Physician Education: Bridging Clinical Research and Patient Care

Faculty Profile

Assistant Professor
Stanford University
Stanford, California        

Topics of Professional Interest:
  • HIV drug resistance
  • HIV evolution
  • Medical genomics
  • HIV drug therapy 
Current Professional Summary:

Dr Shafer is an Assistant Professor of Medicine at Stanford University, Stanford, California, and is the medical director of the HIV antiretroviral testing program at Stanford University Hospital. His research is on the mechanisms and consequences of HIV evolution within human populations with an emphasis on HIV drug resistance. Dr Shafer has created a publicly available database that catalogs evolutionary and drug-related HIV reverse transcriptase and protease sequence variation and correlates sequence variation with drug susceptibility data and drug treatment histories. The database Web site also contains an on-line gene-specific mutation search engine and expert system for the analysis and interpretation of HIV reverse-transcriptase and protease sequences. Dr Shafer is the principal investigator of an NIH-funded proposal to isolate and characterize multidrug-resistant HIV isolates and is chair of an ACTG clinical trial.

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.