Robert W. Shafer

Publications

• Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance. Babrzadeh F, Varghese V, Pacold M, Liu TF, Nyrén P, Schiffer C, Fessel WJ, Shafer RW. J Antimicrob Chemother. 2013; 68 (2): 414-8
• Low-level persistence of drug resistance mutations in hepatitis B virus-infected subjects with a past history of Lamivudine treatment. Margeridon-Thermet S, Svarovskaia ES, Babrzadeh F, Martin R, Liu TF, Pacold M, Reuman EC, Holmes SP, Borroto-Esoda K, Shafer RW. Antimicrob Agents Chemother. 2013; 57 (1): 343-9
• A review of the virological efficacy of the 4 World Health Organization-recommended tenofovir-containing regimens for initial HIV therapy. Tang MW, Kanki PJ, Shafer RW. Clin Infect Dis. 2012; 54 (6): 862-75
• HIV-1 antiretroviral resistance: scientific principles and clinical applications. Tang MW, Shafer RW. Drugs. 2012; 72 (9): e1-25
• Panel of prototypical recombinant infectious molecular clones resistant to nevirapine, efavirenz, etravirine, and rilpivirine. Balamane M, Varghese V, Melikian GL, Fessel WJ, Katzenstein DA, Shafer RW. Antimicrob Agents Chemother. 2012; 56 (8): 4522-4
• HIV-1 integrase inhibitor resistance and its clinical implications. Blanco JL, Varghese V, Rhee SY, Gatell JM, Shafer RW. J Infect Dis. 2011; 203 (9): 1204-14
• The efficacy of an anti-CD4 monoclonal antibody for HIV-1 treatment. Fessel WJ, Anderson B, Follansbee SE, Winters MA, Lewis ST, Weinheimer SP, Petropoulos CJ, Shafer RW. Antiviral Res. 2011; 92 (3): 484-7
• Comparison of the Mechanisms of Drug Resistance among HIV, Hepatitis B, and Hepatitis C. Margeridon-Thermet S, Shafer RW. Viruses. 2010; 2 (12): 2696-739
• HIV-1 protease mutations and protease inhibitor cross-resistance. Rhee SY, Taylor J, Fessel WJ, Kaufman D, Towner W, Troia P, Ruane P, Hellinger J, Shirvani V, Zolopa A, Shafer RW. Antimicrob Agents Chemother. 2010; 54 (10): 4253-61
• Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update. Bennett DE, Camacho RJ, Otelea D, Kuritzkes DR, Fleury H, Kiuchi M, Heneine W, Kantor R, Jordan MR, Schapiro JM, Vandamme AM, Sandstrom P, Boucher CA, van de Vijver D, Rhee SY, Liu TF, Pillay D, Shafer RW. PLoS One. 2009; 4 (3): e4724
• Low-abundance drug-resistant HIV-1 variants: finding significance in an era of abundant diagnostic and therapeutic options. Shafer RW, J Infect Dis. 2009; 199 (5): 610-2
• 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 SY, Liu T, Simen BB, Egholm M, Hanczaruk B, Blake LA, Gharizadeh B, Babrzadeh F, Bachmann MH, Fessel WJ, Shafer RW. J Acquir Immune Defic Syndr. 2009; 52 (3): 309-15
• Nonpolymorphic human immunodeficiency virus type 1 protease and reverse transcriptase treatment-selected mutations. Shahriar R, Rhee SY, Liu TF, Fessel WJ, Scarsella A, Towner W, Holmes SP, Zolopa AR, Shafer RW. Antimicrob Agents Chemother. 2009; 53 (11): 4869-78
• Predictive value of HIV-1 genotypic resistance test interpretation algorithms. Rhee SY, Fessel WJ, Liu TF, Marlowe NM, Rowland CM, Rode RA, Vandamme AM, Van Laethem K, Brun-Vezinet F, Calvez V, Taylor J, Hurley L, Horberg M, Shafer RW. J Infect Dis. 2009; 200 (3): 453-63
• 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 NS, Ahmed A, Shahriar R, Liu T, Wang C, Holmes SP, Babrzadeh F, Gharizadeh B, Hanczaruk B, Simen BB, Egholm M, Shafer RW. J Infect Dis. 2009; 199 (9): 1275-85
• A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Gifford RJ, Katzourakis A, Tristem M, Pybus OG, Winters M, Shafer RW. Proc Natl Acad Sci U S A. 2008; 105 (51): 20362-7
• Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW. Genome Res. 2007; 17 (8): 1195-201
• HIV-1 subtype B protease and reverse transcriptase amino acid covariation. Rhee SY, Liu TF, Holmes SP, Shafer RW. PLoS Comput Biol. 2007; 3 (5): e87
• Genotypic predictors of human immunodeficiency virus type 1 drug resistance. Rhee SY, Taylor J, Wadhera G, Ben-Hur A, Brutlag DL, Shafer RW. Proc Natl Acad Sci U S A. 2006; 103 (46): 17355-60
• HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes. Rhee SY, Kantor R, Katzenstein DA, Camacho R, Morris L, Sirivichayakul S, Jorgensen L, Brigido LF, Schapiro JM, Shafer RW. AIDS. 2006; 20 (5): 643-51
• Rationale and uses of a public HIV drug-resistance database. Shafer RW, J Infect Dis. 2006: 194 Suppl 1 S51-8
• Web resources for HIV type 1 genotypic-resistance test interpretation. Liu TF, Shafer RW. Clin Infect Dis. 2006; 42 (11): 1608-18
• Drug resistance and antiretroviral drug development. Shafer RW, Schapiro JM. J Antimicrob Chemother. 2005; 55 (6): 817-20
• HIV-1 Protease and reverse-transcriptase mutations: correlations with antiretroviral therapy in subtype B isolates and implications for drug-resistance surveillance. Rhee SY, Fessel WJ, Zolopa AR, Hurley L, Liu T, Taylor J, Nguyen DP, Slome S, Klein D, Horberg M, Flamm J, Follansbee S, Schapiro JM, Shafer RW. J Infect Dis. 2005; 192 (3): 456-65
• Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotype: results of a global collaboration. Kantor R, Katzenstein DA, Efron B, Carvalho AP, Wynhoven B, Cane P, Clarke J, Sirivichayakul S, Soares MA, Snoeck J, Pillay C, Rudich H, Rodrigues R, Holguin A, Ariyoshi K, Bouzas MB, Cahn P, Sugiura W, Soriano V, Brigido LF, Grossman Z, Morris L, Vandamme AM, Tanuri A, Phanuphak P, Weber JN, Pillay D, Harrigan PR, Camacho R, Schapiro JM, Shafer RW. PLoS Med. 2005; 2 (4): e112
• Panel of prototypical infectious molecular HIV-1 clones containing multiple nucleoside reverse transcriptase inhibitor resistance mutations. Johnston E, Dupnik KM, Gonzales MJ, Winters MA, Rhee SY, Imamichi T, Shafer RW. AIDS. 2005; 19 (7): 731-3
• Colinearity of reverse transcriptase inhibitor resistance mutations detected by population-based sequencing. Gonzales MJ, Johnson E, Dupnik KM, Imamichi T, Shafer RW. J Acquir Immune Defic Syndr. 2003; 34 (4): 398-402
• Comparison of four-drug regimens and pairs of sequential three-drug regimens as initial therapy for HIV-1 infection. Shafer RW, Smeaton LM, Robbins GK, De Gruttola V, Snyder SW, D'Aquila RT, Johnson VA, Morse GD, Nokta MA, Martinez AI, Gripshover BM, Kaul P, Haubrich R, Swingle M, McCarty SD, Vella S, Hirsch MS, Merigan TC. N Engl J Med. 2003; 349 (24): 2304-15
• Extended spectrum of HIV-1 reverse transcriptase mutations in patients receiving multiple nucleoside analog inhibitors. Gonzales MJ, Wu TD, Taylor J, Belitskaya I, Kantor R, Israelski D, Chou S, Zolopa AR, Fessel WJ, Shafer RW. AIDS. 2003; 17 (6): 791-9
• Human immunodeficiency virus reverse transcriptase and protease sequence database. Rhee SY, Gonzales MJ, Kantor R, Betts BJ, Ravela J, Shafer RW. Nucleic Acids Res. 2003; 31 (1): 298-303
• Lack of detectable human immunodeficiency virus type 1 superinfection during 1072 person-years of observation. Gonzales MJ, Delwart E, Rhee SY, Tsui R, Zolopa AR, Taylor J, Shafer RW. J Infect Dis. 2003; 188 (3): 397-405
• Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments. Wu TD, Schiffer CA, Gonzales MJ, Taylor J, Kantor R, Chou S, Israelski D, Zolopa AR, Fessel WJ, Shafer RW. J Virol. 2003; 77 (8): 4836-47
• Genotypic testing for human immunodeficiency virus type 1 drug resistance. Shafer RW, Clin Microbiol Rev. 2002; 15 (2): 247-77
• Human immunodeficiency virus type 1 reverse transcriptase and protease mutation search engine for queries. Shafer RW, Jung DR, Betts BJ. Nat Med. 2000; 6 (11): 1290-2
• HIV-1 genotypic resistance patterns predict response to saquinavir-ritonavir therapy in patients in whom previous protease inhibitor therapy had failed. Zolopa AR, Shafer RW, Warford A, Montoya JG, Hsu P, Katzenstein D, Merigan TC, Efron B. Ann Intern Med. 1999; 131 (11): 813-21
• Sequence and drug susceptibility of subtype C protease from human immunodeficiency virus type 1 seroconverters in Zimbabwe. Shafer RW, Chuang TK, Hsu P, White CB, Katzenstein DA. AIDS Res Hum Retroviruses. 1999; 15 (1): 65-9
• Multiple concurrent reverse transcriptase and protease mutations and multidrug resistance of HIV-1 isolates from heavily treated patients. Shafer RW, Winters MA, Palmer S, Merigan TC. Ann Intern Med. 1998; 128 (11): 906-11
• Sequence and drug susceptibility of subtype C reverse transcriptase from human immunodeficiency virus type 1 seroconverters in Zimbabwe. Shafer RW, Eisen JA, Merigan TC, Katzenstein DA. J Virol. 1997; 71 (7): 5441-8
• Predictors of survival in HIV-infected tuberculosis patients. Shafer RW, Bloch AB, Larkin C, Vasudavan V, Seligman S, Dehovitz JD, DiFerdinando G, Stoneburner R, Cauthen G. AIDS. 1996; 10 (3): 269-72
• Tuberculosis in patients infected with human immunodeficiency virus: perspective on the past decade. Shafer RW, Edlin BR. Clin Infect Dis. 1996; 22 (4): 683-704
• Temporal trends and transmission patterns during the emergence of multidrug-resistant tuberculosis in New York City: a molecular epidemiologic assessment. Shafer RW, Small PM, Larkin C, Singh SP, Kelly P, Sierra MF, Schoolnik G, Chirgwin KD. J Infect Dis. 1995; 171 (1): 170-6
• Combination therapy with zidovudine and didanosine selects for drug-resistant human immunodeficiency virus type 1 strains with unique patterns of pol gene mutations. Shafer RW, Kozal MJ, Winters MA, Iversen AK, Katzenstein DA, Ragni MV, Meyer WA, Gupta P, Rasheed S, Coombs R. J Infect Dis. 1994; 169 (4): 722-9
• Exogenous reinfection with multidrug-resistant Mycobacterium tuberculosis in patients with advanced HIV infection. Small PM, Shafer RW, Hopewell PC, Singh SP, Murphy MJ, Desmond E, Sierra MF, Schoolnik GK. N Engl J Med. 1993; 328 (16): 1137-44
• Extrapulmonary tuberculosis in patients with human immunodeficiency virus infection. Shafer RW, Kim DS, Weiss JP, Quale JM. Medicine (Baltimore). 1991; 70 (6): 384-97
• Development of elvitegravir resistance and linkage of integrase inhibitor mutations with protease and reverse transcriptase resistance mutations. Winters MA, Lloyd RM, Shafer RW, Kozal MJ, Miller MD, Holodniy M. PLoS One. 2012; 7 (7): e40514
• Standardized comparison of the relative impacts of HIV-1 reverse transcriptase (RT) mutations on nucleoside RT inhibitor susceptibility. Melikian GL, Rhee SY, Taylor J, Fessel WJ, Kaufman D, Towner W, Troia-Cancio PV, Zolopa A, Robbins GK, Kagan R, Israelski D, Shafer RW. Antimicrob Agents Chemother. 2012; 56 (5): 2305-13
• The HIVdb system for HIV-1 genotypic resistance interpretation. Tang MW, Liu TF, Shafer RW. Intervirology. 2012; 55 (2): 98-101
• 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, Nyren P, Shafer RW, Basso LC, de Amorim HV, de Oliveira AJ, Davis RW, Ronaghi M, Gharizadeh B, Stambuk BU. Mol Genet Genomics. 2012; 287 (6): 485-94
• A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes. Doherty KM, Nakka P, King BM, Rhee SY, Holmes SP, Shafer RW, Radhakrishnan ML. BMC Bioinformatics. 2011: 12 477
• 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 ML, Aoki-Ogata H, Amano M, Das D, Shafer RW, Ghosh AK, Mitsuya H. J Virol. 2011; 85 (19): 10079-89
• Mitochondrial genomics and CD4 T-cell count recovery after antiretroviral therapy initiation in AIDS clinical trials group study 384. Grady BJ, Samuels DC, Robbins GK, Selph D, Canter JA, Pollard RB, Haas DW, Shafer R, Kalams SA, Murdock DG, Ritchie MD, Hulgan T. J Acquir Immune Defic Syndr. 2011; 58 (4): 363-70
• A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads. Reuman EC, Margeridon-Thermet S, Caudill HB, Liu T, Borroto-Esoda K, Svarovskaia ES, Holmes SP, Shafer RW. Bioinformatics. 2010; 26 (23): 2929-32
• African mitochondrial DNA subhaplogroups and peripheral neuropathy during antiretroviral therapy. Canter JA, Robbins GK, Selph D, Clifford DB, Kallianpur AR, Shafer R, Levy S, Murdock DG, Ritchie MD, Haas DW, Hulgan T. J Infect Dis. 2010; 201 (11): 1703-7
• Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations. Reuman EC, Rhee SY, Holmes SP, Shafer RW. J Antimicrob Chemother. 2010; 65 (7): 1477-85
• HIV-1 integrase sequence variability in antiretroviral naïve patients and in triple-class experienced patients subsequently treated with raltegravir. Varghese V, Liu TF, Rhee SY, Libiran P, Trevino C, Fessel WJ, Shafer RW. AIDS Res Hum Retroviruses. 2010; 26 (12): 1323-6
• Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery. Rhee SY, Margeridon-Thermet S, Nguyen MH, Liu TF, Kagan RM, Beggel B, Verheyen J, Kaiser R, Shafer RW. Antiviral Res. 2010; 88 (3): 269-75
• Long-term increase in CD4+ T-cell counts during combination antiretroviral therapy for HIV-1 infection. Lok JJ, Bosch RJ, Benson CA, Collier AC, Robbins GK, Shafer RW, Hughes MD. AIDS. 2010; 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 MH, Shahriar R, Liu T, Mappala SJ, Gharizadeh B, Fessel WJ, Katzenstein D, Kassaye S, Shafer RW. PLoS One. 2010; 5 (6): e10992
• Panel of prototypical raltegravir-resistant infectious molecular clones in a novel integrase-deleted cloning vector. Reuman EC, Bachmann MH, Varghese V, Fessel WJ, Shafer RW. Antimicrob Agents Chemother. 2010; 54 (2): 934-6
• 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 JG, Liu TF, Charest H, Brenner B, Roger M, Shafer R, Cantin R, Zolopa A. Antimicrob Agents Chemother. 2010; 54 (6): 2473-9
• Public database for HIV drug resistance in southern Africa. de Oliveira T, Shafer RW, Seebregts C. Nature. 2010; 464 (7289): 673
• The challenge of antiretroviral drug resistance in HIV-1-infected children. Shafer RW, J Pediatr (Rio J). 2009 Mar-Apr; 85 (2): 91-4
• Biomarker discovery using targeted maximum-likelihood estimation: application to the treatment of antiretroviral-resistant HIV infection. Bembom O, Petersen ML, Rhee SY, Fessel WJ, Sinisi SE, Shafer RW, van der Laan MJ. Stat Med. 2009; 28 (1): 152-72
• 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 MH, Fessel WJ, Kagan RM, Shafer RW. Antimicrob Agents Chemother. 2009; 53 (5): 2196-8
• Incomplete reconstitution of T cell subsets on combination antiretroviral therapy in the AIDS Clinical Trials Group protocol 384. Robbins GK, Spritzler JG, Chan ES, Asmuth DM, Gandhi RT, Rodriguez BA, Skowron G, Skolnik PR, Shafer RW, Pollard RB. Clin Infect Dis. 2009; 48 (3): 350-61
• Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database. Altmann A, Däumer M, Beerenwinkel N, Peres Y, Schülter E, Büch J, Rhee SY, Sönnerborg A, Fessel WJ, Shafer RW, Zazzi M, Kaiser R, Lengauer T. J Infect Dis. 2009; 199 (7): 999-1006
• The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance. Gifford RJ, Liu TF, Rhee SY, Kiuchi M, Hue S, Pillay D, Shafer RW. Bioinformatics. 2009; 25 (9): 1197-8
• HIV-1 drug resistance mutations: an updated framework for the second decade of HAART. Shafer RW, Schapiro JM. AIDS Rev. 2008 Apr-Jun; 10 (2): 67-84
• A highly divergent picornavirus in a marine mammal. Kapoor A, Victoria J, Simmonds P, Wang C, Shafer RW, Nims R, Nielsen O, Delwart E. J Virol. 2008; 82 (1): 311-20
• A highly prevalent and genetically diversified Picornaviridae genus in South Asian children. Kapoor A, Victoria J, Simmonds P, Slikas E, Chieochansin T, Naeem A, Shaukat S, Sharif S, Alam MM, Angez M, Wang C, Shafer RW, Zaidi S, Delwart E. Proc Natl Acad Sci U S A. 2008; 105 (51): 20482-7
• Bayesian network analyses of resistance pathways against efavirenz and nevirapine. Deforche K, Camacho RJ, Grossman Z, Soares MA, Van Laethem K, Katzenstein DA, Harrigan PR, Kantor R, Shafer R, Vandamme AM. AIDS. 2008; 22 (16): 2107-15
• Consensus drug resistance mutations for epidemiological surveillance: basic principles and potential controversies. Shafer RW, Rhee SY, Bennett DE. Antivir Ther. 2008: 13 Suppl 2 59-68
• Dynamics of total, linear nonintegrated, and integrated HIV-1 DNA in vivo and in vitro. Koelsch KK, Liu L, Haubrich R, May S, Havlir D, Günthard HF, Ignacio CC, Campos-Soto P, Little SJ, Shafer R, Robbins GK, D'Aquila RT, Kawano Y, Young K, Dao P, Spina CA, Richman DD, Wong JK. J Infect Dis. 2008; 197 (3): 411-9
• Hemochromatosis gene polymorphisms, mitochondrial haplogroups, and peripheral lipoatrophy during antiretroviral therapy. Hulgan T, Tebas P, Canter JA, Mulligan K, Haas DW, Dubé M, Grinspoon S, Robbins GK, Motsinger AA, Kallianpur AR. J Infect Dis. 2008; 197 (6): 858-66
• 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 TF, Holmes SP, Jayakumar P, Gharizadeh B, Ronaghi M, Klein D, Fessel WJ, Shafer RW. J Virol. 2008; 82 (21): 10747-55
• Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patients. Kapoor A, Shapiro B, Shafer RW, Shulman N, Rhee SY, Delwart EL. Retrovirology. 2008: 5 7
• Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors. Rhee SY, Liu TF, Kiuchi M, Zioni R, Gifford RJ, Holmes SP, Shafer RW. Retrovirology. 2008: 5 74
• Rational use of antiretroviral therapy in low-income and middle-income countries: optimizing regimen sequencing and switching. Elliott JH, Lynen L, Calmy A, De Luca A, Shafer RW, Zolfo M, Clotet B, Huffam S, Boucher CA, Cooper DA, Schapiro JM. AIDS. 2008; 22 (16): 2053-67
• Sequence editing by Apolipoprotein B RNA-editing catalytic component [corrected] and epidemiological surveillance of transmitted HIV-1 drug resistance. Gifford RJ, Rhee SY, Eriksson N, Liu TF, Kiuchi M, Das AK, Shafer RW. AIDS. 2008; 22 (6): 717-25
• The mitochondrial pharmacogenomics of haplogroup T: MTND2*LHON4917G and antiretroviral therapy-associated peripheral neuropathy. Canter JA, Haas DW, Kallianpur AR, Ritchie MD, Robbins GK, Shafer RW, Clifford DB, Murdock DG, Hulgan T. Pharmacogenomics J. 2008; 8 (1): 71-7
• Viral population estimation using pyrosequencing. Eriksson N, Pachter L, Mitsuya Y, Rhee SY, Wang C, Gharizadeh B, Ronaghi M, Shafer RW, Beerenwinkel N. PLoS Comput Biol. 2008; 4 (4): e1000074
• Virologic response to lopinavir-ritonavir-based antiretroviral regimens in a multicenter international clinical cohort: comparison of genotypic interpretation scores. Grant P, Wong EC, Rode R, Shafer R, De Luca A, Nadler J, Hawkins T, Cohen C, Harrington R, Kempf D, Zolopa A. Antimicrob Agents Chemother. 2008; 52 (11): 4050-6
• Case files from Stanford University Medical Center: ten years of HAART: a long wait for full HIV suppression. Shulman N, Shafer RW. MedGenMed. 2007; 9 (1): 10
• Educational attainment and response to HAART during initial therapy for HIV-1 infection. Marc LG, Testa MA, Walker AM, Robbins GK, Shafer RW, Anderson NB, Berkman LF. J Psychosom Res. 2007; 63 (2): 207-16
• HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance. Shafer RW, Rhee SY, Pillay D, Miller V, Sandstrom P, Schapiro JM, Kuritzkes DR, Bennett D. AIDS. 2007; 21 (2): 215-23
• Knowledge integration of software for HIV drug resistance research. Hernandez G, Rhee SY, Shafer RW, Das AK. AMIA Annu Symp Proc. 2007: 973
• Prevalence of darunavir resistance-associated mutations: patterns of occurrence and association with past treatment. Mitsuya Y, Liu TF, Rhee SY, Fessel WJ, Shafer RW. J Infect Dis. 2007; 196 (8): 1177-9
• Simple PCR assays improve the sensitivity of HIV-1 subtype B drug resistance testing and allow linking of resistance mutations. Johnson JA, Li JF, Wei X, Lipscomb J, Bennett D, Brant A, Cong ME, Spira T, Shafer RW, Heneine W. PLoS One. 2007; 2 (7): e638
• Virologic efficacy of boosted double versus boosted single protease inhibitor therapy. Petersen ML, Wang Y, van der Laan MJ, Rhee SY, Shafer RW, Fessel WJ. AIDS. 2007; 21 (12): 1547-54
• World Antimalarial Resistance Network (WARN) III: molecular markers for drug resistant malaria. Plowe CV, Roper C, Barnwell JW, Happi CT, Joshi HH, Mbacham W, Meshnick SR, Mugittu K, Naidoo I, Price RN, Shafer RW, Sibley CH, Sutherland CJ, Zimmerman PA, Rosenthal PJ. Malar J. 2007: 6 121
• A combined data mining approach for infrequent events: analyzing HIV mutation changes based on treatment history. Lin RS, Rhee SY, Shafer RW, Das AK. Comput Syst Bioinformatics Conf. 2006: 385-8
• Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity. Gifford R, de Oliveira T, Rambaut A, Myers RE, Gale CV, Dunn D, Shafer R, Vandamme AM, Kellam P, Pillay D. AIDS. 2006; 20 (11): 1521-9
• Butting heads with resistance. Shafer RW, IAPAC Mon. 2006; 12 (6): 180-9
• 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 RW, Nguyen DP, Fessel WJ. MedGenMed. 2006; 8 (3): 32
• 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 AR, Shafer RW. MedGenMed. 2006; 8 (1): 24
• 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 RW, Van Laethem K, Deforche K, Carvalho AP, Wynhoven B, Soares MA, Cane P, Clarke J, Pillay C, Sirivichayakul S, Ariyoshi K, Holguin A, Rudich H, Rodrigues R, Bouzas MB, Brun-Vézinet F, Reid C, Cahn P, Brigido LF, Grossman Z, Soriano V, Sugiura W, Phanuphak P, Morris L, Weber J, Pillay D, Tanuri A, Harrigan RP, Camacho R, Schapiro JM, Katzenstein D, Vandamme AM. Antimicrob Agents Chemother. 2006; 50 (2): 694-701
• 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 RT, Spritzler J, Chan E, Asmuth DM, Rodriguez B, Merigan TC, Hirsch MS, Shafer RW, Robbins GK, Pollard RB. J Acquir Immune Defic Syndr. 2006; 42 (4): 426-34
• HIV-1 drug resistance genotype results in patients with plasma samples with HIV-1 RNA levels less than 75 copies/mL. Mitsuya Y, Winters MA, Fessel WJ, Rhee SY, Slome S, Flamm J, Horberg M, Hurley L, Klein D, Shafer RW. J Acquir Immune Defic Syndr. 2006; 43 (1): 56-9
• Hemochromatosis (HFE) gene mutations and peripheral neuropathy during antiretroviral therapy. Kallianpur AR, Hulgan T, Canter JA, Ritchie MD, Haines JL, Robbins GK, Shafer RW, Clifford DB, Haas DW. AIDS. 2006; 20 (11): 1503-13
• Multilocus genetic interactions and response to efavirenz-containing regimens: an adult AIDS clinical trials group study. Motsinger AA, Ritchie MD, Shafer RW, Robbins GK, Morse GD, Labbe L, Wilkinson GR, Clifford DB, D'Aquila RT, Johnson VA, Pollard RB, Merigan TC, Hirsch MS, Donahue JP, Kim RB, Haas DW. Pharmacogenet Genomics. 2006; 16 (11): 837-45
• 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 MA, Fessel WJ, Rhee SY, Hurley L, Horberg M, Schiffer CA, Zolopa AR, Shafer RW. AIDS Res Hum Retroviruses. 2006; 22 (12): 1300-5
• Oxidant stress and peripheral neuropathy during antiretroviral therapy: an AIDS clinical trials group study. Hulgan T, Hughes M, Sun X, Smeaton LM, Terry E, Robbins GK, Shafer RW, Clifford DB, McComsey GA, Canter JA, Morrow JD, Haas DW. J Acquir Immune Defic Syndr. 2006; 42 (4): 450-4
• Prediction of HIV mutation changes based on treatment history. Lin RS, Rhee SY, Shafer RW, Das AK. AMIA Annu Symp Proc. 2006: 1011
• Accuracy, precision, and consistency of expert HIV type 1 genotype interpretation: an international comparison (The GUESS Study). Zolopa AR, Lazzeroni LC, Rinehart A, Vezinet FB, Clavel F, Collier A, Conway B, Gulick RM, Holodniy M, Perno CF, Shafer RW, Richman DD, Wainberg MA, Kuritzkes DR. Clin Infect Dis. 2005; 41 (1): 92-9
• Comparison of the precision and sensitivity of the Antivirogram and PhenoSense HIV drug susceptibility assays. Zhang J, Rhee SY, Taylor J, Shafer RW. J Acquir Immune Defic Syndr. 2005; 38 (4): 439-44
• Detection of minority populations of HIV-1 expressing the K103N resistance mutation in patients failing nevirapine. Lecossier D, Shulman NS, Morand-Joubert L, Shafer RW, Joly V, Zolopa AR, Clavel F, Hance AJ. J Acquir Immune Defic Syndr. 2005; 38 (1): 37-42
• Glucose metabolism, lipid, and body fat changes in antiretroviral-naive subjects randomized to nelfinavir or efavirenz plus dual nucleosides. Dubé MP, Parker RA, Tebas P, Grinspoon SK, Zackin RA, Robbins GK, Roubenoff R, Shafer RW, Wininger DA, Meyer WA, Snyder SW, Mulligan K. AIDS. 2005; 19 (16): 1807-18
• Mitochondrial haplogroups and peripheral neuropathy during antiretroviral therapy: an adult AIDS clinical trials group study. Hulgan T, Haas DW, Haines JL, Ritchie MD, Robbins GK, Shafer RW, Clifford DB, Kallianpur AR, Summar M, Canter JA. AIDS. 2005; 19 (13): 1341-9
• Nonnucleoside reverse transcriptase inhibitor phenotypic hypersusceptibility can be demonstrated in different assays. Shulman NS, Delgado J, Bosch RJ, Winters MA, Johnston E, Shafer RW, Katzenstein DA, Merigan TC. J Acquir Immune Defic Syndr. 2005; 39 (1): 78-81
• Pharmacogenetics of long-term responses to antiretroviral regimens containing Efavirenz and/or Nelfinavir: an Adult Aids Clinical Trials Group Study. Haas DW, Smeaton LM, Shafer RW, Robbins GK, Morse GD, Labbe L, Wilkinson GR, Clifford DB, D'Aquila RT, De Gruttola V, Pollard RB, Merigan TC, Hirsch MS, George AL, Donahue JP, Kim RB. J Infect Dis. 2005; 192 (11): 1931-42
• 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 PF, Robbins GK, Shafer RW, Wu H, Yu S, Hirsch MS, Merigan TC, Park JG, Forrest A, Fischl MA, Morse GD. Antimicrob Agents Chemother. 2005; 49 (8): 3558-61
• 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 RW, Katzenstein D. MedGenMed. 2005; 7 (1): 71
• Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistance. Johnston E, Winters MA, Rhee SY, Merigan TC, Schiffer CA, Shafer RW. Antimicrob Agents Chemother. 2004; 48 (12): 4864-8
• Comparative evaluation of three computerized algorithms for prediction of antiretroviral susceptibility from HIV type 1 genotype. Zazzi M, Romano L, Venturi G, Shafer RW, Reid C, Dal Bello F, Parolin C, Palù G, Valensin PE. J Antimicrob Chemother. 2004; 53 (2): 356-60
• Distribution of human immunodeficiency virus type 1 protease and reverse transcriptase mutation patterns in 4,183 persons undergoing genotypic resistance testing. Rhee SY, Liu T, Ravela J, Gonzales MJ, Shafer RW. Antimicrob Agents Chemother. 2004; 48 (8): 3122-6
• Evolution of resistance to drugs in HIV-1-infected patients failing antiretroviral therapy. Kantor R, Shafer RW, Follansbee S, Taylor J, Shilane D, Hurley L, Nguyen DP, Katzenstein D, Fessel WJ. AIDS. 2004; 18 (11): 1503-11
• 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 RW, Rhee SY, Kazanjian P, Delwart EL. J Virol. 2004; 78 (13): 7112-23
• Drug resistance mutations in HIV-1. D'Aquila RT, Schapiro JM, Brun-Vézinet F, Clotet B, Conway B, Demeter LM, Grant RM, Johnson VA, Kuritzkes DR, Loveday C, Shafer RW, Richman DD. Top HIV Med. 2003 May-Jun; 11 (3): 92-6
• HIV sequence databases. Kuiken C, Korber B, Shafer RW. AIDS Rev. 2003 Jan-Mar; 5 (1): 52-61
• Algorithm specification interface for human immunodeficiency virus type 1 genotypic interpretation. Betts BJ, Shafer RW. J Clin Microbiol. 2003; 41 (6): 2792-4
• Comparison of sequential three-drug regimens as initial therapy for HIV-1 infection. Robbins GK, De Gruttola V, Shafer RW, Smeaton LM, Snyder SW, Pettinelli C, Dubé MP, Fischl MA, Pollard RB, Delapenha R, Gedeon L, van der Horst C, Murphy RL, Becker MI, D'Aquila RT, Vella S, Merigan TC, Hirsch MS. N Engl J Med. 2003; 349 (24): 2293-303
• HIV-1 protease and reverse transcriptase mutation patterns responsible for discordances between genotypic drug resistance interpretation algorithms. Ravela J, Betts BJ, Brun-Vézinet F, Vandamme AM, Descamps D, van Laethem K, Smith K, Schapiro JM, Winslow DL, Reid C, Shafer RW. J Acquir Immune Defic Syndr. 2003; 33 (1): 8-14
• 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 MJ, Belitskaya I, Dupnik KM, Rhee SY, Shafer RW. AIDS Res Hum Retroviruses. 2003; 19 (10): 909-15
• Drug Resistance Mutations in HIV-1. D'Aquila RT, , Schapiro JM, Brun-Vézinet F, Clotet B, Conway B, Demeter LM, Grant RM, Johnson VA, Kuritzkes DR, Loveday C, Shafer RW, Richman DD. Top HIV Med. 2002 Nov-Dec; 10 (5): 21-25
• Evolution of primary protease inhibitor resistance mutations during protease inhibitor salvage therapy. Kantor R, Fessel WJ, Zolopa AR, Israelski D, Shulman N, Montoya JG, Harbour M, Schapiro JM, Shafer RW. Antimicrob Agents Chemother. 2002; 46 (4): 1086-92
• HIV-1 subtype C reverse transcriptase and protease genotypes in Zimbabwean patients failing antiretroviral therapy. Kantor R, Zijenah LS, Shafer RW, Mutetwa S, Johnston E, Lloyd R, von Lieven A, Israelski D, Katzenstein DA. AIDS Res Hum Retroviruses. 2002; 18 (18): 1407-13
• Identification of Ugandan HIV type 1 variants with unique patterns of recombination in pol involving subtypes A and D. Eshleman SH, Gonzales MJ, Becker-Pergola G, Cunningham SC, Guay LA, Jackson JB, Shafer RW. AIDS Res Hum Retroviruses. 2002; 18 (7): 507-11
• Reverse transcriptase and protease sequence evolution in two HIV-1-infected couples. Palmer S, Vuitton D, Gonzales MJ, Bassignot A, Shafer RW. J Acquir Immune Defic Syndr. 2002; 31 (3): 285-90
• Subtle decreases in stavudine phenotypic susceptibility predict poor virologic response to stavudine monotherapy in zidovudine-experienced patients. Shulman NS, Hughes MD, Winters MA, Shafer RW, Zolopa AR, Hellmann NS, Bates M, Whitcomb JM, Katzenstein DA. J Acquir Immune Defic Syndr. 2002; 31 (2): 121-7
• Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN). Gonzales MJ, Dugan JM, Shafer RW. Bioinformatics. 2002; 18 (6): 886-7
• ACTG (AIDS Clinical Trials Group) 384: a strategy trial comparing consecutive treatments for HIV-1. Smeaton LM, DeGruttola V, Robbins GK, Shafer RW. Control Clin Trials. 2001; 22 (2): 142-59
• Genotypic correlates of a virologic response to stavudine after zidovudine monotherapy. Shulman NS, Machekano RA, Shafer RW, Winters MA, Zolopa AR, Liou SH, Hughes M, Katzenstein DA. J Acquir Immune Defic Syndr. 2001; 27 (4): 377-80
• High degree of interlaboratory reproducibility of human immunodeficiency virus type 1 protease and reverse transcriptase sequencing of plasma samples from heavily treated patients. Shafer RW, Hertogs K, Zolopa AR, Warford A, Bloor S, Betts BJ, Merigan TC, Harrigan R, Larder BA. J Clin Microbiol. 2001; 39 (4): 1522-9
• 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 MJ, Dupnik K, Schapiro JM, Shafer RW. Nucleic Acids Res. 2001; 29 (1): 296-9
• 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 MJ, Machekano RN, Shafer RW. J Infect Dis. 2001; 184 (8): 998-1006
• 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 AR, Passaro D, Shafer RW, Huang W, Katzenstein D, Israelski DM, Hellmann N, Petropoulos C, Whitcomb J. AIDS. 2001; 15 (9): 1125-32
• 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 LM, Shafer RW, Meehan PM, Holden-Wiltse J, Fischl MA, Freimuth WW, Para MF, Reichman RC. Antimicrob Agents Chemother. 2000; 44 (3): 794-7
• Efavirenz- and adefovir dipivoxil-based salvage therapy in highly treatment-experienced patients: clinical and genotypic predictors of virologic response. Shulman NS, Zolopa AR, Passaro DJ, Murlidharan U, Israelski DM, Brosgart CL, Miller MD, Van Doren S, Shafer RW, Katzenstein DA. J Acquir Immune Defic Syndr. 2000; 23 (3): 221-6
• HIV type 1 envelope subtype C sequences from recent seroconverters in Zimbabwe. Batra M, Tien PC, Shafer RW, Contag CH, Katzenstein DA. AIDS Res Hum Retroviruses. 2000; 16 (10): 973-9
• Human immunodeficiency virus on the web: a guided tour. Shafer RW, Deresinski SC. Clin Infect Dis. 2000; 31 (2): 568-77
• Human immunodeficiency virus reverse transcriptase and protease sequence database. Shafer RW, Jung DR, Betts BJ, Xi Y, Gonzales MJ. Nucleic Acids Res. 2000; 28 (1): 346-8
• 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 RW, Warford A, Winters MA, Gonzales MJ. J Virol Methods. 2000; 86 (2): 143-53
• The Genetic Basis of HIV-1 Resistance to Reverse Transcriptase and Protease Inhibitors. Shafer RW, Kantor R, Gonzales MJ. AIDS Rev. 2000; 2 (4): 211-228
• Highly active antiretroviral therapy (HAART) for the treatment of infection with human immunodeficiency virus type 1. Shafer RW, Vuitton DA. Biomed Pharmacother. 1999; 53 (2): 73-86
• Highly drug-resistant HIV-1 clinical isolates are cross-resistant to many antiretroviral compounds in current clinical development. Palmer S, Shafer RW, Merigan TC. AIDS. 1999; 13 (6): 661-7
• Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database. Shafer RW, Stevenson D, Chan B. Nucleic Acids Res. 1999; 27 (1): 348-52
• 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 RW, Merigan TC. Antimicrob Agents Chemother. 1999; 43 (8): 2046-50
• Identification of biased amino acid substitution patterns in human immunodeficiency virus type 1 isolates from patients treated with protease inhibitors. Shafer RW, Hsu P, Patick AK, Craig C, Brendel V. J Virol. 1999; 73 (7): 6197-202
• A 6-basepair insert in the reverse transcriptase gene of human immunodeficiency virus type 1 confers resistance to multiple nucleoside inhibitors. Winters MA, Coolley KL, Girard YA, Levee DJ, Hamdan H, Shafer RW, Katzenstein DA, Merigan TC. J Clin Invest. 1998; 102 (10): 1769-75
• An update on the diagnosis and treatment of HIV, 1998. Shafer RW, Kroodsma K. Drugs Today (Barc). 1998; 34 (8): 663-72
• A novel approach to assessing the drug susceptibility and replication of human immunodeficiency virus type 1 isolates. Jellinger RM, Shafer RW, Merigan TC. J Infect Dis. 1997; 175 (3): 561-6
• Comparison of QIAamp HCV kit spin columns, silica beads, and phenol-chloroform for recovering human immunodeficiency virus type 1 RNA from plasma. Shafer RW, Levee DJ, Winters MA, Richmond KL, Huang D, Merigan TC. J Clin Microbiol. 1997; 35 (2): 520-2
• Human immunodeficiency virus type 1 reverse transcriptase genotype and drug susceptibility changes in infected individuals receiving dideoxyinosine monotherapy for 1 to 2 years. Winters MA, Shafer RW, Jellinger RA, Mamtora G, Gingeras T, Merigan TC. Antimicrob Agents Chemother. 1997; 41 (4): 757-62
• 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 RW, Winters MA, Iversen AK, Merigan TC. Antimicrob Agents Chemother. 1996; 40 (12): 2887-90
• Interlaboratory comparison of sequence-specific PCR and ligase detection reaction to detect a human immunodeficiency virus type 1 drug resistance mutation. The AIDS Clinical Trials Group Virology Committee Drug Resistance Working Group. Shafer RW, Winters MA, Mayers DL, Japour AJ, Kuritzkes DR, Weislow OS, White F, Erice A, Sannerud KJ, Iversen A, Pena F, Dimitrov D, Frenkel LM, Reichelderfer PS. J Clin Microbiol. 1996; 34 (7): 1849-53
• Multidrug-resistant human immunodeficiency virus type 1 strains resulting from combination antiretroviral therapy. Iversen AK, Shafer RW, Wehrly K, Winters MA, Mullins JI, Chesebro B, Merigan TC. J Virol. 1996; 70 (2): 1086-90
• Zidovudine resistance reverse transcriptase mutations during didanosine monotherapy. Shafer RW, Winters MA, Jellinger RM, Merigan TC. J Infect Dis. 1996; 174 (2): 448-9
• Clarification of a method to reverse transcribe human immunodeficiency virus RNA. Kozal MJ, Shafer RW, Winters MA, Katzenstein DA, Merigan TC. J Infect Dis. 1995; 171 (4): 1072
• Drug resistance and heterogeneous long-term virologic responses of human immunodeficiency virus type 1-infected subjects to zidovudine and didanosine combination therapy. The AIDS Clinical Trials Group 143 Virology Team. Shafer RW, Iversen AK, Winters MA, Aguiniga E, Katzenstein DA, Merigan TC. J Infect Dis. 1995; 172 (1): 70-8
• Exogenous reinfection with multidrug-resistant Mycobacterium tuberculosis in an immunocompetent patient. Shafer RW, Singh SP, Larkin C, Small PM. Tuber Lung Dis. 1995; 76 (6): 575-7
• HIV virology for clinical trials. Shafer RW, Merigan TC. AIDS. 1995: 9 Suppl A S193-202
• New virologic tools for the design and analysis of clinical trials. Shafer RW, Merigan TC. J Infect Dis. 1995; 171 (5): 1325-8
• Quantitative analysis of syncytium-inducing and non-syncytium-inducing virus in patients infected with human immunodeficiency virus type 1. Shafer RW, Aguiniga E, Merigan TC. J Clin Microbiol. 1995; 33 (1): 212-4
• Didanosine resistance in HIV-infected patients switched from zidovudine to didanosine monotherapy. Kozal MJ, Kroodsma K, Winters MA, Shafer RW, Efron B, Katzenstein DA, Merigan TC. Ann Intern Med. 1994; 121 (4): 263-8
• HIV-1 syncytium-inducing phenotype, virus burden, codon 215 reverse transcriptase mutation and CD4 cell decline in zidovudine-treated patients. Kozal MJ, Shafer RW, Winters MA, Katzenstein DA, Aguiniga E, Halpern J, Merigan TC. J Acquir Immune Defic Syndr. 1994; 7 (8): 832-8
• Prevalence of HIV-1 syncytium-inducing phenotype. Kozal MJ, Ramachandran RV, Shafer RW. Ann Intern Med. 1994; 120 (9): 811
• A mutation in human immunodeficiency virus reverse transcriptase and decline in CD4 lymphocyte numbers in long-term zidovudine recipients. Kozal MJ, Shafer RW, Winters MA, Katzenstein DA, Merigan TC. J Infect Dis. 1993; 167 (3): 526-32
• 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, Ragni M, Merigan TC. J Acquir Immune Defic Syndr. 1993; 6 (4): 366-9
• Zidovudine susceptibility testing of human immunodeficiency virus type 1 (HIV) clinical isolates. Shafer RW, Kozal MJ, Katzenstein DA, Lipil WH, Johnstone IF, Merigan TC. J Virol Methods. 1993; 41 (3): 297-310
• Mycobacterium xenopi, Mycobacterium fortuitum, Mycobacterium kansasii, and other nontuberculous mycobacteria in an area of endemicity for AIDS. Shafer RW, Sierra MF. Clin Infect Dis. 1992; 15 (1): 161-2
• HIV prevalence, immunosuppression, and drug resistance in patients with tuberculosis in an area endemic for AIDS. Shafer RW, Chirgwin KD, Glatt AE, Dahdouh MA, Landesman SH, Suster B. AIDS. 1991; 5 (4): 399-405
• Relapse of tuberculosis in a patient with the acquired immunodeficiency syndrome despite 12 months of antituberculous therapy and continuation of isoniazid. Shafer RW, Jones WD. Tubercle. 1991; 72 (2): 149-51
• A life-threatening gonococcal infection. Shafer RW, Razavi MH, Zenilman JM. Hosp Pract (Off Ed). 1989; 24 (5): 26, 29
• Frequency of Mycobacterium tuberculosis bacteremia in patients with tuberculosis in an area endemic for AIDS. Shafer RW, Goldberg R, Sierra M, Glatt AE. Am Rev Respir Dis. 1989; 140 (6): 1611-3
• Q fever endocarditis: delay in diagnosis due to an apparent clinical response to corticosteroids. Shafer RW, Braverman ER. Am J Med. 1989; 86 (6 Pt 1): 729
• Successful prophylaxis of Pneumocystis carinii pneumonia with trimethoprim-sulfamethoxazole in AIDS patients with previous allergic reactions. Shafer RW, Seitzman PA, Tapper ML. J Acquir Immune Defic Syndr. 1989; 2 (4): 389-93