Ajay N. Jain, PhD

Professor, UCSF, Department of Bioengineering and Therapeutic Sciences.

Member, UCSF Helen Diller Family Comprehensive Cancer Center, Program in Quantitative Biology (iPQB)

Dr. Jain is an internationally known expert in the area of computer-aided drug design. His research is focused on the development of computerized methods for efficiently developing effective drugs. His formal training is in Computer Science, and he spent a number of years during the Cold War developing methods for military target recognition. These methods found a new use as he transitioned from defense applications to drug discovery in a series of biopharmaceutical start-up companies, beginning with Arris Pharmaceutical in 1992. After several years in Bay Area biotechnology, Dr. Jain joined UCSF in 1999.

Hundreds of collaborating laboratories make use of the Jain lab's computational methods for modeling the shapes of drug molecules and predicting their biological effects, including a number of laboratories actively involved in cancer drug discovery.

Dr. Jain received his PhD in Computer Science in 1991 from Carnegie Mellon University following BS degrees in both Computer Science and Biochemistry from the University of Minnesota.


Ann E. Cleves (Jain), PhD, Senior Staff Scientist
Dr. Cleves has extensive experience in molecular and cellular biology in both academic and commercial settings. Her PhD work, in the lab of Vytas Bankaitis, focused on the role of the SEC14 and SAC1 proteins in Golgi function in yeast. She was a Helen Hay Whitney postdoctoral Fellow in the lab of Reg Kelly at UCSF and worked on both mammalian synaptic vesicle biogenesis and nonclassical secretion in yeast. Her industry experience began with developing in vitro assays for inhibitors of multiple drug resistance transporters and evolved into a specific interest in the relationship between molecular structure and pharmacology. These interests, and her biological expertise in therapeutics, led to a shift in research area from pure molecular and cell biology to applied computational chemistry and biology.

Her role involves three primary aspects: 1) testing and application of sophisticated algorithms for computational modeling of small molecules and protein binding sites, especially as is relevant to therapeutic discovery; 2) development and curation of a database of protein/ligand interactions, describing both on-target and off-target effects, annotated at a level of specific binding sites on protein assemblies; and 3) authorship of peer-reviewed studies to describe research results and didactic books to illustrate the theory and best practices in therapeutically oriented molecular modeling.

Post-Doctoral Researchers
We are not adding new post-doctoral personnel at the moment. If you are interested in a pre-doctoral position, please apply directly to the UCSF (iPQB) Graduate Program.

Graduate Students
We graduated our most recent trio of PhD students in 2013.

Former Lab Members
Former students:
Lawrence Hon, PhD, UCSF Biological and Medical Informatics (2005), now at PacBio
Chris Kingsley, PhD, UCSF Biological and Medical Informatics (2005), now at Ariosa Diagnostics
Barbara Novak, PhD, UCSF Biological and Medical Informatics (2007), now at Agilent
Tuan Pham, PhD, UCSF Biological and Medical Informatics (2007), now at a stealth-mode startup
Russell Spitzer, PhD, Bioinformatics, iPQB Program (2013), now at DataStax
Rocco Varela, PhD, Bioinformatics, iPQB Program (2013), now at DataStax
Emmanuel Yera, PhD Bioinformatics, iPQB Program (2013), now at Quid

Former post-docs:
Jane Fridlyand, PhD, now at Genentech
James Langham, PhD
Adam Olshen, PhD, now faculty at UCSF in Epidemiology and Biostatistics
Taku Tokuyasu, PhD, now at the Center for Synthetic Biology Engineering Research (China)


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