 Ajay Jain, PhD
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| Title | Professor in Residence |
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| School | UCSF School of Medicine |
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| Department | HDF Comprehensive Cancer Center |
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| Address | 1450 3rd Street
San Francisco CA 94158
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| Phone | 415-502-7242 |
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 Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications.
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Varela R, Walters WP, Goldman BB, Jain AN. Iterative refinement of a binding pocket model: active computational steering of lead optimization. J Med Chem. 2012 Oct 25; 55(20):8926-42.
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Spitzer R, Jain AN. Surflex-Dock: Docking benchmarks and real-world application. J Comput Aided Mol Des. 2012 Jun; 26(6):687-99.
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Jones DA, Weerackody R, Rathod K, Behar J, Gallagher S, Knight CJ, Kapur A, Jain AK, Rothman MT, Thompson CA, Mathur A, Wragg A, Smith EJ. Successful recanalization of chronic total occlusions is associated with improved long-term survival. JACC Cardiovasc Interv. 2012 Apr; 5(4):380-8.
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Jain AN, Cleves AE. Does your model weigh the same as a duck? J Comput Aided Mol Des. 2012 Jan; 26(1):57-67.
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Jones DA, Jain AK. Percutaneous balloon pericardiotomy for recurrent malignant pericardial effusion. J Thorac Oncol. 2011 Dec; 6(12):2138-9.
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Yera ER, Cleves AE, Jain AN. Chemical structural novelty: on-targets and off-targets. J Med Chem. 2011 Oct 13; 54(19):6771-85.
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Spitzer R, Cleves AE, Jain AN. Surface-based protein binding pocket similarity. Proteins. 2011 Sep; 79(9):2746-63.
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Jain AN. QMOD: physically meaningful QSAR. J Comput Aided Mol Des. 2010 Oct; 24(10):865-78.
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Nicholls A, McGaughey GB, Sheridan RP, Good AC, Warren G, Mathieu M, Muchmore SW, Brown SP, Grant JA, Haigh JA, Nevins N, Jain AN, Kelley B. Molecular shape and medicinal chemistry: a perspective. J Med Chem. 2010 May 27; 53(10):3862-86.
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Langham JJ, Cleves AE, Spitzer R, Kirshner D, Jain AN. Physical binding pocket induction for affinity prediction. J Med Chem. 2009 Oct 8; 52(19):6107-25.
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Jain AN. Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation. J Comput Aided Mol Des. 2009 Jun; 23(6):355-74.
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Langham JJ, Jain AN. Accurate and interpretable computational modeling of chemical mutagenicity. J Chem Inf Model. 2008 Sep; 48(9):1833-9.
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Jain AN, Nicholls A. Recommendations for evaluation of computational methods. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):133-9.
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Pham TA, Jain AN. Customizing scoring functions for docking. J Comput Aided Mol Des. 2008 May; 22(5):269-86.
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Jain AN. Bias, reporting, and sharing: computational evaluations of docking methods. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):201-12.
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Cleves AE, Jain AN. Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):147-59.
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Jain AN. Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. J Comput Aided Mol Des. 2007 May; 21(5):281-306.
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Kingsley CB, Kuo WL, Polikoff D, Berchuck A, Gray JW, Jain AN. 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 Inform. 2006; 2:10-21.
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Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL, Lapuk A, Neve RM, Qian Z, Ryder T, Chen F, Feiler H, Tokuyasu T, Kingsley C, Dairkee S, Meng Z, Chew K, Pinkel D, Jain A, Ljung BM, Esserman L, Albertson DG, Waldman FM, Gray JW. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell. 2006 Dec; 10(6):529-41.
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Pham TA, Jain AN. Parameter estimation for scoring protein-ligand interactions using negative training data. J Med Chem. 2006 Oct 5; 49(20):5856-68.
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Jain AN. Scoring functions for protein-ligand docking. Curr Protein Pept Sci. 2006 Oct; 7(5):407-20.
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Cleves AE, Jain AN. Robust ligand-based modeling of the biological targets of known drugs. J Med Chem. 2006 May 18; 49(10):2921-38.
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Fridlyand J, Snijders AM, Ylstra B, Li H, Olshen A, Segraves R, Dairkee S, Tokuyasu T, Ljung BM, Jain AN, McLennan J, Ziegler J, Chin K, Devries S, Feiler H, Gray JW, Waldman F, Pinkel D, Albertson DG. Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer. 2006; 6:96.
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Bussey KJ, Chin K, Lababidi S, Reimers M, Reinhold WC, Kuo WL, Gwadry F. Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel. Mol Cancer Ther. 2006 Apr; 5(4):853-67.
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Hon LS, Jain AN. A deterministic motif finding algorithm with application to the human genome. Bioinformatics. 2006 May 1; 22(9):1047-54.
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Novak BA, Jain AN. Pathway recognition and augmentation by computational analysis of microarray expression data. Bioinformatics. 2006 Jan 15; 22(2):233-41.
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Mehta KR, Nakao K, Zuraek MB, Ruan DT, Bergsland EK, Venook AP, Moore DH, Tokuyasu TA, Jain AN, Warren RS, Terdiman JP, Waldman FM. Fractional genomic alteration detected by array-based comparative genomic hybridization independently predicts survival after hepatic resection for metastatic colorectal cancer. Clin Cancer Res. 2005 Mar 1; 11(5):1791-7.
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Snijders AM, Nowak NJ, Huey B, Fridlyand J, Law S, Conroy J, Tokuyasu T, Demir K, Chiu R, Mao JH, Jain AN, Jones SJ, Balmain A, Pinkel D, Albertson DG. Mapping segmental and sequence variations among laboratory mice using BAC array CGH. Genome Res. 2005 Feb; 15(2):302-11.
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Rosen DG, Wang L, Jain AN, Lu KH, Luo RZ, Yu Y, Liu J, Bast RC. Expression of the tumor suppressor gene ARHI in epithelial ovarian cancer is associated with increased expression of p21WAF1/CIP1 and prolonged progression-free survival. Clin Cancer Res. 2004 Oct 1; 10(19):6559-66.
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Jain AN. Virtual screening in lead discovery and optimization. Curr Opin Drug Discov Devel. 2004 Jul; 7(4):396-403.
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Paris PL, Andaya A, Fridlyand J, Jain AN, Weinberg V, Kowbel D, Brebner JH, Simko J, Watson JE, Volik S, Albertson DG, Pinkel D, Alers JC, van der Kwast TH, Vissers KJ, Schroder FH, Wildhagen MF, Febbo PG, Chinnaiyan AM, Pienta KJ, Carroll PR, Rubin MA, Collins C, van Dekken H. Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors. Hum Mol Genet. 2004 Jul 1; 13(13):1303-13.
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Nakao K, Mehta KR, Fridlyand J, Moore DH, Jain AN, Lafuente A, Wiencke JW, Terdiman JP, Waldman FM. High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization. Carcinogenesis. 2004 Aug; 25(8):1345-57.
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Jain AN. Ligand-based structural hypotheses for virtual screening. J Med Chem. 2004 Feb 12; 47(4):947-61.
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Maldonado JL, Fridlyand J, Patel H, Jain AN, Busam K, Kageshita T, Ono T, Albertson DG, Pinkel D, Bastian BC. Determinants of BRAF mutations in primary melanomas. J Natl Cancer Inst. 2003 Dec 17; 95(24):1878-90.
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Hon LS, Jain AN. Compositional structure of repetitive elements is quantitatively related to co-expression of gene pairs. J Mol Biol. 2003 Sep 12; 332(2):305-10.
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Hackett CS, Hodgson JG, Law ME, Fridlyand J, Osoegawa K, de Jong PJ, Nowak NJ, Pinkel D, Albertson DG, Jain A, Jenkins R, Gray JW, Weiss WA. Genome-wide array CGH analysis of murine neuroblastoma reveals distinct genomic aberrations which parallel those in human tumors. Cancer Res. 2003 Sep 1; 63(17):5266-73.
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Snijders AM, Fridlyand J, Mans DA, Segraves R, Jain AN, Pinkel D, Albertson DG. Shaping of tumor and drug-resistant genomes by instability and selection. Oncogene. 2003 Jul 10; 22(28):4370-9.
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Snijders AM, Nowee ME, Fridlyand J, Piek JM, Dorsman JC, Jain AN, Pinkel D, van Diest PJ, Verheijen RH, Albertson DG. Genome-wide-array-based comparative genomic hybridization reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in fallopian tube carcinoma. Oncogene. 2003 Jul 3; 22(27):4281-6.
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Veltman JA, Fridlyand J, Pejavar S, Olshen AB, Korkola JE, DeVries S, Carroll P, Kuo WL, Pinkel D, Albertson D, Cordon-Cardo C, Jain AN, Waldman FM. Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors. Cancer Res. 2003 Jun 1; 63(11):2872-80.
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Paris PL, Albertson DG, Alers JC, Andaya A, Carroll P, Fridlyand J, Jain AN, Kamkar S, Kowbel D, Krijtenburg PJ, Pinkel D, Schröder FH, Vissers KJ, Watson VJ, Wildhagen MF, Collins C, Van Dekken H. High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays. Am J Pathol. 2003 Mar; 162(3):763-70.
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Jain AN. Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J Med Chem. 2003 Feb 13; 46(4):499-511.
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Olshen AB, Jain AN. Deriving quantitative conclusions from microarray expression data. Bioinformatics. 2002 Jul; 18(7):961-70.
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Massion PP, Kuo WL, Stokoe D, Olshen AB, Treseler PA, Chin K, Chen C, Polikoff D, Jain AN, Pinkel D, Albertson DG, Jablons DM, Gray JW. Genomic copy number analysis of non-small cell lung cancer using array comparative genomic hybridization: implications of the phosphatidylinositol 3-kinase pathway. Cancer Res. 2002 Jul 1; 62(13):3636-40.
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Wilhelm M, Veltman JA, Olshen AB, Jain AN, Moore DH, Presti JC, Kovacs G, Waldman FM. Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer. Cancer Res. 2002 Feb 15; 62(4):957-60.
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Jain AN, Tokuyasu TA, Snijders AM, Segraves R, Albertson DG, Pinkel D. Fully automatic quantification of microarray image data. Genome Res. 2002 Feb; 12(2):325-32.
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Ghuloum AM, Sage CR, Jain AN. Molecular hashkeys: a novel method for molecular characterization and its application for predicting important pharmaceutical properties of molecules. J Med Chem. 1999 May 20; 42(10):1739-48.
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Mount J, Ruppert J, Welch W, Jain AN. IcePick: a flexible surface-based system for molecular diversity. J Med Chem. 1999 Jan 14; 42(1):60-6.
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Ruppert J, Welch W, Jain AN. Automatic identification and representation of protein binding sites for molecular docking. Protein Sci. 1997 Mar; 6(3):524-33.
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Jain AN. Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities. J Comput Aided Mol Des. 1996 Oct; 10(5):427-40.
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Welch W, Ruppert J, Jain AN. Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. Chem Biol. 1996 Jun; 3(6):449-62.
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Jain AN, Harris NL, Park JY. Quantitative binding site model generation: compass applied to multiple chemotypes targeting the 5-HT1A receptor. J Med Chem. 1995 Apr 14; 38(8):1295-308.
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Jain AN, Dietterich TG, Lathrop RH, Chapman D, Critchlow RE, Bauer BE, Webster TA, Lozano-Perez T. A shape-based machine learning tool for drug design. J Comput Aided Mol Des. 1994 Dec; 8(6):635-52.
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Jain AN, Koile K, Chapman D. Compass: predicting biological activities from molecular surface properties. Performance comparisons on a steroid benchmark. J Med Chem. 1994 Jul 22; 37(15):2315-27.
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