Robert W. Shafer

Professional Education

Residency: Lenox Hill Hospital (1986) NY

Medical Education: New York University - School Of Medicine (1983) NY

Fellowship: Stanford University School of Medicine (1993) CA

Fellowship: SUNY at Brooklyn School Of Medicine (1988) NY

Board Certification: Infectious Disease, American Board of Internal Medicine (1988)

Board Certification: Internal Medicine, American Board of Internal Medicine (1986)

Internship: Lenox Hill Hospital (1984) NY

Non-nucleoside reverse transcriptase inhibitor (NNRTI) cross-resistance: implications for preclinical evaluation of novel NNRTIs and clinical genotypic resistance testing
Melikian, G. L., Rhee, S.-Y., Varghese, V., Porter, D., White, K., & Shafer, R. W. (2014). Non-nucleoside reverse transcriptase inhibitor (NNRTI) cross-resistance: implications for preclinical evaluation of novel NNRTIs and clinical genotypic resistance testing. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 69(1), 12-20.

Prototypical Recombinant Multi-Protease-Inhibitor-Resistant Infectious Molecular Clones of Human Immunodeficiency Virus Type 1
Varghese, V., Mitsuya, Y., Fessel, W. J., Liu, T. F., Melikian, G. L., & Shafer, R. W. (2013). Prototypical Recombinant Multi-Protease-Inhibitor-Resistant Infectious Molecular Clones of Human Immunodeficiency Virus Type 1. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 57(9), 4290-4299.

Trends in Genotypic HIV-1 Antiretroviral Resistance between 2006 and 2012 in South African Patients Receiving First- and Second-Line Antiretroviral Treatment Regimens
van Zyl, G. U., Liu, T. F., Claassen, M., Engelbrecht, S., de Oliveira, T., & Shafer, R. W. (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, 8(6).

Nucleoside reverse transcriptase inhibitor resistance mutations associated with first-line Stavudine-containing antiretroviral therapy: programmatic implications for countries phasing out Stavudine.
Tang, M. W., Rhee, S.-Y., Bertagnolio, S., Ford, N., Holmes, S., & Shafer, R. W. (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, 207, S70-7.

Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance
Babrzadeh, F., Varghese, V., Pacold, M., Liu, T. F., Nyren, P., & Shafer, R. W. (2013). Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 68(2), 414-418.

Low-Level Persistence of Drug Resistance Mutations in Hepatitis B Virus-Infected Subjects with a Past History of Lamivudine Treatment
Margeridon-Thermet, S., Svarovskaia, E. S., Babrzadeh, F., Martin, R., Liu, T. F., & Shafer, R. W. (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, 57(1), 343-349.

Panel of Prototypical Recombinant Infectious Molecular Clones Resistant to Nevirapine, Efavirenz, Etravirine, and Rilpivirine
Balamane, M., Varghese, V., Melikian, G. L., Fessel, W. J., Katzenstein, D. A., & Shafer, R. W. (2012). Panel of Prototypical Recombinant Infectious Molecular Clones Resistant to Nevirapine, Efavirenz, Etravirine, and Rilpivirine. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 56(8), 4522-4524.

A Review of the Virological Efficacy of the 4 World Health Organization-Recommended Tenofovir-Containing Regimens for Initial HIV Therapy
Tang, M. W., Kanki, P. J., & Shafer, R. W. (2012). A Review of the Virological Efficacy of the 4 World Health Organization-Recommended Tenofovir-Containing Regimens for Initial HIV Therapy. CLINICAL INFECTIOUS DISEASES, 54(6), 862-875.

HIV-1 Antiretroviral Resistance: Scientific Principles and Clinical Applications
Tang, M. W., & Shafer, R. W. (2012). HIV-1 Antiretroviral Resistance: Scientific Principles and Clinical Applications. DRUGS, 72(9), E1-E25.

The efficacy of an anti-CD4 monoclonal antibody for HIV-1 treatment
Fessel, W. J., Anderson, B., Follansbee, S. E., Winters, M. A., Lewis, S. T., & Shafer, R. W. (2011). The efficacy of an anti-CD4 monoclonal antibody for HIV-1 treatment. ANTIVIRAL RESEARCH, 92(3), 484-487.

HIV-1 Integrase Inhibitor Resistance and Its Clinical Implications
Blanco, J.-L., Varghese, V., Rhee, S.-Y., Gatell, J. M., & Shafer, R. W. (2011). HIV-1 Integrase Inhibitor Resistance and Its Clinical Implications. JOURNAL OF INFECTIOUS DISEASES, 203(9), 1204-1214.

Comparison of the Mechanisms of Drug Resistance among HIV, Hepatitis B, and Hepatitis C
Margeridon-Thermet, S., & Shafer, R. W. (2010). Comparison of the Mechanisms of Drug Resistance among HIV, Hepatitis B, and Hepatitis C. VIRUSES-BASEL, 2(12), 2696-2739.

HIV-1 Protease Mutations and Protease Inhibitor Cross-Resistance
Rhee, S.-Y., Taylor, J., Fessel, W. J., Kaufman, D., Towner, W., & Shafer, R. W. (2010). HIV-1 Protease Mutations and Protease Inhibitor Cross-Resistance. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 54(10), 4253-4261.

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
Varghese, V., Shahriar, R., Rhee, S.-Y., Liu, T., Simen, B. B., & Shafer, R. W. (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-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES, 52(3), 309-315.

Nonpolymorphic Human Immunodeficiency Virus Type 1 Protease and Reverse Transcriptase Treatment-Selected Mutations
Shahriar, R., Rhee, S.-Y., Liu, T. F., Fessel, W. J., Scarsella, A., & Shafer, R. W. (2009). Nonpolymorphic Human Immunodeficiency Virus Type 1 Protease and Reverse Transcriptase Treatment-Selected Mutations. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 53(11), 4869-4878.

Predictive Value of HIV-1 Genotypic Resistance Test Interpretation Algorithms
Rhee, S.-Y., Fessel, W. J., Liu, T. F., Marlowe, N. M., Rowland, C. M., & Shafer, R. W. (2009). Predictive Value of HIV-1 Genotypic Resistance Test Interpretation Algorithms. JOURNAL OF INFECTIOUS DISEASES, 200(3), 453-463.

Ultra-Deep Pyrosequencing of Hepatitis B Virus Quasispecies from Nucleoside and Nucleotide Reverse-Transcriptase Inhibitor (NRTI)-Treated Patients and NRTI-Naive Patients
Margeridon-Thermet, S., Shulman, N. S., Ahmed, A., Shahriar, R., Liu, T., & Shafer, R. W. (2009). 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, 199(9), 1275-1285.

Drug Resistance Mutations for Surveillance of Transmitted HIV-1 Drug-Resistance: 2009 Update
Bennett, D. E., Camacho, R. J., Otelea, D., Kuritzkes, D. R., Fleury, H., & Shafer, R. W. (2009). Drug Resistance Mutations for Surveillance of Transmitted HIV-1 Drug-Resistance: 2009 Update. PLOS ONE, 4(3).

Low-Abundance Drug-Resistant HIV-1 Variants: Finding Significance in an Era of Abundant Diagnostic and Therapeutic Options
Shafer, R. W. (2009). Low-Abundance Drug-Resistant HIV-1 Variants: Finding Significance in an Era of Abundant Diagnostic and Therapeutic Options. JOURNAL OF INFECTIOUS DISEASES, 199(5), 610-612.

A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution
Gifford, R. J., Katzourakis, A., Tristem, M., Pybus, O. G., Winters, M., & Shafer, R. W. (2008). A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105(51), 20362-20367.

Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance
Wang, C., Mitsuya, Y., Gharizadeh, B., Ronaghi, M., & Shafer, R. W. (2007). Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance. GENOME RESEARCH, 17(8), 1195-1201.

HIV-1 subtype B protease and reverse transcriptase amino acid covariation
Rhee, S.-Y., Liu, T. F., Holmes, S. P., & Shafer, R. W. (2007). HIV-1 subtype B protease and reverse transcriptase amino acid covariation. PLOS COMPUTATIONAL BIOLOGY, 3(5), 836-843.

Genotypic predictors of human immunodeficiency virus type 1 drug resistance
Rhee, S.-Y., Taylor, J., Wadhera, G., Ben-Hur, A., Brutlag, D. L., & Shafer, R. W. (2006). Genotypic predictors of human immunodeficiency virus type 1 drug resistance. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103(46), 17355-17360.

Rationale and uses of a public HIV drug-resistance database
Shafer, R. W. (2006). Rationale and uses of a public HIV drug-resistance database. JOURNAL OF INFECTIOUS DISEASES, 194, S51-S58.

Web resources for HIV type 1 genotypic-resistance test interpretation
Liu, T. F., & Shafer, R. W. (2006). Web resources for HIV type 1 genotypic-resistance test interpretation. CLINICAL INFECTIOUS DISEASES, 42(11), 1608-1618.

HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes
Rhee, S. Y., Kantor, R., Katzenstein, D. A., Camacho, R., Morris, L., & Shafer, R. W. (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.

HIV-1 protease and reverse-transcriptase mutations: Correlations with antiretroviral therapy in subtype B isolates and implications for drug-resistance surveillance
Rhee, S. Y., Fessel, W. J., Zolopa, A. R., Hurley, L., Liu, T., & Shafer, R. W. (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, 192(3), 456-465.

Drug resistance and antiretroviral drug development
Shafer, R. W., & Schapiro, J. M. (2005). Drug resistance and antiretroviral drug development. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 55(6), 817-820.

Panel of prototypical infectious molecular HIV-1 clones containing multiple nucleoside reverse transcriptase inhibitor resistance mutations
Johnston, E., Dupnik, K. M., Gonzales, M. J., Winters, M. A., Rhee, S. Y., & Shafer, R. W. (2005). Panel of prototypical infectious molecular HIV-1 clones containing multiple nucleoside reverse transcriptase inhibitor resistance mutations. AIDS, 19(7), 731-733.

Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotype: Results of a global collaboration
Kantor, R., Katzenstein, D. A., Efron, B., CARVALHO, A. P., Wynhoven, B., & Shafer, R. W. (2005). Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotype: Results of a global collaboration. PLOS MEDICINE, 2(4), 325-337.

Comparison of four-drug regimens and pairs of sequential three-drug regimens as initial therapy for HIV-1 infection
Shafer, R. W., Smeaton, L. M., Robbins, G. K., De Gruttola, V., Snyder, S. W., & Doolan, A. (2003). Comparison of four-drug regimens and pairs of sequential three-drug regimens as initial therapy for HIV-1 infection. NEW ENGLAND JOURNAL OF MEDICINE, 349(24), 2304-2315.

Colinearity of reverse transcriptase inhibitor resistance mutations detected by population-based sequencing
Gonzales, M. J., JOHNSON, E., Dupnik, K. M., Imamichi, T., & Shafer, R. W. (2003). Colinearity of reverse transcriptase inhibitor resistance mutations detected by population-based sequencing. JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES, 34(4), 398-402.

Lack of detectable human immunodeficiency virus type 1 superinfection during 1072 person-years of observation
Gonzales, M. J., Delwart, E., Rhee, S. Y., Tsui, R., Zolopa, A. R., & Shafer, R. W. (2003). Lack of detectable human immunodeficiency virus type 1 superinfection during 1072 person-years of observation. JOURNAL OF INFECTIOUS DISEASES, 188(3), 397-405.

Extended spectrum of HIV-1 reverse transcriptase mutations in patients receiving multiple nucleoside analog inhibitors
Gonzales, M. J., Wu, T. D., Taylor, J., Belitskaya, F., Kantor, R., & Shafer, R. W. (2003). Extended spectrum of HIV-1 reverse transcriptase mutations in patients receiving multiple nucleoside analog inhibitors. AIDS, 17(6), 791-799.

Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments
Wu, T. D., Schiffer, C. A., Gonzales, M. J., Taylor, J., Kantor, R., & Shafer, R. W. (2003). Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments. JOURNAL OF VIROLOGY, 77(8), 4836-4847.

Human immunodeficiency virus reverse transcriptase and protease sequence database
Rhee, S. Y., Gonzales, M. J., Kantor, R., Betts, B. J., Ravela, J., & Shafer, R. W. (2003). Human immunodeficiency virus reverse transcriptase and protease sequence database. NUCLEIC ACIDS RESEARCH, 31(1), 298-303.

Genotypic testing for human immunodeficiency virus type 1 drug resistance
Shafer, R. W. (2002). Genotypic testing for human immunodeficiency virus type 1 drug resistance. CLINICAL MICROBIOLOGY REVIEWS, 15(2), 247-?.

Human immunodeficiency virus type 1 reverse transcriptase and protease mutation search engine for queries
Shafer, R. W., Jung, D. R., & Betts, B. J. (2000). Human immunodeficiency virus type 1 reverse transcriptase and protease mutation search engine for queries. NATURE MEDICINE, 6(11), 1290-1292.

HIV-1 genotypic resistance patterns predict response to saquinavir-ritonavir therapy in patients in whom previous protease inhibitor therapy had failed
Zolopa, A. R., Shafer, R. W., Warford, A., Montoya, J. G., Hsu, P., & Efron, B. (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-?.

Sequence and drug susceptibility of subtype C protease from human immunodeficiency virus type 1 seroconverters in Zimbabwe
Shafer, R. W., Chuang, T. K., Hsu, P., White, C. B., & Katzenstein, D. A. (1999). Sequence and drug susceptibility of subtype C protease from human immunodeficiency virus type 1 seroconverters in Zimbabwe. AIDS RESEARCH AND HUMAN RETROVIRUSES, 15(1), 65-69.

Multiple concurrent reverse transcriptase and protease mutations and multidrug resistance of HIV-1 isolates from heavily treated patients
Shafer, R. W., Winters, M. A., Palmer, S., & Merigan, T. C. (1998). Multiple concurrent reverse transcriptase and protease mutations and multidrug resistance of HIV-1 isolates from heavily treated patients. ANNALS OF INTERNAL MEDICINE, 128(11), 906-911.

Sequence and drug susceptibility of subtype C reverse transcriptase from human immunodeficiency virus type 1 seroconverters in Zimbabwe
Shafer, R. W., Eisen, J. A., Merigan, T. C., & Katzenstein, D. A. (1997). Sequence and drug susceptibility of subtype C reverse transcriptase from human immunodeficiency virus type 1 seroconverters in Zimbabwe. JOURNAL OF VIROLOGY, 71(7), 5441-5448.

Tuberculosis in patients infected with human immunodeficiency virus: Perspective on the past decade
Shafer, R. W., & Edlin, B. R. (1996). Tuberculosis in patients infected with human immunodeficiency virus: Perspective on the past decade. CLINICAL INFECTIOUS DISEASES, 22(4), 683-704.

Predictors of survival in HIV-infected tuberculosis patients
Shafer, R. W., Bloch, A. B., Larkin, C., VASUDAVAN, V., SELIGMAN, S., & Cauthen, G. (1996). Predictors of survival in HIV-infected tuberculosis patients. AIDS, 10(3), 269-272.

TEMPORAL TRENDS AND TRANSMISSION PATTERNS DURING THE EMERGENCE OF MULTIDRUG-RESISTANT TUBERCULOSIS IN NEW-YORK-CITY - A MOLECULAR EPIDEMIOLOGIC ASSESSMENT
Shafer, R. W., Small, P. M., Larkin, C., Singh, S. P., Kelly, P., & Chirgwin, K. D. (1995). TEMPORAL TRENDS AND TRANSMISSION PATTERNS DURING THE EMERGENCE OF MULTIDRUG-RESISTANT TUBERCULOSIS IN NEW-YORK-CITY - A MOLECULAR EPIDEMIOLOGIC ASSESSMENT. JOURNAL OF INFECTIOUS DISEASES, 171(1), 170-176.

COMBINATION THERAPY WITH ZIDOVUDINE AND DIDANOSINE SELECTS FOR DRUG-RESISTANT HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1 STRAINS WITH UNIQUE PATTERNS OF POL GENE-MUTATIONS
Shafer, R. W., Kozal, M. J., Winters, M. A., Iversen, A. Kn., Katzenstein, D. A., & Merigan, T. C. (1994). COMBINATION THERAPY WITH ZIDOVUDINE AND DIDANOSINE SELECTS FOR DRUG-RESISTANT HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1 STRAINS WITH UNIQUE PATTERNS OF POL GENE-MUTATIONS. JOURNAL OF INFECTIOUS DISEASES, 169(4), 722-729.

EXOGENOUS REINFECTION WITH MULTIDRUG-RESISTANT MYCOBACTERIUM-TUBERCULOSIS IN PATIENTS WITH ADVANCED HIV-INFECTION
Small, P. M., Shafer, R. W., Hopewell, P. C., Singh, S. P., MURPHY, M. J., & SCHOOLNIK, G. K. (1993). EXOGENOUS REINFECTION WITH MULTIDRUG-RESISTANT MYCOBACTERIUM-TUBERCULOSIS IN PATIENTS WITH ADVANCED HIV-INFECTION. NEW ENGLAND JOURNAL OF MEDICINE, 328(16), 1137-1144.

EXTRAPULMONARY TUBERCULOSIS IN PATIENTS WITH HUMAN-IMMUNODEFICIENCY-VIRUS INFECTION
Shafer, R. W., Kim, D. S., Weiss, J. P., & Quale, J. M. (1991). EXTRAPULMONARY TUBERCULOSIS IN PATIENTS WITH HUMAN-IMMUNODEFICIENCY-VIRUS INFECTION. MEDICINE, 70(6), 384-397.

HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure.
Sangeda, R. Z., Theys, K., Beheydt, G., Rhee, S.-Y., Deforche, K., & Vandamme, A.-M. (2013). HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 19, 349-360.

Drug Resistance Mutations in HIV-1.
D'Aquila, R. T., Schapiro, J. M., Brun-Vézinet, F., Clotet, B., & Richman, D. D. Drug Resistance Mutations in HIV-1. Topics in HIV medicine : a publication of the International AIDS Society, USA, 10(5), 21-25.

In Vitro HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitors & In Silico Phenotypic Analysis
Rath, B. A., Yousef, K. P., Katzenstein, D. K., Shafer, R. W., Schuette, C., & Merigan, T. C. (2013). In Vitro HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitors & In Silico Phenotypic Analysis. PLOS ONE, 8(4).

Cooperative Effects of Drug-Resistance Mutations in the Flap Region of HIV-1 Protease
Foulkes-Murzycki, J. E., Rosi, C., Yilmaz, N. K., Shafer, R. W., & Schiffer, C. A. (2013). Cooperative Effects of Drug-Resistance Mutations in the Flap Region of HIV-1 Protease. ACS CHEMICAL BIOLOGY, 8(3), 513-518.

Update of the drug resistance mutations in HIV-1: March 2013.
Johnson, V. A., Calvez, V., Gunthard, H. F., Paredes, R., Pillay, D., & Richman, D. D. (2013). Update of the drug resistance mutations in HIV-1: March 2013. Topics in antiviral medicine, 21(1), 6-14.

In vitro HIV-1 evolution in response to triple reverse transcriptase inhibitors & in silico phenotypic analysis.
Rath, B. A., Yousef, K. P., Katzenstein, D. K., Shafer, R. W., Schütte, C., & Merigan, T. C. (2013). In vitro HIV-1 evolution in response to triple reverse transcriptase inhibitors & in silico phenotypic analysis. PloS one, 8(4).

T Cell Activation Markers and African Mitochondrial DNA Haplogroups among Non-Hispanic Black Participants in AIDS Clinical Trials Group Study 384
Hulgan, T., Robbins, G. K., Kalams, S. A., Samuels, D. C., Grady, B., & Pollard, R. B. (2012). T Cell Activation Markers and African Mitochondrial DNA Haplogroups among Non-Hispanic Black Participants in AIDS Clinical Trials Group Study 384. PLOS ONE, 7(8).

Development of Elvitegravir Resistance and Linkage of Integrase Inhibitor Mutations with Protease and Reverse Transcriptase Resistance Mutations
Winters, M. A., Lloyd, R. M., Shafer, R. W., Kozal, M. J., Miller, M. D., & Holodniy, M. (2012). Development of Elvitegravir Resistance and Linkage of Integrase Inhibitor Mutations with Protease and Reverse Transcriptase Resistance Mutations. PLOS ONE, 7(7).

Automating HIV Drug Resistance Genotyping with RECall, a Freely Accessible Sequence Analysis Tool
Woods, C. K., Brumme, C. J., Liu, T. F., Chui, C. Ks., Chu, A. L., & Harrigan, P. R. (2012). Automating HIV Drug Resistance Genotyping with RECall, a Freely Accessible Sequence Analysis Tool. JOURNAL OF CLINICAL MICROBIOLOGY, 50(6), 1936-1942.

Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1
Babrzadeh, F., Jalili, R., Wang, C., Shokralla, S., Pierce, S., & Stambuk, B. U. (2012). Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1. MOLECULAR GENETICS AND GENOMICS, 287(6), 485-494.

Standardized representation, visualization and searchable repository of antiretroviral treatment-change episodes
Rhee, S.-Y., Luis Blanco, J., Liu, T. F., Pere, I., Kaiser, R., & Shafer, R. W. (2012). Standardized representation, visualization and searchable repository of antiretroviral treatment-change episodes. AIDS RESEARCH AND THERAPY, 9.

Standardized Comparison of the Relative Impacts of HIV-1 Reverse Transcriptase (RT) Mutations on Nucleoside RT Inhibitor Susceptibility
Melikian, G. L., Rhee, S.-Y., Taylor, J., Fessel, W. J., Kaufman, D., & Shafer, R. W. (2012). Standardized Comparison of the Relative Impacts of HIV-1 Reverse Transcriptase (RT) Mutations on Nucleoside RT Inhibitor Susceptibility. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 56(5), 2305-2313.

The HIVdb System for HIV-1 Genotypic Resistance Interpretation
Tang, M. W., Liu, T. F., & Shafer, R. W. (2012). The HIVdb System for HIV-1 Genotypic Resistance Interpretation. INTERVIROLOGY, 55(2), 98-101.

A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes
Doherty, K. M., Nakka, P., King, B. M., Rhee, S.-Y., Holmes, S. P., & Radhakrishnan, M. L. (2011). A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes. BMC BIOINFORMATICS, 12.

2011 update of the drug resistance mutations in HIV-1.
Johnson, V. A., Calvez, V., Günthard, H. F., Paredes, R., Pillay, D., & Richman, D. D. (2011). 2011 update of the drug resistance mutations in HIV-1. Topics in antiviral medicine, 19(4), 156-164.

Loss of Protease Dimerization Inhibition Activity of Darunavir Is Associated with the Acquisition of Resistance to Darunavir by HIV-1
Koh, Y., Aoki, M., Danish, M. L., Aoki-Ogata, H., Amano, M., & Mitsuya, H. (2011). Loss of Protease Dimerization Inhibition Activity of Darunavir Is Associated with the Acquisition of Resistance to Darunavir by HIV-1. JOURNAL OF VIROLOGY, 85(19), 10079-10089.

Prediction of response to antiretroviral therapy by human experts and by the EuResist data-driven expert system (the EVE study)
Zazzi, M., Kaiser, R., Sonnerborg, A., Struck, D., Altmann, A., & Incardona, F. (2011). Prediction of response to antiretroviral therapy by human experts and by the EuResist data-driven expert system (the EVE study). HIV MEDICINE, 12(4), 211-218.

Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery
Rhee, S.-Y., Margeridon-Thermet, S., Nguyen, M. H., Liu, T. F., Kagan, R. M., & Shafer, R. W. (2010). Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery. ANTIVIRAL RESEARCH, 88(3), 269-275.

A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads
Reuman, E. C., Margeridon-Thermet, S., Caudill, H. B., Liu, T., Borroto-Esoda, K., & Shafer, R. W. (2010). A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads. BIOINFORMATICS, 26(23), 2929-2932.

HIV-1 Integrase Sequence Variability in Antiretroviral Naive Patients and in Triple-Class Experienced Patients Subsequently Treated with Raltegravir
Varghese, V., Liu, T. F., Rhee, S.-Y., Libiran, P., Trevino, C., & Shafer, R. W. (2010). HIV-1 Integrase Sequence Variability in Antiretroviral Naive Patients and in Triple-Class Experienced Patients Subsequently Treated with Raltegravir. AIDS RESEARCH AND HUMAN RETROVIRUSES, 26(12), 1323-1326.

Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape
Theys, K., Deforche, K., Beheydt, G., Moreau, Y., Van Laethem, K., & Vandamme, A.-M. (2010). Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape. BMC BIOINFORMATICS, 11.

Long-term increase in CD4(+) T-cell counts during combination antiretroviral therapy for HIV-1 infection
Lok, J. J., Bosch, R. J., Benson, C. A., Collier, A. C., Robbins, G. K., & Hughes, M. D. (2010). Long-term increase in CD4(+) T-cell counts during combination antiretroviral therapy for HIV-1 infection. AIDS, 24(12), 1867-1876.

Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations
Reuman, E. C., Rhee, S.-Y., Holmes, S. P., & Shafer, R. W. (2010). Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 65(7), 1477-1485.

Nucleic Acid Template and the Risk of a PCR-Induced HIV-1 Drug Resistance Mutation
Varghese, V., Wang, E., Babrzadeh, F., Bachmann, M. H., Shahriar, R., & Shafer, R. W. (2010). Nucleic Acid Template and the Risk of a PCR-Induced HIV-1 Drug Resistance Mutation. PLOS ONE, 5(6).

African Mitochondrial DNA Subhaplogroups and Peripheral Neuropathy during Antiretroviral Therapy
Canter, J. A., Robbins, G. K., Selph, D., Clifford, D. B., Kallianpur, A. R., & Hulgan, T. (2010). African Mitochondrial DNA Subhaplogroups and Peripheral Neuropathy during Antiretroviral Therapy. JOURNAL OF INFECTIOUS DISEASES, 201(11), 1703-1707.

Predicting Tipranavir and Darunavir Resistance Using Genotypic, Phenotypic, and Virtual Phenotypic Resistance Patterns: an Independent Cohort Analysis of Clinical Isolates Highly Resistant to All Other Protease Inhibitors
Talbot, A., Grant, P., Taylor, J., Baril, J.-G., Liu, T. F., & Zolopa, A. (2010). Predicting Tipranavir and Darunavir Resistance Using Genotypic, Phenotypic, and Virtual Phenotypic Resistance Patterns: an Independent Cohort Analysis of Clinical Isolates Highly Resistant to All Other Protease Inhibitors. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 54(6), 2473-2479.

Public database for HIV drug resistance in southern Africa
de Oliveira, T., Shafer, R. W., & Seebregts, C. (2010). Public database for HIV drug resistance in southern Africa. NATURE, 464(7289), 673-673.

Panel of Prototypical Raltegravir-Resistant Infectious Molecular Clones in a Novel Integrase-Deleted Cloning Vector
Reuman, E. C., Bachmann, M. H., Varghese, V., Fessel, W. J., & Shafer, R. W. (2010). Panel of Prototypical Raltegravir-Resistant Infectious Molecular Clones in a Novel Integrase-Deleted Cloning Vector. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 54(2), 934-936.

The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance
Gifford, R. J., Liu, T. F., Rhee, S.-Y., Kiuchi, M., Hue, S., & Shafer, R. W. (2009). The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance. BIOINFORMATICS, 25(9), 1197-1198.

Human Immunodeficiency Virus Type 1 Isolates with the Reverse Transcriptase (RT) Mutation Q145M Retain Nucleoside and Nonnucleoside RT Inhibitor Susceptibility
Varghese, V., Mitsuya, Y., Shahriar, R., Bachmann, M. H., Fessel, W. J., & Shafer, R. W. (2009). Human Immunodeficiency Virus Type 1 Isolates with the Reverse Transcriptase (RT) Mutation Q145M Retain Nucleoside and Nonnucleoside RT Inhibitor Susceptibility. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 53(5), 2196-2198.

Predicting the Response to Combination Antiretroviral Therapy: Retrospective Validation of geno2pheno-THEO on a Large Clinical Database
Altmann, A., Daeumer, M., Beerenwinkel, N., Peres, Y., Schuelter, E., & Lengauer, T. (2009). Predicting the Response to Combination Antiretroviral Therapy: Retrospective Validation of geno2pheno-THEO on a Large Clinical Database. JOURNAL OF INFECTIOUS DISEASES, 199(7), 999-1006.

The challenge of antiretroviral drug resistance in HIV-1-infected children
Shafer, R. W. (2009). The challenge of antiretroviral drug resistance in HIV-1-infected children. JORNAL DE PEDIATRIA, 85(2), 91-94.

Incomplete Reconstitution of T Cell Subsets on Combination Antiretroviral Therapy in the AIDS Clinical Trials Group Protocol 384
Robbins, G. K., Spritzler, J. G., Chan, E. S., Asmuth, D. M., Gandhi, R. T., & Pollard, R. B. (2009). Incomplete Reconstitution of T Cell Subsets on Combination Antiretroviral Therapy in the AIDS Clinical Trials Group Protocol 384. CLINICAL INFECTIOUS DISEASES, 48(3), 350-361.

Biomarker discovery using targeted maximum-likelihood estimation: Application to the treatment of antiretroviral-resistant HIV infection
Bembom, O., Petersen, M. L., Rhee, S.-Y., Fessel, W. J., Sinisi, S. E., & Van der Laan, M. J. (2009). Biomarker discovery using targeted maximum-likelihood estimation: Application to the treatment of antiretroviral-resistant HIV infection. STATISTICS IN MEDICINE, 28(1), 152-172.

Advantages of predicted phenotypes and statistical learning models in inferring virological response to antiretroviral therapy from HIV genotype
Altmann, A., Sing, T., Vermeiren, H., Winters, B., Van Craenenbroeck, E., & Lengauer, T. (2009). Advantages of predicted phenotypes and statistical learning models in inferring virological response to antiretroviral therapy from HIV genotype. ANTIVIRAL THERAPY, 14(2), 273-283.

A highly prevalent and genetically diversified Picornaviridae genus in South Asian children
Kapoor, A., Victoria, J., Simmonds, P., Slikas, E., Chieochansin, T., & Delwart, E. (2008). A highly prevalent and genetically diversified Picornaviridae genus in South Asian children. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105(51), 20482-20487.

Virologic Response to Lopinavir-Ritonavir-Based Antiretroviral Regimens in a Multicenter International Clinical Cohort: Comparison of Genotypic Interpretation Scores
Grant, P., Wong, E. C., Rode, R., Shafer, R., De Luca, A., & Zolopa, A. (2008). Virologic Response to Lopinavir-Ritonavir-Based Antiretroviral Regimens in a Multicenter International Clinical Cohort: Comparison of Genotypic Interpretation Scores. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 52(11), 4050-4056.

Minority Human Immunodeficiency Virus Type 1 Variants in Antiretroviral-Naive Persons with Reverse Transcriptase Codon 215 Revertant Mutations
Mitsuya, Y., Varghese, V., Wang, C., Liu, T. F., Holmes, S. P., & Shafer, R. W. (2008). Minority Human Immunodeficiency Virus Type 1 Variants in Antiretroviral-Naive Persons with Reverse Transcriptase Codon 215 Revertant Mutations. JOURNAL OF VIROLOGY, 82(21), 10747-10755.

Bayesian network analyses of resistance pathways against efavirenz and nevirapine
Deforche, K., Camacho, R. J., Grossman, Z., Soares, M. A., Van Laethem, K., & Vandamme, A.-M. (2008). Bayesian network analyses of resistance pathways against efavirenz and nevirapine. AIDS, 22(16), 2107-2115.

Rational use of antiretroviral therapy in low-income and middle-income countries: optimizing regimen sequencing and switching
Elliott, J. H., Lynen, L., Calmy, A., De Luca, A., Shafer, R. W., & Schapiro, J. M. (2008). Rational use of antiretroviral therapy in low-income and middle-income countries: optimizing regimen sequencing and switching. AIDS, 22(16), 2053-2067.

Natural variation of HIV-1 group M integrase: Implications for a new class of antiretroviral inhibitors
Rhee, S.-Y., Liu, T. F., Kiuchi, M., Zioni, R., Gifford, R. J., & Shafer, R. W. (2008). Natural variation of HIV-1 group M integrase: Implications for a new class of antiretroviral inhibitors. RETROVIROLOGY, 5.

Viral population estimation using pyrosequencing
Eriksson, N., Pachter, L., Mitsuya, Y., Rhee, S.-Y., Wang, C., & Beerenwinkel, N. (2008). Viral population estimation using pyrosequencing. PLOS COMPUTATIONAL BIOLOGY, 4(5).

Viral population estimation using pyrosequencing.
Eriksson, N., Pachter, L., Mitsuya, Y., Rhee, S.-Y., Wang, C., & Beerenwinkel, N. (2008). Viral population estimation using pyrosequencing. PLoS computational biology, 4(4).

HIV-1 drug resistance mutations: an updated framework for the second decade of HAART
Shafer, R. W., & Schapiro, J. M. (2008). HIV-1 drug resistance mutations: an updated framework for the second decade of HAART. AIDS REVIEWS, 10(2), 67-84.

Sequence editing by Apolipoprotein B RNA-editing catalytic component-B and epidemiological surveillance of transmitted HIV-1 drug resistance
Gifford, R. J., Rhee, S.-Y., Eriksson, N., Liu, T. F., Kiuchi, M., & Shafer, R. W. (2008). Sequence editing by Apolipoprotein B RNA-editing catalytic component-B and epidemiological surveillance of transmitted HIV-1 drug resistance. AIDS, 22(6), 717-725.

Hemochromatosis gene polymorphisms, mitochondrial haplogroups, and peripheral lipoatrophy during antiretroviral therapy
Hulgan, T., Tebas, P., Canter, J. A., Mulligan, K., Haas, D. W., & Kallianpur, A. R. (2008). Hemochromatosis gene polymorphisms, mitochondrial haplogroups, and peripheral lipoatrophy during antiretroviral therapy. JOURNAL OF INFECTIOUS DISEASES, 197(6), 858-866.

The mitochondrial pharmacogenomics of haplogroup T: MTND2*LHON4917G and antiretroviral therapy-associated peripheral neuropathy
Canter, J. A., Haas, D. W., Kallianpur, A. R., Ritchie, M. D., Robbins, G. K., & Hulgan, T. (2008). The mitochondrial pharmacogenomics of haplogroup T: MTND2*LHON4917G and antiretroviral therapy-associated peripheral neuropathy. PHARMACOGENOMICS JOURNAL, 8(1), 71-77.

Dynamics of total, linear nonintegrated, and integrated HIV-1 DNA in vivo and in vitro
Koelsch, K. K., Liu, L., Haubrich, R., May, S., Havlir, D., & Wong, J. K. (2008). Dynamics of total, linear nonintegrated, and integrated HIV-1 DNA in vivo and in vitro. JOURNAL OF INFECTIOUS DISEASES, 197(3), 411-419.

Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patients
Kapoor, A., Shapiro, B., Shafer, R. W., Shulman, N., Rhee, S.-Y., & Delwart, E. L. (2008). Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patients. RETROVIROLOGY, 5.

Consensus drug resistance mutations for epidemiological surveillance: basic principles and potential controversies
Shafer, R. W., Rhee, S.-Y., & Bennett, D. E. (2008). Consensus drug resistance mutations for epidemiological surveillance: basic principles and potential controversies. ANTIVIRAL THERAPY, 13, 59-68.

A highly divergent picornavirus in a marine mammal
Kapoor, A., Victoria, J., Simmonds, P., Wang, C., Shafer, R. W., & Delwart, E. (2008). A highly divergent picornavirus in a marine mammal. JOURNAL OF VIROLOGY, 82(1), 311-320.

Prevalence of darunavir resistance-associated mutations: Patterns of occurrence and association with past treatment
Mitsuya, Y., Liu, T. F., Rhee, S.-Y., Fessel, W. J., & Shafer, R. W. (2007). Prevalence of darunavir resistance-associated mutations: Patterns of occurrence and association with past treatment. JOURNAL OF INFECTIOUS DISEASES, 196(8), 1177-1179.

World antimalarial resistance network (WARN) III: Molecular markers for drug resistant malaria
Plowe, C. V., Roper, C., Barnwell, J. W., Happi, C. T., Joshi, H. H., & Rosenthal, P. J. (2007). World antimalarial resistance network (WARN) III: Molecular markers for drug resistant malaria. MALARIA JOURNAL, 6.

Educational attainment and response to HAART during initial therapy for HIV-1 infection
Marc, L. G., Testa, M. A., Walker, A. M., Robbins, G. K., Shafer, R. W., & Berkman, L. F. (2007). Educational attainment and response to HAART during initial therapy for HIV-1 infection. JOURNAL OF PSYCHOSOMATIC RESEARCH, 63(2), 207-216.

Virologic efficacy of boosted double versus boosted single protease inhibitor therapy
Petersen, M. L., Wang, Y., Van der Laan, M. J., Rhee, S.-Y., Shafer, R. W., & Fessel, W. J. (2007). Virologic efficacy of boosted double versus boosted single protease inhibitor therapy. AIDS, 21(12), 1547-1554.

Simple PCR Assays Improve the Sensitivity of HIV-1 Subtype B Drug Resistance Testing and Allow Linking of Resistance Mutations
Johnson, J. A., Li, J.-F., Wei, X., Lipscomb, J., Bennett, D., & Heneine, W. (2007). Simple PCR Assays Improve the Sensitivity of HIV-1 Subtype B Drug Resistance Testing and Allow Linking of Resistance Mutations. PLOS ONE, 2(7).

HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance
Shafer, R. W., Rhee, S.-Y., Pillay, D., Miller, V., Sandstrom, P., & Bennett, D. (2007). HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance. AIDS, 21(2), 215-223.

Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance
Altmann, A., Beerenwinkel, N., Sing, T., Savenkov, I., Daeumer, M., & Lengauer, T. (2007). Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance. ANTIVIRAL THERAPY, 12(2), 169-178.

Knowledge integration of software for HIV drug resistance research.
Hernandez, G., Rhee, S.-Y., Shafer, R. W., & Das, A. K. (2007). Knowledge integration of software for HIV drug resistance research. AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium, 973-?.

Case files from Stanford University Medical Center: ten years of HAART: a long wait for full HIV suppression.
Shulman, N., & Shafer, R. W. (2007). Case files from Stanford University Medical Center: ten years of HAART: a long wait for full HIV suppression. MedGenMed : Medscape general medicine, 9(1), 10-?.

N88D facilitates the co-occurrence of D30N and L90M and the development of multidrug resistance in HIV type 1 protease following nelfinavir treatment failure
Mitsuya, Y., Winters, M. A., Fessel, W. J., Rhee, S.-Y., Hurley, L., & Shafer, R. W. (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 RESEARCH AND HUMAN RETROVIRUSES, 22(12), 1300-1305.

Multilocus genetic interactions and response to efavirenz-containing regimens: an Adult AIDS Clinical Trials Group study
Motsinger, A. A., Ritchie, M. D., Shafer, R. W., Robbins, G. K., Morse, G. D., & Haas, D. W. (2006). Multilocus genetic interactions and response to efavirenz-containing regimens: an Adult AIDS Clinical Trials Group study. PHARMACOGENETICS AND GENOMICS, 16(11), 837-845.

HIV-1 drug resistance genotype results in patients with plasma samples with HIV-1 RNA levels less than 75 copies/mL
Mitsuya, Y., Winters, M. A., Fessel, W. J., Rhee, S.-Y., Slome, S., & Shafer, R. W. (2006). HIV-1 drug resistance genotype results in patients with plasma samples with HIV-1 RNA levels less than 75 copies/mL. JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES, 43(1), 56-59.

Effect of baseline- and treatment-related factors on immunologic recovery after initiation of antiretroviral therapy in HIV-1-positive subjects: Results from ACTG 384
Gandhi, R. T., Spritzler, J., Chan, E., Asmuth, D. M., Rodriguez, B., & Pollard, R. B. (2006). Effect of baseline- and treatment-related factors on immunologic recovery after initiation of antiretroviral therapy in HIV-1-positive subjects: Results from ACTG 384. JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES, 42(4), 426-434.

Oxidant stress and peripheral neuropathy during antiretroviral therapy: An AIDS Clinical Trials Group Study
Hulgan, T., Hughes, M., Xin Sun, S., Smeaton, L. M., Terry, E., & Haas, D. W. (2006). Oxidant stress and peripheral neuropathy during antiretroviral therapy: An AIDS Clinical Trials Group Study. JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES, 42(4), 450-454.

Hemochromatosis (HFE) gene mutations and peripheral neuropathy during antiretroviral therapy
Kallianpur, A. R., Hulgan, T., Canter, J. A., Ritchie, M. D., Haines, J. L., & Haas, D. W. (2006). Hemochromatosis (HFE) gene mutations and peripheral neuropathy during antiretroviral therapy. AIDS, 20(11), 1503-1513.

Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity
Gifford, R., de Oliveira, T., Rambaut, A., Myers, R. E., Gale, C. V., & Pillay, D. (2006). Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity. AIDS, 20(11), 1521-1529.

Discordances between interpretation algorithms for genotypic resistance to protease and reverse transcriptase inhibitors of human immunodeficiency virus are subtype dependent
Snoeck, J., Kantor, R., Shafer, R. W., Van Laethem, K., Deforche, K., & Vandamme, A. M. (2006). Discordances between interpretation algorithms for genotypic resistance to protease and reverse transcriptase inhibitors of human immunodeficiency virus are subtype dependent. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 50(2), 694-701.

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.
Shafer, R. W., Nguyen, D. P., & Fessel, W. J. (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. MedGenMed : Medscape general medicine, 8(3), 32-?.

A combined data mining approach for infrequent events: analyzing HIV mutation changes based on treatment history.
Lin, R. S., Rhee, S.-Y., Shafer, R. W., & Das, A. K. (2006). A combined data mining approach for infrequent events: analyzing HIV mutation changes based on treatment history. Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference, 385-388.

Case files from Stanford University Medical Center: the initial presentation of HIV-1 infection--where public and personal health meet.
Liu, M., Holodniy, M., Zolopa, A. R., & Shafer, R. W. (2006). Case files from Stanford University Medical Center: the initial presentation of HIV-1 infection--where public and personal health meet. MedGenMed : Medscape general medicine, 8(1), 24-?.

Prediction of HIV mutation changes based on treatment history.
Lin, R. S., Rhee, S.-Y., Shafer, R. W., & Das, A. K. (2006). Prediction of HIV mutation changes based on treatment history. AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium, 1011-?.

Pharmacogenetics of long-term responses to antiretroviral regimens containing efavirenz and/or nelfinavir: An adult AIDS clinical trials group study
Haas, D. W., Smeaton, L. M., Shafer, R. W., Robbins, G. K., Morse, G. D., & Kim, R. B. (2005). Pharmacogenetics of long-term responses to antiretroviral regimens containing efavirenz and/or nelfinavir: An adult AIDS clinical trials group study. JOURNAL OF INFECTIOUS DISEASES, 192(11), 1931-1942.

Glucose metabolism, lipid, and body fat changes in antiretroviral-naive subjects randomized to nelfinavir or efavirenz plus dual nucleosides
Dube, M. P., Parker, R. A., Tebas, P., Grinspoon, S. K., Zackin, R. A., & Mulligan, K. (2005). Glucose metabolism, lipid, and body fat changes in antiretroviral-naive subjects randomized to nelfinavir or efavirenz plus dual nucleosides. AIDS, 19(16), 1807-1818.

Mitochondrial haplogroups and peripheral neuropathy during antiretroviral therapy: an adult AIDS clinical trials group study
Hulgan, T., Haas, D. W., Haines, J. L., Ritchie, M. D., Robbins, G. K., & Canter, J. A. (2005). Mitochondrial haplogroups and peripheral neuropathy during antiretroviral therapy: an adult AIDS clinical trials group study. AIDS, 19(13), 1341-1349.

Pharmacokinetics of nelfinavir and efavirenz in antiretroviral-naive, human immunodeficiency virus-infected subjects when administered alone or in combination with nucleoside analog reverse transcriptase inhibitors
Smith, P. F., Robbins, G. K., Shafer, R. W., Wu, H. L., Yu, S., & Morse, G. D. (2005). Pharmacokinetics of nelfinavir and efavirenz in antiretroviral-naive, human immunodeficiency virus-infected subjects when administered alone or in combination with nucleoside analog reverse transcriptase inhibitors. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 49(8), 3558-3561.

Accuracy, precision, and consistency of expert HIV type 1 genotype interpretation: An international comparison (The GUESS Study)
Zolopa, A. R., Lazzeroni, L. C., Rinehart, A., Vezinet, F. B., Clavel, F., & Kuritzkes, D. R. (2005). Accuracy, precision, and consistency of expert HIV type 1 genotype interpretation: An international comparison (The GUESS Study). CLINICAL INFECTIOUS DISEASES, 41(1), 92-99.

Nonnucleoside reverse transcriptase inhibitor phenotypic hypersusceptibility can be demonstrated in different assays
Shulman, N. S., Delgado, D., Bosch, R. J., Winters, M. A., Johnston, E., & Merigan, T. C. (2005). Nonnucleoside reverse transcriptase inhibitor phenotypic hypersusceptibility can be demonstrated in different assays. JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES, 39(1), 78-81.

Comparison of the precision and sensitivity of the antivirogram and PhenoSense HIV drug susceptibility assays
Zhang, J., Rhee, S. Y., Taylor, J., & Shafer, R. W. (2005). Comparison of the precision and sensitivity of the antivirogram and PhenoSense HIV drug susceptibility assays. JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES, 38(4), 439-444.

Detection of minority populations of HIV-1 expressing the K103N resistance mutation in patients failing nevirapine
Lecossier, D., Shulman, N. S., Morand-Joubert, L., Shafer, R. W., Joly, V., & Hance, A. J. (2005). Detection of minority populations of HIV-1 expressing the K103N resistance mutation in patients failing nevirapine. JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES, 38(1), 37-42.

The HIV-1 Non-subtype B Workgroup: an international collaboration for the collection and analysis of HIV-1 non-subtype B data.
Kantor, R., Shafer, R. W., & Katzenstein, D. (2005). The HIV-1 Non-subtype B Workgroup: an international collaboration for the collection and analysis of HIV-1 non-subtype B data. MedGenMed : Medscape general medicine, 7(1), 71-?.

Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistance
Johnston, E., Winters, M. A., Rhee, S. Y., Merigan, T. C., Schiffer, C. A., & Shafer, R. W. (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), 4864-4868.

Clinically validated genotype analysis: guiding principles and statistical concerns
Brun-Vezinet, F., Costagliolo, D., Khaled, M. A., Calvez, V., Clavel, F., & DeGruttola, V. (2004). Clinically validated genotype analysis: guiding principles and statistical concerns. ANTIVIRAL THERAPY, 9(4), 465-478.

Distribution of human immunodeficiency virus type 1 protease and reverse transcriptase mutation patterns in 4,183 persons undergoing genotypic resistance testing
Rhee, S. Y., Liu, T., Ravela, J., Gonzales, M. J., & Shafer, R. W. (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.

Evolution of resistance to drugs in HIV-1-infected patients failing antiretroviral therapy
Kantor, R., Shafer, R. W., Follansbee, S., Taylor, J., Shilane, D., & Fessel, W. J. (2004). Evolution of resistance to drugs in HIV-1-infected patients failing antiretroviral therapy. AIDS, 18(11), 1503-1511.

Sequencing-Based detection of low-frequency human immunodeficiency virus type 1 drug-resistant mutants by an RNA/DNA heteroduplex generator-tracking assay
Kapoor, A., Jones, M., Shafer, R. W., Rhee, S. Y., Kazanjian, P., & Delwart, E. L. (2004). Sequencing-Based detection of low-frequency human immunodeficiency virus type 1 drug-resistant mutants by an RNA/DNA heteroduplex generator-tracking assay. JOURNAL OF VIROLOGY, 78(13), 7112-7123.

Comparative evaluation of three computerized algorithms for prediction of antiretroviral susceptibility from HIV type 1 genotype
Zazzi, M., Romano, L., Venturi, G., Shafer, R. W., Reid, C., & Valensin, P. E. (2004). Comparative evaluation of three computerized algorithms for prediction of antiretroviral susceptibility from HIV type 1 genotype. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 53(2), 356-360.

Comparison of sequential three-drug regimens as initial therapy for HIV-1 infection
Robbins, G. K., De Gruttola, V., Shafer, R. W., Smeaton, L. M., Snyder, S. W., & Doolan, A. (2003). Comparison of sequential three-drug regimens as initial therapy for HIV-1 infection. NEW ENGLAND JOURNAL OF MEDICINE, 349(24), 2293-2303.

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
Gonzales, M. J., Belitskaya, I., Dupnik, K. M., Rhee, S. Y., & Shafer, R. W. (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 RESEARCH AND HUMAN RETROVIRUSES, 19(10), 909-915.

Algorithm specification interface for human immunodefiency virus type 1 genotypic interpretation
Betts, B. J., & Shafer, R. W. (2003). Algorithm specification interface for human immunodefiency virus type 1 genotypic interpretation. JOURNAL OF CLINICAL MICROBIOLOGY, 41(6), 2792-2794.

HIV-1 protease and reverse transcriptase mutation patterns responsible for discordances between genotypic drug resistance interpretation algorithms
Ravela, J., Betts, B. J., Brun-Vezinet, F., Vandamme, A. M., Descamps, T., & Shafer, R. W. (2003). HIV-1 protease and reverse transcriptase mutation patterns responsible for discordances between genotypic drug resistance interpretation algorithms. JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES, 33(1), 8-14.

Drug resistance mutations in HIV-1.
D'Aquila, R. T., Schapiro, J. M., Brun-Vézinet, F., Clotet, B., Conway, B., & Richman, D. D. (2003). Drug resistance mutations in HIV-1. Topics in HIV medicine : a publication of the International AIDS Society, USA, 11(3), 92-96.

HIV sequence databases.
Kuiken, C., Korber, B., & Shafer, R. W. (2003). HIV sequence databases. AIDS reviews, 5(1), 52-61.

HIV-1 subtype C reverse transcriptase and protease genotypes in Zimbabwean patients failing antiretroviral therapy
Kantor, R., Zijenah, L. S., Shafer, R. W., Mutetwa, S., Johnston, E., & Katzenstein, D. A. (2002). HIV-1 subtype C reverse transcriptase and protease genotypes in Zimbabwean patients failing antiretroviral therapy. AIDS RESEARCH AND HUMAN RETROVIRUSES, 18(18), 1407-1413.

Reverse transcriptase and protease sequence evolution in two HIV-1-infected couples
Palmer, S., Vuitton, D., Gonzales, M. J., Bassignot, A., & Shafer, R. W. (2002). Reverse transcriptase and protease sequence evolution in two HIV-1-infected couples. JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES, 31(3), 285-290.

Subtle decreases in stavudine phenotypic susceptibility predict poor virologic response to stavudine monotherapy in zidovudine-experienced patients
Shulman, N. S., Hughes, M. D., Winters, M. A., Shafer, R. W., Zolopa, A. R., & Katzenstein, D. A. (2002). Subtle decreases in stavudine phenotypic susceptibility predict poor virologic response to stavudine monotherapy in zidovudine-experienced patients. JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES, 31(2), 121-127.

Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN)
Gonzales, M. J., Dugan, J. M., & Shafer, R. W. (2002). Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN). BIOINFORMATICS, 18(6), 886-887.

Identification of Ugandan HIV type 1 variants with unique patterns of recombination in pol involving subtypes A and D
Eshleman, S. H., Gonzales, M. J., Becker-Pergola, G., Cunningham, S. C., Guay, L. A., & Shafer, R. W. (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(7), 507-511.

Evolution of primary protease inhibitor resistance mutations during protease inhibitor salvage therapy
Kantor, R., Fessel, W. J., Zolopa, A. R., Israelski, D., Shulman, N., & Shafer, R. W. (2002). Evolution of primary protease inhibitor resistance mutations during protease inhibitor salvage therapy. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 46(4), 1086-1092.

Human immunodeficiency virus type 1 reverse-transcriptase and protease subtypes: Classification, amino acid mutation patterns, and prevalence in a northern California clinic-based population
Gonzales, M. J., Machekano, R. N., & Shafer, R. W. (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(8), 998-1006.

Genotypic correlates of a virologic response to stavudine after zidovudine monotherapy
Shulman, N. S., Machekano, R. A., Shafer, R. W., Winters, M. A., Zolopa, A. R., & Katzenstein, D. A. (2001). Genotypic correlates of a virologic response to stavudine after zidovudine monotherapy. JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES, 27(4), 377-380.

Phenotypic hypersusceptibility to non-nucleoside reverse transcriptase inhibitors in treatment-experienced HIV-infected patients: impact on virological response to efavirenz-based therapy
Shulman, N., Zolopa, A. R., Passaro, D., Shafer, R. W., Huang, W., & Whitcomb, J. (2001). Phenotypic hypersusceptibility to non-nucleoside reverse transcriptase inhibitors in treatment-experienced HIV-infected patients: impact on virological response to efavirenz-based therapy. AIDS, 15(9), 1125-1132.

High degree of interlaboratory reproducibility of human immunodeficiency virus type 1 protease and reverse transcriptase sequencing of plasma samples from heavily treated patients
Shafer, R. W., Hertogs, K., Zolopa, A. R., Warford, A., Bloor, S., & Larder, B. A. (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), 1522-1529.

ACTG (AIDS Clinical Trials Group) 384: A strategy trial comparing consecutive treatments for HIV-1
Smeaton, L. M., DeGruttola, V., Robbins, G. K., & Shafer, R. W. (2001). ACTG (AIDS Clinical Trials Group) 384: A strategy trial comparing consecutive treatments for HIV-1. CONTROLLED CLINICAL TRIALS, 22(2), 142-159.

Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs
Kantor, R., Machekano, R., Gonzales, M. J., Dupnik, K., Schapiro, J. M., & Shafer, R. W. (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.

Human immunodeficiency virus on the Web: A guided tour
Shafer, R. W., & Deresinski, S. C. (2000). Human immunodeficiency virus on the Web: A guided tour. CLINICAL INFECTIOUS DISEASES, 31(2), 568-577.

HIV type 1 envelope subtype C sequences from recent seroconverters in Zimbabwe
Batra, M., Tien, P. C., Shafer, R. W., Contag, C. H., & Katzenstein, D. A. (2000). HIV type 1 envelope subtype C sequences from recent seroconverters in Zimbabwe. AIDS RESEARCH AND HUMAN RETROVIRUSES, 16(10), 973-979.

Reproducibility of human immunodeficiency virus type 1 (HIV-1) protease and reverse transcriptase sequencing of plasma samples from heavily treated HIV-1-infected individuals
Shafer, R. W., Warford, A., Winters, M. A., & Gonzales, M. J. (2000). Reproducibility of human immunodeficiency virus type 1 (HIV-1) protease and reverse transcriptase sequencing of plasma samples from heavily treated HIV-1-infected individuals. JOURNAL OF VIROLOGICAL METHODS, 86(2), 143-153.

Efavirenz- and adefovir dipivoxil-based salvage therapy in highly treatment-experienced patients: Clinical and genotypic predictors of virologic response
Shulman, N. S., Zolopa, A. R., Passaro, D. J., Murlidharan, U., Israelski, D. M., & Katzenstein, D. A. (2000). Efavirenz- and adefovir dipivoxil-based salvage therapy in highly treatment-experienced patients: Clinical and genotypic predictors of virologic response. JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES, 23(3), 221-226.

Delavirdine susceptibilities and associated reverse transcriptase mutations in human immunodeficiency virus type 1 isolates from patients in a phase I/II trial of delavirdine monotherapy (ACTG 260)
Demeter, L. M., Shafer, R. W., Meehan, P. M., Holden-Wiltse, J., Fischl, M. A., & Reichman, R. C. (2000). Delavirdine susceptibilities and associated reverse transcriptase mutations in human immunodeficiency virus type 1 isolates from patients in a phase I/II trial of delavirdine monotherapy (ACTG 260). ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 44(3), 794-797.

The Genetic Basis of HIV-1 Resistance to Reverse Transcriptase and Protease Inhibitors.
Shafer, R. W., Kantor, R., & Gonzales, M. J. (2000). The Genetic Basis of HIV-1 Resistance to Reverse Transcriptase and Protease Inhibitors. AIDS reviews, 2(4), 211-228.

Human immunodeficiency virus reverse transcriptase and protease sequence database
Shafer, R. W., Jung, D. R., Betts, B. J., Xi, Y. O., & Gonzales, M. J. (2000). Human immunodeficiency virus reverse transcriptase and protease sequence database. NUCLEIC ACIDS RESEARCH, 28(1), 346-348.

Hydroxyurea enhances the activities of didanosine, 9-[2(phosphonylmethoxy)ethyl] adenine, and 9-[2(phosphonylmethoxy)propyl]adenine against drug-susceptible and drug-resistant human immunodeficiency virus isolates
Palmer, S., Shafer, R. W., & Merigan, T. C. (1999). Hydroxyurea enhances the activities of didanosine, 9-[2(phosphonylmethoxy)ethyl] adenine, and 9-[2(phosphonylmethoxy)propyl]adenine against drug-susceptible and drug-resistant human immunodeficiency virus isolates. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 43(8), 2046-2050.

Identification of biased amino acid substitution patterns in human immunodeficiency virus type 1 isolates from patients treated with protease inhibitors
Shafer, R. W., Hsu, P., Patick, A. K., Craig, C., & Brendel, V. (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(7), 6197-6202.

ACTG 260: a randomized, phase I-II, dose-ranging trial of the anti-human immunodeficiency virus activity of delavirdine monotherapy
Para, M. F., Meehan, P., Holden-Wiltse, J., Fischl, M., Morse, G., & Freimuth, W. W. (1999). ACTG 260: a randomized, phase I-II, dose-ranging trial of the anti-human immunodeficiency virus activity of delavirdine monotherapy. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 43(6), 1373-1378.

Highly drug-resistant HIV-1 clinical isolates are cross-resistant to many antiretroviral compounds in current clinical development
Palmer, S., Shafer, R. W., & Merigan, T. C. (1999). Highly drug-resistant HIV-1 clinical isolates are cross-resistant to many antiretroviral compounds in current clinical development. AIDS, 13(6), 661-667.

Highly active antiretroviral therapy (HAART) for the treatment of infection with human immunodeficiency virus type 1
Shafer, R. W., & Vuitton, D. A. (1999). Highly active antiretroviral therapy (HAART) for the treatment of infection with human immunodeficiency virus type 1. BIOMEDICINE & PHARMACOTHERAPY, 53(2), 73-86.

Human immunodeficiency virus reverse transcriptase and protease sequence database
Shafer, R. W., Stevenson, D., & Chan, B. (1999). Human immunodeficiency virus reverse transcriptase and protease sequence database. NUCLEIC ACIDS RESEARCH, 27(1), 348-352.

A 6-basepair insert in the reverse transcriptase gene of human immunodeficiency virus type 1 confers resistance to multiple nucleoside inhibitors
Winters, M. A., Coolley, K. L., Girard, Y. A., Levee, D. J., Hamdan, H., & Merigan, T. C. (1998). A 6-basepair insert in the reverse transcriptase gene of human immunodeficiency virus type 1 confers resistance to multiple nucleoside inhibitors. JOURNAL OF CLINICAL INVESTIGATION, 102(10), 1769-1775.

Interlaboratory concordance of DNA sequence analysis to detect reverse transcriptase mutations in HIV-1 proviral DNA
Demeter, L. M., D'Aquila, R., WEISLOW, O., Lorenzo, E., ERICE, A., & Japour, A. (1998). Interlaboratory concordance of DNA sequence analysis to detect reverse transcriptase mutations in HIV-1 proviral DNA. JOURNAL OF VIROLOGICAL METHODS, 75(1), 93-104.

An update on the diagnosis and treatment of HIV, 1998
Shafer, R. W., & Kroodsma, K. (1998). An update on the diagnosis and treatment of HIV, 1998. DRUGS OF TODAY, 34(8), 663-672.

Human immunodeficiency virus type 1 reverse transcriptase genotype and drug susceptibility changes in infected individuals receiving dideoxyinosine monotherapy for 1 to 2 years
Winters, M. A., Shafer, R. W., Jellinger, R. A., Mamtora, G., Gingeras, T., & Merigan, T. C. (1997). Human immunodeficiency virus type 1 reverse transcriptase genotype and drug susceptibility changes in infected individuals receiving dideoxyinosine monotherapy for 1 to 2 years. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 41(4), 757-762.

A novel approach to assessing the drug susceptibility and replication of human immunodeficiency virus type 1 isolates
Jellinger, R. M., Shafer, R. W., & Merigan, T. C. (1997). A novel approach to assessing the drug susceptibility and replication of human immunodeficiency virus type 1 isolates. JOURNAL OF INFECTIOUS DISEASES, 175(3), 561-566.

Comparison of QIAamp HCV kit spin columns, silica beads, and phenol-chloroform for recovering human immunodeficiency virus type 1 RNA from plasma
Shafer, R. W., Levee, D. J., Winters, M. A., Richmond, K. L., Huang, D., & Merigan, T. C. (1997). Comparison of QIAamp HCV kit spin columns, silica beads, and phenol-chloroform for recovering human immunodeficiency virus type 1 RNA from plasma. JOURNAL OF CLINICAL MICROBIOLOGY, 35(2), 520-522.

Genotypic and phenotypic changes during culture of a multinucleoside-resistant human immunodeficiency virus type 1 strain in the presence and absence of additional reverse transcriptase inhibitors
Shafer, R. W., Winters, M. A., Iversen, A. Kn., & Merigan, T. C. (1996). Genotypic and phenotypic changes during culture of a multinucleoside-resistant human immunodeficiency virus type 1 strain in the presence and absence of additional reverse transcriptase inhibitors. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 40(12), 2887-2890.

Zidovudine resistance reverse transcriptase mutations during didanosine monotherapy
Shafer, R. W., Winters, M. A., Jellinger, R. M., & Merigan, T. C. (1996). Zidovudine resistance reverse transcriptase mutations during didanosine monotherapy. JOURNAL OF INFECTIOUS DISEASES, 174(2), 448-449.

Interlaboratory comparison of sequence-specific PCR and ligase detection reaction to detect a human immunodeficiency virus type 1 drug resistance mutation
Shafer, R. W., Winters, M. A., MAYERS, D. L., JAPOUR, A. J., Kuritzkes, D. R., & REICHELDERFER, P. S. (1996). Interlaboratory comparison of sequence-specific PCR and ligase detection reaction to detect a human immunodeficiency virus type 1 drug resistance mutation. JOURNAL OF CLINICAL MICROBIOLOGY, 34(7), 1849-1853.

Multidrug-resistant human immunodeficiency virus type 1 strains resulting from combination antiretroviral therapy
Iversen, A. Kn., Shafer, R. W., Wehrly, K., Winters, M. A., Mullins, J. I., & Merigan, T. C. (1996). Multidrug-resistant human immunodeficiency virus type 1 strains resulting from combination antiretroviral therapy. JOURNAL OF VIROLOGY, 70(2), 1086-1090.

Exogenous reinfection with multidrug-resistant Mycobacterium tuberculosis in an immunocompetent patient
Shafer, R. W., Singh, S. P., Larkin, C., & Small, P. M. (1995). Exogenous reinfection with multidrug-resistant Mycobacterium tuberculosis in an immunocompetent patient. TUBERCLE AND LUNG DISEASE, 76(6), 575-577.

DRUG-RESISTANCE AND HETEROGENEOUS LONG-TERM VIROLOGICAL RESPONSES OF HUMAN-IMMUNODEFICIENCY-VIRUS TYPE 1-INFECTED SUBJECTS TO ZIDOVUDINE AND DIDANOSINE COMBINATION THERAPY
Shafer, R. W., Iversen, A. Kn., Winters, M. A., Aguiniga, E., Katzenstein, D. A., & Merigan, T. C. (1995). DRUG-RESISTANCE AND HETEROGENEOUS LONG-TERM VIROLOGICAL RESPONSES OF HUMAN-IMMUNODEFICIENCY-VIRUS TYPE 1-INFECTED SUBJECTS TO ZIDOVUDINE AND DIDANOSINE COMBINATION THERAPY. JOURNAL OF INFECTIOUS DISEASES, 172(1), 70-78.

RANDOMIZED STUDY OF DIDANOSINE MONOTHERAPY AND COMBINATION THERAPY WITH ZIDOVUDINE IN HEMOPHILIC AND NONHEMOPHILIC SUBJECTS WITH ASYMPTOMATIC HUMAN IMMUNODEFICIENCY VIRUS-1 INFECTION
Ragni, M. V., LOFARO, M. L., DeGruttola, V., VANDERHORST, C., Eyster, M. E., & Morse, G. (1995). RANDOMIZED STUDY OF DIDANOSINE MONOTHERAPY AND COMBINATION THERAPY WITH ZIDOVUDINE IN HEMOPHILIC AND NONHEMOPHILIC SUBJECTS WITH ASYMPTOMATIC HUMAN IMMUNODEFICIENCY VIRUS-1 INFECTION. BLOOD, 85(9), 2337-2346.

NEW VIROLOGICAL TOOLS FOR THE DESIGN AND ANALYSIS OF CLINICAL-TRIALS
Shafer, R. W., & Merigan, T. C. (1995). NEW VIROLOGICAL TOOLS FOR THE DESIGN AND ANALYSIS OF CLINICAL-TRIALS. JOURNAL OF INFECTIOUS DISEASES, 171(5), 1325-1328.

CLARIFICATION OF A METHOD TO REVERSE TRANSCRIBE HUMAN-IMMUNODEFICIENCY-VIRUS RNA
Kozal, M. J., Shafer, R. W., Winters, M. A., Katzenstein, D. A., & Merigan, T. C. (1995). CLARIFICATION OF A METHOD TO REVERSE TRANSCRIBE HUMAN-IMMUNODEFICIENCY-VIRUS RNA. JOURNAL OF INFECTIOUS DISEASES, 171(4), 1072-1072.

HIV virology for clinical trials.
Shafer, R. W., & Merigan, T. C. (1995). HIV virology for clinical trials. AIDS , 9, S193-202.

QUANTITATIVE-ANALYSIS OF SYNCYTIUM-INDUCING AND NON-SYNCYTIUM-INDUCING VIRUS IN PATIENTS INFECTED WITH HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1
Shafer, R. W., Aguiniga, E., & Merigan, T. C. (1995). QUANTITATIVE-ANALYSIS OF SYNCYTIUM-INDUCING AND NON-SYNCYTIUM-INDUCING VIRUS IN PATIENTS INFECTED WITH HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1. JOURNAL OF CLINICAL MICROBIOLOGY, 33(1), 212-214.

DIDANOSINE RESISTANCE IN HIV-INFECTED PATIENTS SWITCHED FROM ZIDOVUDINE TO DIDANOSINE MONOTHERAPY
Kozal, M. J., Kroodsma, K., Winters, M. A., Shafer, R. W., Efron, B., & Merigan, T. C. (1994). DIDANOSINE RESISTANCE IN HIV-INFECTED PATIENTS SWITCHED FROM ZIDOVUDINE TO DIDANOSINE MONOTHERAPY. ANNALS OF INTERNAL MEDICINE, 121(4), 263-268.

HIV-1 SYNCYTIUM-INDUCING PHENOTYPE, VIRUS BURDEN CODON-215 REVERSE-TRANSCRIPTASE MUTATION AND CD4 CELL DECLINE IN ZIDOVUDINE-TREATED PATIENTS
Kozal, M. J., Shafer, R. W., Winters, M. A., Katzenstein, D. A., Aguiniga, E., & Merigan, T. C. (1994). HIV-1 SYNCYTIUM-INDUCING PHENOTYPE, VIRUS BURDEN CODON-215 REVERSE-TRANSCRIPTASE MUTATION AND CD4 CELL DECLINE IN ZIDOVUDINE-TREATED PATIENTS. JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES AND HUMAN RETROVIROLOGY, 7(8), 832-838.

PREVALENCE OF HIV-1 SYNCYTIUM-INDUCING PHENOTYPE
Kozal, M. J., Ramachandran, R. V., & Shafer, W. (1994). PREVALENCE OF HIV-1 SYNCYTIUM-INDUCING PHENOTYPE. ANNALS OF INTERNAL MEDICINE, 120(9), 811-811.

MEASUREMENT OF HIV VIRUS LOAD AND GENOTYPIC RESISTANCE BY GENE AMPLIFICATION IN ASYMPTOMATIC SUBJECTS TREATED WITH COMBINATION THERAPY
Holodniy, M., KATZENSTEIN, D., Winters, M., Montoya, J., Shafer, R., & Merigan, T. C. (1993). MEASUREMENT OF HIV VIRUS LOAD AND GENOTYPIC RESISTANCE BY GENE AMPLIFICATION IN ASYMPTOMATIC SUBJECTS TREATED WITH COMBINATION THERAPY. JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES, 6(4), 366-369.

ZIDOVUDINE SUSCEPTIBILITY TESTING OF HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1 (HIV) CLINICAL ISOLATES
Shafer, R. W., Kozal, M. J., Katzenstein, D. A., LIPIL, W. H., JOHNSTONE, I. F., & Merigan, T. C. (1993). ZIDOVUDINE SUSCEPTIBILITY TESTING OF HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1 (HIV) CLINICAL ISOLATES. JOURNAL OF VIROLOGICAL METHODS, 41(3), 297-310.

A MUTATION IN HUMAN-IMMUNODEFICIENCY-VIRUS REVERSE-TRANSCRIPTASE AND DECLINE IN LYMPHOCYTE-CD4 NUMBERS IN LONG-TERM ZIDOVUDINE RECIPIENTS
Kozal, M. J., Shafer, R. W., Winters, M. A., Katzenstein, D. A., & Merigan, T. C. (1993). A MUTATION IN HUMAN-IMMUNODEFICIENCY-VIRUS REVERSE-TRANSCRIPTASE AND DECLINE IN LYMPHOCYTE-CD4 NUMBERS IN LONG-TERM ZIDOVUDINE RECIPIENTS. JOURNAL OF INFECTIOUS DISEASES, 167(3), 526-532.

MYCOBACTERIUM-XENOPI, MYCOBACTERIUM-FORTUITUM, MYCOBACTERIUM-KANSASII, AND OTHER NONTUBERCULOUS MYCOBACTERIA IN AN AREA OF ENDEMICITY FOR AIDS
Shafer, R. W., & Sierra, M. F. (1992). MYCOBACTERIUM-XENOPI, MYCOBACTERIUM-FORTUITUM, MYCOBACTERIUM-KANSASII, AND OTHER NONTUBERCULOUS MYCOBACTERIA IN AN AREA OF ENDEMICITY FOR AIDS. CLINICAL INFECTIOUS DISEASES, 15(1), 161-162.

RELAPSE OF TUBERCULOSIS IN A PATIENT WITH THE ACQUIRED-IMMUNODEFICIENCY-SYNDROME DESPITE 12 MONTHS OF ANTITUBERCULOUS THERAPY AND CONTINUATION OF ISONIAZID
Shafer, R. W., & Jones, W. D. (1991). RELAPSE OF TUBERCULOSIS IN A PATIENT WITH THE ACQUIRED-IMMUNODEFICIENCY-SYNDROME DESPITE 12 MONTHS OF ANTITUBERCULOUS THERAPY AND CONTINUATION OF ISONIAZID. TUBERCLE, 72(2), 149-151.

HIV PREVALENCE, IMMUNOSUPPRESSION, AND DRUG-RESISTANCE IN PATIENTS WITH TUBERCULOSIS IN AN AREA ENDEMIC FOR AIDS
Shafer, R. W., Chirgwin, K. D., Glatt, A. E., DAHDOUH, M. A., Landesman, S. H., & Suster, B. (1991). HIV PREVALENCE, IMMUNOSUPPRESSION, AND DRUG-RESISTANCE IN PATIENTS WITH TUBERCULOSIS IN AN AREA ENDEMIC FOR AIDS. AIDS, 5(4), 399-405.

FREQUENCY OF MYCOBACTERIUM-TUBERCULOSIS BACTEREMIA IN PATIENTS WITH TUBERCULOSIS IN AN AREA ENDEMIC FOR AIDS
Shafer, R. W., Goldberg, R., Sierra, M., & Glatt, A. E. (1989). FREQUENCY OF MYCOBACTERIUM-TUBERCULOSIS BACTEREMIA IN PATIENTS WITH TUBERCULOSIS IN AN AREA ENDEMIC FOR AIDS. AMERICAN REVIEW OF RESPIRATORY DISEASE, 140(6), 1611-1613.

Q-FEVER ENDOCARDITIS - DELAY IN DIAGNOSIS DUE TO AN APPARENT CLINICAL-RESPONSE TO CORTICOSTEROIDS
Shafer, R. W., & Braverman, E. R. (1989). Q-FEVER ENDOCARDITIS - DELAY IN DIAGNOSIS DUE TO AN APPARENT CLINICAL-RESPONSE TO CORTICOSTEROIDS. AMERICAN JOURNAL OF MEDICINE, 86(6), 729-729.

A LIFE-THREATENING GONOCOCCAL-INFECTION
Shafer, R. W., RAZAVI, M. H., & Zenilman, J. M. (1989). A LIFE-THREATENING GONOCOCCAL-INFECTION. HOSPITAL PRACTICE, 24(5), 26-?.

SUCCESSFUL PROPHYLAXIS OF PNEUMOCYSTIS-CARINII PNEUMONIA WITH TRIMETHOPRIM SULFAMETHOXAZOLE IN AIDS PATIENTS WITH PREVIOUS ALLERGIC REACTIONS
Shafer, R. W., SEITZMAN, P. A., & Tapper, M. L. (1989). SUCCESSFUL PROPHYLAXIS OF PNEUMOCYSTIS-CARINII PNEUMONIA WITH TRIMETHOPRIM SULFAMETHOXAZOLE IN AIDS PATIENTS WITH PREVIOUS ALLERGIC REACTIONS. JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES AND HUMAN RETROVIROLOGY, 2(4), 389-393.