Research Topics
Species | A N JainSummaryAffiliation: University of California Country: USA Publications
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Detail Information
Publications
Breast tumor copy number aberration phenotypes and genomic instabilityJane 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...
Virtual screening in lead discovery and optimizationAjay 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...- Ligand-based structural hypotheses for virtual screeningAjay 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... - Morphological similarity: a 3D molecular similarity method correlated with protein-ligand recognitionA 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... - Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engineAjay 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... - Fully automatic quantification of microarray image dataAjay 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... - Effects of protein conformation in docking: improved pose prediction through protein pocket adaptationAjay 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... - Pathway recognition and augmentation by computational analysis of microarray expression dataBarbara 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..AVAILABILITY: The software is available for academic research use free of charge by email request. SUPPLEMENTARY INFORMATION: Data used in the paper may be downloaded from http://www.jainlab.org/downloads.html.. - Parameter estimation for scoring protein-ligand interactions using negative training dataTuan 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... - Fractional genomic alteration detected by array-based comparative genomic hybridization independently predicts survival after hepatic resection for metastatic colorectal cancerKshama 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..CONCLUSIONS: Both FGA and CRS are independent predictors of survival in patients with resected hepatic colorectal cancer metastases. The greater the FGA, the more likely the patient is to survive... - Robust ligand-based modeling of the biological targets of known drugsAnn 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... - Customizing scoring functions for dockingTuan 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... - Quantitative analysis of chromosomal CGH in human breast tumors associates copy number abnormalities with p53 status and patient survivalA 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... - Mapping segmental and sequence variations among laboratory mice using BAC array CGHAntoine 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... - Genomic copy number analysis of non-small cell lung cancer using array comparative genomic hybridization: implications of the phosphatidylinositol 3-kinase pathwayPierre 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... - Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumorsPamela 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... - Scoring functions for protein-ligand dockingAjay 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... - Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based searchAjay 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.... - Genome-wide-array-based comparative genomic hybridization reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in fallopian tube carcinomaAntoine 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... - High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarraysPamela 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... - Deriving quantitative conclusions from microarray expression dataAdam 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..AVAILABILITY: The software and supplementary information are available freely to researchers at academic and non-profit institutions at http://cc.ucsf.edu/jain/public.. - Assembly of microarrays for genome-wide measurement of DNA copy numberA 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... - Bias, reporting, and sharing: computational evaluations of docking methodsAjay 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... - Physical binding pocket induction for affinity predictionJames J Langham
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158 9001, USA
J Med Chem 52:6107-25. 2009.... - Compositional structure of repetitive elements is quantitatively related to co-expression of gene pairsLawrence 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.... - A deterministic motif finding algorithm with application to the human genomeLawrence 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... - Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancerMonica 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... - Accurate and interpretable computational modeling of chemical mutagenicityJames 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... - Recommendations for evaluation of computational methodsAjay 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... - Shaping of tumor and drug-resistant genomes by instability and selectionAntoine M Snijders
Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
Oncogene 22:4370-9. 2003.... - Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumorsJoris A Veltman
Cancer Center, University of California-San Francisco, California 94143-0808, USA
Cancer Res 63:2872-80. 2003.... - Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discoveryAnn 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... - High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridizationKentaro 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... - Expression of the tumor suppressor gene ARHI in epithelial ovarian cancer is associated with increased expression of p21WAF1/CIP1 and prolonged progression-free survivalDaniel 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..CONCLUSIONS: Persistence of ARHI expression in epithelial ovarian cancers correlated with prolonged disease free survival and expression of the cyclin dependent kinase inhibitor p21(WAF1/CIP1)...