UCSF Helen Diller Family Comprehensive Cancer Center - People

Professor, Cancer Research Institute, Department of Biopharmaceutical Sciences and Department of Laboratory Medicine
Executive Committee, Program in Biological and Medical Informatics (BMI), UCSF
Director, Informatics Core Facility, UCSF Helen Diller Family Comprehensive Cancer Center

CONTACT

ajain@jainlab.org
(415) 502-7242 (voice)
(415) 240-1781 (fax)

Box 0128, UCSF; San Francisco, CA 94143-0128

additional websites:

Jain Lab Website

EDUCATION
University of Minnesota, St. Paul, MN, BS, 1986, Biochemistry University of Minnesota, Minneapolis, MN, BS, 1986, Computer Science Carnegie Mellon University, Pittsburgh, PA, MS, 1989, Computer Science Carnegie Mellon University, Pittsburgh, PA, PhD, 1991, Computer Science
PROFESSIONAL EXPERIENCE
1983-1986	Research Engineer, Machine Vision Technology, Honeywell, Minneapolis, MN
1992	Principal Research Scientist, Multi-Sensor Signal Processing. Alliant Techsystems (formerly Honeywell), Minneapolis, MN
1992-1996	Senior Scientist and Group Leader of Computational Sciences, Arris Pharmaceutical, So. San Francisco, CA
1996-1997	Principal Scientist and Group Leader of Computational Sciences, MetaXen LLC, Hayward, CA
1997-present	Founder and Chief Scientist, BioPharmics, San Mateo, CA
1998-1999	Director of Applied Computing, Iconix Pharmaceuticals, Mountain View, CA
1999-present	Full Member, UCSF Cancer Center, University of California, San Francisco, CA
1999-2002	Director of Informatics, UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
1999-2002	Associate Adjunct Professor, Cancer Research Institute and Department of Laboratory Medicine, University of California, San Francisco, CA
2002-present	Director, Informatics Core, UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
2002-2007	Associate Professor, Cancer Research Institute and Department of Laboratory Medicine, University of California, San Francisco, CA
2004-2007	Associate Professor, Department of Biopharmaceutical Sciences, University of California, San Francisco, CA
2007-present	Professor, Cancer Research Institute, Department of Biopharmaceutical Sciences, and Department of Laboratory Medicine, University of California, San Francisco, CA
SELECTED PUBLICATIONS
A. N. Jain. Parsing Complex Sentences with Structured Connectionist Networks. Neural Computation 3(1): 110-20, 1991.
A. N. Jain, K. Koile, D. Chapman. Compass: Predicting Biological Activities from Molecular Surface Properties; Performance Comparisons on a Steroid Benchmark. J. Med. Chem. 37: 2315-2327, 1994.
A. N. Jain, T. G. Dietterich, R. L. Lathrop, D. Chapman, R. E. Critchlow, B. E. Bauer, T. A. Webster, and T. Lozano-Perez. Compass: A Shape-Based Machine Learning Tool for Drug Design. Journal of Computer-Aided Molecular Design 8(6): 635-652, 1994.
A. N. Jain, N. L. Harris, and J. Y. Park. Quantitative Binding Site Model Generation: Compass Applied to Multiple Chemotypes Targeting the 5HTlA Receptor. J. Med. Chem. 38: 1295-1307, 1995.
J. Ruppert, W. Welch, and A. N. Jain. Automatic Characterization and Identification of Protein Binding Pockets for Molecular Docking. Protein Science 6: 524-533, 1996.
W. Welch, J. Ruppert, and A. N. Jain. Hammerhead: Fast, Fully Automated Docking of Flexible Ligands to Protein Binding Sites. Chemistry and Biology 3: 449-462, 1996.
A. N. Jain. Scoring Non-Covalent Ligand-Protein Interactions: A Continuous Differentiable Function Tuned to Compute Binding Affinities. Journal of Computer-Aided Molecular Design 10:5, 427-440, 1996.
J. Mount, J. Ruppert, W. Welch, and A. N. Jain. IcePick: A Flexible Surface-Based System for Molecular Diversity. J. Med. Chem. 42: 60-66, 1999.
A. Ghuloum, C. R. Sage, and A. N. Jain. Molecular Hashkeys: A Novel Method for Molecular Characterization and its Application to Predicting Important Pharmaceutical Properties of Molecules. J. Med. Chem. 42: 1739-1748, 1999.
A. N. Jain. Morphological Similarity: A 3D Molecular Similarity Method Correlated with Protein-Ligand Recognition. Journal of Computer-Aided Molecular Design 14: 199-213, 2000.
A. N. Jain, K. Chin, A. B¿rresen-Dale, B. K. Erikstein, P. E. Lonning, R. Kaaresen, and J. W. Gray. Quantitative Analysis of Chromosomal CGH in Human Breast Tumors Associates Copy Number Abnormalities with p53 Status and Patient Survival. PNAS 98: 7952-7957, 2001.
A. M. Snijders, N. Nowak, R. Segraves, S. Blackwood, N. Brown, J. Conroy, G. Hamilton, A. K. Hindle, B. Huey, K. Kimura, S. Law, K. Myambo, J. Palmer, B. Ylstra, J. P. Yue, J. W. Gray, A. N. Jain, D. Pinkel, and D. G. Albertson. Assembly of microarrays for genome-wide measurement of DNA copy number by CGH. Nature Genetics 29: 263-264, 2001.
A. N. Jain, T. A. Tokuyasu, A. M. Snijders, R. Segraves, D. G. Albertson, and D. Pinkel. Fully Automatic Quantification of Microarray Image Data. Genome Research 12: 325-332, 2002.
A. B. Olshen and A. N. Jain. Deriving Quantitative Conclusions from Microarray Expression Data. Bioinformatics 18: 961-970, 2002.
A. N. Jain. Surflex: Fully Automatic Flexible Molecular Docking using a Molecular Similarity-Based Search Engine. J Med Chem. 46: 499-511, 2003.
L.S. Hon and A. N. Jain. Compositional Structure of Repetitive Elements is Quantitatively Related to Co-Expression of Gene Pairs. Journal of Molecular Biology, 332: 305-310, 2003.
J. Fridlyand, A.M. Snijders, D. Pinkel, D.G. Albertson, and A.N. Jain. Hidden Markov Model Analysis of Array CGH Data. Journal of Multivariate Analysis, 90, 132-153, 2004.
A. N. Jain. Ligand-Based Structural Hypotheses for Virtual Screening. J Med Chem, 47, 947-961, 2004.
A. N. Jain. Virtual Screening in Lead Discovery and Optimization. Curr Op Drug Discovery & Dev 7: 396-403, 2004.
T.A. Pham and A. N. Jain. Parameter Estimation for Scoring Protein-Ligand Interactions using Negative Training Data. J Med Chem., 49, 5856-68, 2006.
C. B. Kingsley, W.-L. Kuo, D. Polikoff, A. Berchuck, J.W. Gray, and A. N. Jain. 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, 2006
B.A. Novak and A.N. Jain. Pathway Recognition and Augmentation by Computational Analysis of Microarray Expression Data. Bioinformatics, 22, 233-241, 2006.
L.S. Hon and A.N. Jain. A Deterministic Motif Finding Algorithm With Application to the Human Genome. Bioinformatics, 22, 1047-54, 2006.
A.E. Cleves and A.N. Jain. Robust Ligand-Based Modeling of the Biological Targets of Known Drugs. J Med Chem., 49, 2921-38, 2006.
A.N. Jain. Scoring Functions for Protein-Ligand Docking. Curr Protein Pept Sci., 7:407-20, 2006.
J. Fridlyand, A.M. Snijders, B. Ylstra, H. Li, A. Olshen, R. Segraves, S. Dairkee, T. Tokuyasu, B.M. Ljung, A.N. Jain, J. Mclennan, J. Ziegler, K. Chin, S. Devries, H. Feiler, J.W. Gray, F. Waldman, D. Pinkel, and D.G. Albertson. Breast Tumor Copy Number Aberration Phenotypes and Genomic Instability. BMC Cancer, 6, 96, 2006.
K. Chin, S. DeVries, J. Fridlyand, P.T. Spellman, R. Roydasgupta, W.L. Kuo, A. Lapuk, R.M. Neve, Z. Qian, T. Ryder, F. Chen, H. Feiler, T. Tokuyasu, C. Kingsley, S. Dairkee, Z. Meng, K. Chew, D. Pinkel, A.N. Jain, B.M. Ljung, L. Esserman, D.G. Albertson, F.M. Waldman, and J.W. Gray. Genomic and Transcriptional Aberrations Linked to Breast Cancer Pathophysiologies. Cancer Cell, 10: 529-41, 2006.
A.N. Jain. Surflex-Dock 2.1: Robust Performance from Ligand Energetic Modeling, Ring Flexibility, and Knowledge-based Search. J Comput Aided Mol Des., 21: 281-306, 2007.
5/21/08

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