A N Jain

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Breast tumor copy number aberration phenotypes and genomic instability
    Jane Fridlyand
    Department of Epidemiology and Biostatistics, University of California San Francisco, CA 94143, USA
    BMC Cancer 6:96. 2006
  2. ncbi Virtual screening in lead discovery and optimization
    Ajay N Jain
    University of California, San Francisco, Cancer Research Institute and Comprehensive Cancer Center, Box 0128, San Francisco, CA 94143 0128, USA
    Curr Opin Drug Discov Devel 7:396-403. 2004
  3. ncbi Ligand-based structural hypotheses for virtual screening
    Ajay N Jain
    UCSF Cancer Research Institute and Comprehensive Cancer Center, University of California, San Francisco, California 94143 0128, USA
    J Med Chem 47:947-61. 2004
  4. ncbi Morphological similarity: a 3D molecular similarity method correlated with protein-ligand recognition
    A N Jain
    UCSF Cancer Center, San Francisco, CA 94143 0128, USA
    J Comput Aided Mol Des 14:199-213. 2000
  5. ncbi Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine
    Ajay N Jain
    UCSF Cancer Research Institute and Comprehensive Cancer Center, University of California, San Francisco, California 94143 0128, USA
    J Med Chem 46:499-511. 2003
  6. pmc Fully automatic quantification of microarray image data
    Ajay N Jain
    Comprehensive Cancer Center, University of California, San Francisco, California 94143, USA
    Genome Res 12:325-32. 2002
  7. pmc Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation
    Ajay N Jain
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158 9001, USA
    J Comput Aided Mol Des 23:355-74. 2009
  8. ncbi Pathway recognition and augmentation by computational analysis of microarray expression data
    Barbara A Novak
    UCSF Cancer Research Institute and Comprehensive Cancer Center, University of California at San Francisco San Francisco, CA 94143 0128, USA
    Bioinformatics 22:233-41. 2006
  9. ncbi Parameter estimation for scoring protein-ligand interactions using negative training data
    Tuan A Pham
    Cancer Research Institute, Department of Biopharmaceutical Sciences, University of California, San Francisco, 2340 Sutter Street, San Francisco, California 94143 0128, USA
    J Med Chem 49:5856-68. 2006
  10. ncbi Fractional genomic alteration detected by array-based comparative genomic hybridization independently predicts survival after hepatic resection for metastatic colorectal cancer
    Kshama R Mehta
    Comprehensive Cancer Center, Department of Surgery, University of California San Francisco, 2340 Sutter Street, San Francisco, CA 94143, USA
    Clin Cancer Res 11:1791-7. 2005

Collaborators

Detail Information

Publications34

  1. pmc Breast tumor copy number aberration phenotypes and genomic instability
    Jane Fridlyand
    Department of Epidemiology and Biostatistics, University of California San Francisco, CA 94143, USA
    BMC Cancer 6:96. 2006
    ..g. those involved in mitosis, replication, repair, and telomeres) are rarely mutated in chromosomally unstable sporadic tumors, even though such mutations are associated with some heritable cancer prone syndromes...
  2. ncbi Virtual screening in lead discovery and optimization
    Ajay N Jain
    University of California, San Francisco, Cancer Research Institute and Comprehensive Cancer Center, Box 0128, San Francisco, CA 94143 0128, USA
    Curr Opin Drug Discov Devel 7:396-403. 2004
    ..This review will discuss recent advances in both domains of virtual screening, including theoretical and practical advances and the implications for their application...
  3. ncbi Ligand-based structural hypotheses for virtual screening
    Ajay N Jain
    UCSF Cancer Research Institute and Comprehensive Cancer Center, University of California, San Francisco, California 94143 0128, USA
    J Med Chem 47:947-61. 2004
    ..The methods are practically applicable for rational design of ligands and for high-throughput virtual screening and offer competitive performance to many structure-based docking algorithms...
  4. ncbi Morphological similarity: a 3D molecular similarity method correlated with protein-ligand recognition
    A N Jain
    UCSF Cancer Center, San Francisco, CA 94143 0128, USA
    J Comput Aided Mol Des 14:199-213. 2000
    ..Further, MS agrees with crystallographic observation of bound ligand states, independent of information about bound states. MS is efficient to compute and can be practically applied to large libraries of compounds...
  5. ncbi Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine
    Ajay N Jain
    UCSF Cancer Research Institute and Comprehensive Cancer Center, University of California, San Francisco, California 94143 0128, USA
    J Med Chem 46:499-511. 2003
    ..Docking time was roughly linear in number of rotatable bonds, beginning with a few seconds for rigid molecules and adding approximately 10 s per rotatable bond...
  6. pmc Fully automatic quantification of microarray image data
    Ajay N Jain
    Comprehensive Cancer Center, University of California, San Francisco, California 94143, USA
    Genome Res 12:325-32. 2002
    ..The software, called, runs on Windows platforms and is available free of charge for academic use...
  7. pmc Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation
    Ajay N Jain
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158 9001, USA
    J Comput Aided Mol Des 23:355-74. 2009
    ..Consideration of the best of two pose families (from alternate scoring regimes) yields a 75% mean success rate...
  8. ncbi Pathway recognition and augmentation by computational analysis of microarray expression data
    Barbara A Novak
    UCSF Cancer Research Institute and Comprehensive Cancer Center, University of California at San Francisco San Francisco, CA 94143 0128, USA
    Bioinformatics 22:233-41. 2006
    ..QPACA supports data visualization and both fine- and coarse-grained specifications, but, more importantly, addresses the problems of pathway recognition and pathway augmentation...
  9. ncbi Parameter estimation for scoring protein-ligand interactions using negative training data
    Tuan A Pham
    Cancer Research Institute, Department of Biopharmaceutical Sciences, University of California, San Francisco, 2340 Sutter Street, San Francisco, California 94143 0128, USA
    J Med Chem 49:5856-68. 2006
    ..Maximal enrichment of true ligands over nonligands exceeded 20-fold in over 80% of cases, with enrichment of greater than 100-fold in over 50% of cases...
  10. ncbi Fractional genomic alteration detected by array-based comparative genomic hybridization independently predicts survival after hepatic resection for metastatic colorectal cancer
    Kshama R Mehta
    Comprehensive Cancer Center, Department of Surgery, University of California San Francisco, 2340 Sutter Street, San Francisco, CA 94143, USA
    Clin Cancer Res 11:1791-7. 2005
    ..Identification of molecular markers that predict patients at highest risk for recurrence may help to target further therapy...
  11. ncbi Robust ligand-based modeling of the biological targets of known drugs
    Ann E Cleves
    UCSF Cancer Research Institute and Department of Biopharmaceutical Sciences, University of California, San Francisco, California 94143, USA
    J Med Chem 49:2921-38. 2006
    ..Predicted activities derived from crossing drugs against modeled targets identified a number of known side effects, drug specificities, and drug-drug interactions that have a rational basis in molecular structure...
  12. pmc Customizing scoring functions for docking
    Tuan A Pham
    University of California, San Francisco, Box 0128, San Francisco, CA 94143 0128, USA
    J Comput Aided Mol Des 22:269-86. 2008
    ..Analysis of the changes to the scoring function suggest that modifications can be learned that are related to protein-specific features such as active-site mobility...
  13. pmc Quantitative analysis of chromosomal CGH in human breast tumors associates copy number abnormalities with p53 status and patient survival
    A N Jain
    UCSF Cancer Center, University of California, San Francisco, Box 0128, San Francisco, CA 94143-0128, USA
    Proc Natl Acad Sci U S A 98:7952-7. 2001
    ..The 9q and 5q losses suggest the possibility of gene products involved in breast cancer progression. The analytical techniques are general and also are applicable to the analysis of array-based expression data...
  14. pmc Mapping segmental and sequence variations among laboratory mice using BAC array CGH
    Antoine M Snijders
    Cancer Research Institute, University of California San Francisco, San Francisco, California 94143, USA
    Genome Res 15:302-11. 2005
    ..1) distinguish homozygous and heterozygous regions of the genome in interspecific backcross mice, providing an efficient method for genotyping progeny of backcrosses...
  15. ncbi Genomic copy number analysis of non-small cell lung cancer using array comparative genomic hybridization: implications of the phosphatidylinositol 3-kinase pathway
    Pierre P Massion
    UCSF Comprehensive Cancer Center, University of California, San Francisco, California 94143 0808, USA
    Cancer Res 62:3636-40. 2002
    ..75), suggesting that these copy number increases contribute to activation of PI3K signaling in SqCas of the lung...
  16. ncbi Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors
    Pamela L Paris
    Comprehensive Cancer Center, University of California at San Francisco, 94115, USA
    Hum Mol Genet 13:1303-13. 2004
    ..Moreover, comparison with an independent set of metastases revealed approximately 40 candidate markers associated with metastatic potential. Copy number aberrations at these loci may define metastatic genotypes...
  17. ncbi Scoring functions for protein-ligand docking
    Ajay N Jain
    UCSF Cancer Research Institute, Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143 0218, USA
    Curr Protein Pept Sci 7:407-20. 2006
    ..Generally, performance is not good enough to correctly rank among true ligands. Strategies for improvement are discussed...
  18. ncbi Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search
    Ajay N Jain
    Department of Biopharmaceutical Sciences, UCSF Cancer Research Institute, University of California San Francisco, Box 0128, San Francisco, CA 94143 0128, USA
    J Comput Aided Mol Des 21:281-306. 2007
    ....
  19. ncbi Genome-wide-array-based comparative genomic hybridization reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in fallopian tube carcinoma
    Antoine M Snijders
    Cancer Research Institute, University of California San Francisco, San Francisco, CA, USA
    Oncogene 22:4281-6. 2003
    ..The FTC were remarkably homogeneous, with some recurrent aberrations occurring in more than 70% of samples, which suggests a stereotyped pattern of tumor evolution...
  20. pmc High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays
    Pamela L Paris
    Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California 94115, USA
    Am J Pathol 162:763-70. 2003
    ..We present a straightforward protocol and demonstrate the utility of archived tissue for array comparative genomic hybridization with a 2400 element BAC array that provides high-resolution detection of both deletions and amplifications...
  21. ncbi Deriving quantitative conclusions from microarray expression data
    Adam B Olshen
    Comprehensive Cancer Center, Cancer Research Institute, and Department of Laboratory Medicine, University of California, San Francisco, CA 94143 0128, USA
    Bioinformatics 18:961-70. 2002
    ..While many methods have been developed to analyze such data, most have been visualization-based. Methods that yield quantitative conclusions have been diverse and complex...
  22. ncbi Assembly of microarrays for genome-wide measurement of DNA copy number
    A M Snijders
    Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94143, USA
    Nat Genet 29:263-4. 2001
    ..d. of log2 ratios=0.05-0.10) in cell lines and clinical material, so that we can reliably detect and quantify high-level amplifications and single-copy alterations in diploid, polyploid and heterogeneous backgrounds...
  23. ncbi Bias, reporting, and sharing: computational evaluations of docking methods
    Ajay N Jain
    University of California San Francisco, Box 0128, San Francisco, CA 94143 0128, USA
    J Comput Aided Mol Des 22:201-12. 2008
    ..This paper presents detailed examples of pitfalls in each area and makes recommendations as to best practices...
  24. pmc Physical binding pocket induction for affinity prediction
    James J Langham
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158 9001, USA
    J Med Chem 52:6107-25. 2009
    ....
  25. ncbi Compositional structure of repetitive elements is quantitatively related to co-expression of gene pairs
    Lawrence S Hon
    Cancer Research Institute, University of California, 2340 Sutter Street S 336, Box 0128, San Francisco, CA 94143 0128, USA
    J Mol Biol 332:305-10. 2003
    ....
  26. ncbi A deterministic motif finding algorithm with application to the human genome
    Lawrence S Hon
    UCSF Cancer Research Institute and Comprehensive Cancer Center, University of California San Francisco, CA, USA
    Bioinformatics 22:1047-54. 2006
    ..MaMF is a very fast algorithm, suitable for application to large numbers of interesting gene sets...
  27. ncbi Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer
    Monica Wilhelm
    Cancer Center and Departments of Laboratory Medicine and Urology, University of California San Francisco, San Francisco, California 94143 0808, USA
    Cancer Res 62:957-60. 2002
    ..These results indicate that array-based CGH is capable of diagnosing the vast majority of renal cell carcinomas based on their genetic profiles...
  28. pmc Accurate and interpretable computational modeling of chemical mutagenicity
    James J Langham
    Cancer Research Institute, University of California, San Francisco, 2340 Sutter Street, San Francisco, California 94143 0128, USA
    J Chem Inf Model 48:1833-9. 2008
    ..While we have focused on chemical mutagenicity in demonstrating this method, we anticipate that it may be more generally useful in modeling other molecular properties such as other types of chemical toxicity...
  29. pmc Recommendations for evaluation of computational methods
    Ajay N Jain
    University of California San Francisco, Box 0128, San Francisco, CA 94143 0128, USA
    J Comput Aided Mol Des 22:133-9. 2008
    ..Here we propose a modest beginning, with recommendations for requirements on statistical reporting, requirements for data sharing, and best practices for benchmark preparation and usage...
  30. ncbi Shaping of tumor and drug-resistant genomes by instability and selection
    Antoine M Snijders
    Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143 0808, USA
    Oncogene 22:4370-9. 2003
    ....
  31. ncbi Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors
    Joris A Veltman
    Cancer Center, University of California San Francisco, California 94143 0808, USA
    Cancer Res 63:2872-80. 2003
    ....
  32. ncbi Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery
    Ann E Cleves
    BioPharmics LLC, 36 Avila Road, San Mateo, CA 94402, USA
    J Comput Aided Mol Des 22:147-59. 2008
    ..We propose specific strategies to explicitly address the problems posed by inductive bias considerations...
  33. ncbi High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization
    Kentaro Nakao
    Second Department of Surgery, Showa University School of Medicine, Tokyo, Japan
    Carcinogenesis 25:1345-57. 2004
    ..Array-based CGH was also able to identify DNA copy number changes in MSI-H tumors...
  34. ncbi Expression of the tumor suppressor gene ARHI in epithelial ovarian cancer is associated with increased expression of p21WAF1/CIP1 and prolonged progression-free survival
    Daniel G Rosen
    Department of Pathology, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
    Clin Cancer Res 10:6559-66. 2004
    ..To determine the relevance of these observations to clinical cancer, we have now measured ARHI expression in normal, benign and malignant ovarian tissues using immunohistochemistry and in situ hybridization...