Joel T Dudley

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Translational bioinformatics in the cloud: an affordable alternative
    Joel T Dudley
    Program in Biomedical Informatics, Stanford University School of Medicine, 251 Campus Drive, Stanford, CA 94305, USA
    Genome Med 2:51. 2010
  2. pmc FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease
    Rong Chen
    Stanford Center for Biomedical Informatics Research, 251 Cmpus Drive, Stanford, CA 94305, USA
    Genome Biol 9:R170. 2008
  3. pmc Phased whole-genome genetic risk in a family quartet using a major allele reference sequence
    Frederick E Dewey
    Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
    PLoS Genet 7:e1002280. 2011
  4. pmc Content-based microarray search using differential expression profiles
    Jesse M Engreitz
    Department of Bioengineering, Stanford University School of Medicine, CA, USA
    BMC Bioinformatics 11:603. 2010
  5. pmc Discovery and preclinical validation of drug indications using compendia of public gene expression data
    Marina Sirota
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 251 Campus Drive, Stanford, CA 94305 5415, USA
    Sci Transl Med 3:96ra77. 2011
  6. pmc Integrative approach to pain genetics identifies pain sensitivity loci across diseases
    David Ruau
    Department of Anesthesia, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Comput Biol 8:e1002538. 2012
  7. pmc Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases
    Rong Chen
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Genet 8:e1002621. 2012
  8. pmc ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression
    Jesse M Engreitz
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 27:3317-8. 2011
  9. pmc Systematic functional regulatory assessment of disease-associated variants
    Konrad J Karczewski
    Biomedical Informatics Training Program, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 110:9607-12. 2013
  10. pmc Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions
    Rong Chen
    Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Comput Biol 6:. 2010

Detail Information

Publications28

  1. pmc Translational bioinformatics in the cloud: an affordable alternative
    Joel T Dudley
    Program in Biomedical Informatics, Stanford University School of Medicine, 251 Campus Drive, Stanford, CA 94305, USA
    Genome Med 2:51. 2010
    ....
  2. pmc FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease
    Rong Chen
    Stanford Center for Biomedical Informatics Research, 251 Cmpus Drive, Stanford, CA 94305, USA
    Genome Biol 9:R170. 2008
    ..We propose to use the more than 200,000 microarray studies in the Gene Expression Omnibus to systematically prioritize candidate SNPs from GWASs...
  3. pmc Phased whole-genome genetic risk in a family quartet using a major allele reference sequence
    Frederick E Dewey
    Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
    PLoS Genet 7:e1002280. 2011
    ..These ethnicity-specific, family-based approaches to interpretation of genetic variation are emblematic of the next generation of genetic risk assessment using whole-genome sequencing...
  4. pmc Content-based microarray search using differential expression profiles
    Jesse M Engreitz
    Department of Bioengineering, Stanford University School of Medicine, CA, USA
    BMC Bioinformatics 11:603. 2010
    ....
  5. pmc Discovery and preclinical validation of drug indications using compendia of public gene expression data
    Marina Sirota
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 251 Campus Drive, Stanford, CA 94305 5415, USA
    Sci Transl Med 3:96ra77. 2011
    ..This computational method provides a systematic approach for repositioning established drugs to treat a wide range of human diseases...
  6. pmc Integrative approach to pain genetics identifies pain sensitivity loci across diseases
    David Ruau
    Department of Anesthesia, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Comput Biol 8:e1002538. 2012
    ..This data-derived list of pain gene candidates enables additional focused and efficient biological studies validating additional candidates...
  7. pmc Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases
    Rong Chen
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Genet 8:e1002621. 2012
    ..Our results indicate that the differential frequencies of T2D risk alleles may contribute to the observed disparity in T2D incidence rates across ethnic populations...
  8. pmc ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression
    Jesse M Engreitz
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 27:3317-8. 2011
    ..This analysis identifies statistical links to similar expression experiments from the vast array of publicly available data on diseases, drugs, phenotypes and other experimental conditions...
  9. pmc Systematic functional regulatory assessment of disease-associated variants
    Konrad J Karczewski
    Biomedical Informatics Training Program, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 110:9607-12. 2013
    ..Thus, using this integrative approach, we provide a unique means to assign putative function to many disease-associated SNPs...
  10. pmc Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions
    Rong Chen
    Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Comput Biol 6:. 2010
    ....
  11. pmc Human genomic disease variants: a neutral evolutionary explanation
    Joel T Dudley
    Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, California 94305, USA
    Genome Res 22:1383-94. 2012
    ....
  12. pmc Personal omics profiling reveals dynamic molecular and medical phenotypes
    Rui Chen
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Cell 148:1293-307. 2012
    ..This study demonstrates that longitudinal iPOP can be used to interpret healthy and diseased states by connecting genomic information with additional dynamic omics activity...
  13. pmc Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets
    Silpa Suthram
    Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
    PLoS Comput Biol 6:e1000662. 2010
    ....
  14. ncbi request reprint Disease risk factors identified through shared genetic architecture and electronic medical records
    Li Li
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, Stanford, CA 94305, USA
    Sci Transl Med 6:234ra57. 2014
    ..Disease-trait associations identify traits that could serve as future prognostics, if validated through EMR and subsequent prospective trials. ..
  15. pmc Exploiting drug-disease relationships for computational drug repositioning
    Joel T Dudley
    Stanford University, Stanford, CA, USA
    Brief Bioinform 12:303-11. 2011
    ..Newer algorithms for computational drug repositioning will likely span these two axes, will take advantage of newer types of molecular measurements, and will certainly play a role in reducing the global burden of disease...
  16. pmc Identification of cell surface targets through meta-analysis of microarray data
    Henry Haeberle
    Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
    Neoplasia 14:666-9. 2012
    ..This bioinformatics method has broad utility for the identification of accessible molecular targets in a variety of cancers and will enable probe development for guided resection...
  17. pmc Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease
    Joel T Dudley
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 251 Campus Drive, Stanford, CA 94305 5415, USA
    Sci Transl Med 3:96ra76. 2011
    ..These findings suggest that topiramate might serve as a therapeutic option for IBD in humans and support the use of public molecular data and computational approaches to discover new therapeutic options for disease...
  18. pmc An integrative method for scoring candidate genes from association studies: application to warfarin dosing
    Nicholas P Tatonetti
    Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, CA, USA
    BMC Bioinformatics 11:S9. 2010
    ..We then define a summary score for each gene based on allele frequencies and train linear and logistic regression classifiers to predict drug response phenotypes...
  19. pmc Computational prediction and experimental validation associating FABP-1 and pancreatic adenocarcinoma with diabetes
    Ravi N Sharaf
    Department of Gastroenterology and Hepatology, Stanford University School of Medicine, Alway Building, Room M211, 300 Pasteur Drive, MC 5187, Stanford, CA 94305 5187, USA
    BMC Gastroenterol 11:5. 2011
    ..We identified fatty acid binding protein-1 (FABP-1) as one of several candidates. The primary aim of this pilot study was to experimentally validate the predicted association between FABP-1 with PaC and PaC with diabetes...
  20. pmc STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud
    Konrad J Karczewski
    Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, California, United States of America Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 9:e84860. 2014
    ..We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2. ..
  21. pmc Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery
    Joel T Dudley
    Program in Biomedical Informatics, Stanford University School of Medicine
    Mol Biol Evol 29:2087-94. 2012
    ....
  22. pmc Clinical assessment incorporating a personal genome
    Euan A Ashley
    Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
    Lancet 375:1525-35. 2010
    ..The cost of genomic information has fallen steeply, but the clinical translation of genetic risk estimates remains unclear. We aimed to undertake an integrated analysis of a complete human genome in a clinical context...
  23. pmc Quantifying multi-ethnic representation in genetic studies of high mortality diseases
    Rong Chen
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
    AMIA Summits Transl Sci Proc 2012:11-8. 2012
    ..Our results demonstrate that diseases killing most Americans are still lacking genetic studies across ethnicities...
  24. doi request reprint Drug discovery in a multidimensional world: systems, patterns, and networks
    Joel T Dudley
    Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, CA, USA
    J Cardiovasc Transl Res 3:438-47. 2010
    ..When available, specific applications to cardiovascular drug discovery are highlighted and discussed...
  25. pmc Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays
    David P Chen
    Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, CA 94305, USA
    BMC Bioinformatics 11:S4. 2010
    ..Knowledge of these factors could be used to improve assessment of disease severity and help to refine strategies for diagnosis and monitoring disease progression...
  26. pmc Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets
    David Ruau
    Division of Systems Medicine, Department of Pediatrics, Stanford, CA 94305, USA
    J Biomed Inform 44:S39-43. 2011
    ....
  27. pmc Dynamism in gene expression across multiple studies
    Alexander A Morgan
    Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
    Physiol Genomics 40:128-40. 2010
    ....