Robert W. Shafer, MD

Assistant Professor
Stanford University
Stanford, California

Committees and Organizations

  • AIDS Clinical Trials Group
  • American College of Physicians
  • American Society for Microbiology
  • Infectious Diseases Society of America


  • Columbia University, BA, Computer Science (1979)
  • New York University, MD (1983)
  • New York Medical College, Residency, Internal Medicine (1983–1986)
  • SUNY-Health Sciences Center of Brooklyn, Fellow in Infectious Diseases (1986–1988)
  • Stanford University Medical Center, AIDS Research Fellow (1990–1993)

Selected Publications

  1. Shafer RW, Kim DS, Weiss JP, Quale JD. Extrapulmonary tuberculosis in patients with HIV infection. Medicine. 1991;70:384-397.
  2. Small PM, Shafer RW, Hopewell PC, Singh SP, Murphy MJ, Desmond E, Sierra MF, Schoolnik GK. Exogenous reinfection with multidrug-resistant tuberculosis in patients with advanced HIV infection. N Engl J Med. 1993;328:1137-1144.
  3. Shafer RW, Kozal MJ, Winters MA, Iversen AK, Katzenstein DA, Fiscus S, Katzman M, Gupta P, Meyer R, Rasheed S, Coombs R, Ragni MV, Merigan TC. Combination therapy with zidovudine and didanosine selects for drug-resistant HIV-1 strains with unique patterns of pol gene mutation. J Infect Dis. 1994;169:722-729.
  4. Shafer RW, Small PM, Larkin C, Singh SP, Kelly P, Sierra MF, Schoolnik G, Chirgwin KD. Temporal trends and transmission patterns during the emergence of multidrug-resistant tuberculosis at a New York City hospital: a molecular epidemiological assessment. J Infect Dis.1995;171:170-176.
  5. Shafer RW, Winters MA, Palmer S, Merigan TC. Multiple concurrent reverse transcriptase and protease mutations, and multidrug resistance of HIV-1 isolates from heavily treated patients. Ann Intern Med. 1998;128:906-911.
  6. Shafer RW, Stevenson D, Chan B. HIV reverse transcriptase and protease sequence database. Nucleic Acids Res. 1999;27:348-352.
  7. Shafer RW, Hsu P, Patick AK, Craig C, Brendel V. Identification of biased amino acid substitution patterns in human immunodeficiency virus type 1 isolates from patients treated with protease inhibitors. J Virol. 1999;73:6197-6202.
  8. Zolopa AR, Shafer RW, Montoya JG, Warford A, Merigan TC, Efron BA. HIV genotypic predictors of response to saquinavir/ritonavir combination therapy in patients who have failed prior protease inhibitors: A clinical cohort study. Ann Intern Med. 1999;131:813-821.
  9. Shafer RW, Jung DR, Betts BJ. Human immunodeficiency virus type 1 reverse transcriptase and protease mutation search engine for queries (HIV-SEQ). Nat Med. 2000;6:1290-1292.
  10. Shafer RW, Hertogs K, Zolopa AR, Warford A, Betts BJ, Bloor S, Merigan TC, Harrigan R, Larder BA. High degree of interlaboratory reproducibility of HIV-1 protease and reverse transcriptase sequencing of plasma samples from heavily treated patients. J Clin Microbiol. 2001;39:1522-1529.