873595; PMCID: PMC8647652.
      View in: PubMed   Mentions:
    36. Characteristics and growth of the genetic HIV transmission network of Mexico City during 2020. J Int AIDS Soc. 2021 11; 24(11):e25836. Dávila-Conn V, García-Morales C, Matías-Florentino M, López-Ortiz E, Paz-Juárez HE, Beristain-Barreda Á, Cárdenas-Sandoval M, Tapia-Trejo D, López-Sánchez DM, Becerril-Rodríguez M, García-Esparza P, Macías-González I, Iracheta-Hernández P, Weaver S, Wertheim JO, Reyes-Terán G, González-Rodríguez A, Ávila-Ríos S. PMID: 34762774; PMCID: PMC8583431.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    37. Incorporating metadata in HIV transmission network reconstruction: A machine learning feasibility assessment. PLoS Comput Biol. 2021 09; 17(9):e1009336. Mazrouee S, Little SJ, Wertheim JO. PMID: 34550966; PMCID: PMC8457453.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    38. Prevalence of resistance-associated substitutions and phylogenetic analysis of hepatitis C virus infection in Russia. Int J Infect Dis. 2021 Dec; 113:36-42. Isakov V, Hedskog C, Wertheim JO, Hostager RE, Parhy B, Schneider AB, Suri V, Mo H, Geivandova N, Morozov V, Bessonova E, Gankina N, Zhdanov K, Abdurakhmanov D, Svarovskaia E. PMID: 34560266.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    39. The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Cell. 2021 09 30; 184(20):5189-5200.e7. Martin DP, Weaver S, Tegally H, San JE, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ, NGS-SA, COVID-19 Genomics UK (COG-UK), Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, Kosakovsky Pond SL. PMID: 34537136; PMCID: PMC8421097.
      View in: PubMed   Mentions: 144     Fields:    Translation:HumansCellsPHPublic Health
    40. The origins of SARS-CoV-2: A critical review. Cell. 2021 09 16; 184(19):4848-4856. Holmes EC, Goldstein SA, Rasmussen AL, Robertson DL, Crits-Christoph A, Wertheim JO, Anthony SJ, Barclay WS, Boni MF, Doherty PC, Farrar J, Geoghegan JL, Jiang X, Leibowitz JL, Neil SJD, Skern T, Weiss SR, Worobey M, Andersen KG, Garry RF, Rambaut A. PMID: 34480864; PMCID: PMC8373617.
      View in: PubMed   Mentions: 212     Fields:    Translation:HumansAnimalsCells
    41. Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Nat Commun. 2021 08 09; 12(1):4886. 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, Gaebler C, Caskey M, Nussenzweig MC, Keeffe JR, Bjorkman PJ. PMID: 34373458; PMCID: PMC8352861.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansCells
    42. The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. medRxiv. 2021 Jul 25. Martin DP, Weaver S, Tegally H, San EJ, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ, NGS-SA, COVID-19 Genomics UK (COG-UK), Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, Kosakovsky Pond SL. PMID: 33688681; PMCID: PMC7941658.
      View in: PubMed   Mentions: 1  
    43. Characterization of HIV Risk Behaviors and Clusters Using HIV-Transmission Cluster Engine Among a Cohort of Persons Living with HIV in Washington, DC. AIDS Res Hum Retroviruses. 2021 09; 37(9):706-715. Wilbourn B, Saafir-Callaway B, Jair K, Wertheim JO, Laeyendeker O, Jordan JA, Kharfen M, Castel A, DC Cohort Executive Committee. PMID: 34157853; PMCID: PMC8501467.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansPHPublic Health
    44. Discovery of Novel Herpes Simplexviruses in Wild Gorillas, Bonobos, and Chimpanzees Supports Zoonotic Origin of HSV-2. Mol Biol Evol. 2021 06 25; 38(7):2818-2830. 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, Kuehl H, Langergraber KE, Lee K, Madinda NF, Metzger S, Ormsby LJ, Robbins MM, Sommer V, Stoinski T, Wessling EG, Wittig RM, Yuh YG, Leendertz FH, Calvignac-Spencer S. PMID: 33720357; PMCID: PMC8233514.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    45. Author Correction: Methodological synthesis of Bayesian phylodynamics, HIV-TRACE, and GEE: HIV-1 transmission epidemiology in a racially/ethnically diverse Southern U.S. context. Sci Rep. 2021 May 10; 11(1):10336. 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. PMID: 33976320; PMCID: PMC8113263.
      View in: PubMed   Mentions:    Fields:    
    46. Interplay Between Geography and HIV Transmission Clusters in Los Angeles County. Open Forum Infect Dis. 2021 Jun; 8(6):ofab211. Skaathun B, Ragonnet-Cronin M, Poortinga K, Sheng Z, Hu YW, Wertheim JO. PMID: 34159215; PMCID: PMC8212943.
      View in: PubMed   Mentions: 2  
    47. Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. bioRxiv. 2021 Apr 22. 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, Gaebler C, Caskey M, Nussenzweig MC, Keeffe JR, Bjorkman PJ. PMID: 33907745; PMCID: PMC8077570.
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    48. Increasing Capacity to Detect Clusters of Rapid HIV Transmission in Varied Populations-United States. Viruses. 2021 03 30; 13(4). 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. PMID: 33808053; PMCID: PMC8066706.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCellsPHPublic Health
    49. Timing the SARS-CoV-2 index case in Hubei province. Science. 2021 04 23; 372(6540):412-417. Pekar J, Worobey M, Moshiri N, Scheffler K, Wertheim JO. PMID: 33737402; PMCID: PMC8139421.
      View in: PubMed   Mentions: 75     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    50. Sorting by Race/Ethnicity Across HIV Genetic Transmission Networks in Three Major Metropolitan Areas in the United States. AIDS Res Hum Retroviruses. 2021 10; 37(10):784-792. Ragonnet-Cronin M, Benbow N, Hayford C, Poortinga K, Ma F, Forgione LA, Sheng Z, Hu YW, Torian LV, Wertheim JO. PMID: 33349132; PMCID: PMC8573809.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    51. Methodological synthesis of Bayesian phylodynamics, HIV-TRACE, and GEE: HIV-1 transmission epidemiology in a racially/ethnically diverse Southern U.S. context. Sci Rep. 2021 02 08; 11(1):3325. 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. PMID: 33558579; PMCID: PMC7870963.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    52. Analysis of Hepatitis B Virus Genotype D in Greenland Suggests the Presence of a Novel Quasi-Subgenotype. Front Microbiol. 2020; 11:602296. de Bernardi Schneider A, Osiowy C, Hostager R, Krarup H, Børresen M, Tanaka Y, Morriseau T, Wertheim JO. PMID: 33519744; PMCID: PMC7843931.
      View in: PubMed   Mentions: 4  
    53. The Relationship Between the Human Immunodeficiency Virus-1 Transmission Network and the HIV Care Continuum in Los Angeles County. Clin Infect Dis. 2020 12 03; 71(9):e384-e391. Hassan A, De Gruttola V, Hu YW, Sheng Z, Poortinga K, Wertheim JO. PMID: 32020172; PMCID: PMC7904072.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    54. Timing the SARS-CoV-2 Index Case in Hubei Province. bioRxiv. 2020 Nov 24. Pekar J, Worobey M, Moshiri N, Scheffler K, Wertheim JO. PMID: 33269353; PMCID: PMC7709179.
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    55. Addressing Ethical Challenges in US-Based HIV Phylogenetic Research. J Infect Dis. 2020 11 13; 222(12):1997-2006. 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, Sweeney P, Torian LV, Wertheim JO. PMID: 32525980; PMCID: PMC7661760.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCellsPHPublic Health
    56. The emergence of SARS-CoV-2 in Europe and North America. Science. 2020 10 30; 370(6516):564-570. Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO, Lemey P. PMID: 32912998; PMCID: PMC7810038.
      View in: PubMed   Mentions: 234     Fields:    Translation:HumansCellsPHPublic Health
    57. A Glimpse Into the Origins of Genetic Diversity in the Severe Acute Respiratory Syndrome Coronavirus 2. Clin Infect Dis. 2020 07 28; 71(15):721-722. Wertheim JO. PMID: 32129842; PMCID: PMC7108145.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCellsPHPublic Health
    58. Incident infection in high-priority HIV molecular transmission clusters in the United States. AIDS. 2020 07 01; 34(8):1187-1193. Wertheim JO, Panneer N, France AM, Saduvala N, Oster AM. PMID: 32287065; PMCID: PMC8580737.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCellsPHPublic Health
    59. The emergence of SARS-CoV-2 in Europe and the US. bioRxiv. 2020 May 23. Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO, Lemey P. PMID: 32511416; PMCID: PMC7265688.
      View in: PubMed   Mentions: 1  
    60. Brief Report: Temporal Changes in HIV Transmission Patterns Among Young Men Who Have Sex With Men, United States, 2009-2016. J Acquir Immune Defic Syndr. 2020 05 01; 84(1):1-4. Panneer N, France AM, Whiteside YO, Zhang T, Wertheim JO, Oster AM. PMID: 31977598.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    61. Use of molecular HIV surveillance data and predictive modeling to prioritize persons for transmission-reduction interventions. AIDS. 2020 03 01; 34(3):459-467. Xia Q, Wertheim JO, Braunstein SL, Misra K, Udeagu CC, Torian LV. PMID: 31794522; PMCID: PMC8580888.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansPHPublic Health
    62. StrainHub: a phylogenetic tool to construct pathogen transmission networks. Bioinformatics. 2020 02 01; 36(3):945-947. de Bernardi Schneider A, Ford CT, Hostager R, Williams J, Cioce M, Çatalyürek ÜV, Wertheim JO, Janies D. PMID: 31418766; PMCID: PMC8215912.
      View in: PubMed   Mentions: 23     Fields:    Translation:Humans
    63. Natural selection favoring more transmissible HIV detected in United States molecular transmission network. Nat Commun. 2019 12 19; 10(1):5788. Wertheim JO, Oster AM, Switzer WM, Zhang C, Panneer N, Campbell E, Saduvala N, Johnson JA, Heneine W. PMID: 31857582; PMCID: PMC6923435.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    64. Characteristics of a cohort of high-risk men who have sex with men on pre-exposure prophylaxis reporting transgender sexual partners. Medicine (Baltimore). 2019 Dec; 98(50):e18232. Hassan A, Wertheim JO, Blumenthal JS, Ellorin E, Dube MP, Corado K, Moore DJ, Morris SR. PMID: 31852085; PMCID: PMC6922495.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansPHPublic Health
    65. Hepatitis C virus genotype 1 and 2 recombinant genomes and the phylogeographic history of the 2k/1b lineage. Virus Evol. 2019 Jul; 5(2):vez041. Hostager R, Ragonnet-Cronin M, Murrell B, Hedskog C, Osinusi A, Susser S, Sarrazin C, Svarovskaia E, Wertheim JO. PMID: 31616569; PMCID: PMC6785677.
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    66. HIV co-infection is associated with increased transmission risk in patients with chronic hepatitis C virus. J Viral Hepat. 2019 11; 26(11):1351-1354. Ragonnet-Cronin M, Hostager R, Hedskog C, Osinusi A, Svarovskaia E, Wertheim JO. PMID: 31194901; PMCID: PMC6800583.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    67. Consent and criminalisation concerns over phylogenetic analysis of surveillance data - Authors' reply. Lancet HIV. 2019 07; 6(7):e420-e421. Wertheim JO, Morris S, Ragonnet-Cronin M. PMID: 31272659.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    68. FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences. Bioinformatics. 2019 06 01; 35(11):1852-1861. Moshiri N, Ragonnet-Cronin M, Wertheim JO, Mirarab S. PMID: 30395173; PMCID: PMC6931354.
      View in: PubMed   Mentions: 28     Fields:    Translation:Humans
    69. Comparative analysis of HIV sequences in real time for public health. Curr Opin HIV AIDS. 2019 05; 14(3):213-220. Wertheim JO, Chato C, Poon AFY. PMID: 30882486.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCellsPHPublic Health
    70. Understanding disclosed and cryptic HIV transmission risk via genetic analysis: what are we missing and when does it matter? Curr Opin HIV AIDS. 2019 05; 14(3):205-212. Ragonnet-Cronin M, Hodcroft EB, Wertheim JO. PMID: 30946142.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    71. Transmission Patterns in a Low HIV-Morbidity State - Wisconsin, 2014-2017. MMWR Morb Mortal Wkly Rep. 2019 Feb 15; 68(6):149-152. Grande KM, Schumann CL, Bañez Ocfemia MC, Vergeront JM, Wertheim JO, Oster AM. PMID: 30763299; PMCID: PMC6375656.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansPHPublic Health
    72. HIV transmission networks among transgender women in Los Angeles County, CA, USA: a phylogenetic analysis of surveillance data. Lancet HIV. 2019 03; 6(3):e164-e172. Ragonnet-Cronin M, Hu YW, Morris SR, Sheng Z, Poortinga K, Wertheim JO. PMID: 30765313; PMCID: PMC6887514.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCellsPHPublic Health
    73. Identifying Clusters of Recent and Rapid HIV Transmission Through Analysis of Molecular Surveillance Data. J Acquir Immune Defic Syndr. 2018 12 15; 79(5):543-550. Oster AM, France AM, Panneer N, Bañez Ocfemia MC, Campbell E, Dasgupta S, Switzer WM, Wertheim JO, Hernandez AL. PMID: 30222659; PMCID: PMC6231979.
      View in: PubMed   Mentions: 83     Fields:    Translation:HumansCells
    74. Maintenance and reappearance of extremely divergent intra-host HIV-1 variants. Virus Evol. 2018 Jul; 4(2):vey030. Wertheim JO, Oster AM, Murrell B, Saduvala N, Heneine W, Switzer WM, Johnson JA. PMID: 30538823; PMCID: PMC6279948.
      View in: PubMed   Mentions: 5  
    75. Growth of HIV-1 Molecular Transmission Clusters in New York City. J Infect Dis. 2018 11 05; 218(12):1943-1953. Wertheim JO, Murrell B, Mehta SR, Forgione LA, Kosakovsky Pond SL, Smith DM, Torian LV. PMID: 30010850; PMCID: PMC6217720.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansCellsPHPublic Health
    76. Phosphoserine acidic cluster motifs bind distinct basic regions on the μ subunits of clathrin adaptor protein complexes. J Biol Chem. 2018 10 05; 293(40):15678-15690. Singh R, Stoneham C, Lim C, Jia X, Guenaga J, Wyatt R, Wertheim JO, Xiong Y, Guatelli J. PMID: 30135209; PMCID: PMC6177606.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    77. HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens. Mol Biol Evol. 2018 07 01; 35(7):1812-1819. Kosakovsky Pond SL, Weaver S, Leigh Brown AJ, Wertheim JO. PMID: 29401317; PMCID: PMC5995201.
      View in: PubMed   Mentions: 143     Fields:    Translation:HumansCells
    78. Size, Composition, and Evolution of HIV DNA Populations during Early Antiretroviral Therapy and Intensification with Maraviroc. J Virol. 2018 02 01; 92(3). 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. PMID: 29142136; PMCID: PMC5774877.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    79. Intrapatient viral diversity and treatment outcome in patients with genotype 3a hepatitis C virus infection on sofosbuvir-containing regimens. J Viral Hepat. 2018 04; 25(4):344-353. 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, Svarovskaia ES. PMID: 29112331.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCellsCTClinical Trials
    80. HIV Transmission Dynamics Among Foreign-Born Persons in the United States. J Acquir Immune Defic Syndr. 2017 12 15; 76(5):445-452. Valverde EE, Oster AM, Xu S, Wertheim JO, Hernandez AL. PMID: 28902072; PMCID: PMC5680123.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    81. 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). Chaillon A, Nakazawa M, Wertheim JO, Little SJ, Smith DM, Mehta SR, Gianella S. PMID: 28794047; PMCID: PMC5640831.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    82. Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas. PLoS Negl Trop Dis. 2017 Aug; 11(8):e0005693. 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. PMID: 28771475; PMCID: PMC5557581.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    83. Identification of major routes of HIV transmission throughout Mesoamerica. Infect Genet Evol. 2017 10; 54:98-107. 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, Mesoamerican Project Group. PMID: 28645708; PMCID: PMC5610625.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    84. Transmission fitness of drug-resistant HIV revealed in a surveillance system transmission network. Virus Evol. 2017 Jan; 3(1):vex008. Wertheim JO, Oster AM, Johnson JA, Switzer WM, Saduvala N, Hernandez AL, Hall HI, Heneine W. PMID: 28458918; PMCID: PMC5399924.
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    85. Short Communication: HIV-1 Transmission Networks Across South Korea. AIDS Res Hum Retroviruses. 2017 08; 33(8):827-831. 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. PMID: 28346838; PMCID: PMC5564048.
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    86. Increasing HIV-1 subtype diversity in seven states, United States, 2006-2013. Ann Epidemiol. 2017 04; 27(4):244-251.e1. Oster AM, Switzer WM, Hernandez AL, Saduvala N, Wertheim JO, Nwangwu-Ike N, Ocfemia MC, Campbell E, Hall HI. PMID: 28318764.
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    87. Viral Evolution: Mummy Virus Challenges Presumed History of Smallpox. Curr Biol. 2017 Feb 06; 27(3):R119-R120. Wertheim JO. PMID: 28171759.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    88. Social and Genetic Networks of HIV-1 Transmission in New York City. PLoS Pathog. 2017 01; 13(1):e1006000. Wertheim JO, Kosakovsky Pond SL, Forgione LA, Mehta SR, Murrell B, Shah S, Smith DM, Scheffler K, Torian LV. PMID: 28068413; PMCID: PMC5221827.
      View in: PubMed   Mentions: 114     Fields:    Translation:HumansCellsPHPublic Health
    89. HIV transmission clusters among injecting drug users in Romania. Rom Biotechnol Lett. 2017 Jan-Feb; 22(1):12307-12315. Temereanca A, Oprea C, Wertheim JO, Ianache I, Ceausu E, Cernescu C, Mehta SR, Ruta S. PMID: 29213206; PMCID: PMC5713907.
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    90. Identifying Transmission Clusters with Cluster Picker and HIV-TRACE. AIDS Res Hum Retroviruses. 2017 03; 33(3):211-218. Rose R, Lamers SL, Dollar JJ, Grabowski MK, Hodcroft EB, Ragonnet-Cronin M, Wertheim JO, Redd AD, German D, Laeyendecker O. PMID: 27824249; PMCID: PMC5333565.
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    91. Concurrency and HIV transmission network characteristics among MSM with recent HIV infection. AIDS. 2016 11 28; 30(18):2875-2883. Pines HA, Wertheim JO, Liu L, Garfein RS, Little SJ, Karris MY. PMID: 27662550; PMCID: PMC5279958.
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    92. A molecular transmission network of recent hepatitis C infection in people with and without HIV: Implications for targeted treatment strategies. J Viral Hepat. 2017 05; 24(5):404-411. Bartlett SR, Wertheim JO, Bull RA, Matthews GV, Lamoury FM, Scheffler K, Hellard M, Maher L, Dore GJ, Lloyd AR, Applegate TL, Grebely J. PMID: 27882678; PMCID: PMC5400687.
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    93. Assessing Host-Virus Codivergence for Close Relatives of Merkel Cell Polyomavirus Infecting African Great Apes. J Virol. 2016 10 01; 90(19):8531-41. 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. PMID: 27440885; PMCID: PMC5021428.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    94. 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. Murrell B, Vollbrecht T, Guatelli J, Wertheim JO. PMID: 27356902; PMCID: PMC5008085.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansAnimalsCells
    95. 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. Wertheim JO, Oster AM, Hernandez AL, Saduvala N, Bañez Ocfemia MC, Hall HI. PMID: 27105549; PMCID: PMC5067842.
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    96. 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 07 01; 63(1):101-107. 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. PMID: 27174704; PMCID: PMC4901863.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCellsPHPublic Health
    97. 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. Chin BS, Chaillon A, Mehta SR, Wertheim JO, Kim G, Shin HS, Smith DM. PMID: 26990771; PMCID: PMC4969179.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    98. 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. Panichsillapakit T, Smith DM, Wertheim JO, Richman DD, Little SJ, Mehta SR. PMID: 26413846; PMCID: PMC4712087.
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    99. 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. Oster AM, Wertheim JO, Hernandez AL, Ocfemia MC, Saduvala N, Hall HI. PMID: 26302431; PMCID: PMC4878401.
      View in: PubMed   Mentions: 96     Fields:    Translation:HumansCellsPHPublic Health
    100. 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. Whiteside YO, Song R, Wertheim JO, Oster AM. PMID: 26558547; PMCID: PMC4862399.
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    101. HIV Transmission Networks in the San Diego-Tijuana Border Region. EBioMedicine. 2015 Oct; 2(10):1456-63. 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. PMID: 26629540; PMCID: PMC4634195.
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    102. 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. Wang X, Wu Y, Mao L, Xia W, Zhang W, Dai L, Mehta SR, Wertheim JO, Dong X, Zhang T, Wu H, Smith DM. PMID: 26129754; PMCID: PMC4599390.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCellsPHPublic Health
    103. The Sordid Affair Between Human Herpesvirus and HIV. J Infect Dis. 2015 Sep 15; 212(6):845-52. Gianella S, Massanella M, Wertheim JO, Smith DM. PMID: 25748324; PMCID: PMC4548466.
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    104. 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. Smith MD, Wertheim JO, Weaver S, Murrell B, Scheffler K, Kosakovsky Pond SL. PMID: 25697341; PMCID: PMC4408413.
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    105. Gene-wide identification of episodic selection. Mol Biol Evol. 2015 May; 32(5):1365-71. 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. PMID: 25701167; PMCID: PMC4408417.
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    106. RELAX: detecting relaxed selection in a phylogenetic framework. Mol Biol Evol. 2015 Mar; 32(3):820-32. Wertheim JO, Murrell B, Smith MD, Kosakovsky Pond SL, Scheffler K. PMID: 25540451; PMCID: PMC4327161.
      View in: PubMed   Mentions: 323     Fields:    Translation:AnimalsCells
    107. Evolutionary origins of human herpes simplex viruses 1 and 2. Mol Biol Evol. 2014 Sep; 31(9):2356-64. Wertheim JO, Smith MD, Smith DM, Scheffler K, Kosakovsky Pond SL. PMID: 24916030; PMCID: PMC4137711.
      View in: PubMed   Mentions: 73     Fields:    Translation:HumansAnimalsCells
    108. Using HIV networks to inform real time prevention interventions. PLoS One. 2014; 9(6):e98443. Little SJ, Kosakovsky Pond SL, Anderson CM, Young JA, Wertheim JO, Mehta SR, May S, Smith DM. PMID: 24901437; PMCID: PMC4047027.
      View in: PubMed   Mentions: 108     Fields:    Translation:HumansCellsPHPublic Health
    109. 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 Jul - Sep; 761:15-30. Benndorf R, Martin JL, Kosakovsky Pond SL, Wertheim JO. PMID: 24607769; PMCID: PMC4157968.
      View in: PubMed   Mentions: 23     Fields:    
    110. HIV migration between blood and cerebrospinal fluid or semen over time. J Infect Dis. 2014 May 15; 209(10):1642-52. Chaillon A, Gianella S, Wertheim JO, Richman DD, Mehta SR, Smith DM. PMID: 24302756; PMCID: PMC3997580.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    111. The global transmission network of HIV-1. J Infect Dis. 2014 Jan 15; 209(2):304-13. Wertheim JO, Leigh Brown AJ, Hepler NL, Mehta SR, Richman DD, Smith DM, Kosakovsky Pond SL. PMID: 24151309; PMCID: PMC3873788.
      View in: PubMed   Mentions: 137     Fields:    Translation:HumansCellsPHPublic Health
    112. Dynamics of viral evolution and neutralizing antibody response after HIV-1 superinfection. J Virol. 2013 Dec; 87(23):12737-44. 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. PMID: 24049166; PMCID: PMC3838120.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    113. A case for the ancient origin of coronaviruses. J Virol. 2013 Jun; 87(12):7039-45. Wertheim JO, Chu DK, Peiris JS, Kosakovsky Pond SL, Poon LL. PMID: 23596293; PMCID: PMC3676139.
      View in: PubMed   Mentions: 102     Fields:    Translation:HumansAnimalsCells
    114. 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. Koeppel AF, Wertheim JO, Barone L, Gentile N, Krizanc D, Cohan FM. PMID: 23364353; PMCID: PMC3660680.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    115. Phylogenetic relatedness of HIV-1 donor and recipient populations. J Infect Dis. 2013 Apr; 207(7):1181-2. Wertheim JO, Scheffler K, Choi JY, Smith DM, Kosakovsky Pond SL. PMID: 23315327; PMCID: PMC3583277.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    116. Detecting individual sites subject to episodic diversifying selection. PLoS Genet. 2012; 8(7):e1002764. Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, Kosakovsky Pond SL. PMID: 22807683; PMCID: PMC3395634.
      View in: PubMed   Mentions: 861     Fields:    Translation:Animals
    117. Using HIV transmission networks to investigate community effects in HIV prevention trials. PLoS One. 2011; 6(11):e27775. Wertheim JO, Kosakovsky Pond SL, Little SJ, De Gruttola V. PMID: 22114692; PMCID: PMC3218056.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    118. Inconsistencies in estimating the age of HIV-1 subtypes due to heterotachy. Mol Biol Evol. 2012 Feb; 29(2):451-6. Wertheim JO, Fourment M, Kosakovsky Pond SL. PMID: 22045998; PMCID: PMC3258043.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansCells
    119. Purifying selection can obscure the ancient age of viral lineages. Mol Biol Evol. 2011 Dec; 28(12):3355-65. Wertheim JO, Kosakovsky Pond SL. PMID: 21705379; PMCID: PMC3247791.
      View in: PubMed   Mentions: 114     Fields:    Translation:Cells
    120. Using phylogeography to characterize the origins of the HIV-1 subtype F epidemic in Romania. Infect Genet Evol. 2011 Jul; 11(5):975-9. Mehta SR, Wertheim JO, Delport W, Ene L, Tardei G, Duiculescu D, Pond SL, Smith DM. PMID: 21439403; PMCID: PMC3104099.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCellsPHPublic Health
    121. Estimating diversification rates: how useful are divergence times? Evolution. 2011 Feb; 65(2):309-20. Wertheim JO, Sanderson MJ. PMID: 21044059; PMCID: PMC3057369.
      View in: PubMed   Mentions: 11     Fields:    
    122. Evolutionary history of chimpanzees inferred from complete mitochondrial genomes. Mol Biol Evol. 2011 Jan; 28(1):615-23. Bjork A, Liu W, Wertheim JO, Hahn BH, Worobey M. PMID: 20802239; PMCID: PMC3108604.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansAnimalsCells
    123. 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. Wertheim JO. PMID: 20567599; PMCID: PMC2887442.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    124. Relaxed molecular clocks, the bias-variance trade-off, and the quality of phylogenetic inference. Syst Biol. 2010 Jan; 59(1):1-8. Wertheim JO, Sanderson MJ, Worobey M, Bjork A. PMID: 20525616; PMCID: PMC2909785.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    125. When pigs fly: the avian origin of a 'swine flu'. Environ Microbiol. 2009 Sep; 11(9):2191-2. Wertheim JO. PMID: 19737300.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    126. A quick fuse and the emergence of Taura syndrome virus. Virology. 2009 Aug 01; 390(2):324-9. Wertheim JO, Tang KF, Navarro SA, Lightner DV. PMID: 19524995.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    127. Dating the age of the SIV lineages that gave rise to HIV-1 and HIV-2. PLoS Comput Biol. 2009 May; 5(5):e1000377. Wertheim JO, Worobey M. PMID: 19412344; PMCID: PMC2669881.
      View in: PubMed   Mentions: 68     Fields:    Translation:HumansAnimalsCells
    128. Relaxed selection and the evolution of RNA virus mucin-like pathogenicity factors. J Virol. 2009 May; 83(9):4690-4. Wertheim JO, Worobey M. PMID: 19224988; PMCID: PMC2668480.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    129. A challenge to the ancient origin of SIVagm based on African green monkey mitochondrial genomes. PLoS Pathog. 2007 Jul; 3(7):e95. Wertheim JO, Worobey M. PMID: 17616975; PMCID: PMC1904472.
      View in: PubMed   Mentions: 31     Fields:    Translation:AnimalsCells
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