Kaiming Tao, Philip L Tzou, Malaya K Sahoo, Charles B Hare, Benjamin A Pinsky, Robert W Shafer (2026). HIV-1 subtype diversity trends in a Northern California cohort AIDS. 2026 Apr.

Van Zyl G, Prochazka M, Schmidt HMA, Orrell C, Schapiro JM, McCluskey SM, Vitoria M, Kantor R, Parikh UM, Rodolph M, Jordan MR, Shafer RW (2025). Lenacapavir-associated drug resistance: implications for scaling up long-acting HIV pre-exposure prophylaxis The Lancet HIV. 2025 Jun.

Tao K, Zhou J, Getaneh Y, Shafer RW (2025). GenBank2PubMed: Bridging Viral Genomic Data and the Scientific Literature with AI-Assisted Curation Scientific reports. 2025 Nov.

Tao K, Zhou J, Osman ZA, Ahluwalia V, Sabati C, Shafer RW (2024). Fine-tuned large language models for answering questions about full-text biomedical research studies. Medrxiv. 2024 Oct.

Nagarajan P, Zhou J, Todoro GD, Incardona F, Segui-Devaux C, Kaiser R, Abecasis AB, Gomes P, Tao K, Zazzi M, Shafer RW (2024). Spectrum of Non-Nucleoside Reverse Transcriptase Inhibitor-Associated Drug Resistance Mutations in Persons Living with HIV-1 Receiving Rilpivirine Viruses. 2024 Oct.

Tao K, Zhou J, Nagarajan P, Tzou PL, Shafer RW (2024). Comprehensive database of HIV mutations selected during antiretroviral in vitro passage experiments. Antiviral Research. 2024 Oct.

Chu C, Tao K, Kouamou V, Avalos A, Scott J, Grant PM, Rhee SY, McCluskey SM, Jordan MR, Morgan RL, Shafer RW (2024). Prevalence of Emergent Dolutegravir Resistance Mutations in People Living with HIV: A Rapid Scoping Review. Viruses. 2024 Mar.

Tao J, Osman, ZA, Tzou PL, Rhee SY, Ahluwalia V, Shafer RW (2024). GPT-4 Performance on Querying Scientific Publications: Reproducibility, Accuracy, and Impact of an Instruction Sheet BMC Medical Research Methodology. 2024 Jan.

Nouhin J, Tzou PL, Rhee SY, Sahoo MK, Pinsky BA, Krupkin M, Puglisi JD, Puglisi EV, Shafer RW (2023). Human immunodeficiency virus 1 5′-leader mutations in plasma viruses before and after the development of reverse transcriptase inhibitor-resistance mutations Journal of General Virology. 2023 Oct.

Inzaule SC, Siedner MJ, Little SJ, Avilla-Rios S, Ayitewala A, Bosch RJ, Calvez V, Ceccherini-Silberstein F, Charpentier C, Descamps D, Eschleman SH, Fokam J, Frenkel LM, Gupta KR, Ioannidis JPA, Kaleebu P, Kantor R, Kassaye SG, Pond SLK, 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 (2023). Recommendations on data sharing in HIV drug resistance research PLOS Medicine. 2023 Sep.

Tao K, Rhee SY, Chu C, Avalos A, Ahluwalia AK, Gupta RK, Jordan MR, Shafer RW (2023). Treatment Emergent Dolutegravir Resistance Mutations in Individuals Naïve to HIV-1 Integrase Inhibitors: A Rapid Scoping Review Viruses. 2023 Aug.

Tao K, Rhee SY, Tzou PL, Osman ZA, Pond SLK, Holmes SP, Shafer RW (2023). HIV-1 Group M Capsid Amino Acid Variability: Implications for Sequence Quality Control of Genotypic Resistance Testing Viruses. 2023 Apr.

Rhee SY, Schapiro JM, Saladini F, Zazzi M, Khoo S, Shafer RW (2023). Potential role of doravirine for the treatment of HIV-1-infected persons with transmitted drug resistance. AIDS Res Ther. 2023 Feb.

Tao K, Rhee SY, Tzou PL, Holmes SP, Shafer RW (2023). Highly Ambiguous HIV-1 Pol Positions Encoding Multiple Amino Acids Usually Result from Antiviral or Immune Selection Pressure AIDS Res Hum Retroviruses. 2023 Jan.

Rhee SY, Parkin N, Harrigan PR, Holmes S, Shafer RW (2022). Genotypic correlates of resistance to the HIV-1 strand transfer integrase inhibitor cabotegravir. Antiviral Res. 2022 Sep.

Chu C, Armenia D, Walworth C, Santoro MM, Shafer RW (2022). Genotypic Resistance Testing of HIV-1 DNA in Peripheral Blood Mononuclear Cells. Clin Microbiol Rev. 2022 Sep.

Rhee SY, Boehm M, Tarasova O, Di Teodoro G, Abecasis AB, Sönnerborg A, Bailey AJ, Kireev D, Zazzi M, The EuResist Network Study Group, Shafer RW (2022). Spectrum of atazanavir-selected protease inhibitor-resistance mutations. Pathogens. 2022 May.

Rhee SY, Kassaye SG, Jordan MR, Kouamou V, Katzenstein D, Shafer RW (2022). Public availability of HIV-1 drug resistance sequence and treatment data: a systematic review. Lancet Microbe. 2022 January.

Rhee SY, Tzou PL, Shafer RW (2021). Temporal Trends in HIV-1 Mutations Used for the Surveillance of Transmitted Drug Resistance. Viruses. 2021 May.

Bailey AJ, Rhee SY, Shafer RW (2021). Integrase Strand Transfer Inhibitor Resistance in Integrase Strand Transfer Inhibitor-Naive Persons. AIDS Research and Human Retroviruses. 2021 Apr.

Rhee SY, Kassaye SG, Barrow G, Sundaramurthi JC, Jordan MR, Shafer RW (2020). HIV-1 transmitted drug resistance surveillance: shifting trends in study design and prevalence estimates. J Int AIDS Soc. 2020 Sep.

Rhee SY, Clutter D, Hare CB, Tchakoute CT, Sainani K, Fessel WJ, Hurley L, Slome S, Pinsky BA, Silverberg MJ, Shafer RW (2020). Virological Failure and Acquired Genotypic Resistance Associated With Contemporary Antiretroviral Treatment Regimens. Open Forum Infect Dis. 2020 Sep.

Tzou PL, Descamps D, Rhee SY, Raugi DN, Charpentier C, Taveira N, Smith RA, Soriano V, de Mendoza C, Holmes SP, Gottlieb GS, Shafer RW (2020). Expanded Spectrum of Antiretroviral-Selected Mutations in Human Immunodeficiency Virus Type 2. J Infect Dis. 2020 Jun 11.

Tzou PL, Kosakovsky Pond SL, Avila-Rios S, Holmes SP, Kantor R, Shafer RW (2020). Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences PLoS One. 2020 Feb 26.

Rhee SY, Grant PM, Tzou PL, Barrow G, Harrigan PR, Ioannidis JPA, Shafer RW (2019). A systematic review of the genetic mechanisms of dolutegravir resistance. J Antimicrob Chemother. 2019 Jul 5.

Tzou PL, Rhee SY, Shafer RW (2019). Amino Acid Prevalence of HIV-1 pol Mutations by Direct Polymerase Chain Reaction and Single Genome Sequencing. AIDS Research and Human Retroviruses 2019 Oct 1.

Tzou PL, Rhee SY, Descamps D, Clutter DS, Hare B, Mor O, Grude M, Parkin N, Jordan MR, Bertagnolio S, Schapiro JM, Harrigan PR, Geretti AM, Marcelin A, Shafer RW (2019). Integrase strand transfer inhibitor (INSTI)-resistance mutations for the surveillance of transmitted HIV-1 drug resistance. J Antimicrob Chemother. 2019 Oct 16.

Clutter DS, Mazarei G, Sinha R, Manasa J, Nouhin J, LaPrade E, Bolouki S, Tzou PL, Hannita-Hui J, Sahoo MK, Kuimelis P, Kuimelis RG, Pinsky BA, Schoolnik GK, Hassibi A, Shafer RW (2019). Multiplex Solid-Phase Melt Curve Analysis for the Point-of-Care Detection of HIV-1 Drug Resistance. J Mol Diagn. 2019 Apr 23.

Rhee SY, Magalis BR, Hurley L, Silverberg MJ, Marcus JL, Slome S, Kosakovsky Pond SL, Shafer RW (2019). National and International Dimensions of Human Immunodeficiency Virus-1 Sequence Clusters in a Northern California Clinical Cohort. Open Forum Infect Dis. 2019 Mar 14.

Rhee SY and Shafer RW (2018). Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences. Scientific Data. 2018 July 31.

Tzou PL, Rhee SY, Pond SLK, Manasa J, Shafer RW (2018). Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy. Scientific Data. 2018 July 24.

Rhee SY, Clutter D, Fessel WJ, Klein D, Slome S, Pinsky BA, Marcus JL, Hurley L, Silverberg MJ, Kosakovsky Pond SL, Shafer RW (2018). Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance in a Large U.S. Clinic Population. Clin Infect Dis. 2018 May 26.

Tzou PL, Ariyaratne P, Varghese V, Lee C, Rakhmanaliev E, Villy C, Yee M, Tan K, Michel G, Pinsky BA, Shafer RW (2018). Comparison of an In Vitro Diagnostic Next-Generation Sequencing Assay with Sanger Sequencing for HIV-1 Genotypic Resistance Testing. Journal of Clinical Microbiology 2018 May 25;56(6)

Manasa J, Varghese V, Pond SLK, Rhee SY, Tzou PL, Fessel WJ, Jang KS, White E, Rognvaldsson T, Katzenstein DA, Shafer RW (2017). Evolution of gag and gp41 in Patients Receiving Ritonavir-Boosted Protease Inhibitors. Sci Rep., 2017 Sep 14.

Clutter DS, Zhou S, Varghese V, Rhee SY, Pinsky BA, Jeffrey Fessel W, Klein DB, Spielvogel E, Holmes SP, Hurley LB, Silverberg MJ, Swanstrom R, Shafer RW (2017). Prevalence of Drug-Resistant Minority Variants in Untreated HIV-1-Infected Individuals With and Those Without Transmitted Drug Resistance Detected by Sanger Sequencing. J Infect Dis., 2017 Aug 1.

Rhee SY, Varghese V, Holmes SP, Van Zyl GU, Steegen K, Boyd MA, Cooper DA, Nsanzimana S, Saravanan S, Charpentier C, de Oliveira T, Etiebet MA, Garcia F, Goedhals D, Gomes P, Gunthard HF, Hamers RL, Hoffmann CJ, Hunt G, Jiamsakul A, Kaleebu P, Kanki P, Kantor R, Kerschberger B, Marconi VC, D'amour Ndahimana J, Ndembi N, Ngo-Giang-Huong N, Rokx C, Santoro MM, Schapiro JM, Schmidt D, Seu L, Sigaloff KC, Sirivichayakul S, Skhosana L, Sunpath H, Tang M, Yang C, Carmona S, Gupta RK, Shafer RW (2017). Mutational correlates of virological failure in individuals receiving a WHO-recommended tenofovir-containing first-line regimen: An international collaboration. EBioMedicine, 2017 Mar 19.

Rhee SY, Sankaran K, Varghese V, Winters M, Hurt CB, Eron JJ, Parkin N, Holmes SP, Holodniy M, Shafer RW (2016). HIV-1 Protease, Reverse Transcriptase, and Integrase Variation. J Virol., 2016 Apr 20.

Varghese V, Pinsky BA, Smith DS, Klein D, Shafer RW (2016). Q148N, a Novel Integrase Inhibitor Resistance Mutation Associated with Low-Level Reduction in Elvitegravir Susceptibility. AIDS Res Hum Retroviruses, 2016 Apr 19.

Feder AF, Rhee SY, Holmes SP, Shafer RW, Petrov DA, Pennings PS (2016). More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1. Elife, 2016 Feb 15.

Clutter DS, Sanchez PR, Rhee SY, Shafer RW (2016). Genetic Variability of HIV-1 for Drug Resistance Assay Development. Viruses, 2016 Feb 11.

Clutter DS, Fessel WJ, Rhee SY, Hurley LB, Klein DB, Ioannidis JP, Silverberg MJ, Shafer RW (2016). Response to Therapy in Antiretroviral Therapy-Naïve Patients with Isolated Nonnucleoside Reverse-Transcriptase Inhibitor-Associated Transmitted Drug Resistance. J Acquir Immune Defic Syndr., 2016 Feb 5.

Rhee SY, Jordan MR, Raizes E, Chua A, Parkin N, Kantor R, Van Zyl GU, Mukui I, Hosseinipour MC, Frenkel LM, Ndembi N, Hamers RL, Rinke de Wit TF, Wallis CL, Gupta RK, Fokam J, Zeh C, Schapiro JM, Carmona S, Katzenstein D, Tang M, Aghokeng AF, De Oliveira T, Wensing AM, Gallant JE, Wainberg MA, Richman DD, Fitzgibbon JE, Schito M, Bertagnolio S, Yang C, Shafer RW (2015). HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing. PLoS ONE, 2015 Dec 30.

Rhee SY, Blanco JL, Jordan MR, Taylor J, Lemey P, Varghese V, Hamers RL, Bertagnolio S, de Wit TF, Aghokeng AF, Albert J, Avi R, Avila-Rios S, Bessong PO, Brooks JI, Boucher CA, Brumme ZL, Busch MP, Bussmann H, Chaix ML, Chin BS, D'Aquin TT, De Gascun CF, Derache A, Descamps D, Deshpande AK, Djoko CF, Eshleman SH, Fleury H, Frange P, Fujisaki S, Harrigan PR, Hattori J, Holguin A, Hunt GM, Ichimura H, Kaleebu P, Katzenstein D, Kiertiburanakul S, Kim JH, Kim SS, Li Y, Lutsar I, Morris L, Ndembi N, Ng KP, Paranjape RS, Peeters M, Poljak M, Price MA, Ragonnet-Cronin ML, Reyes-Teran G, Rolland M, Sirivichayakul S, Smith DM, Soares MA, Soriano VV, Ssemwanga D, Stanojevic M, Stefani MA, Sugiura W, Sungkanuparph S, Tanuri A, Tee KK, Truong HH, van de Vijver DA, Vidal N, Yang C, Yang R, Yebra G, Ioannidis JPA, Vandamme AM, Shafer RW (2015). Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis. PLoS Med, 2015 Apr 7.

Kolomeets AN, Varghese V, Lemey P, Bobkova MR, Shafer RW (2014). A uniquely prevalent nonnucleoside reverse transcriptase inhibitor resistance mutation in Russian subtype A HIV-1 viruses. AIDS, 2014 Nov 13.

Melikian GL, Rhee SY, Varghese V, Porter D, White K, Taylor J, Towner W, Troia P, Burack J, Dejesus E, Robbins GK, Razzeca K, Kagan R, Liu TF, Fessel WJ, Israelski D, Shafer RW (2013). Non-nucleoside reverse transcriptase inhibitor (NNRTI) cross-resistance: implications for preclinical evaluation of novel NNRTIs and clinical genotypic resistance testing. J Antimicrob Chemother, 2013 Aug 9.

Van Zyl GU, Liu TF, Claassen M, Engelbrecht S, de Oliveira T, Preiser W, Wood NT, Travers S, Shafer RW (2013). Trends in Genotypic HIV-1 Antiretroviral Resistance between 2006 and 2012 in South African Patients Receiving First- and Second-Line Antiretroviral Treatment Regimens. PLoS One, 2013 Jun 26.

Varghese V, Mitsuya Y, Fessel WJ, Liu TF, Melikian GL, Katzenstein DA, Schiffer CA, Holmes SP, Shafer RW (2013). Prototypical Recombinant Multi-Protease Inhibitor Resistant Infectious Molecular Clones of Human Immunodeficiency Virus Type-1. Antimicrobial Agents and Chemotherapy, 2013 Jun 24.

Tang MW, Rhee SY, Bertagnolio S, Ford N, Holmes S, Sigaloff KC, Hamers RL, de Wit TF, Fleury HJ, Kanki PJ, Ruxrungtham K, Hawkins CA, Wallis CL, Stevens W, van Zyl GU, Manosuthi W, Hosseinipour MC, Ngo-Giang-Huong N, Belec L, Peeters M, Aghokeng A, Bunupuradah T, Burda S, Cane P, Cappelli G, Charpentier C, Dagnra AY, Deshpande AK, El-Katib Z, Eshleman SH, Fokam J, Gody JC, Katzenstein D, Koyalta DD, Kumwenda JJ, Lallemant M, Lynen L, Marconi VC, Margot NA, Moussa S, Ndung'u T, Nyambi PN, Orrell C, Schapiro JM, Schuurman R, Sirivichayakul S, Smith D, Zolfo M, Jordan MR, Shafer RW (2013). Nucleoside reverse transcriptase inhibitor resistance mutations associated with first-line stavudine-containing antiretroviral therapy: programmatic implications for countries phasing out stavudine. Journal of Infectious Diseases, 2013 Jun 15.

Babrzadeh F, Varghese V, Pacold M, Liu TF, Nyren P, Schiffer C, Fessel WJ, Shafer RW (2012). Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance. J Antimicrob Chemother. 2012 Oct 19.

Balamane M, Varghese V, Melikian GL, Fessel WJ, Katzenstein DA, Shafer RW (2012). Panel of prototypical recombinant infectious molecular clones resistant to nevirapine, efavirenz, etravirine, and rilpivirine. Antimicrobial Agents and Chemother. 2012 Aug;56(8):4522-4.

Rhee SY, Blanco JL, Liu TF, Pere I, Kaiser R, Zazzi M, Incardona F, Towner W, Gatell JM, De Luca A, Fessel WJ, Shafer RW (2012). Standardized representation, visualization and searchable repository of antiretroviral treatment-change episodes. AIDS Res Ther. 2012 May 3;9(1):13.

Melikian GL, Rhee SY, Taylor J, Fessel WJ, Kaufman D, Towner W, Troia-Cancio PV, Zolopa A, Robbins GK, Kagan R, Israelski D, Shafer RW (2012). Standardized comparison of the relative impacts of HIV-1 reverse transcriptase (RT) mutations on nucleoside RT inhibitor susceptibility. Antimicrobial Agents and Chemother. 2012 May;56(5):2305-13.

Tang MW, Kanki PJ, Shafer RW (2012). A Review of the Virological Efficacy of the 4 World Health Organization-Recommended Tenofovir-Containing Regimens for Initial HIV Therapy. Clin Infect Dis. 2012 Mar;54(6):862-75.

Doherty KM, Nakka P, King BM, Rhee SY, Holmes SP, Shafer RW, Radhakrishnan ML (2011). A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes. BMC Bioinformatics2011 Dec 15;12(1):477

Fessel WJ, Anderson B, Follansbee SE, Winters MA, Lewis ST, Weinheimer SP, Petropoulos CJ, Shafer RW (2011). The efficacy of an anti-CD4 monoclonal antibody for HIV-1 treatment. Antiviral Res. 2011 Dec;92(3):484-7. Epub 2011 Oct 4.

Varghese V, Liu TF, Rhee SY, Libiran P, Trevino C, Fessel WJ, Shafer RW. (2010). HIV-1 Integrase Sequence Variability in Antiretroviral Naive Patients and in Triple-Class Experienced Patients Subsequently Treated with Raltegravir. AIDS Res Hum Retroviruses, 2010 Oct

Rhee SY, Taylor J, Fessel WJ, Kaufman D, Towner W, Troia P, Ruane P, Hellinger J, Shirvani V, Zolopa A, Shafer RW. (2010). HIV-1 protease mutations and protease inhibitor cross-resistance. Antimicrobial Agents and Chemotherapy, 2010 Oct

Varghese V, Wang E, Babrzadeh F, Bachmann MH, Shahriar R, Liu T, Mappala SJ, Gharizadeh B, Fessel WJ, Katzenstein D, Kassaye S, Shafer RW. (2010). Nucleic acid template and the risk of a PCR-Induced HIV-1 drug resistance mutation. PLoS One, 2010 Jun 7

Reuman EC, Rhee SY, Holmes SP, Shafer RW (2010). Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations. Journal of Antinicrobial Chemotherapy, 2010 May 12

Reuman EC, Bachmann MH, Varghese V, Fessel WJ, Shafer RW (2010). Panel of prototypical raltegravir-resistant infectious molecular clones in a novel integrase-deleted cloning vector. Antimicrobial Agents and Chemotherapy,2010 Feb;54(2):934-6.

Varghese V, Shahriar R, Rhee SY, Liu T, Simen BB, Egholm M, Hanczaruk B, Blake LA, Gharizadeh B, Babrzadeh F, Bachmann MH, Fessel WJ, Shafer RW (2009). Minority Variants Associated with Transmitted and Acquired HIV-1 Nonnucleoside Reverse Transcriptase Inhibitor Resistance: Implications for the Use of Second-Generation Nonnucleoside Reverse Transcriptase Inhibitors. JAIDS, 2009 Sep 3

Shahriar R, Rhee SY, Liu TF, Fessel WJ, Scarcella A, Towner W, Holmes SP, Zolopa AR, Shafer RW (2009). Nonpolymorphic HIV-1 Protease and RT Treatment-Selected Mutations. Antimicrobial Agents and Chemotherapy, 2009 Aug 31

Rhee SY, Fessel WJ, Liu TF, Marlowe NM, Rowland CM, Rode RA, Vandamme AM, Van Laethem K, Brun-Vezinet F, Calvez V, Taylor J, Hurley L, Horberg M, Shafer RW (2009). Predictive Value of HIV-1 Genotypic Resistance Test Interpretation Algorithms. Journal of Infectious Diseases, 2009 Aug 1;200(3):453-463

Bennett DE, Camacho RJ, Otelea D, Kuritzkes DR, Fleury H, Kiuchi M, Heneine W, Kantor R, Jordan MR, Schapiro JM, Vandamme AM, Sandstrom P, Boucher CA, van de Vijver D, Rhee SY, Liu TF, Pillay D, Shafer RW (2009). Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update. PLoS ONE, 2009;4(3):e4724

Varghese V, Mitsuya Y, Shahriar R, Bachmann MH, Fessel WJ, Kagan RM, Shafer RW (2009). HIV-1 Isolates with the RT Mutation Q145M Retain Nucleoside and Non-Nucleoside RT Inhibitor Susceptibility. Antimicrobial Agents and Chemotherapy, 2009 Feb 17

Rhee SY, Liu TF, Kiuchi M, Zioni R, Gifford RJ, Holmes SP, Shafer RW (2008). Natural Variation of HIV-1 Group M Integrase: Implications for a New Class of Antiretroviral Inhibitors. Retrovirology, 2008 Aug 7;5:74

Mitsuya Y, Varghese V, Wang C, Liu TF, Holmes SP, Jayakumar R, Gharizadeh B, Ronaghi M, Klein D, Fessel WJ, Shafer RW (2008). Minority HIV-1 Variants in Antiretroviral Naive Persons with Reverse Transcriptase Codon 215 Revertant Mutations. Journal of Virology, 2008 Aug 20 Epub

Bembom O, Petersen ML, Rhee SY, Fessel WJ, Sinisi SE, Shafer RW, van der Laan MJ (2008). Biomarker Discovery using Targeted Maximum-Likelihood Estimation: Application to the treatment of Antiretroviral-Resistant HIV Infection. Statistics in Medicine, 2008 Sep 29 Epub

Gifford RJ, Rhee SY, Eriksson N, Liu TF, Kiuchi M, Das AK, Shafer RW (2008). Sequence Editing by Apolipoprotein B RNA-editing Catalytic Component-B and Epidemiological Surveillance of Transmitted HIV-1 Drug Resistance. AIDS, 2008 Mar 30;22(6):717-25

Shafer RW, Rhee SY, Bennett DE (2008). Consensus Drug Resistance Mutations for Epidemiological Surveillance: Basic Principles and Potential Controversies. Antiviral Therapy, Vol. 13 (2008) Suppl 2:59-68

Mitsuya Y, Liu TF, Rhee SY, Fessel WJ, Shafer RW (2007). Prevalence of Darunavir Resistance-Associated Mutations: Patterns of Occurrence and Association with Past Treatment. Journal of Infectious Diseases, Oct 15, 2007 196:1177-9

Petersen ML, Wang Y, van der Laan MJ, Rhee SY, Shafer RW, Fessel WJ (2007). Virologic Efficacy of Boosted Double Versus Boosted Single Protease Inhibitor Therapy. AIDS July 31, 2007 ISSN 0269-9370

Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW (2007). Characterization of Mutation Spectra with Ultra-Deep Pyrosequencing: Application to HIV-1 Drug Resistance. Genome Research June 28, 2007 ISSN 1088-9051/07

Rhee SY, Liu TF, Holmes SP, Shafer RW (2007). HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation. PLoS Computational Biology May 2007 3:5(e87)

Shafer RW, Rhee SY, Pillay D, Miller V, Sandstrom P, Schaprio JM, Kuritzkes DR, Bennett D.(2006). HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance. AIDS Jan 11, 2007

Mitsuya Y, Winters MA, Fessel WJ, Rhee SY, Hurley L, Horberg M, Schiffer CA, Zolopa AR, Shafer RW.(2006). N88D Facilitates the Co-occurrence of D30N and L90M and the Development of Multidrug Resistance in HIV Type 1 Protease following Nelfinavir Treatment Failure. AIDS Res Hum Retroviruses 22(12):1300-5

Rhee SY, Taylor J, Wadhera G, Ben-Hur A, Brutlag DL, Shafer RW(2006). Genotypic predictors of human immunodeficiency virus type 1 drug resistance. Proceedings of National Academy of Sciences of the United States of America Oct 25, 2006

Click here to access the data sets and the results.

Mitsuya Y, Winters MA, Fessel WJ, Rhee SY, Slome S, Flamm J, Horberg M, Hurley L, Klein D, Shafer RW(2006). HIV-1 Drug Resistance Genotype Results in Patients With Plasma Samples With HIV-1 RNA Levels Less than 75 Copies/mL. JAIDS 43(1):56-9

Rhee SY, Kantor R, Katzenstein DA, Camacho R, Morris L,Sirivichayakul S,Jorgensen L, Brigido LF, Schapiro JM,and Shafer RW for the international Non Subtype B HIV-1 Working Group(2006). HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes. AIDS 20(5):643-651, March 21, 2006

Click here to access the HIVseq program

Rhee SY, Fessel WJ, Zolopa AR, Hurley L, Liu T, Taylor J, Nguyen DP, Slome S, Klein D, Horberg M, Flamm J, Follansbee S, Schapiro JM, Shafer RW (2005). HIV-1 Protease and Reverse-Transcriptase Mutations: Correlations with Antiretroviral Therapy in Subtype B Isolates and Implications for Drug-Resistance Surveillance. Journal of Infectious Diseases, Aug 1;192(3):456-65. Epub 2005 Jul 5.

Kantor R, Katzenstein DA, Efron B, Carvalho AP, Wynhoven B, Cane P, Clarke J, Sirivichayakul S, Soares MA, Snoeck J, Pillay C, Rudich H, Rodrigues R, Holguin A, Ariyoshi K, Bouzas MB, Cahn P, Sugiura W, Soriano V, Brigido LF, Grossman Z, Morris L, Vandamme AM, Tanuri A, Phanuphak P, Weber JN, Pillay D, Harrigan PR, Camacho R, Schapiro JM and Shafer RW (2005). Impact of HIV-1 Subtype and Antiretroviral Therapy on Protease and Reverse Transcriptase Genotype: Results of a Global Collaboration. PLoS Med. Apr;2(4):e112.

Johnston E, Dupnik KM, Gonzales MJ, Winters MA, Rhee SY, Imamichi T and Shafer RW (2005). Panel of prototypical infectious molecular HIV-1 clones containing multiple nucleoside reverse transcriptase inhibitor resistance mutations. AIDS 19(7):731-3.

Click here to access sequences.

Jie Zhang, Soo-Yon Rhee, Jonathan Taylor and Robert W. Shafer (2005). Comparison of the Precision and Sensitivity of the Antivirogram and PhenoSense HIV Drug Susceptibility Assays. JAIDS 38(4):439-444.

Click here to access data sets and statistical analyses used.

Johnston E, Winters MA, Rhee SY, Merigan TC, Schiffer CA and Shafer RW. (2004). Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistance. Antimicrobial Agents and Chemotherapy 48(12):4864-8.

Soo-Yon Rhee, Tommy Liu, Jaideep Ravela, Matthew J. Gonzales and Robert W. Shafer (2004). Distribution of Human Immunodeficiency Virus Type 1 Protease and Reverse Transcriptase Mutation Patterns in 4,183 Persons Undergoing Genotypic Resistance Testing. Antimicrobial Agents and Chemotherapy 48(8):3122-3126.

Rami Kantor, Robert W. Shafer, Stephen Follansbee, Jonathan Taylor, David Shilane, Leo Hurley, Dong-Phuong Nguyen, David Katzenstein, and W. Jeffrey Fessel (2004). Evolution of resistance to drugs in HIV-1-infected patients failing antiretroviral therapy. AIDS 18(11):1503-1511.

Amit Kapoor, Morris Jones, Robert W. Shafer, Soo-Yon Rhee, Powel Kazanjian, and Eric L. Delwart (2004). Sequencing-based detection of low-frequency human immunodeficiency virus type 1 drug-resistant mutants by an RNA/DNA heteroduplex generator-tracking assay.

Gonzales MJ, Johnson E, Dupnik KM, Imamichi T, Shafer RW.(2003) Colinearity of reverse transcriptase inhibitor resistance mutations detected by population-based sequencing. JAIDS,1;34(4):398-402

Matthew J. Gonzales, Ilana Belitskaya, Kathryn M. Dupnik, Soo-Yon Rhee and Robert W. Shafer. (2003) Protease and Reverse Transcriptase Mutation Patterns in HIV Type 1 Isolates from Heavily Treated Persons: Comparison of Isolates from Northern California with Isolates from Other Regions. AIDS Res Hum Retroviruses, 19:909-915

Matthew J. Gonzales, Eric Delwart, Soo-Yon Rhee, Rose Tsui, Andrew R. Zolopa, Jonathan Taylor, and Robert W. Shafer. (2003) Lack of Detectable Human Immunodeficiency Virus Type 1 Superinfection during 1072 Person-Years of Observation. Journal of Infectious Diseases, 188(3):397-405

Jaideep Ravela, Bradley J. Betts, Francoise Brun-Vézinet, Anne-Mieke Vandamme, Diane Descamps, Kristel Van Laethem, Kate Smith, Jonathan M. Schapiro, Dean Winslow, Caroline Reid, Robert W. Shafer (2003). HIV-1 Protease and Reverse Transcriptase Mutation Patterns Responsible for Discordances Between Genotypic Drug Resistance Interpretation Algorithms JAIDS 33(1):8-14

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Thomas D. Wu, Celia A. Schiffer, Matthew J. Gonzales, Jonathan Taylor, Rami Kantor, Sunwen Chou, Dennis Israelski, Andrew R. Zolopa, W. Jeffrey Fessel, and Robert W. Shafer (2003). Mutation Patterns and Structural Correlates in HIV-1 Protease Following Varying Degrees of Protease Inhibitor Treatment J. Virol. 77(8): 4836-4847.

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Matthew J. Gonzales, Thomas D. Wu, Jonathan Taylor, Ilana Belitskaya, Rami Kantor, Dennis Israelski, Sunwen Chou, Andrew R. Zolopa, W. Jeffrey Fessel, and Robert W. Shafer (2003). Extended spectrum of HIV-1 reverse transcriptase mutations in patients receiving multiple nucleoside analog inhibitors AIDS 17(6):791-799.

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Rami Kantor, Lynn S. Zijenah, Robert W. Shafer, Solomon Mutetwa, Elizabeth Johnston, Robert Lloyd, Andrea Von Lieven, Dennis Israelski, and David A. Katzenstein (2002). HIV-1 subtype C reverse transcriptase and protease genotypes in Zimbabwean patients failing antiretroviral therapy AIDS Res Hum Retroviruses, 18(18):1407-13.

Sarah Palmer, Dominique Vuitton, Matthew J. Gonzales, Agnés Bassignot, and Robert W. Shafer (2002) Reverse Transcriptase and Protease Sequence Evolution in Two HIV-1-Infected Couples JAIDS, 31(3):285-290.

Susan H. Eshleman, Matthew J. Gonzales, Graziella Becker-Pergola, Shawn C. Cunningham, Laura A. Guay, G. Brooks Jackson, and Robert W. Shafer (2002) Identification of Ugandan HIV Type 1 Variants with Unique Patterns of Recombination in pol Involving Subtypes A and D AIDS Research and Human Retroviruses, 18:507-511.

Rami Kantor, W. Jeffrey Fessel, Andrew R. Zolopa, Dennis Israelski, Nancy Shulman, Jose G. Montoya Michael Harbour, Jonathan M. Schapiro and Robert W. Shafer. (2002) Evolution of primary protease inhibitor resistance mutations during protease inhibitor salvage therapy Antimicrobial Agents and Chemotherapy, 46:1086-1092.

Matthew J. Gonzales, Rhoderick N. Machekano, and Robert W. Shafer. (2001) Human immunodeficiency virus type 1 reverse-transcriptase and protease subtypes: classification, amino acid mutation patterns, and prevalence in a northern california clinic-based population. Journal of Infectious Diseases, 184:998-1006.

Shafer RW, Hertogs K, Zolopa AR, Warford A, Bloor S, Betts BJ, Merigan TC, Harrigan R, Larder BA(2001). High Degree of Interlaboratory Reproducibility of Human Immunodeficiency Virus Type 1 Protease and Reverse Transcriptase Sequencing of Plasma Samples from Heavily Treated Patients. Journal of Clinical Microbiology 39(4):1522-9

Robert W. Shafer, Phillip Hsu, Amy K. Patick, Charles Craig, and Volker Brendel. (1999) Identification of biased amino acid substitution patterns in human immunodeficiency virus type 1 isolates from patients treated with protease inhibitors. Journal of Virology, 73:6197-6202.

Andrew R. Zolopa, MD; Robert W. Shafer, MD; Ann Warford, PhD; Jose G. Montoya, MD; Philip Hsu, BA; David Katzentein, MD; Thomas C. Merigan, MD; and Brad Efron, PhD. (1999) HIV-1 Genotypic Resistance Patterns Predict Response to Saquinavir-Ritonavir Therapy in Patients in Whom Previous Protease Inhibitor Therapy Had Failed. Annals of Internal Medicine, 131(11):813-21

Paredes R, Tzou PL, van Zyl G, Barrow G, Camacho R, Carmona S, Grant PM, Gupta RK, Hamers RL, Harrigan PR, Jordan MR, Kantor R, Katzenstein DA, Kuritzkes DR, Maldarelli F, Otelea D, Wallis CL, Schapiro JM, Shafer RW (2017). Collaborative update of a rule-based expert system for HIV-1 genotypic resistance test interpretation. PLoS One., 2017 Jul 28.

Tzou PL, Huang X, Shafer RW (2017). NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences. BMC Bioinformatics, 2017 March 1

Tang MW, Liu TF, Shafer RW. (2012). The HIVdb system for HIV-1 genotypic resistance interpretation. Intervirology 2012;55(2):98-101. Epub 2012 Jan 24

de Oliveira T, Shafer RW, Seebregts C (2010). Public database for HIV drug resistance in southern Africa. Nature, 2010 Apr 1;464(7289):673

Gifford RJ, Liu TF, Rhee SY, Kiuchi M, Hue S, Pillay D, Shafer RW (2009). The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance. Bioinformatics, 2009 Mar 20.

Bradley J. Betts and Robert W. Shafer, (2003) Algorithm Specification Interface for Human Immunodeficiency Virus Type 1 Genotypic Interpretation. Journal of Clinical Microbiology, 41(6), 2792-4.

Soo-Yon Rhee, Matthew J. Gonzales, Rami Kantor, Bradley J. Betts, Jaideep Ravela, and Robert W. Shafer (2003) Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Research, 31(1), 298-303.

Matthew J. Gonzales, Jonathan M. Dugan, and Robert W. Shafer (2002) Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN) Bioinformatics, 18(6), 886-887.

Rami Kantor, Rhoderick Machekano, Matthew J. Gonzales, Kathryn Dupnik, Jonathan M. Shapiro, and Robert W. Shafer. (2001) Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs Nucleic Acids Research, 29(1), 296-299.

Robert W. Shafer, Duane R. Jung, and Bradley J. Betts. (2000) Human immunodeficiency virus type 1 reverse transcriptase and protease mutation search engine for queries. Nature Medicine, 6(11), 1290-1292.

Robert W. Shafer, Duane R. Jung, Bradley J. Betts, Yinong Xi, and Matthew J. Gonzales. (2000) Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Research, 28(1), 346-348.

Robert W. Shafer, Derek Stevenson, and Bryan Chan. (1999) Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Research, 27(1), 348-352.

Shafer RW and Frenkel LM (2018). The Clinical Implications of Pretreatment Drug Resistance—A Moving Target. Clinical Infect Dis., 2018 Oct 10.

Shafer RW (2017). Human Immunodeficiency Virus Type 1 Drug Resistance Mutations Update. J Infect Dis., 2017 Sep 15.

Clutter DS, Jordan MR, Bertagnolio S, Shafer RW (2016). HIV-1 drug resistance and resistance testing. Infect Genet Evol. 2016 Dec

Sean E. Collins, Philip M. Grant, Robert W. Shafer (2016). Modifying Antiretroviral Therapy in Virologically Suppressed HIV-1-Infected Patients. Drugs 2016 Jan;76(1):75-98

Pennings PS, Holmes SP, Shafer RW (2014). HIV-1 transmission networks in a small world. JID. 2014 Jan 15

Tang MW, and Shafer RW (2012). HIV-1 Antiretroviral Resistance: Scientific Principles and Clinical Applications. Drugs 2012 Jun 18;72(9)

Blanco JL, Varghese V, Rhee SY, Gatell JM, Shafer RW (2011). HIV-1 integrase inhibitor resistance and its clinical implications. JID 2011 May 1;203(9):1204-14

Shafer RW (2009). The challenge of antiretroviral drug resistance in HIV-1-infected children. Jornal de pediatria 2009 Mar-Apr;85(2):91-4

Shafer RW (2009). Low-abundance drug-resistant HIV-1 variants: finding significance in an era of abundant diagnostic and therapeutic options. Journal of Infectious Diseases 2009 Mar 1;199(5):610-2

Shafer RW, Schapiro JM (2008). HIV-1 Drug Resistance Mutations: an Updated Framework for the Second Decade of HAART. AIDS, Rev. 2008;10:67-84

Shafer RW(2006). Rationale and Uses of a Public HIV Drug-Resistance Database. Journal of Infectious Diseases 194 Suppl 1:S51-8

Liu TF, Shafer RW(2006). Web Resources for HIV type 1 Genotypic-Resistance Test Interpretation. Clin Infect Dis 42(11):1608-18. Epub 2006 Apr 28

Shafer RW and Schapiro JM. (2005) Drug resistance and antiretroviral drug development. J Antimicrob Chemother

Robert W. Shafer (2002) Genotypic testing for human immunodeficiency virus type 1 drug resistance Clinical Microbiology Reviews 15:247-277

Robert W. Shafer, Kathryn M. Dupnik, Mark A. Winters, and Susan H. Eshleman. (2001) A guide to HIV-1 reverse transcriptase and protease sequencing for drug resistance studies. Human Retroviruses and AIDS, Theoretical Biology and Biophysics. Los Alamos National Laboratories.

Robert W. Shafer, Rami Kantor, and Matthew J. Gonzales. (2000) The genetic basis of HIV-1 resistance to reverse transcriptase and protease inhibitors AIDS Reviews, 2, 211-228.

Robert W. Shafer, Stanley C. Deresinski (2000) Human immunodeficiency virus information on the web: A guided tour. Clin Infect Dis, 31(2):568-77.

Margeridon-Thermet S, Svarovskaia ES, Babrzadeh F, Martin R, Liu TF, Pacold M, Reuman EC, Holmes SP, Borroto-Esoda K, Shafer RW (2013). Low-level persistence of drug resistance mutations in hepatitis B virus-infected subjects with a past history of Lamivudine treatment. Antimicrobial Agents and Chemotherapy, 2013 Jan.

Margeridon-Thermet S, Shafer RW. (2010). Comparison of the Mechanisms of Drug Resistance among HIV, Hepatitis B, and Hepatitis C.   Viruses, 2010 Dec.

Reuman EC, Margeridon-Thermet S, Caudill HB, Liu T, Borroto-Esoda K, Svarovskaia ES, Holmes S, Shafer RW. (2010). A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads.   Bioinformatics, 2010 Oct.

Rhee SY, Margeridon-Thermet S, Nguyen MH, Liu TF, Kagan RM, Beggel B, Verheyen J, Kaiser R, Shafer RW. (2010). Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery.   Antiviral Res., 2010 Sept.

Margeridon-Thermet S, Shulman NS, Ahmed A, Shahriar R, Liu T, Wang C, Holmes SP, Babrzadeh F, Gharizadeh F, Hanczaruk B, Simen BB, Egholm M and Shafer RW (2009) Nancy Shulman, Robert W. Shafer (2007) Ultra-Deep Pyrosequencing of Hepatitis B Virus Quasispecies from Nucleoside and Nucleotide Reverse-Transcriptase Inhibitor (NRTI)-Treated Patients and NRTI-Naive Patients   Journal of Infectious Diseases, 2009 May 1;199(9):1275-85.

Gifford RJ, Katzourakis A, Tristem M, Pybus OG, Winters M, Shafer RW (2008). A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proceedings of National Academy of Sciences of the United States of America, 2008 Dec 23;105(51):20362-7

Tzou PL, Tao K, Sahoo MK, Pond SK, Pinsky BA, Shafer RW (2022). Sierra SARS-CoV-2 sequence and antiviral resistance analysis program Journal of Clinical Virology. 2022 Dec.

Tao K, Tzou PL, Pond SK, Ioannidis JPA, Shafer RW (2022). Susceptibility of SARS-CoV-2 Omicron Variants to Therapeutic Monoclonal Antibodies: Systematic Review and Meta-analysis Microbiology Spectrum. 2022 Jun.

Tzou PL, Tao K, Pond SK, Shafer RW (2022). Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons PLOS ONE. 2022 Mar.

Tao K, Tzou PL, Nouhin J, Gupta RK, Oliveira T, Pond SK, Fera D, Shafer RW (2021). The biological and clinical significance of emerging SARS-CoV-2 variants Nature Review Genetics. 2021 Sep.

Tao K, Tzou PL, Nouhin J, Bonilla H, Jagannathan P, Shafer RW (2021). SARS-CoV-2 Antiviral Therapy Clinical Microbiology Reviews. 2021 Jul.

Shafer RW (2020). A SARS-CoV-2 antiviral therapy score card Global Health & Medicine. 2020 Sep.

Tzou PL, Tao K, Nouhin J, Rhee SY, Hu BD, Pai S, Parkin N, Shafer RW (2020). Coronavirus Antiviral Research Database (CoV-RDB): An Online Database Designed to Facilitate Comparisons between Candidate Anti-Coronavirus Compounds Viruses. 2020 Sep.

Nancy Shulman, Robert W. Shafer (2007) Case files from Stanford University Medical Center: Ten Years of HAART: A Long Wait for Full HIV Suppression   Medscape General Medicine 2007;9(1):10.

Robert W. Shafer, Dong Phuong Nguyen, Jeffrey Fessel (2006) Case files from Stanford University Medical Center: Drug Resistance Testing in Previously Untreated Patients with HIV -- Knowing What to Look for and Choosing Appropriate Therapy   Medscape General Medicine 2006;8(3):32.

Minghsun Liu, Mark Holodniy, Andrew R. Zolopa, Robert W. Shafer (2006) Case files from Stanford University Medical Center: The Initial Presentation of HIV-1 Infection -- Where Public and Personal Health Meet   Medscape General Medicine 2006;8(1):24.