Biography
Professional Summary
Education & Certifications
- Medical Education: NYU Grossman School of Medicine (1983) NY
- Fellowship: Stanford University School of Medicine (1993) CA
- Board Certification: American Board of Internal Medicine, Infectious Disease (1988)
- Fellowship: SUNY at Brooklyn School Of Medicine (1988) NY
- Board Certification: American Board of Internal Medicine, Internal Medicine (1986)
- Residency: Lenox Hill Hospital (1986) NY
- Internship: Lenox Hill Hospital (1984) NY
Publications
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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. -
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. -
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. -
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. -
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. -
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. -
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., KATZENSTEIN, D., … 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-? -
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., Freimuth, W. W., … 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. -
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., Brosgart, C. L., … 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), 221–26. -
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), 973–79. -
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. -
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. -
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. -
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., Betts, B. J., … 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. -
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., KATZENSTEIN, D., … 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. -
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., Liou, S. H., … Katzenstein, D. A. (2001). Genotypic correlates of a virologic response to stavudine after zidovudine monotherapy. JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES, 27(4), 377–80. -
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. -
Evolution of primary protease inhibitor resistance mutations during protease inhibitor salvage therapy
Kantor, R., Fessel, W. J., Zolopa, A. R., Israelski, D., Shulman, N., Montoya, J. G., … Shafer, R. W. (2002). Evolution of primary protease inhibitor resistance mutations during protease inhibitor salvage therapy. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 46(4), 1086–92. -
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-? -
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., Jackson, J. B., & 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. -
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), 886–87. -
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., Hellmann, N. S., … 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), 121–27. -
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. -
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., Lloyd, R., … 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), 1407–13. -
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. -
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., Israelski, D., … Shafer, R. W. (2003). Extended spectrum of HIV-1 reverse transcriptase mutations in patients receiving multiple nucleoside analog inhibitors. AIDS, 17(6), 791–99. -
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., Chou, S. W., … 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), 4836–47. -
Drug Resistance Mutations in HIV-1.
D'Aquila, R. T., Schapiro, J. M., Brun-Vézinet, F., Clotet, B., Conway, B., Demeter, L. M., … Richman, D. D. (2002). Drug Resistance Mutations in HIV-1. Topics in HIV Medicine : a Publication of the International AIDS Society, USA, 10(5), 21–25. -
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., Van Laethem, K., … 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., Demeter, L. M., … 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. -
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., Taylor, J., & 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. -
HIV sequence databases.
Kuiken, C., Korber, B., & Shafer, R. W. (2003). HIV sequence databases. AIDS Reviews, 5(1), 52–61. -
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), 909–15. -
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. -
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., Pettinelli, C., … 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. -
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., D'Aquila, R. T., … 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), 2304–15. -
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., Dal Bello, F., … 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. -
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. -
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), 7112–23. -
Evolution of resistance to drugs in HIV-1-infected patients failing antiretroviral therapy
Kantor, R., Shafer, R. W., Follansbee, S., Taylor, J., Shilane, D., Hurley, L., … Fessel, W. J. (2004). Evolution of resistance to drugs in HIV-1-infected patients failing antiretroviral therapy. AIDS, 18(11), 1503–11. -
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), 3122–26. -
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), 4864–68. -
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., Zolopa, A. R., … 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. -
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), 439–44. -
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., Imamichi, T., & Shafer, R. W. (2005). Panel of prototypical infectious molecular HIV-1 clones containing multiple nucleoside reverse transcriptase inhibitor resistance mutations. AIDS, 19(7), 731–33. -
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., Cane, P., … 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), 325–37. -
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), 817–20. -
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., Shafer, R. W., … 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. -
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., Collier, A., … 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. -
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., Taylor, J., … 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), 456–65. -
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., Hirsch, M. 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. -
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., Shafer, R. W., … Canter, J. A. (2005). Mitochondrial haplogroups and peripheral neuropathy during antiretroviral therapy: an adult AIDS clinical trials group study. AIDS, 19(13), 1341–1349. -
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. -
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., Robbins, G. K., … 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. -
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., Labbe, L., … 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. BOSTON,MA,MA,MA,MA,MA,MA,MA,MA: UNIV CHICAGO PRESS. -
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-? -
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., CARVALHO, A. P., … 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. -
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., Sirivichayakul, S., … 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), 643–51. -
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), 1608–18. -
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. -
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., Robbins, G. K., … 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), 450–54. -
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., Merigan, T. C., … 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), 426–34. -
Hemochromatosis (HFE) gene mutations and peripheral neuropathy during antiretroviral therapy
Kallianpur, A. R., Hulgan, T., Canter, J. A., Ritchie, M. D., Haines, J. L., Robbins, G. K., … 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., Dunn, D., … Pillay, D. (2006). Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity. AIDS, 20(11), 1521–1529. -
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., Flamm, J., … 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. -
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-? -
Rationale and uses of a public HIV drug-resistance database
Shafer, R. W. (2006). Rationale and uses of a public HIV drug-resistance database. Presented at the Symposium on Bridging Generations Toward an Understanding of Infectious Disease Pathogenesis, Stanford,CA,CA,CA,CA,CA,CA: UNIV CHICAGO PRESS. -
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., Labbe, L., … Haas, D. W. (2006). Multilocus genetic interactions and response to efavirenz-containing regimens: an Adult AIDS Clinical Trials Group study. PHARMACOGENETICS AND GENOMICS. DENVER,CO,CO,CO,CO,CO,CO,CO,CO,CO: LIPPINCOTT WILLIAMS & WILKINS. -
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), 17355–60. -
HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance
Shafer, R. W., Rhee, S.-Y., Pillay, D., Miller, V., Sandstrom, P., Schapiro, J. M., … Bennett, D. (2007). HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance. AIDS, 21(2), 215–23. -
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., Horberg, M., … 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. -
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-? -
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, 385–88. -
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-? -
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-? -
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), 836–43. -
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., Kaiser, R., … Lengauer, T. (2007). Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance. ANTIVIRAL THERAPY, 12(2), 169–78. -
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. -
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), 1547–54. -
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., Brant, A., … 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). -
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., Anderson, N. B., & 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. -
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., Shafer, R. W., … Hulgan, T. (2008). The mitochondrial pharmacogenomics of haplogroup T: MTND2*LHON4917G and antiretroviral therapy-associated peripheral neuropathy. PHARMACOGENOMICS JOURNAL, 8(1), 71–77. -
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., Mbacham, W., … Rosenthal, P. J. (2007). World antimalarial resistance network (WARN) III: Molecular markers for drug resistant malaria. MALARIA JOURNAL, 6. -
A highly divergent picornavirus in a marine mammal
Kapoor, A., Victoria, J., Simmonds, P., Wang, C., Shafer, R. W., Nims, R., … 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), 1177–79. -
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. -
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., Guenthard, H. F., … Wong, J. K. (2008). Dynamics of total, linear nonintegrated, and integrated HIV-1 DNA in vivo and in vitro. JOURNAL OF INFECTIOUS DISEASES. BANGKOK,THAILAND,THAILAND,THAILAND,THAILAND: OXFORD UNIV PRESS INC. -
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., Das, A. K., & 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), 717–25. -
Hemochromatosis gene polymorphisms, mitochondrial haplogroups, and peripheral lipoatrophy during antiretroviral therapy
Hulgan, T., Tebas, P., Canter, J. A., Mulligan, K., Haas, D. W., Dube, M., … Kallianpur, A. R. (2008). Hemochromatosis gene polymorphisms, mitochondrial haplogroups, and peripheral lipoatrophy during antiretroviral therapy. JOURNAL OF INFECTIOUS DISEASES, 197(6), 858–866. -
Viral population estimation using pyrosequencing.
Eriksson, N., Pachter, L., Mitsuya, Y., Rhee, S.-Y., Wang, C., Gharizadeh, B., … Beerenwinkel, N. (2008). Viral population estimation using pyrosequencing. PLoS Computational Biology, 4(4). -
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. -
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. -
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., Holmes, S. P., & Shafer, R. W. (2008). Natural variation of HIV-1 group M integrase: Implications for a new class of antiretroviral inhibitors. RETROVIROLOGY, 5. -
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-? -
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., Nadler, J., … 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), 4050–56. -
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., Jayakumar, 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), 10747–55. -
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., Zolfo, M., … 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. -
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., Shafer, R. W., & 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. -
Bayesian network analyses of resistance pathways against efavirenz and nevirapine
Deforche, K., Camacho, R. J., Grossman, Z., Soares, M. A., Van Laethem, K., Katzenstein, D. A., … Vandamme, A.-M. (2008). Bayesian network analyses of resistance pathways against efavirenz and nevirapine. AIDS, 22(16), 2107–15. -
A highly prevalent and genetically diversified Picornaviridae genus in South Asian children
Kapoor, A., Victoria, J., Simmonds, P., Slikas, E., Chieochansin, T., Naeem, A., … 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), 20482–87. -
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), 20362–67. -
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), 211–28. -
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., Rodriguez, B. A., … 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. -
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. -
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., Kagan, R. M., & 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), 2196–98. -
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., Buech, J., … 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. -
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., Kiuchi, M., … Shafer, R. W. (2009). Drug Resistance Mutations for Surveillance of Transmitted HIV-1 Drug-Resistance: 2009 Update. PLOS ONE, 4(3). -
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., Wang, C., … 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), 1275–85. -
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., Pillay, D., & Shafer, R. W. (2009). The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance. BIOINFORMATICS, 25(9), 1197–98. -
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. -
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., Van der Borght, K., … 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. -
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. -
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., Rode, R. A., … Shafer, R. W. (2009). Predictive Value of HIV-1 Genotypic Resistance Test Interpretation Algorithms. JOURNAL OF INFECTIOUS DISEASES, 200(3), 453–63. -
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. -
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., Towner, W., … Shafer, R. W. (2009). Nonpolymorphic Human Immunodeficiency Virus Type 1 Protease and Reverse Transcriptase Treatment-Selected Mutations. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 53(11), 4869–78. -
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., Egholm, M., … 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), 309–15. -
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), 934–36. -
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. -
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., Charest, H., … 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. -
African Mitochondrial DNA Subhaplogroups and Peripheral Neuropathy during Antiretroviral Therapy
Canter, J. A., Robbins, G. K., Selph, D., Clifford, D. B., Kallianpur, A. R., Shafer, R., … Hulgan, T. (2010). African Mitochondrial DNA Subhaplogroups and Peripheral Neuropathy during Antiretroviral Therapy. JOURNAL OF INFECTIOUS DISEASES, 201(11), 1703–1707. -
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), 1477–85. -
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., Shafer, R. W., & Hughes, M. D. (2010). Long-term increase in CD4(+) T-cell counts during combination antiretroviral therapy for HIV-1 infection. AIDS, 24(12), 1867–76. -
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., Liu, T., … Shafer, R. W. (2010). Nucleic Acid Template and the Risk of a PCR-Induced HIV-1 Drug Resistance Mutation. PLOS ONE, 5(6). -
HIV-1 Protease Mutations and Protease Inhibitor Cross-Resistance
Rhee, S.-Y., Taylor, J., Fessel, W. J., Kaufman, D., Towner, W., Troia, P., … Shafer, R. W. (2010). HIV-1 Protease Mutations and Protease Inhibitor Cross-Resistance. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 54(10), 4253–61. -
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., Beggel, B., … Shafer, R. W. (2010). Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery. ANTIVIRAL RESEARCH, 88(3), 269–75. -
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., Svarovskaia, E. S., … Shafer, R. W. (2010). A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads. BIOINFORMATICS, 26(23), 2929–32. -
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., Fessel, W. J., & 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), 1323–26. -
The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation
Pereyra, F., Jia, X., McLaren, P. J., Telenti, A., de Bakker, P. I. W., Walker, B. D., … Zhao, M. (2010). The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation. SCIENCE, 330(6010), 1551–57. -
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 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. -
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., Das, D., … 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), 10079–89. -
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., Weinheimer, S. P., … Shafer, R. W. (2011). The efficacy of an anti-CD4 monoclonal antibody for HIV-1 treatment. ANTIVIRAL RESEARCH, 92(3), 484–487. -
A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes
Doherty, K. M., Nakka, P., King, B. M., Rhee, S.-Y., Holmes, S. P., Shafer, R. W., & Radhakrishnan, M. L. (2011). A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes. BMC BIOINFORMATICS, 12. -
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. -
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., Towner, W., … 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), 2305–13. -
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), 862–75. -
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., Robinson-Mosher, A., … 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), 485–94. -
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), 4522–24. -
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. -
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). -
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., Schiffer, C., … 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), 414–18. -
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., Pacold, M., … 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), 343–49. -
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. -
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., Vercauteren, J., … 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. -
Update of the drug resistance mutations in HIV-1: March 2013.
Johnson, V. A., Calvez, V., Gunthard, H. F., Paredes, R., Pillay, D., Shafer, R. W., … 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., von Kleist, M., & Merigan, T. C. (2013). In vitro HIV-1 evolution in response to triple reverse transcriptase inhibitors & in silico phenotypic analysis. PloS One, 8(4). -
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., Sigaloff, K. C., … 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. -
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-? -
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. -
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. -
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. -
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., Halpern, J., & 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), 832–38. -
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., Katzenstein, D. A., & Merigan, T. C. (1994). DIDANOSINE RESISTANCE IN HIV-INFECTED PATIENTS SWITCHED FROM ZIDOVUDINE TO DIDANOSINE MONOTHERAPY. ANNALS OF INTERNAL MEDICINE, 121(4), 263–68. -
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. K. N., 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. -
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), 526–32. -
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. -
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), 1072–72. -
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. -
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., Sierra, M. F., … 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), 170–76. -
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), 811–11. -
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., Kozal, M., … 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), 366–69. -
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., Desmond, E., … SCHOOLNIK, G. K. (1993). EXOGENOUS REINFECTION WITH MULTIDRUG-RESISTANT MYCOBACTERIUM-TUBERCULOSIS IN PATIENTS WITH ADVANCED HIV-INFECTION. NEW ENGLAND JOURNAL OF MEDICINE, 328(16), 1137–44. -
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. -
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. K. N., Katzenstein, D. A., Ragni, M. V., … 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), 722–29. -
Multidrug-resistant human immunodeficiency virus type 1 strains resulting from combination antiretroviral therapy
Iversen, A. K. N., Shafer, R. W., Wehrly, K., Winters, M. A., Mullins, J. I., Chesebro, B., & 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. -
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. -
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. -
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., Weislow, O. S., … 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. -
HIV virology for clinical trials.
Shafer, R. W., & Merigan, T. C. (1995). HIV virology for clinical trials. AIDS , 9, S193–202. -
Predictors of survival in HIV-infected tuberculosis patients
Shafer, R. W., Bloch, A. B., Larkin, C., VASUDAVAN, V., SELIGMAN, S., Dehovitz, J. D., … Cauthen, G. (1996). Predictors of survival in HIV-infected tuberculosis patients. AIDS, 10(3), 269–272. -
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), 520–22. -
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. -
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. -
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. K. N., & 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. -
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), 5441–48. -
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. -
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., Shafer, R. W., … 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. -
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), 348–52. -
Viral population estimation using pyrosequencing
Eriksson, N., Pachter, L., Mitsuya, Y., Rhee, S.-Y., Wang, C., Gharizadeh, B., … Beerenwinkel, N. (2008). Viral population estimation using pyrosequencing. PLOS COMPUTATIONAL BIOLOGY, 4(5). -
Clinically validated genotype analysis: guiding principles and statistical concerns
Brun-Vezinet, F., Costagliolo, D., Khaled, M. A., Calvez, V., Clavel, F., Clotet, B., … DeGruttola, V. (2004). Clinically validated genotype analysis: guiding principles and statistical concerns. ANTIVIRAL THERAPY, 9(4), 465–78. -
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., Shafer, R., … 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. -
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., Shafer, R., … 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). -
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., Fitzgibbon, J., … 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. -
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., Prosperi, M., … 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. -
2011 update of the drug resistance mutations in HIV-1.
Johnson, V. A., Calvez, V., Günthard, H. F., Paredes, R., Pillay, D., Shafer, R., … Richman, D. D. (2011). 2011 update of the drug resistance mutations in HIV-1. Topics in Antiviral Medicine, 19(4), 156–164. -
Spectrum of HIV-1 reverse transcriptase mutations selected by nucleoside reverse transcriptase inhibitor treatment is greater than previously reported
Gonzales, M. J., Wu, T., Taylor, J., Belitskaya, I., Kantor, R., Israelski, D., … Shafer, R. W. (2002). Spectrum of HIV-1 reverse transcriptase mutations selected by nucleoside reverse transcriptase inhibitor treatment is greater than previously reported. INT MEDICAL PRESS LTD. -
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., Lemey, P., … Vandamme, A.-M. (2010). Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape. BMC BIOINFORMATICS, 11. -
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., Preiser, W., … 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). -
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., Kessler, C. M., … 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), 2337–46. -
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., Katzenstein, D. A., … 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), 4290–99. -
Automating HIV Drug Resistance Genotyping with RECall, a Freely Accessible Sequence Analysis Tool
Woods, C. K., Brumme, C. J., Liu, T. F., Chui, C. K. S., Chu, A. L., Wynhoven, B., … 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. -
Standardized representation, visualization and searchable repository of antiretroviral treatment-change episodes
Rhee, S.-Y., Luis Blanco, J., Liu, T. F., Pere, I., Kaiser, R., Zazzi, M., … Shafer, R. W. (2012). Standardized representation, visualization and searchable repository of antiretroviral treatment-change episodes. AIDS RESEARCH AND THERAPY, 9. -
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., von Kleist, M., & Merigan, T. C. (2013). In Vitro HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitors & In Silico Phenotypic Analysis. PloS One, 8(4). -
HIV-1 transmission networks in a small world.
Pennings, P. S., Holmes, S. P., & Shafer, R. W. (2014). HIV-1 transmission networks in a small world. Journal of Infectious Diseases, 209(2), 180–82. -
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., Taylor, J., … 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. -
Genome-wide association study of peripheral neuropathy with D-drug-containing regimens in AIDS Clinical Trials Group protocol 384
Leger, P. D., Johnson, D. H., Robbins, G. K., Shafer, R. W., Clifford, D. B., Li, J., … Haas, D. W. (2014). Genome-wide association study of peripheral neuropathy with D-drug-containing regimens in AIDS Clinical Trials Group protocol 384. JOURNAL OF NEUROVIROLOGY, 20(3), 304–8. -
2014 update of the drug resistance mutations in HIV-1.
Wensing, A. M., Calvez, V., Günthard, H. F., Johnson, V. A., Paredes, R., Pillay, D., … Richman, D. D. (2014). 2014 update of the drug resistance mutations in HIV-1. Topics in Antiviral Medicine, 22(3), 642–50. -
Similar Prevalence of Low-Abundance Drug-Resistant Variants in Treatment-Naive Patients with Genotype 1a and 1b Hepatitis C Virus Infections as Determined by Ultradeep Pyrosequencing
Margeridon-Thermet, S., Le Pogam, S., Li, L., Liu, T. F., Shulman, N., Shafer, R. W., & Najera, I. (2014). Similar Prevalence of Low-Abundance Drug-Resistant Variants in Treatment-Naive Patients with Genotype 1a and 1b Hepatitis C Virus Infections as Determined by Ultradeep Pyrosequencing. PLOS ONE, 9(8). -
A uniquely prevalent nonnucleoside reverse transcriptase inhibitor resistance mutation in Russian subtype A HIV-1 viruses
Kolomeets, A. N., Varghese, V., Lemey, P., Bobkova, M. R., & Shafer, R. W. (2014). A uniquely prevalent nonnucleoside reverse transcriptase inhibitor resistance mutation in Russian subtype A HIV-1 viruses. AIDS, 28(17), F1–F8. -
Lower prevalence of drug resistance mutations at first-line virological failure to first-line therapy with atripla vs. tenofovir plus emtricitabine/lamivudine plus efavirenz administered on a multiple tablet therapy
Blanco, J. L., Montaner, J. S. G., Marconi, V. C., Santoro, M. M., Campos-Loza, A. E., Shafer, R. W., … Gatell, J. M. (2014). Lower prevalence of drug resistance mutations at first-line virological failure to first-line therapy with atripla vs. tenofovir plus emtricitabine/lamivudine plus efavirenz administered on a multiple tablet therapy. AIDS, 28(17), 2531–39. -
Impact of Drug Resistance-Associated Amino Acid Changes in HIV-1 Subtype C on Susceptibility to Newer Nonnucleoside Reverse Transcriptase Inhibitors
Basson, A. E., Rhee, S.-Y., Parry, C. M., El-Khatib, Z., Charalambous, S., de Oliveira, T., … Morris, L. (2015). Impact of Drug Resistance-Associated Amino Acid Changes in HIV-1 Subtype C on Susceptibility to Newer Nonnucleoside Reverse Transcriptase Inhibitors. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 59(2), 960–71. -
Lower prevalence of drug resistance mutations at first-line virological failure to first-line therapy with atripla vs. tenofovir?+?emtricitabine/lamivudine?+?efavirenz administered on a multiple tablet therapy.
Blanco, J. L., Montaner, J. S. G., Marconi, V. C., Santoro, M. M., Campos-Loza, A. E., Shafer, R. W., … Gatell, J. M. (2014). Lower prevalence of drug resistance mutations at first-line virological failure to first-line therapy with atripla vs. tenofovir?+?emtricitabine/lamivudine?+?efavirenz administered on a multiple tablet therapy. AIDS , 28(17), 2531–39. -
A uniquely prevalent nonnucleoside reverse transcriptase inhibitor resistance mutation in Russian subtype A HIV-1 viruses.
Kolomeets, A. N., Varghese, V., Lemey, P., Bobkova, M. R., & Shafer, R. W. (2014). A uniquely prevalent nonnucleoside reverse transcriptase inhibitor resistance mutation in Russian subtype A HIV-1 viruses. AIDS , 28(17), F1–8. -
BLASTOMYCOSIS IN PATIENTS WITH THE ACQUIRED-IMMUNODEFICIENCY-SYNDROME
Pappas, P. G., Pottage, J. C., Powderly, W. G., Fraser, V. J., Stratton, C. W., McKenzie, S., … Dismukes, W. E. (1992). BLASTOMYCOSIS IN PATIENTS WITH THE ACQUIRED-IMMUNODEFICIENCY-SYNDROME. ANNALS OF INTERNAL MEDICINE, 116(10), 847–853. -
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.
Rhee, S.-Y., Blanco, J. L., Jordan, M. R., Taylor, J., Lemey, P., Varghese, V., … Shafer, R. W. (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 Medicine, 12(4). -
Modifying Antiretroviral Therapy in Virologically Suppressed HIV-1-Infected Patients
Collins, S. E., Grant, P. M., & Shafer, R. W. (2016). Modifying Antiretroviral Therapy in Virologically Suppressed HIV-1-Infected Patients. DRUGS, 76(1), 75–98. -
2015 Update of the Drug Resistance Mutations in HIV-1.
Wensing, A. M., Calvez, V., Günthard, H. F., Johnson, V. A., Paredes, R., Pillay, D., … Richman, D. D. (2015). 2015 Update of the Drug Resistance Mutations in HIV-1. Topics in Antiviral Medicine, 23(4), 132–41. -
HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing.
Rhee, S.-Y., Jordan, M. R., Raizes, E., Chua, A., Parkin, N., Kantor, R., … Shafer, R. W. (2015). HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing. PloS One, 10(12). -
Response to Therapy in Antiretroviral Therapy-Naive Patients With Isolated Nonnucleoside Reverse Transcriptase Inhibitor-Associated Transmitted Drug Resistance
Clutter, D. S., Fessel, W. J., Rhee, S.-Y., Hurley, L. B., Klein, D. B., Ioannidis, J. P. A., … Shafer, R. W. (2016). Response to Therapy in Antiretroviral Therapy-Naive Patients With Isolated Nonnucleoside Reverse Transcriptase Inhibitor-Associated Transmitted Drug Resistance. JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES, 72(2), 171–76. -
More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1.
Feder, A. F., Rhee, S.-Y., Holmes, S. P., Shafer, R. W., Petrov, D. A., & Pennings, P. S. (2016). More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1. ELife, 5. -
HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing
Rhee, S.-Y., Jordan, M. R., Raizes, E., Chua, A., Parkin, N., Kantor, R., … Shafer, R. W. (2015). HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing. PLOS ONE, 10(12). -
Genetic Variability of HIV-1 for Drug Resistance Assay Development
Clutter, D. S., Rojas Sanchez, P., Rhee, S.-Y., & Shafer, R. W. (2016). Genetic Variability of HIV-1 for Drug Resistance Assay Development. VIRUSES-BASEL, 8(2). -
HIV-1 Protease, Reverse Transcriptase, and Integrase Variation
Rhee, S.-Y., Sankaran, K., Varghese, V., Winters, M. A., Hurt, C. B., Eron, J. J., … Shafer, R. W. (2016). HIV-1 Protease, Reverse Transcriptase, and Integrase Variation. JOURNAL OF VIROLOGY, 90(13), 6058–70. -
Surveillance of HIV Transmitted Drug Resistance in Latin America and the Caribbean: A Systematic Review and Meta-Analysis
Avila-Rios, S., Sued, O., Rhee, S.-Y., Shafer, R. W., Reyes-Teran, G., & Ravasi, G. (2016). Surveillance of HIV Transmitted Drug Resistance in Latin America and the Caribbean: A Systematic Review and Meta-Analysis. PLOS ONE, 11(6). -
Transmitted HIV Drug Resistance Is High and Longstanding in Metropolitan Washington, DC.
Kassaye, S. G., Grossman, Z., Balamane, M., Johnston-White, B., Liu, C., Kumar, P., … Maldarelli, F. (2016). Transmitted HIV Drug Resistance Is High and Longstanding in Metropolitan Washington, DC. Clinical Infectious Diseases , 63(6), 836–43. -
Q148N, a Novel Integrase Inhibitor Resistance Mutation Associated with Low-Level Reduction in Elvitegravir Susceptibility
Varghese, V., Pinsky, B. A., Smith, D. S., Klein, D., & Shafer, R. W. (2016). Q148N, a Novel Integrase Inhibitor Resistance Mutation Associated with Low-Level Reduction in Elvitegravir Susceptibility. AIDS RESEARCH AND HUMAN RETROVIRUSES, 32(7), 702–4. -
Global epidemiology of drug resistance after failure of WHO recommended first-line regimens for adult HIV-1 infection: a multicentre retrospective cohort study
Gregson, J., Tang, M., Ndembi, N., Hamers, R. L., Rhee, S.-Y., Marconi, V. C., … Gupta, R. K. (2016). Global epidemiology of drug resistance after failure of WHO recommended first-line regimens for adult HIV-1 infection: a multicentre retrospective cohort study. LANCET INFECTIOUS DISEASES, 16(5), 565–75. -
HIV-1 drug resistance and resistance testing.
Clutter, D. S., Jordan, M. R., Bertagnolio, S., & Shafer, R. W. (2016). HIV-1 drug resistance and resistance testing. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. -
Evaluation of the Aptima HIV-1 Quant Dx Assay Using Plasma and Dried Blood Spots.
Sahoo, M. K., Varghese, V., White, E., Winslow, M., Katzenstein, D. A., Shafer, R. W., & Pinsky, B. A. (2016). Evaluation of the Aptima HIV-1 Quant Dx Assay Using Plasma and Dried Blood Spots. Journal of Clinical Microbiology, 54(10), 2597–2601. -
Transmitted HIV Drug Resistance Is High and Longstanding in Metropolitan Washington, DC
Kassaye, S. G., Grossman, Z., Balamane, M., Johnston-White, B., Liu, C., Kumar, P., … Maldarelli, F. (2016). Transmitted HIV Drug Resistance Is High and Longstanding in Metropolitan Washington, DC. CLINICAL INFECTIOUS DISEASES, 65(6), 836–43. -
A Guide to HIV-1 Reverse Transcriptase and Protease Sequencing for Drug Resistance Studies.
Shafer, R. W., Dupnik, K., Winters, M. A., & Eshleman, S. H. (2001). A Guide to HIV-1 Reverse Transcriptase and Protease Sequencing for Drug Resistance Studies. HIV Sequence Compendium, 2001, 1–51. -
2017 Update of the Drug Resistance Mutations in HIV-1.
Wensing, A. M., Calvez, V., Günthard, H. F., Johnson, V. A., Paredes, R., Pillay, D., … Richman, D. D. (2017). 2017 Update of the Drug Resistance Mutations in HIV-1. Topics in Antiviral Medicine, 24(4), 132–33. -
Occult HIV-1 drug resistance to thymidine analogues following failure of first-line tenofovir combined with a cytosine analogue and nevirapine or efavirenz in sub Saharan Africa: a retrospective multi-centre cohort study.
Gregson, J., Kaleebu, P., Marconi, V. C., van Vuuren, C., Ndembi, N., Hamers, R. L., … Gupta, R. K. (2017). Occult HIV-1 drug resistance to thymidine analogues following failure of first-line tenofovir combined with a cytosine analogue and nevirapine or efavirenz in sub Saharan Africa: a retrospective multi-centre cohort study. The Lancet. Infectious Diseases, 17(3), 296–304. -
Mutational Correlates of Virological Failure in Individuals Receiving a WHO-Recommended Tenofovir-Containing First-Line Regimen: An International Collaboration.
Rhee, S.-Y., Varghese, V., Holmes, S. P., van Zyl, G. U., Steegen, K., Boyd, M. A., … Shafer, R. W. (2017). Mutational Correlates of Virological Failure in Individuals Receiving a WHO-Recommended Tenofovir-Containing First-Line Regimen: An International Collaboration. EBioMedicine, 18, 225–35. -
NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences
Tzou, P. L., Huang, X., & Shafer, R. W. (2017). NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences. BMC BIOINFORMATICS, 18. -
Collaborative update of a rule-based expert system for HIV-1 genotypic resistance test interpretation.
Paredes, R., Tzou, P. L., van Zyl, G., Barrow, G., Camacho, R., Carmona, S., … Shafer, R. W. (2017). Collaborative update of a rule-based expert system for HIV-1 genotypic resistance test interpretation. PloS One, 12(7), e0181357. -
Prevalence of Drug-Resistant Minority Variants in Untreated HIV-1-Infected Individuals With and Those Without Transmitted Drug Resistance Detected by Sanger Sequencing.
Clutter, D. S., Zhou, S., Varghese, V., Rhee, S.-Y. Y., Pinsky, B. A., Jeffrey Fessel, W., … Shafer, R. W. (2017). Prevalence of Drug-Resistant Minority Variants in Untreated HIV-1-Infected Individuals With and Those Without Transmitted Drug Resistance Detected by Sanger Sequencing. The Journal of Infectious Diseases, 216(3), 387–91. -
Evolution of gag and gp41 in Patients Receiving Ritonavir-Boosted Protease Inhibitors.
Manasa, J., Varghese, V., Pond, S. L., Rhee, S.-Y. Y., Tzou, P. L., Fessel, W. J., … Shafer, R. W. (2017). Evolution of gag and gp41 in Patients Receiving Ritonavir-Boosted Protease Inhibitors. Scientific Reports, 7(1), 11559. -
Human Immunodeficiency Virus Type 1 Drug Resistance Mutations Update.
Shafer, R. W. (2017). Human Immunodeficiency Virus Type 1 Drug Resistance Mutations Update. The Journal of Infectious Diseases. -
Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance in a Large U.S. Clinic Population.
Rhee, S.-Y., Clutter, D., Fessel, W. J., Klein, D., Slome, S., Pinsky, B. A., … Shafer, R. W. (2018). Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance in a Large U.S. Clinic Population. Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America. -
Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery
Aggeli, D., Karas, V. O., Sinnott-Armstrong, N. A., Varghese, V., Shafer, R. W., Greenleaf, W. J., & Sherlock, G. (2018). Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery. NUCLEIC ACIDS RESEARCH, 46(7). -
Comparison of an In Vitro Diagnostic Next-Generation Sequencing Assay with Sanger Sequencing for HIV-1 Genotypic Resistance Testing
Tzou, P. L., Ariyaratne, P., Varghese, V., Lee, C., Rakhmanaliev, E., Villy, C., … Shafer, R. W. (2018). Comparison of an In Vitro Diagnostic Next-Generation Sequencing Assay with Sanger Sequencing for HIV-1 Genotypic Resistance Testing. JOURNAL OF CLINICAL MICROBIOLOGY, 56(6). -
NO DETECTION OF VARIANTS BEARING NS5B S282T MERICITABINE (MCB) RESISTANCE MUTATION IN DAA TREATMENT-NAIVE HCV GENOTYPE 1 (G1)-INFECTED PATIENTS USING ULTRA-DEEP PYROSEQUENCING (UDPS)
Margeridon, S., Le Pogam, S., Liu, T. F., Hanczaruk, B., Simen, B. B., Shulman, N., … Najera, I. (2011). NO DETECTION OF VARIANTS BEARING NS5B S282T MERICITABINE (MCB) RESISTANCE MUTATION IN DAA TREATMENT-NAIVE HCV GENOTYPE 1 (G1)-INFECTED PATIENTS USING ULTRA-DEEP PYROSEQUENCING (UDPS). HEPATOLOGY, 54, 532A. -
ULTRA-DEEP SEQUENCING OF THE NS3 AND NS5B REGIONS DETECTS PRE-EXISTING RESISTANT VARIANTS TO DIRECT ACTING ANTIVIRALS (DAA) IN HCV GENOTYPE 1 INFECTED PATIENTS NAIVE
Margeridon, S., Le Pogam, S., Liu, T. F., Hanczaruk, B., Arnold, T. E., Simen, B. B., … Najera, I. (2010). ULTRA-DEEP SEQUENCING OF THE NS3 AND NS5B REGIONS DETECTS PRE-EXISTING RESISTANT VARIANTS TO DIRECT ACTING ANTIVIRALS (DAA) IN HCV GENOTYPE 1 INFECTED PATIENTS NAIVE. HEPATOLOGY, 52(4), 714A. -
LOW-LEVEL PERSISTENCE OF HBV DRUG RESISTANCE MUTATIONS IN PATIENTS WITH A PAST HISTORY OF LAMIVUDINE (LAM) TREATMENT
Margeridon, S., Svarovskaia, E. S., Martin, S. R., Liu, T. F., Borroto-Esoda, K., & Shafer, R. W. (2010). LOW-LEVEL PERSISTENCE OF HBV DRUG RESISTANCE MUTATIONS IN PATIENTS WITH A PAST HISTORY OF LAMIVUDINE (LAM) TREATMENT. HEPATOLOGY, 52(4), 505A–506A. -
Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy.
Tzou, P. L., Rhee, S.-Y., Pond, S. L., Manasa, J., & Shafer, R. W. (2018). Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy. Scientific Data, 5, 180147. -
Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences.
Rhee, S.-Y., & Shafer, R. W. (2018). Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences. Scientific Data, 5, 180148. -
The clinical implications of pretreatment drug resistance -- a moving target.
Shafer, R. W., & Frenkel, L. M. (2018). The clinical implications of pretreatment drug resistance -- a moving target. Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America. -
Baseline dasabuvir resistance in Hepatitis C virus from the genotypes 1, 2 and 3 and modeling of the NS5B-dasabuvir complex by the in silico approach.
Akaberi, D., Bergfors, A., Kjellin, M., Kameli, N., Lidemalm, L., Kolli, B., … Lennerstrand, J. (2018). Baseline dasabuvir resistance in Hepatitis C virus from the genotypes 1, 2 and 3 and modeling of the NS5B-dasabuvir complex by the in silico approach. Infection Ecology & Epidemiology, 8(1), 1528117. -
Moderate to high levels of pre-treatment HIV drug resistance in KwaZulu-Natal Province, South Africa.
Chimukangara, B., Kharsany, A. B., Lessells, R. J., Naidoo, K., Rhee, S.-Y., Manasa, J., … de Oliveira, T. (2018). Moderate to high levels of pre-treatment HIV drug resistance in KwaZulu-Natal Province, South Africa. AIDS Research and Human Retroviruses. -
Reply to Ambrosioni et al.
Gunthard, H. F., Calvez, V., Paredes, R., Pillay, D., Shafer, R. W., Wensing, A. M., … Richman, D. D. (2018). Reply to Ambrosioni et al. Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America. -
Human Immunodeficiency Virus Drug Resistance: 2018 Recommendations of the International Antiviral Society-USA Panel
Gunthard, H. F., Calvez, V., Paredes, R., Pillay, D., Shafer, R. W., Wensing, A. M., … Richman, D. D. (2019). Human Immunodeficiency Virus Drug Resistance: 2018 Recommendations of the International Antiviral Society-USA Panel. CLINICAL INFECTIOUS DISEASES, 68(2), 177–87. -
Mechanisms of Resistance to Antiviral Agents
Shafer, R. W., Einav, S., & Chou, S. (2007). Mechanisms of Resistance to Antiviral Agents. MANUAL OF CLINICAL MICROBIOLOGY, 9TH ED, 1689–1704. -
Curbing the rise of HIV drug resistance in low-income and middle-income countries: the role of dolutegravir-containing regimens.
Inzaule, S. C., Hamers, R. L., Doherty, M., Shafer, R. W., Bertagnolio, S., & Rinke de Wit, T. F. (2019). Curbing the rise of HIV drug resistance in low-income and middle-income countries: the role of dolutegravir-containing regimens. The Lancet. Infectious Diseases. -
Modifying Antiretroviral Therapy in Virologically Suppressed HIV-1-Infected Patients.
Collins, S. E., Grant, P. M., & Shafer, R. W. (2016). Modifying Antiretroviral Therapy in Virologically Suppressed HIV-1-Infected Patients. Drugs, 76(1), 75–98. -
Multiplex Solid-Phase Melt Curve Analysis for the Point-of-Care Detection of HIV-1 Drug Resistance.
Clutter, D. S., Mazarei, G., Sinha, R., Manasa, J., Nouhin, J., LaPrade, E., … Shafer, R. W. (2019). Multiplex Solid-Phase Melt Curve Analysis for the Point-of-Care Detection of HIV-1 Drug Resistance. The Journal of Molecular Diagnostics : JMD. -
National and International Dimensions of Human Immunodeficiency Virus-1 Sequence Clusters in a Northern California Clinical Cohort.
Rhee, S.-Y., Magalis, B. R., Hurley, L., Silverberg, M. J., Marcus, J. L., Slome, S., … Shafer, R. W. (2019). National and International Dimensions of Human Immunodeficiency Virus-1 Sequence Clusters in a Northern California Clinical Cohort. Open Forum Infectious Diseases, 6(4), ofz135. -
Moderate-to-High Levels of Pretreatment HIV Drug Resistance in KwaZulu-Natal Province, South Africa
Chimukangara, B., Kharsany, A. B. M., Lessells, R. J., Naidoo, K., Rhee, S.-Y., Manasa, J., … de Oliveira, T. (2019). Moderate-to-High Levels of Pretreatment HIV Drug Resistance in KwaZulu-Natal Province, South Africa. AIDS RESEARCH AND HUMAN RETROVIRUSES, 35(2), 129–38. -
Trends in Pretreatment HIV-1 Drug Resistance in Antiretroviral Therapy-naive Adults in South Africa, 2000-2016: A Pooled Sequence Analysis.
Chimukangara, B., Lessells, R. J., Rhee, S.-Y., Giandhari, J., Kharsany, A. B., Naidoo, K., … de Oliveira, T. (2019). Trends in Pretreatment HIV-1 Drug Resistance in Antiretroviral Therapy-naive Adults in South Africa, 2000-2016: A Pooled Sequence Analysis. EClinicalMedicine, 9, 26–34. -
Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted Human Immunodeficiency Virus Type 1 Drug Resistance in a Large US Clinic Population
Rhee, S.-Y., Clutter, D., Fessel, W. J., Klein, D., Slome, S., Pinsky, B. A., … Shafer, R. W. (2019). Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted Human Immunodeficiency Virus Type 1 Drug Resistance in a Large US Clinic Population. CLINICAL INFECTIOUS DISEASES, 68(2), 213–21. -
Resistance Testing for Integrase Strand Transfer Inhibitors in Naive, Human Immunodeficiency Virus-infected Individuals Reply
Gunthard, H. F., Calvez, V., Paredes, R., Pillay, D., Shafer, R. W., Wensing, A. M., … Richman, D. D. (2019). Resistance Testing for Integrase Strand Transfer Inhibitors in Naive, Human Immunodeficiency Virus-infected Individuals Reply. CLINICAL INFECTIOUS DISEASES, 68(11), 1977–78. -
A systematic review of the genetic mechanisms of dolutegravir resistance.
Rhee, S.-Y. Y., Grant, P. M., Tzou, P. L., Barrow, G., Harrigan, P. R., Ioannidis, J. P., & Shafer, R. W. (2019). A systematic review of the genetic mechanisms of dolutegravir resistance. The Journal of Antimicrobial Chemotherapy. -
Curbing the rise of HIV drug resistance in low-income and middle-income countries: the role of dolutegravir-containing regimens
Inzaule, S. C., Hamers, R. L., Doherty, M., Shafer, R. W., Bertagnolio, S., & de Wit, T. F. R. (2019). Curbing the rise of HIV drug resistance in low-income and middle-income countries: the role of dolutegravir-containing regimens. LANCET INFECTIOUS DISEASES, 19(7), E246–E252. -
Amino Acid Prevalence of HIV-1 pol Mutations by Direct PCR and Single Genome Sequencing.
Tzou, P. L., Rhee, S.-Y., & Shafer, R. (2019). Amino Acid Prevalence of HIV-1 pol Mutations by Direct PCR and Single Genome Sequencing. AIDS Research and Human Retroviruses. -
National and International Dimensions of Human Immunodeficiency Virus-1 Sequence Clusters in a Northern California Clinical Cohort
Rhee, S.-Y., Magalis, B. R., Hurley, L., Silverberg, M. J., Marcus, J. L., Slome, S., … Shafer, R. W. (2019). National and International Dimensions of Human Immunodeficiency Virus-1 Sequence Clusters in a Northern California Clinical Cohort. OPEN FORUM INFECTIOUS DISEASES, 6(4). -
Multiplex Solid-Phase Melt Curve Analysis for the Point-of-Care Detection of HIV-1 Drug Resistance
Clutter, D. S., Mazarei, G., Sinha, R., Manasa, J., Nouhin, J., LaPrade, E., … Shafer, R. W. (2019). Multiplex Solid-Phase Melt Curve Analysis for the Point-of-Care Detection of HIV-1 Drug Resistance. JOURNAL OF MOLECULAR DIAGNOSTICS, 21(4), 580–92. -
Prospective Evaluation of the Vela Diagnostics Next-Generation Sequencing Platform for HIV-1 Genotypic Resistance Testing.
Weber, J., Volkova, I., Sahoo, M. K., Tzou, P. L., Shafer, R. W., & Pinsky, B. A. (2019). Prospective Evaluation of the Vela Diagnostics Next-Generation Sequencing Platform for HIV-1 Genotypic Resistance Testing. The Journal of Molecular Diagnostics : JMD. -
The Clinical Implications of Pretreatment Drug Resistance-A Moving Target
Shafer, R. W., & Frenkel, L. M. (2019). The Clinical Implications of Pretreatment Drug Resistance-A Moving Target. CLINICAL INFECTIOUS DISEASES, 69(2), 215–17. -
Integrase strand transfer inhibitor (INSTI)-resistance mutations for the surveillance of transmitted HIV-1 drug resistance.
Tzou, P. L., Rhee, S.-Y. Y., Descamps, D., Clutter, D. S., Hare, B., Mor, O., … Shafer, R. W. (2019). Integrase strand transfer inhibitor (INSTI)-resistance mutations for the surveillance of transmitted HIV-1 drug resistance. The Journal of Antimicrobial Chemotherapy. -
2019 update of the drug resistance mutations in HIV-1.
Wensing, A. M., Calvez, V., Ceccherini-Silberstein, F., Charpentier, C., Gunthard, H. F., Paredes, R., … Richman, D. D. (2019). 2019 update of the drug resistance mutations in HIV-1. Topics in Antiviral Medicine, 27(3), 111–21. -
Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences
Rhee, S.-Y., & Shafer, R. W. (2018). Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences. SCIENTIFIC DATA, 5. -
Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy
Tzou, P. L., Rhee, S.-Y., Pond, S. L. K., Manasa, J., & Shafer, R. W. (2018). Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy. SCIENTIFIC DATA, 5. -
DOLUTEGRAVIR ROLLOUT AND EXPECTED PREVALENCE OF PRETREATMENT DRUG RESISTANCE TO ANTIRETROVIRAL THERAPY AMONG KENYAN WOMEN
Duarte, H., Enns, E., Stauffer, D., Shafer, R., & Bendavid, E. (2019). DOLUTEGRAVIR ROLLOUT AND EXPECTED PREVALENCE OF PRETREATMENT DRUG RESISTANCE TO ANTIRETROVIRAL THERAPY AMONG KENYAN WOMEN. SEXUALLY TRANSMITTED INFECTIONS, 95, A137–A138. -
Expanded Spectrum of Antiretroviral-Selected Mutations in Human Immunodeficiency Virus Type 2.
Tzou, P. L., Descamps, D., Rhee, S.-Y., Raugi, D. N., Charpentier, C., Taveira, N., … Shafer, R. W. (2020). Expanded Spectrum of Antiretroviral-Selected Mutations in Human Immunodeficiency Virus Type 2. The Journal of Infectious Diseases. -
Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences.
Tzou, P. L., Kosakovsky Pond, S. L., Avila-Rios, S., Holmes, S. P., Kantor, R., & Shafer, R. W. (2020). Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences. PloS One, 15(2), e0225352. -
Cost-effectiveness analysis of pre-ART HIV drug resistance testing in Kenyan women.
Duarte, H. A., Babigumira, J. B., Enns, E. A., Stauffer, D. C., Shafer, R. W., Beck, I. A., … Bendavid, E. (2020). Cost-effectiveness analysis of pre-ART HIV drug resistance testing in Kenyan women. EClinicalMedicine, 22, 100355. -
Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations.
Avila-Rios, S., Parkin, N., Swanstrom, R., Paredes, R., Shafer, R., Ji, H., & Kantor, R. (2020). Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations. Viruses, 12(6). -
Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing.
Noguera-Julian, M., Lee, E. R., Shafer, R. W., Kantor, R., & Ji, H. (2020). Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing. Viruses, 12(6). -
Virological Failure and Acquired Genotypic Resistance Associated With Contemporary Antiretroviral Treatment Regimens.
Rhee, S.-Y. Y., Clutter, D., Hare, C. B., Tchakoute, C. T., Sainani, K., Fessel, W. J., … Shafer, R. W. (2020). Virological Failure and Acquired Genotypic Resistance Associated With Contemporary Antiretroviral Treatment Regimens. Open Forum Infectious Diseases, 7(9), ofaa316. -
Coronavirus Antiviral Research Database (CoV-RDB): An Online Database Designed to Facilitate Comparisons between Candidate Anti-Coronavirus Compounds.
Tzou, P. L., Tao, K., Nouhin, J., Rhee, S.-Y. Y., Hu, B. D., Pai, S., … Shafer, R. W. (2020). Coronavirus Antiviral Research Database (CoV-RDB): An Online Database Designed to Facilitate Comparisons between Candidate Anti-Coronavirus Compounds. Viruses, 12(9). -
HIV-1 transmitted drug resistance surveillance: shifting trends in study design and prevalence estimates.
Rhee, S.-Y. Y., Kassaye, S. G., Barrow, G., Sundaramurthi, J. C., Jordan, M. R., & Shafer, R. W. (2020). HIV-1 transmitted drug resistance surveillance: shifting trends in study design and prevalence estimates. Journal of the International AIDS Society, 23(9), e25611. -
In vitro cross-resistance to doravirine in a panel of HIV-1 clones harbouring multiple NNRTI resistance mutations.
Saladini, F., Giammarino, F., Hosseini, B. A., Giannini, A., Boccuto, A., Dragoni, F., … Zazzi, M. (2020). In vitro cross-resistance to doravirine in a panel of HIV-1 clones harbouring multiple NNRTI resistance mutations. The Journal of Antimicrobial Chemotherapy. -
Predictors of first-line antiretroviral therapy failure among adults and adolescents living with HIV/AIDS in a large prevention and treatment program in Nigeria.
Ndembi, N., Murtala-Ibrahim, F., Tola, M., Jumare, J., Aliyu, A., Alabi, P., … Dakum, P. (2020). Predictors of first-line antiretroviral therapy failure among adults and adolescents living with HIV/AIDS in a large prevention and treatment program in Nigeria. AIDS Research and Therapy, 17(1), 64. -
A SARS-CoV-2 antiviral therapy score card.
Shafer, R. W. (2020). A SARS-CoV-2 antiviral therapy score card. Global Health & Medicine, 2(6), 346–49. -
Integrase Strand Transfer Inhibitor Resistance in Integrase Strand Transfer Inhibitor-Naïve Persons.
Bailey, A. J., Rhee, S.-Y. Y., & Shafer, R. W. (2021). Integrase Strand Transfer Inhibitor Resistance in Integrase Strand Transfer Inhibitor-Naïve Persons. AIDS Research and Human Retroviruses. -
Temporal Trends in HIV-1 Mutations Used for the Surveillance of Transmitted Drug Resistance.
Rhee, S.-Y., Tzou, P. L., & Shafer, R. W. (2021). Temporal Trends in HIV-1 Mutations Used for the Surveillance of Transmitted Drug Resistance. Viruses, 13(5). -
SARS-CoV-2 Neutralization Resistance Mutations in Patient with HIV/AIDS, California, USA.
Hoffman, S. A., Costales, C., Sahoo, M. K., Palanisamy, S., Yamamoto, F., Huang, C. H., … Pinsky, B. A. (2021). SARS-CoV-2 Neutralization Resistance Mutations in Patient with HIV/AIDS, California, USA. Emerging Infectious Diseases, 27(10). -
SARS-CoV-2 Antiviral Therapy.
Tao, K., Tzou, P. L., Nouhin, J., Bonilla, H., Jagannathan, P., & Shafer, R. W. (2021). SARS-CoV-2 Antiviral Therapy. Clinical Microbiology Reviews, e0010921. -
The biological and clinical significance of emerging SARS-CoV-2 variants.
Tao, K., Tzou, P. L., Nouhin, J., Gupta, R. K., de Oliveira, T., Kosakovsky Pond, S. L., … Shafer, R. W. (2021). The biological and clinical significance of emerging SARS-CoV-2 variants. Nature Reviews. Genetics. -
SARS-CoV-2 Variants and Their Relevant Mutational Profiles: Update Summer 2021.
Alkhatib, M., Svicher, V., Salpini, R., Ambrosio, F. A., Bellocchi, M. C., Carioti, L., … Ceccherini-Silberstein, F. (2021). SARS-CoV-2 Variants and Their Relevant Mutational Profiles: Update Summer 2021. Microbiology Spectrum, e0109621. -
Adherence to contemporary antiretroviral treatment regimens and impact on immunological and virologic outcomes in a US healthcare system.
T Tchakoute, C., Rhee, S.-Y., Hare, C. B., Shafer, R. W., & Sainani, K. (2022). Adherence to contemporary antiretroviral treatment regimens and impact on immunological and virologic outcomes in a US healthcare system. PloS One, 17(2), e0263742. -
Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons.
Tzou, P. L., Tao, K., Pond, S. L., & Shafer, R. W. (2022). Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons. PloS One, 17(3), e0261045. -
Selection analysis identifies clusters of unusual mutational changes in Omicron lineage BA.1 that likely impact Spike function.
Martin, D. P., Lytras, S., Lucaci, A. G., Maier, W., Grüning, B., Shank, S. D., … Kosakovsky Pond, S. L. (2022). Selection analysis identifies clusters of unusual mutational changes in Omicron lineage BA.1 that likely impact Spike function. Molecular Biology and Evolution. -
Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function.
Martin, D. P., Lytras, S., Lucaci, A. G., Maier, W., Grüning, B., Shank, S. D., … Kosakovsky Pond, S. L. (2022). Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function. BioRxiv : the Preprint Server for Biology. -
A Partially Multiplexed HIV Drug Resistance (HIVDR) Assay for Monitoring HIVDR Mutations of the Protease, Reverse-Transcriptase (PRRT), and Integrase (INT).
DeVos, J., McCarthy, K., Sewe, V., Akinyi, G., Junghae, M., Opollo, V., … Chang, J. (2022). A Partially Multiplexed HIV Drug Resistance (HIVDR) Assay for Monitoring HIVDR Mutations of the Protease, Reverse-Transcriptase (PRRT), and Integrase (INT). Microbiology Spectrum, e0177621. -
Public availability of HIV-1 drug resistance sequence and treatment data: a systematic review.
Rhee, S.-Y., Kassaye, S. G., Jordan, M. R., Kouamou, V., Katzenstein, D., & Shafer, R. W. (2022). Public availability of HIV-1 drug resistance sequence and treatment data: a systematic review. The Lancet. Microbe, 3(5), e392–e398. -
Spectrum of Atazanavir-Selected Protease Inhibitor-Resistance Mutations.
Rhee, S.-Y., Boehm, M., Tarasova, O., Di Teodoro, G., Abecasis, A. B., Sonnerborg, A., … Shafer, R. W. (2022). Spectrum of Atazanavir-Selected Protease Inhibitor-Resistance Mutations. Pathogens (Basel, Switzerland), 11(5). -
Susceptibility of SARS-CoV-2 Omicron Variants to Therapeutic Monoclonal Antibodies: Systematic Review and Meta-analysis.
Tao, K., Tzou, P. L., Kosakovsky Pond, S. L., Ioannidis, J. P., & Shafer, R. W. (2022). Susceptibility of SARS-CoV-2 Omicron Variants to Therapeutic Monoclonal Antibodies: Systematic Review and Meta-analysis. Microbiology Spectrum, e0092622. -
Infectious Diseases Society of America Guidelines on the Treatment and Management of Patients with COVID-19.
Bhimraj, A., Morgan, R. L., Shumaker, A. H., Baden, L., Cheng, V. C., Edwards, K. M., … Falck-Ytter, Y. (2022). Infectious Diseases Society of America Guidelines on the Treatment and Management of Patients with COVID-19. Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America. -
Genotypic Resistance Testing of HIV-1 DNA in Peripheral Blood Mononuclear Cells.
Chu, C., Armenia, D., Walworth, C., Santoro, M. M., & Shafer, R. W. (2022). Genotypic Resistance Testing of HIV-1 DNA in Peripheral Blood Mononuclear Cells. Clinical Microbiology Reviews, e0005222. -
Genotypic correlates of resistance to the HIV-1 strand transfer integrase inhibitor cabotegravir.
Rhee, S.-Y., Parkin, N., Harrigan, P. R., Holmes, S., & Shafer, R. W. (2022). Genotypic correlates of resistance to the HIV-1 strand transfer integrase inhibitor cabotegravir. Antiviral Research, 105427. -
Sierra SARS-CoV-2 sequence and antiviral resistance analysis program.
Tzou, P. L., Tao, K., Sahoo, M. K., Kosakovsky Pond, S. L., Pinsky, B. A., & Shafer, R. W. (2022). Sierra SARS-CoV-2 sequence and antiviral resistance analysis program. Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology, 157, 105323. -
2022 update of the drug resistance mutations in HIV-1.
Wensing, A. M., Calvez, V., Ceccherini-Silberstein, F., Charpentier, C., Gunthard, H. F., Paredes, R., … Richman, D. D. (2022). 2022 update of the drug resistance mutations in HIV-1. Topics in Antiviral Medicine, 30(4), 559–574. -
Highly Ambiguous HIV-1 pol Positions Encoding Multiple Amino Acids Usually Result from Antiviral or Immune Selection Pressure.
Tao, K., Rhee, S.-Y., Tzou, P. L., Holmes, S., & Shafer, R. W. (2022). Highly Ambiguous HIV-1 pol Positions Encoding Multiple Amino Acids Usually Result from Antiviral or Immune Selection Pressure. AIDS Research and Human Retroviruses. -
Predicted effects of the introduction of long-acting injectable cabotegravir pre-exposure prophylaxis in sub-Saharan Africa: a modelling study.
Smith, J., Bansi-Matharu, L., Cambiano, V., Dimitrov, D., Bershteyn, A., van de Vijver, D., … Phillips, A. N. (2023). Predicted effects of the introduction of long-acting injectable cabotegravir pre-exposure prophylaxis in sub-Saharan Africa: a modelling study. The Lancet. HIV. -
Insights into HIV-1 Transmission Dynamics Using Routinely Collected Data in the Mid-Atlantic United States.
Kassaye, S. G., Grossman, Z., Vengurlekar, P., Chai, W., Wallace, M., Rhee, S.-Y. Y., … Maldarelli, F. (2022). Insights into HIV-1 Transmission Dynamics Using Routinely Collected Data in the Mid-Atlantic United States. Viruses, 15(1). -
Potential role of doravirine for the treatment of HIV-1-infected persons with transmitted drug resistance.
Rhee, S.-Y., Schapiro, J. M., Saladini, F., Zazzi, M., Khoo, S., & Shafer, R. W. (2023). Potential role of doravirine for the treatment of HIV-1-infected persons with transmitted drug resistance. AIDS Research and Therapy, 20(1), 8. -
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome is common in post-acute sequelae of SARS-CoV-2 infection (PASC): Results from a post-COVID-19 multidisciplinary clinic.
Bonilla, H., Quach, T. C., Tiwari, A., Bonilla, A. E., Miglis, M., Yang, P. C., … Geng, L. C. (2023). Myalgic Encephalomyelitis/Chronic Fatigue Syndrome is common in post-acute sequelae of SARS-CoV-2 infection (PASC): Results from a post-COVID-19 multidisciplinary clinic. Frontiers in Neurology, 14, 1090747. -
HIV-1 Group M Capsid Amino Acid Variability: Implications for Sequence Quality Control of Genotypic Resistance Testing.
Tao, K., Rhee, S.-Y. Y., Tzou, P. L., Osman, Z. A., Pond, S. L., Holmes, S. P., & Shafer, R. W. (2023). HIV-1 Group M Capsid Amino Acid Variability: Implications for Sequence Quality Control of Genotypic Resistance Testing. Viruses, 15(4). -
HIV-1 5'-Leader Mutations in Plasma Viruses Before and After the Development of Reverse Transcriptase Inhibitor-Resistance Mutations.
Nouhin, J., Tzou, P., Rhee, S.-Y., Sahoo, M. K., Pinsky, B. A., Krupkin, M. A., … Shafer, R. W. (2023). HIV-1 5'-Leader Mutations in Plasma Viruses Before and After the Development of Reverse Transcriptase Inhibitor-Resistance Mutations. MedRxiv : the Preprint Server for Health Sciences. -
Checklist for studies of HIV drug resistance prevalence or incidence: rationale and recommended use.
Mbuagbaw, L., Garcia, C., Brenner, B., Cecchini, D., Chakroun, M., Djiadeu, P., … Jordan, M. R. (2023). Checklist for studies of HIV drug resistance prevalence or incidence: rationale and recommended use. The Lancet. HIV. -
Recommendations on data sharing in HIV drug resistance research.
Inzaule, S. C., Siedner, M. J., Little, S. J., Avila-Rios, S., Ayitewala, A., Bosch, R. J., … Shafer, R. W. (2023). Recommendations on data sharing in HIV drug resistance research. PLoS Medicine, 20(9), e1004293. -
Treatment Emergent Dolutegravir Resistance Mutations in Individuals Naïve to HIV-1 Integrase Inhibitors: A Rapid Scoping Review.
Tao, K., Rhee, S.-Y. Y., Chu, C., Avalos, A., Ahluwalia, A. K., Gupta, R. K., … Shafer, R. W. (2023). Treatment Emergent Dolutegravir Resistance Mutations in Individuals Naïve to HIV-1 Integrase Inhibitors: A Rapid Scoping Review. Viruses, 15(9). -
Low-dose naltrexone use for the management of post-acute sequelae of COVID-19.
Bonilla, H., Tian, L., Marconi, V. C., Shafer, R., McComsey, G. A., Miglis, M., … Geng, L. N. (2023). Low-dose naltrexone use for the management of post-acute sequelae of COVID-19. International Immunopharmacology, 124(Pt B), 110966. -
Human immunodeficiency virus 1 5'-leader mutations in plasma viruses before and after the development of reverse transcriptase inhibitor-resistance mutations.
Nouhin, J., Tzou, P. L., Rhee, S.-Y., Sahoo, M. K., Pinsky, B. A., Krupkin, M., … Shafer, R. W. (2023). Human immunodeficiency virus 1 5'-leader mutations in plasma viruses before and after the development of reverse transcriptase inhibitor-resistance mutations. The Journal of General Virology, 104(10). -
Prevalence of Emergent Dolutegravir Resistance Mutations in People Living with HIV: A Rapid Scoping Review.
Chu, C., Tao, K., Kouamou, V., Avalos, A., Scott, J., Grant, P. M., … Shafer, R. W. (2024). Prevalence of Emergent Dolutegravir Resistance Mutations in People Living with HIV: A Rapid Scoping Review. Viruses, 16(3).
Practice Locations
(301) Post-Acute COVID-19 Syndrome (PACS) Clinic Atherton, CA
Atherton, CA(301) Post-Acute COVID-19 Syndrome (PACS) Clinic
3351 El Camino Real, Suite 225
Atherton , CA 94027
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Stanford Health Care, Stanford Health Care Tri-Valley, and Stanford Medicine Partners are each independent nonprofit organizations that are affiliated with but separate from each other and from Stanford University. The physicians who provide care at facilities operated by Stanford Health Care, Stanford Health Care Tri-Valley, and Stanford Medicine Partners are faculty, foundation, or community physicians who are not employees, representatives, or agents of Stanford Health Care, Stanford Health Care Tri- Valley, or Stanford Medicine Partners. Stanford Health Care, Stanford Health Care Tri-Valley, and Stanford Medicine Partners do not exercise control over the care provided by such faculty, foundation, and community physicians and are not responsible for their actions.
Referring Physicians
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