Dr. John Cunniff, M.D. Ph.D.



  • U. of Penn Wharton School of Business, BS in Economics 5/85,

  • U. of Florida, MD 6/95

  • U. of Southern California PhD 3/96

  • Stanford University, Residency, Internal Medicine 7/00

  • Palo Alto Foundation Medical Group

  • PAFMG Executive Board Member 2010- 2015


After completing my Internal Medicine residency at Stanford University, I had the opportunity to continue working at Stanford Hospital as a hospitalist for the Palo Alto Medical Foundation. During this time, I had the chance to work closely with Stanford medical students, interns and residents as an attending winning the Stanford Russell Lee teaching award in 2003 and 2004.

I enjoyed the intellectual challenge of teaching and seeing hospitalized patients with the very intelligent, hard-working Stanford residents and interns. After a change of administration, the policy of community physicians working with residency teams was eliminated. I, therefore, decided to get back to basic science research and joined Dr. Roger Kornberg's lab in the Department of Structural Biology at Stanford University working on the structure of RNA polymerase II while continuing my work as a hospitalist at Stanford. More specifically my project involved work on the Rpb4/Rpb7 heterodimer of RNA polymerase II. The Rpb4/Rpb7 heterodimer is a dissociable dimer whose role in transcription is poorly understood and is not currently part of the structural analysis and has been exceedingly difficult to crystalize as part of the overall RNA polymerase II complex.

Roger Kornberg then asked me to join his start-up company, Co-Crystal Discovery, Inc. that is focused on making small molecule inhibitors of viral polymerases. I led a group focused on targeting the influenza polymerase. When the company went public, operations were moved to Seattle and Atlanta and I had to leave the company because of this change in location. It was at that time that I started a company with Michael Levitt (Nobel Prize in Chemistry 2013) and his former post-doc Boris Fain to use Big Data techniques that he and Dr. Fain had pioneered and patented in 2008 to diagnose cancer. The current focus of our company is using Dr. Levitt’s theoretical advances to make breath-based diagnostic screening to diagnose cancer a reality.

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