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Ajay Jain

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Physiology

Gene Expression Regulation, Neoplastic

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Publications

TOP 3
Rocco Varela; W Patrick Walters; Brian B Goldman; Ajay N Jain
Iterative refinement of a binding pocket model: active computational steering of lead optimization.
Russell Spitzer; Ajay N Jain
Surflex-Dock: Docking benchmarks and real-world application.
Ajay N Jain; Ann E Cleves
Does your model weigh the same as a duck?

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All Publications

2012: Rocco Varela; W Patrick Walters; Brian B Goldman; Ajay N Jain
Iterative refinement of a binding pocket model: active computational steering of lead optimization.
Journal of medicinal chemistry 2012;55(20):8926-42.
2012: Russell Spitzer; Ajay N Jain
Surflex-Dock: Docking benchmarks and real-world application.
Journal of computer-aided molecular design 2012;26(6):687-99.
2012: Ajay N Jain; Ann E Cleves
Does your model weigh the same as a duck?
Journal of computer-aided molecular design 2012;26(1):57-67.
2011: Emmanuel R Yera; Ann E Cleves; Ajay N Jain
Chemical structural novelty: on-targets and off-targets.
Journal of medicinal chemistry 2011;54(19):6771-85.
2011: Russell Spitzer; Ann E Cleves; Ajay N Jain
Surface-based protein binding pocket similarity.
Proteins 2011;79(9):2746-63.
2010: Ajay N Jain
QMOD: physically meaningful QSAR.
Journal of computer-aided molecular design 2010;24(10):865-78.
2010: Anthony Nicholls; Georgia B McGaughey; Robert P Sheridan; Andrew C Good; Gregory Warren; Magali Mathieu; Steven W Muchmore; Scott P Brown; J Andrew Grant; James A Haigh; Neysa Nevins; Ajay N Jain; Brian Kelley
Molecular shape and medicinal chemistry: a perspective.
Journal of medicinal chemistry 2010;53(10):3862-86.
2009: James J Langham; Ann E Cleves; Russell Spitzer; Daniel Kirshner; Ajay N Jain
Physical binding pocket induction for affinity prediction.
Journal of medicinal chemistry 2009;52(19):6107-25.
2009: Ajay N Jain
Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation.
Journal of computer-aided molecular design 2009;23(6):355-74.
2008: James J Langham; Ajay N Jain
Accurate and interpretable computational modeling of chemical mutagenicity.
Journal of chemical information and modeling 2008;48(9):1833-9.
2008: Tuan A Pham; Ajay N Jain
Customizing scoring functions for docking.
Journal of computer-aided molecular design 2008;22(5):269-86.
2008: Ajay N Jain; Anthony Nicholls
Recommendations for evaluation of computational methods.
Journal of computer-aided molecular design 2008;22(3-4):133-9.
2008: Ajay N Jain
Bias, reporting, and sharing: computational evaluations of docking methods.
Journal of computer-aided molecular design 2008;22(3-4):201-12.
2008: Ann E Cleves; Ajay N Jain
Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery.
Journal of computer-aided molecular design 2008;22(3-4):147-59.
2007: Ajay N Jain
Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search.
Journal of computer-aided molecular design 2007;21(5):281-306.
2006: Tony A Pham; Ajay N Jain
Parameter estimation for scoring protein-ligand interactions using negative training data.
Journal of medicinal chemistry 2006;49(20):5856-68.
2006: Ajay N Jain
Scoring functions for protein-ligand docking.
Current protein & peptide science 2006;7(5):407-20.
2006: Ann E Cleves; Ajay N Jain
Robust ligand-based modeling of the biological targets of known drugs.
Journal of medicinal chemistry 2006;49(10):2921-38.
2006: Lawrence S Hon; Ajay N Jain
A deterministic motif finding algorithm with application to the human genome.
Bioinformatics (Oxford, England) 2006;22(9):1047-54.
2006: Barbara A Novak; Ajay N Jain
Pathway recognition and augmentation by computational analysis of microarray expression data.
Bioinformatics (Oxford, England) 2006;22(2):233-41.
2006: Christopher Kingsley; Wen-Lin Kuo; Daniel Polikoff; Andrew Berchuck; Joe Gray; Ajay 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 2006;2():10-21.
2006: Jane Fridlyand; Antoine M Snijders; Bauke Ylstra; Hua Li; Adam B Olshen; Richard Segraves; Shanaz H Dairkee; Taku Tokuyasu; Britt-Marie Ljung; Ajay N Jain; Jane McLennan; John Ziegler; Koei Chin; Sandy Devries; Heidi Feiler; Joe Gray; Frederic M Waldman; Daniel Pinkel; Donna G Albertson
Breast tumor copy number aberration phenotypes and genomic instability.
BMC cancer 2006;6():96.
2005: Kshama R Mehta; Kentaro Nakao; Marlene B Zuraek; Daniel T Ruan; Emily K Bergsland; Alan P Venook; Dan H Moore; Taku Tokuyasu; Ajay N Jain; Robert S Warren; Jonathan P Terdiman; Frederic M Waldman
Fractional genomic alteration detected by array-based comparative genomic hybridization independently predicts survival after hepatic resection for metastatic colorectal cancer.
Clinical cancer research : an official journal of the American Association for Cancer Research 2005;11(5):1791-7.
2005: Antoine M Snijders; Norma J Nowak; Bing Huey; Jane Fridlyand; Sindy Law; Jeffrey Conroy; Taku Tokuyasu; Kubilay Demir; Readman Chiu; Jian-Hua Mao; Ajay N Jain; Steven J M Jones; Allan Balmain; Daniel Pinkel; Donna G Albertson
Mapping segmental and sequence variations among laboratory mice using BAC array CGH.
Genome research 2005;15(2):302-11.
2004: Daniel G Rosen; Lin Wang; Ajay N Jain; Karen H Lu; Robert Z Luo; Yinhua Yu; Jinsong Liu; Robert C Bast
Expression of the tumor suppressor gene ARHI in epithelial ovarian cancer is associated with increased expression of p21WAF1/CIP1 and prolonged progression-free survival.
Clinical cancer research : an official journal of the American Association for Cancer Research 2004;10(19):6559-66.
2004: Kentaro Nakao; Kshama R Mehta; Jane Fridlyand; Dan H Moore; Ajay N Jain; Amalia Lafuente; John W Wiencke; Jonathan P Terdiman; Frederic M Waldman
High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization.
Carcinogenesis 2004;25(8):1345-57.
2004: Ajay N Jain
Virtual screening in lead discovery and optimization.
Current opinion in drug discovery & development 2004;7(4):396-403.
2004: Pamela L Paris; Armann Andaya; Jane Fridlyand; Ajay N Jain; Vivian Weinberg; David Kowbel; John H Brebner; Jeff Simko; J E Vivienne Watson; Stanislav Volik; Donna G Albertson; Daniel Pinkel; Janneke C Alers; Theo Van der Kwast; Kees J Vissers; Fritz H Schroder; Mark F Wildhagen; Phillip G Febbo; Arul M Chinnaiyan; Kenneth J Pienta; Peter R Carroll; Mark A Rubin; Colin Collins; Herman van Dekken
Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors.
Human molecular genetics 2004;13(13):1303-13.
2004: Ajay N Jain
Ligand-based structural hypotheses for virtual screening.
Journal of medicinal chemistry 2004;47(4):947-61.
2003: Janet L Maldonado; Jane Fridlyand; Hetal Patel; Ajay N Jain; Klaus J Busam; Toshiro Kageshita; Tomomichi Ono; Donna G Albertson; Daniel Pinkel; Boris C Bastian
Determinants of BRAF mutations in primary melanomas.
Journal of the National Cancer Institute 2003;95(24):1878-90.
2003: Lawrence S Hon; Ajay N Jain
Compositional structure of repetitive elements is quantitatively related to co-expression of gene pairs.
Journal of molecular biology 2003;332(2):305-10.
2003: Antoine M Snijders; Jane Fridlyand; Dorus A Mans; Richard Segraves; Ajay N Jain; Daniel Pinkel; Donna G Albertson
Shaping of tumor and drug-resistant genomes by instability and selection.
Oncogene 2003;22(28):4370-9.
2003: Antoine M Snijders; Marlies E Nowee; Jane Fridlyand; Jurgen M J Piek; Josephine C Dorsman; Ajay N Jain; Daniel Pinkel; Paulus van Diest; René H M Verheijen; Donna G Albertson
Genome-wide-array-based comparative genomic hybridization reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in fallopian tube carcinoma.
Oncogene 2003;22(27):4281-6.
2003: Joris Veltman; Jane Fridlyand; Sunanda Pejavar; Adam B Olshen; James Korkola; Sandy Devries; Peter Carroll; Wen-Lin Kuo; Daniel Pinkel; Donna Albertson; Carlos Cordon-Cardo; Ajay N Jain; Frederic M Waldman
Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors.
Cancer research 2003;63(11):2872-80.
2003: Pamela L Paris; Donna G Albertson; Janneke C Alers; Armann Andaya; Peter Carroll; Jane Fridlyand; Ajay N Jain; Sherwin Kamkar; David Kowbel; Pieter-Jaap Krijtenburg; Daniel Pinkel; Fritz H Schröder; Kees J Vissers; Vivienne J E Watson; Mark F Wildhagen; Colin Collins; Herman van Dekken
High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays.
The American journal of pathology 2003;162(3):763-70.
2003: Ajay N Jain
Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine.
Journal of medicinal chemistry 2003;46(4):499-511.
2002: Adam B Olshen; Ajay N Jain
Deriving quantitative conclusions from microarray expression data.
Bioinformatics (Oxford, England) 2002;18(7):961-70.
2002: Pierre P Massion; Wen-Lin Kuo; David Stokoe; Adam B Olshen; Patrick Treseler; Koei Chin; Chira Chen; Daniel Polikoff; Ajay N Jain; Daniel Pinkel; Donna G Albertson; David M Jablons; Joe Gray
Genomic copy number analysis of non-small cell lung cancer using array comparative genomic hybridization: implications of the phosphatidylinositol 3-kinase pathway.
Cancer research 2002;62(13):3636-40.
2002: Mónica Wilhelm; Joris Veltman; Adam B Olshen; Ajay N Jain; Dan H Moore; Joe C Presti; Gyula Kovacs; Frederic M Waldman
Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer.
Cancer research 2002;62(4):957-60.
2002: Ajay N Jain; Taku Tokuyasu; Antoine M Snijders; Richard Segraves; Donna G Albertson; Daniel Pinkel
Fully automatic quantification of microarray image data.
Genome research 2002;12(2):325-32.
2001: Antoine M Snijders; N Nowak; Richard Segraves; S Blackwood; N Brown; J Conroy; G Hamilton; A K Hindle; Bing Huey; K Kimura; S Law; Kenneth Myambo; J Palmer; Bauke Ylstra; J P Yue; Joe Gray; Ajay N Jain; Daniel Pinkel; Donna G Albertson
Assembly of microarrays for genome-wide measurement of DNA copy number.
Nature genetics 2001;29(3):263-4.
2001: Ajay N Jain; Koei Chin; A L Børresen-Dale; B K Erikstein; P Eynstein Lonning; R Kaaresen; Joe Gray
Quantitative analysis of chromosomal CGH in human breast tumors associates copy number abnormalities with p53 status and patient survival.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(14):7952-7.