Alexander A Morgan

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. ncbi request reprint Multiplex meta-analysis of medulloblastoma expression studies with external controls
    Alexander A Morgan
    Stanford University School of Medicine, Stanford, CA 94305, USA
    Pac Symp Biocomput 19:99-109. 2014
  2. pmc Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays
    Alexander A Morgan
    Department of Biochemistry, Stanford Genome Technology Center, Stanford University, Stanford, California, USA
    J Am Med Inform Assoc 19:e21-7. 2012
  3. pmc Likelihood ratios for genome medicine
    Alexander A Morgan
    Department of Pediatrics and the Department of Medicine, Stanford University School of Medicine, 251 Campus Drive, MS 5415, Stanford, CA 94305 5479, USA
    Genome Med 2:30. 2010
  4. 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
  5. pmc Automating document classification for the Immune Epitope Database
    Peng Wang
    The La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    BMC Bioinformatics 8:269. 2007
  6. 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
  7. pmc A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation
    Purvesh Khatri
    Department of Pediatrics 2 Stanford Cardiovascular Institute 3 Department of Cardiothoracic Surgery 4 Stanford Center for Biomedical Informatics Research, Department of Medicine and 5 Institute for Immunity, Transplant, and Infection Stanford University, Stanford, CA 94305
    J Exp Med 210:2205-21. 2013
  8. 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
  9. 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
  10. 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

Collaborators

Detail Information

Publications22

  1. ncbi request reprint Multiplex meta-analysis of medulloblastoma expression studies with external controls
    Alexander A Morgan
    Stanford University School of Medicine, Stanford, CA 94305, USA
    Pac Symp Biocomput 19:99-109. 2014
    ..We demonstrate this approach on publicly available gene expression datasets from samples of medulloblastoma and normal cerebellar tissue and identify some potential new targets in the treatment of medulloblastoma. ..
  2. pmc Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays
    Alexander A Morgan
    Department of Biochemistry, Stanford Genome Technology Center, Stanford University, Stanford, California, USA
    J Am Med Inform Assoc 19:e21-7. 2012
    ..We investigated the common-disease relevant information obtained from sequencing compared with that reported from genotyping arrays...
  3. pmc Likelihood ratios for genome medicine
    Alexander A Morgan
    Department of Pediatrics and the Department of Medicine, Stanford University School of Medicine, 251 Campus Drive, MS 5415, Stanford, CA 94305 5479, USA
    Genome Med 2:30. 2010
    ..By using well-established methods of evidence based medicine, these very many parallel tests may be combined using likelihood ratios to report a post-test probability of disease for use in patient assessment...
  4. 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...
  5. pmc Automating document classification for the Immune Epitope Database
    Peng Wang
    The La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    BMC Bioinformatics 8:269. 2007
    ..Like similar projects in other knowledge domains, significant effort is spent on identifying which articles are relevant for this purpose...
  6. 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
    ....
  7. pmc A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation
    Purvesh Khatri
    Department of Pediatrics 2 Stanford Cardiovascular Institute 3 Department of Cardiothoracic Surgery 4 Stanford Center for Biomedical Informatics Research, Department of Medicine and 5 Institute for Immunity, Transplant, and Infection Stanford University, Stanford, CA 94305
    J Exp Med 210:2205-21. 2013
    ..In conclusion, we identified a CRM in transplantation that provides new opportunities for diagnosis, drug repositioning, and rational drug design. ..
  8. 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
    ....
  9. 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...
  10. 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...
  11. pmc Multiplex meta-analysis of RNA expression to identify genes with variants associated with immune dysfunction
    Alexander A Morgan
    Biomedical Informatics Graduate Training Program and Division of Systems Medicine, Department of Pediatrics, Stanford University, Stanford, California 94305 5415, USA
    J Am Med Inform Assoc 19:284-8. 2012
    ..We demonstrate a genome-wide method for the integration of many studies of gene expression of phenotypically similar disease processes, a method of multiplex meta-analysis. We use immune dysfunction as an example disease process...
  12. pmc Analysis of the genetic basis of disease in the context of worldwide human relationships and migration
    Erik Corona
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
    PLoS Genet 9:e1003447. 2013
    ..We anticipate that our findings will enable detailed analysis pertaining to the driving forces behind genetic risk differentiation...
  13. pmc Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants
    Alexander A Morgan
    Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
    BMC Bioinformatics 11:S6. 2010
    ....
  14. pmc Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes
    Keiichi Kodama
    Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 109:7049-54. 2012
    ..Genes repeatedly implicated in publicly available experimental data may have unique functionally important roles in T2D and other complex diseases...
  15. 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
    ....
  16. doi request reprint Integrating multiple 'omics' analyses identifies serological protein biomarkers for preeclampsia
    Linda Y Liu
    Department of Pediatrics, Stanford University, 1265 Welch Road, Room X 163 MS 5415, Stanford, CA 94305, USA
    BMC Med 11:236. 2013
    ..Preeclampsia (PE) is a pregnancy-related vascular disorder which is the leading cause of maternal morbidity and mortality. We sought to identify novel serological protein markers to diagnose PE with a multi-'omics' based discovery approach...
  17. pmc Identification of an IFN-γ/mast cell axis in a mouse model of chronic asthma
    Mang Yu
    Department of Pathology, Stanford University School of Medicine, Stanford, California 94305 5176, USA
    J Clin Invest 121:3133-43. 2011
    ..These findings identify a previously unsuspected IFN-γ/mast cell axis in the pathology of chronic allergic inflammation of the airways in mice...
  18. pmc FoxO6 regulates memory consolidation and synaptic function
    Dervis A M Salih
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genes Dev 26:2780-801. 2012
    ..Thus, FoxO6 may promote memory consolidation by regulating a program coordinating neuronal connectivity in the hippocampus, which could have important implications for physiological and pathological age-dependent decline in memory...
  19. doi request reprint Differentiating the roles of STAT5B and STAT5A in human CD4+ T cells
    Jennifer A Jenks
    Division of Immunology and Allergy, Stanford University, Stanford, CA 94305, USA
    Clin Immunol 148:227-36. 2013
    ..These results indicate that STAT5B and STAT5A act partly as non-redundant transcription factors and that STAT5B is more critical for Treg maintenance and function in humans. ..
  20. 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
    ....
  21. pmc Proline: the distribution, frequency, positioning, and common functional roles of proline and polyproline sequences in the human proteome
    Alexander A Morgan
    Department of Biochemistry and Genome Technology Center, Stanford University Medical School, Stanford, California, United States of America
    PLoS ONE 8:e53785. 2013
    ..We also suggest a role for proline in Kruppel-type zinc finger protein control of DNA expression, and in the nucleation and translocation of actin by the formin complex...
  22. pmc Validating pathophysiological models of aging using clinical electronic medical records
    David P Chen
    Center for Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
    J Biomed Inform 43:358-64. 2010
    ..The integration of both epidemiological and clinical data promises to create more robust models that shed new light on physiological processes...