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    Benjamin Murrell

    TitleAssistant Adjunct Professor
    SchoolUniversity of California, San Diego
    DepartmentMedicine
    Address9500 Gilman Drive #0679
    CA La Jolla 92093
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      Collapse Research 
      Collapse Research Activities and Funding
      Viral sequence and dynamic determinants of antibody breadth
      NIH R00AI120851Jun 15, 2015 - Jun 30, 2018
      Role: Principal Investigator
      Viral sequence and dynamic determinants of antibody breadth
      NIH K99AI120851Jun 15, 2015 - Jun 30, 2016
      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. Caskey M, Schoofs T, Gruell H, Settler A, Karagounis T, Kreider EF, Murrell B, Pfeifer N, Nogueira L, Oliveira TY, Learn GH, Cohen YZ, Lehmann C, Gillor D, Shimeliovich I, Unson-O'Brien C, Weiland D, Robles A, Kümmerle T, Wyen C, Levin R, Witmer-Pack M, Eren K, Ignacio C, Kiss S, West AP, Mouquet H, Zingman BS, Gulick RM, Keler T, Bjorkman PJ, Seaman MS, Hahn BH, Fätkenheuer G, Schlesinger SJ, Nussenzweig MC, Klein F. Antibody 10-1074 suppresses viremia in HIV-1-infected individuals. Nat Med. 2017 Jan 16. PMID: 28092665.
        View in: PubMed
      2. 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
      3. Martin DP, Murrell B, Khoosal A, Muhire B. Detecting and Analyzing Genetic Recombination Using RDP4. Methods Mol Biol. 2017; 1525:433-460. PMID: 27896731.
        View in: PubMed
      4. 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 Sep 15; 90(18):8085-9. PMID: 27356902.
        View in: PubMed
      5. MacLeod DT, Choi NM, Briney B, Garces F, Ver LS, Landais E, Murrell B, Wrin T, Kilembe W, Liang CH, Ramos A, Bian CB, Wickramasinghe L, Kong L, Eren K, Wu CY, Wong CH. Early Antibody Lineage Diversification and Independent Limb Maturation Lead to Broad HIV-1 Neutralization Targeting the Env High-Mannose Patch. Immunity. 2016 May 17; 44(5):1215-26. PMID: 27192579.
        View in: PubMed
      6. 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 1; 63(1):101-7. PMID: 27174704.
        View in: PubMed
      7. Murrell B, Murrell D, Murrell H. Discovering General Multidimensional Associations. PLoS One. 2016; 11(3):e0151551. PMID: 26991498.
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      8. de Oliveira MF, Murrell B, Pérez-Santiago J, Vargas M, Ellis RJ, Letendre S, Grant I, Smith DM, Woods SP, Gianella S. Corrigendum: Circulating HIV DNA Correlates With Neurocognitive Impairment in Older HIV-infected Adults on Suppressive ART. Sci Rep. 2016; 6:19387. PMID: 26783252.
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      9. Landais E, Huang X, Havenar-Daughton C, Murrell B, Price MA, Wickramasinghe L, Ramos A, Bian CB, Simek M, Allen S, Karita E, Kilembe W, Lakhi S, Inambao M, Kamali A, Sanders EJ, Anzala O, Edward V, Bekker LG, Tang J, Gilmour J, Kosakovsky-Pond SL, Phung P, Wrin T, Crotty S, Godzik A, Poignard P. Broadly Neutralizing Antibody Responses in a Large Longitudinal Sub-Saharan HIV Primary Infection Cohort. PLoS Pathog. 2016 Jan; 12(1):e1005369. PMID: 26766578.
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      10. Oliveira MF, Murrel B, Pérez-Santiago J, Vargas M, Ellis RJ, Letendre S, Grant I, Smith DM, Woods SP, Gianella S. Circulating HIV DNA Correlates With Neurocognitive Impairment in Older HIV-infected Adults on Suppressive ART. Sci Rep. 2015; 5:17094. PMID: 26603568.
        View in: PubMed
      11. McInnes AM, Khoosal A, Murrell B, Merkle D, Lacerda M, Nyengera R, Coetzee JC, Edwards LC, Ryan PG, Rademan J, van der Westhuizen JJ, Pichegru L. Recreational Fish-Finders-An Inexpensive Alternative to Scientific Echo-Sounders for Unravelling the Links between Marine Top Predators and Their Prey. PLoS One. 2015; 10(11):e0140936. PMID: 26600300.
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      12. Pérez-Santiago J, Schrier RD, de Oliveira MF, Gianella S, Var SR, Day TR, Ramirez-Gaona M, Suben JD, Murrell B, Massanella M, Cherner M, Smith DM, Ellis RJ, Letendre SL, Mehta SR. Cell-free mitochondrial DNA in CSF is associated with early viral rebound, inflammation, and severity of neurocognitive deficits in HIV infection. J Neurovirol. 2016 Apr; 22(2):191-200. PMID: 26428514.
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      13. Frost SD, Murrell B, Hossain AS, Silverman GJ, Pond SL. Assigning and visualizing germline genes in antibody repertoires. Philos Trans R Soc Lond B Biol Sci. 2015 Sep 5; 370(1676). PMID: 26194754.
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      14. 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.
        View in: PubMed
      15. Filloux D, Murrell S, Koohapitagtam M, Golden M, Julian C, Galzi S, Uzest M, Rodier-Goud M, D'Hont A, Vernerey MS, Wilkin P, Peterschmitt M, Winter S, Murrell B, Martin DP, Roumagnac P. The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed. Virus Evol. 2015; 1(1):vev002. PMID: 27774276.
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      16. Martin DP, Murrell B, Golden M, Khoosal A, Muhire B. RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evol. 2015; 1(1):vev003. PMID: 27774277.
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      17. 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.
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      18. 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.
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      19. 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.
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      20. Fisher RG, Smith DM, Murrell B, Slabbert R, Kirby BM, Edson C, Cotton MF, Haubrich RH, Kosakovsky Pond SL, Van Zyl GU. Next generation sequencing improves detection of drug resistance mutations in infants after PMTCT failure. J Clin Virol. 2015 Jan; 62:48-53. PMID: 25542470.
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      21. Hepler NL, Scheffler K, Weaver S, Murrell B, Richman DD, Burton DR, Poignard P, Smith DM, Kosakovsky Pond SL. IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform. PLoS Comput Biol. 2014 Sep; 10(9):e1003842. PMID: 25254639.
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      22. Murrell B, Murrell D, Murrell H. R2-equitability is satisfiable. Proc Natl Acad Sci U S A. 2014 May 27; 111(21):E2160. PMID: 24782547.
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      23. Scheffler K, Murrell B, Kosakovsky Pond SL. On the validity of evolutionary models with site-specific parameters. PLoS One. 2014; 9(4):e94534. PMID: 24722425.
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      24. Lacerda M, Moore PL, Ngandu NK, Seaman M, Gray ES, Murrell B, Krishnamoorthy M, Nonyane M, Madiga M, Wibmer CK, Sheward D, Bailer RT, Gao H, Greene KM, Karim SS, Mascola JR, Korber BT, Montefiori DC, Morris L, Williamson C, Seoighe C. Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models. Virol J. 2013; 10(1):347. PMID: 24295501.
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      25. Muhire BM, Golden M, Murrell B, Lefeuvre P, Lett JM, Gray A, Poon AY, Ngandu NK, Semegni Y, Tanov EP, Monjane AL, Harkins GW, Varsani A, Shepherd DN, Martin DP. Evidence of Pervasive Biologically Functional Secondary Structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses. J Virol. 2014 Feb; 88(4):1972-89. PMID: 24284329.
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      26. Murrell B, Moola S, Mabona A, Weighill T, Sheward D, Kosakovsky Pond SL, Scheffler K. FUBAR: a fast, unconstrained bayesian approximation for inferring selection. Mol Biol Evol. 2013 May; 30(5):1196-205. PMID: 23420840.
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      27. 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.
        View in: PubMed
      28. Murrell B, de Oliveira T, Seebregts C, Kosakovsky Pond SL, Scheffler K. Modeling HIV-1 drug resistance as episodic directional selection. PLoS Comput Biol. 2012; 8(5):e1002507. PMID: 22589711.
        View in: PubMed
      29. Sheward DJ, Murrell B, Williamson C. Degenerate Primer IDs and the birthday problem. Proc Natl Acad Sci U S A. 2012 May 22; 109(21):E1330; author reply E1331. PMID: 22517746.
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      30. Fisher R, van Zyl GU, Travers SA, Kosakovsky Pond SL, Engelbrech S, Murrell B, Scheffler K, Smith D. Deep sequencing reveals minor protease resistance mutations in patients failing a protease inhibitor regimen. J Virol. 2012 Jun; 86(11):6231-7. PMID: 22457522.
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      31. Pond SL, Murrell B, Poon AF. Evolution of viral genomes: interplay between selection, recombination, and other forces. Methods Mol Biol. 2012; 856:239-72. PMID: 22399462.
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      32. Murrell B, Weighill T, Buys J, Ketteringham R, Moola S, Benade G, du Buisson L, Kaliski D, Hands T, Scheffler K. Non-negative matrix factorization for learning alignment-specific models of protein evolution. PLoS One. 2011; 6(12):e28898. PMID: 22216138.
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      33. Kosakovsky Pond SL, Murrell B, Fourment M, Frost SD, Delport W, Scheffler K. A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol. 2011 Nov; 28(11):3033-43. PMID: 21670087.
        View in: PubMed
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