Dapp MJ, Kober KM, Chen L, Westfall DH, Wong K, Zhao H, Hall BM, Deng W, Sibley T, Ghorai S, Kim K, Chen N, McHugh S, Au L, Cohen M, Anastos K, Mullins JI (2017). Patterns and rates of viral evolution in HIV-1 subtype B infected females and males. PloS one, 12(10), e0182443. (pubmed) (doi)

Nakamura KJ, Heath L, Sobrera ER, Wilkinson TA, Semrau K, Kankasa C, Tobin NH, Webb NE, Lee B, Thea DM, Kuhn L, Mullins JI, Aldrovandi GM (2017). Breast milk and in utero transmission of HIV-1 select for envelope variants with unique molecular signatures. Retrovirology, 14(1), 6. (pubmed) (doi)

Wagner TA, McLaughlin S, Garg K, Cheung CY, Larsen BB, Styrchak S, Huang HC, Edlefsen PT, Mullins JI, Frenkel LM (2014). HIV latency. Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection. Science (New York, N.Y.), 345(6196), 570-3. (pubmed) (doi)

Iyer S, Bouzek H, Deng W, Larsen B, Casey E, Mullins JI (2013). Quality score based identification and correction of pyrosequencing errors. PloS one, 8(9), e73015. (pubmed) (doi)

Deng W, Maust BS, Westfall DH, Chen L, Zhao H, Larsen BB, Iyer S, Liu Y, Mullins JI (2013). Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data. Bioinformatics (Oxford, England), 29(19), 2402-9. (pubmed) (doi)

Manocheewa S, Swain JV, Lanxon-Cookson E, Rolland M, Mullins JI (2013). Fitness costs of mutations at the HIV-1 capsid hexamerization interface. PloS one, 8(6), e66065. (pubmed) (doi)

Kunwar P, Hawkins N, Dinges WL, Liu Y, Gabriel EE, Swan DA, Stevens CE, Maenza J, Collier AC, Mullins JI, Hertz T, Yu X, Horton H (2013). Superior control of HIV-1 replication by CD8+ T cells targeting conserved epitopes: implications for HIV vaccine design. PloS one, 8(5), e64405. (pubmed) (doi)

Raugi DN, Smith RA, Ba S, Toure M, Traore F, Sall F, Pan C, Blankenship L, Montano A, Olson J, Dia Badiane NM, Mullins JI, Kiviat NB, Hawes SE, Sow PS, Gottlieb GS, University of Washington-Dakar HIV-2 Study Group (2013). Complex patterns of protease inhibitor resistance among antiretroviral treatment-experienced HIV-2 patients from Senegal: implications for second-line therapy. Antimicrobial agents and chemotherapy, 57(6), 2751-60. (pubmed) (doi)

Bull ME, Heath LM, McKernan-Mullin JL, Kraft KM, Acevedo L, Hitti JE, Cohn SE, Tapia KA, Holte SE, Dragavon JA, Coombs RW, Mullins JI, Frenkel LM (2013). Human immunodeficiency viruses appear compartmentalized to the female genital tract in cross-sectional analyses but genital lineages do not persist over time. The Journal of infectious diseases, 207(8), 1206-15. (pubmed) (doi)

CorQ: Quality score based identification and correction of pyrosequencing errors. Shyamala Iyer, Heather Bouzek, Wenjie Deng, Brendan Larsen, Eleanor Casey, James I. Mullins

Wagner TA, McKernan JL, Tobin NH, Tapia KA, Mullins JI, Frenkel LM (2013). An increasing proportion of monotypic HIV-1 DNA sequences during antiretroviral treatment suggests proliferation of HIV-infected cells. Journal of virology, 87(3), 1770-8. (pubmed) (doi)

Herbeck JT, Rolland M, Liu Y, McLaughlin S, McNevin J, Zhao H, Wong K, Stoddard JN, Raugi D, Sorensen S, Genowati I, Birditt B, McKay A, Diem K, Maust BS, Deng W, Collier AC, Stekler JD, McElrath MJ, Mullins JI (2011). Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes. Journal of virology, 85(15), 7523-34. (pubmed) (doi)

Campbell MS, Mullins JI, Hughes JP, Celum C, Wong KG, Raugi DN, Sorensen S, Stoddard JN, Zhao H, Deng W, Kahle E, Panteleeff D, Baeten JM, McCutchan FE, Albert J, Leitner T, Wald A, Corey L, Lingappa JR, Partners in Prevention HSV/HIV Transmission Study Team (2011). Viral linkage in HIV-1 seroconverters and their partners in an HIV-1 prevention clinical trial. PloS one, 6(3), e16986. (pubmed) (doi)

Curlin ME, Zioni R, Hawes SE, Liu Y, Deng W, Gottlieb GS, Zhu T, Mullins JI (2010). HIV-1 envelope subregion length variation during disease progression. PLoS pathogens, 6(12), e1001228. (pubmed) (doi)

Curlin ME, Zioni R, Hawes SE, Liu Y, Deng W, Gottlieb GS, Zhu T, Mullins JI 2009 HIV-1 envelope subregion length variation during disease progression

Rousseau CM, Lockhart DW, Listgarten J, Maley SN, Kadie C, Learn GH, Nickle DC, Heckerman DE, Deng W, Brander C, Ndung'u T, Coovadia H, Goulder PJ, Korber BT, Walker BD, Mullins JI (2009). Rare HLA drive additional HIV evolution compared to more frequent alleles. AIDS research and human retroviruses, 25(3), 297-303. (pubmed) (doi)

Gottlieb GS, Badiane NM, Hawes SE, Fortes L, Toure M, Ndour CT, Starling AK, Traore F, Sall F, Wong KG, Cherne SL, Anderson DJ, Dye SA, Smith RA, Mullins JI, Kiviat NB, Sow PS, University of Washington-Dakar HIV-2 Study Group (2009). Emergence of multiclass drug-resistance in HIV-2 in antiretroviral-treated individuals in Senegal: implications for HIV-2 treatment in resouce-limited West Africa. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 48(4), 476-83. (pubmed) (doi)

Liu Y, Curlin ME, Diem K, Zhao H, Ghosh AK, Zhu H, Woodward AS, Maenza J, Stevens CE, Stekler J, Collier AC, Genowati I, Deng W, Zioni R, Corey L, Zhu T, Mullins JI (2008). Env length and N-linked glycosylation following transmission of human immunodeficiency virus Type 1 subtype B viruses. Virology, 374(2), 229-33. (pubmed) (doi)

Rolland M, Nickle DC, Mullins JI (2007). HIV-1 group M conserved elements vaccine. PLoS pathogens, 3(11), e157. (pubmed)

Rousseau CM, Learn GH, Bhattacharya T, Nickle DC, Heckerman D, Chetty S, Brander C, Goulder PJ, Walker BD, Kiepiela P, Korber BT, Mullins JI (2007). Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections. Journal of virology, 81(9), 4492-500. (pubmed)

Jensen MA, Coetzer M, van ’t Wout AB, Morris L, Mullins JI (2006). A reliable phenotype predictor for human immunodeficiency virus type 1 subtype C based on envelope V3 sequences. Journal of virology, 80(10), 4698-704. (pubmed)

Herbeck JT, Nickle DC, Learn GH, Gottlieb GS, Curlin ME, Heath L, Mullins JI (2006). Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host. Journal of virology, 80(4), 1637-44. (pubmed)

Doria-Rose NA, Learn GH, Rodrigo AG, Nickle DC, Li F, Mahalanabis M, Hensel MT, McLaughlin S, Edmonson PF, Montefiori D, Barnett SW, Haigwood NL, Mullins JI (2005). Human immunodeficiency virus type 1 subtype B ancestral envelope protein is functional and elicits neutralizing antibodies in rabbits similar to those elicited by a circulating subtype B envelope. Journal of virology, 79(17), 11214-24. (pubmed)

Tobin NH, Learn GH, Holte SE, Wang Y, Melvin AJ, McKernan JL, Pawluk DM, Mohan KM, Lewis PF, Mullins JI, Frenkel LM (2005). Evidence that low-level viremias during effective highly active antiretroviral therapy result from two processes: expression of archival virus and replication of virus. Journal of virology, 79(15), 9625-34. (pubmed)

Gottlieb GS, Nickle DC, Jensen MA, Wong KG, Grobler J, Li F, Liu SL, Rademeyer C, Learn GH, Karim SS, Williamson C, Corey L, Margolick JB, Mullins JI (2004). Dual HIV-1 infection associated with rapid disease progression. Lancet (London, England), 363(9409), 619-22. (pubmed)

Jensen MA, Li FS, van ’t Wout AB, Nickle DC, Shriner D, He HX, McLaughlin S, Shankarappa R, Margolick JB, Mullins JI (2003). Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences. Journal of virology, 77(24), 13376-88. (pubmed)

Anderson JP, Learn GH, Rodrigo AG, He X, Wang Y, Weinstock H, Kalish ML, Robbins KE, Hood L, Mullins JI (2003). Predicting demographic group structures based on DNA sequence data. Molecular biology and evolution, 20(7), 1168-80. (pubmed)

Frenkel LM, Wang Y, Learn GH, McKernan JL, Ellis GM, Mohan KM, Holte SE, De Vange SM, Pawluk DM, Melvin AJ, Lewis PF, Heath LM, Beck IA, Mahalanabis M, Naugler WE, Tobin NH, Mullins JI (2003). Multiple viral genetic analyses detect low-level human immunodeficiency virus type 1 replication during effective highly active antiretroviral therapy. Journal of virology, 77(10), 5721-30. (pubmed)

van ’t Wout AB, Lehrman GK, Mikheeva SA, O'Keeffe GC, Katze MG, Bumgarner RE, Geiss GK, Mullins JI (2003). Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(+)-T-cell lines. Journal of virology, 77(2), 1392-402. (pubmed)

Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, Farzadegan H, Gupta P, Rinaldo CR, Learn GH, He X, Huang XL, Mullins JI (1999). Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. Journal of virology, 73(12), 10489-502. (pubmed)

Frenkel LM, Mullins JI, Learn GH, Manns-Arcuino L, Herring BL, Kalish ML, Steketee RW, Thea DM, Nichols JE, Liu SL, Harmache A, He X, Muthui D, Madan A, Hood L, Haase AT, Zupancic M, Staskus K, Wolinsky S, Krogstad P, Zhao J, Chen I, Koup R, Ho D, Korber B, Apple RJ, Coombs RW, Pahwa S, Roberts NJ (1998). Genetic evaluation of suspected cases of transient HIV-1 infection of infants. Science (New York, N.Y.), 280(5366), 1073-7. (pubmed)

Bachmann MH, Mathiason-Dubard C, Learn GH, Rodrigo AG, Sodora DL, Mazzetti P, Hoover EA, Mullins JI (1997). Genetic diversity of feline immunodeficiency virus: dual infection, recombination, and distinct evolutionary rates among envelope sequence clades. Journal of virology, 71(6), 4241-53. (pubmed)