• Department of Pathology
  • Pathology Staff
• Department of Laboratory Medicine
  • Laboratory Medicine Staff
• Affiliated Hospitals
  • Moffitt-Long
  • Mount Zion Medical Center
  • San Francisco Veterans Affairs Medical Center
  • San Francisco General
• Faculty
  • Pathology
  • Laboratory Medicine

Research and Clinical Interests

Predictive computational modeling encompasses all of the work in the Jain Lab. This ranges from modeling protein ligand interactions to modeling the relationship between variation in quantifiable molecular species to the behavior of complex biological systems. The primary areas of research in the lab are: 1) computational methods for structure-based drug design, 2) computational approaches for modeling human transcription and biological network structure, and 3) computational and statistical methods to derive quantitative conclusions from high-throughput biological measurements. All of the approaches share their roots in the use of empirically derived scoring functions and compute-intensive search, optimization, and enumeration.

Selected Publications

• Pham, T. A. and Jain, A.N. (2006). Parameter Estimation for Scoring Protein-Ligand Interactions using Negative Training Data. J Med Chem, 49, 5856-68.
• Kingsley, C. B., Kuo, W-L., Polikoff, D., Berchuck, A., Gray, J.W., and Jain, A.N. (2006). Magellan: A Web Based System for the Integrated Analysis of Heterogeneous Biological Data and Annotations; Application to DNA Copy Number and Expression Data in Ovarian Cancer. Cancer Informatics, 1, 10-21.
• Novak, B.A. and Jain, A.N. (2006). Pathway Recognition and Augmentation by Computational Analysis of Microarray Expression Data. Bioinformatics, 22, 233-241.
• Hon, L.S. and Jain, A.N. (2006). A Deterministic Motif Finding Algorithm With Application to the Human Genome. Bioinformatics, 22, 1047-54
• Cleves, A.E. and Jain, A.N. (2006). Robust Ligand-Based Modeling of the Biological Targets of Known Drugs. J Med Chem, 49, 2921-38.

• Professor
• Laboratory Medicine
• Biopharmaceutical Sciences and Cancer Research Institute

Specialty Area

• Computational Biology
• Biophysics
• Chemistry

Contact Information

• ajain@jainlab.org
• Phone: 415-502-7242
• Fax: 650-240-1781

• Box 0128

Web Site

• http://www.jainlab.org

Other UCSF Organizational Association(s)

Member and Director of Informatics Core

• UCSF Comprehensive Cancer Center