Photo of Shannon McWeeney, Ph.D.

Shannon McWeeney Ph.D.

  • (503) 494-8347
    • Professor of Medicine School of Medicine
    • Division Head, Bioinformatics and Computational Biology Medical Informatics and Clinical Epidemiology School of Medicine
    • Director, Translational Bioinformatics Program Oregon Clinical and Translational Research Institute
    • Biomedical Informatics Graduate Program School of Medicine
    • M.D./Ph.D. Program Committee School of Medicine

I am a statistical geneticist working at the intersection of computer science, biostatistics and genetics to develop approaches to solve research bottlenecks and novel ways to visualize and interpret information. In my work, my strengths have been in being able to “think outside the box” and my ability to rapidly synthesize information from diverse fields which has allowed me to keep pace with rapidly evolving technology and target key areas early. My work on novel computational methods and frameworks for prioritization is one of my most significant contributions to science. While these methods were initially applied to precision medicine (cancer), they have wide applicability for target identification and therapeutic prioritization for many complex traits. In 2010, I was selected as a Kavli Frontiers Fellow by the US National Academy of Sciences for my contributions.


  • Ph.D., University of California, Berkeley California 2000

Honors and awards

  • 2018 Medical Research Foundation of Oregon Mentor Award


  • "Detection of reciprocal quantitative trait loci for acute ethanol withdrawal and ethanol consumption in heterogeneous stock mice" Psychopharmacology May 2009
  • "Data integration and reproducibility for high-throughput transcriptomics" International Review of Neurobiology  2014
  • "Human Cytomegalovirus miR-UL112-3p Targets TLR2 and Modulates the TLR2/IRAK1/NFκB Signaling Pathway" PLoS Pathogens May 1 2015
  • "TandTRAQ" Bioinformatics December 2007
  • "Expression quantitative trait loci for extreme host response to influenza A in pre-collaborative cross mice" G3: Genes, Genomes, Genetics February 2012
  • "Single-nucleotide polymorphism masking" Alcohol research : current reviews  2008
  • "Modeling Host Genetic Regulation of Influenza Pathogenesis in the Collaborative Cross" PLoS Pathogens February 2013
  • "Maternal high-fat diet and obesity compromise fetal hematopoiesis" Molecular Metabolism January 1 2015
  • "Cancer stem cell tumor model reveals invasive morphology and increased phenotypical heterogeneity" Journal of Cancer Research January 1 2010
  • "Genetic factors involved in risk for methamphetamine intake and sensitization" Mammalian Genome December 2013
  • "Localization of TFIIB binding regions using serial analysis of chromatin occupancy" BMC Molecular Biology November 12 2007
  • "Defining the CREB regulon" Cell December 29 2004
  • "SNPs matter" Nature Methods September 2007
  • "The Plasmodium genome database" Nature October 3 2002
  • "Protein database and quantitative analysis considerations when integrating genetics and proteomics to compare mouse strains" Journal of Proteome Research July 1 2011
  • "A simulation framework to investigate in vitro viral infection dynamics"   2011
  • "The genetics of gene expression in complex mouse crosses as a tool to study the molecular underpinnings of behavior traits" Mammalian Genome  2014
  • "Cytomegalovirus miRNAs target secretory pathway genes to facilitate formation of the virion assembly compartment and reduce cytokine secretion" Cell Host and Microbe March 12 2014
  • "Corepressor Rcor1 is essential for murine erythropoiesis" Blood May 15 2014
  • "Locus and population specific evolution in HLA class II genes" Annals of Human Genetics January 1999
  • "Challenges in secondary analysis of high throughput screening data." Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  2014
  • "Identification of β-catenin binding regions in colon cancer cells using ChIP-Seq" Nucleic Acids Research May 11 2010
  • "Codon usage bias and base composition in MHC genes in humans and common chimpanzees" Immunogenetics  1999
  • "Characterization of the quantitative trait locus for haloperidol-induced catalepsy on distal mouse chromosome 1" Genes, Brain and Behavior March 2008
  • "Translational gene mapping of cognitive decline" Neurobiology of Aging April 2008
  • "Heritability of serum sodium concentration" Physiological Genomics February 2012
  • "A loss-of-function nonsynonymous polymorphism in the osmoregulatory TRPV4 gene is associated with human hyponatremia" Proceedings of the National Academy of Sciences of the United States of America August 18 2009
  • "Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells" Journal of Virology April 2013
  • "Renal gene and protein expression signatures for prediction of kidney disease progression" American Journal of Pathology June 2009
  • "A systems framework for vaccine design." Current Opinion in Immunology October 2013

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