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Steve Miller, MD, PhD

Research and Clinical Interests

I am interested in the use of molecular methods for diagnosis and monitoring of clinical infectious disease, particularly in immunocompromised and transplant patients. Conventional clinical testing often is unable to identify pathogens of interest in patient samples, and my research aims to develop methods to better identify infectious agents, which could improve patient care and public health. Projects include:

  1. Clinical evaluation and implementation of quantitative PCR measurements of viral illness (EBV, BK, JC, CMV) and multiplex identification of these agents in disease or symptom-specific panels.
  2. Development and evaluation of microarray and deep sequencing assays for microbial identification of viral, bacterial, fungal and parasitic pathogens for diagnosis of clinical infection.
  3. 3. Viral and bacterial identification, strain typing, and prediction of phenotypic resistance profiles using microarrays and deep sequencing genomic methods.

Selected Publications

  • Miller S, Liverman CS, Post L, Khan Y and Wright C. Analytical and clinical performance characteristics of the Simplexa BK virus quantitative PCR assay for the diagnosis of polyomavirus-associated nephropathy in renal transplant recipients using plasma and urine specimens. Journal of Clinical Virology 2012;55:310-6.
  • Yu G, Greninger AL, Isa P, Phan TG, Martinez MA, Sanchez ML, Contreras JF, Santos-Preciado JI, Parsonnett J, Miller S, DeRisi JL, Delwart E, Arias CF and Chiu CY. Discovery of a Novel Polyomavirus in Acute Diarrheal Samples from Children. PLoS One 2012;7:e49449.
  • Miller S, Wiita A, Wright C, Reyes H and Liu C. Evaluation of Glutamate Dehydrogease Immunoassay Screening with Toxin Confirmation for the Diagnosis of Clostridium difficile Infection. LabMedicine 2013;44:e65-e71.
  • Naccache SN, Federman S, Veeraraghavan N, Zaharia M, Lee D, Samayoa E, Bouquet J, Greninger AL, Luk K-C, Enge B, Wadford DA, Messenger SL, Genrich GL, Pellegrino K, Grard G, Leroy E, Schneider BS, Fair JN, Martinez MA, Isa P, Crump JA, DeRisi JL, Sittler T, Hackett J, Miller S and Chiu CY. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Research 2014;24:1180-1192.
  • Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, Salamat SM, Somasekar S, Federman S, Miller S, Sokolic R, Garabedian E, Candotti F, Buckley RH, Reed KD, Meyer TL, Seroogy CM, Galloway R, Henderson SL, Gern JE, DeRisi JL and Chiu CY. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. The New England Journal of Medicine 2014;370:2408-2417.

Selected Awards

  • 2006: Paul E. Strandjord Young Investigator Award
  • 2006-2007: College of American Pathologists Foundation Scholar
Steve Miller, MD, PhD
  • Associate Professor and Director, UCSF Clinical Microbiology Laboratory
  • Laboratory Medicine
  • Infectious Disease/Microbial Pathogenesis

Specialty Area

  • Molecular Microbiology

Contact Information

  • 185 Berry Street, Suite 290
  • Box 0100
  • San Francisco, CA 94107

Hospital Affiliation(s)

  • UCSF Medical Center
  • UCSF Childrens Hospital
  • Mt. Zion Medical Center
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