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

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


  • "Gender-Specific Effects of Selection for Drinking in the Dark on the Network Roles of Coding and Noncoding RNAs." Alcoholism: Clinical and Experimental Research  In: , Vol. 42, No. 8, 01.08.2018, p. 1454-1465.
  • "Synthetic lethality of TNK2 inhibition in PTPN11-mutant leukemia." Science Signaling In: , Vol. 11, No. 539, eaao5617, 17.07.2018.
  • "Network-based predictors of progression in head and neck squamous cell carcinoma." Frontiers in Genetics In: , Vol. 9, No. MAY, 183, 29.05.2018.
  • "Targeting of colony-stimulating factor 1 receptor (CSF1R) in the CLL microenvironment yields antineoplastic activity in primary patient samples." Oncotarget In: , Vol. 9, No. 37, 15.05.2018, p. 24576-24589.
  • "LSD1 activates a lethal prostate cancer gene network independently of its demethylase function." Proceedings of the National Academy of Sciences of the United States of America In: , Vol. 115, No. 18, 01.05.2018, p. E4179-E4188.
  • "A single-cell approach to the elusive latent human cytomegalovirus transcriptome." mBio  In: , Vol. 9, No. 3, e01001-18, 01.05.2018.
  • "Working Memory and Vigilance as Multivariate Endophenotypes Related to Common Genetic Risk for Attention-Deficit/Hyperactivity Disorder." Journal of the American Academy of Child and Adolescent Psychiatry  In: , Vol. 57, No. 3, 01.03.2018, p. 175-182.
  • "Characterization of the leukemogenic potential of distal cytoplasmic CSF3R truncation and missense mutations." Leukemia In: , Vol. 31, No. 12, 01.12.2017, p. 2752-2760.
  • "Comprehensive definition of human immunodominant CD8 antigens in tuberculosis." npj Vaccines In: , Vol. 2, No. 1, 8, 01.12.2017.
  • "Extensive Homeostatic T Cell Phenotypic Variation within the Collaborative Cross." Cell Reports In: , Vol. 21, No. 8, 21.11.2017, p. 2313-2325.
  • "Recurrent cyclin D2 mutations in myeloid neoplasms." Leukemia In: , Vol. 31, No. 9, 01.09.2017, p. 2005-2008.
  • "Unpaired extracellular cysteine mutations of CSF3R mediate gain or loss of function." Cancer Research In: , Vol. 77, No. 16, 15.08.2017, p. 4258-4267.
  • "NFAT5 and SLC4A10 loci associate with plasma osmolality." Journal of the American Society of Nephrology In: , Vol. 28, No. 8, 01.08.2017, p. 2311-2321.
  • "Oas1b-dependent immune transcriptional profiles of west nile virus infection in the collaborative cross." G3: Genes, Genomes, Genetics  In: , Vol. 7, No. 6, 01.06.2017, p. 1665-1682.
  • "Alignment of the transcriptome with individual variation in animals selectively bred for High Drinking-In-the-Dark (HDID)." Alcohol  In: , Vol. 60, 01.05.2017.
  • "A microRNA screen identifies the Wnt signaling pathway as a regulator of the interferon response during flavivirus infection." Journal of Virology In: , Vol. 91, No. 8, e02388-16, 01.04.2017.
  • "Identification of Interleukin-1 by Functional Screening as a Key Mediator of Cellular Expansion and Disease Progression in Acute Myeloid Leukemia." Cell Reports  In: , Vol. 18, No. 13, 28.03.2017, p. 3204-3218.
  • "REST corepressors RCOR1 and RCOR2 and the repressor INSM1 regulate the proliferation- differentiation balance in the developing brain." Proceedings of the National Academy of Sciences of the United States of America  In: , Vol. 114, No. 3, 17.01.2017, p. E406-E415.
  • "Integrated functional and mass spectrometry-based flow cytometric phenotyping to describe the immune microenvironment in acute myeloid leukemia." Journal of Immunological Methods In: , 01.01.2017.
  • "Effects of selection for ethanol preference on gene expression in the nucleus accumbens of HS-CC mice." Genes, Brain and Behavior In: , 2017.
  • "On the relationships in rhesus macaques between chronic ethanol consumption and the brain transcriptome." Addiction Biology  In: , 2017.
  • "Identification of Hip BMD Loss and Fracture Risk Markers Through Population-Based Serum Proteomics." Journal of Bone and Mineral Research In: , 2017.
  • "Integration of genomic, transcriptomic and functional profiles of aggressive osteosarcomas across multiple species." Oncotarget  In: , Vol. 8, No. 44, 2017, p. 76241-76256.
  • "Evidence-Based Precision Oncology with the Cancer Targetome." Trends in Pharmacological Sciences In: , 2017.
  • "A Mouse Model of Chronic West Nile Virus Disease." PLoS Pathogens In: , Vol. 12, No. 11, e1005996, 01.11.2016.
  • "The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus." BMC Systems Biology In: , Vol. 10, No. 1, 93, 23.09.2016.
  • "Cover Image, Volume 171B, Number 6, September 2016." American Journal of Medical Genetics, Part B: Neuropsychiatric Genetics  In: , Vol. 171, No. 6, 01.09.2016, p. 1.
  • "Does the urinary microbiome play a role in urgency urinary incontinence and its severity?" Frontiers in cellular and infection microbiology  In: , Vol. 6, No. JUL, 78, 27.07.2016.
  • "HitWalker2 : Visual analytics for precision medicine and beyond." Bioinformatics  In: , Vol. 32, No. 8, 15.04.2016, p. 1253-1255.
  • "IL-10 and integrin signaling pathways are associated with head and neck cancer progression." BMC Genomics  In: , Vol. 17, No. 1, 38, 08.01.2016.

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