Computational Scientist
Computational Scientist


Hugh Mitchell's research involves using computational analysis of omics data to identify key components of biological systems. His analyses focus on network inference and topology and multi-omic data integration and visualization. His work involves data from a diverse array of prokaryotic and eukaryotic organisms. Having a strong background in biology and extensive experience with computational analysis, Mitchell firmly believes in tight partnerships between biologists and computationalists.

Research Interest

  • Network inference from high-throughput data
  • Network topology
  • Multi-omic data integration


  • PhD in Molecular Biology, Mayo Graduate School
  • BS in Molecular Biology, Brigham Young University

Awards and Recognitions

  • Systems Biology Verification IMPROVER challenge, 2013



  • Mensch A.C., H.D. Mitchell, L.M. Markillie, E.D. Laudadio, J.K. Hedlund Orbeck, A. Dohnalkova, M.P. Schwartz, R.J. Hamers, and G. Orr. 2020. “Subtoxic dose of lithium cobalt oxide nanosheets impacts critical molecular pathways in trout gill epithelial cells.” Environmental Science: Nano, in press.
  • Daly P., M. Peng, H.D. Mitchell, Y. Kim, C.K. Ansong, H.M. Brewer, and P. De Gijsel, et al. 2020. "Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation." Environmental Microbiology 22, no. 3:1154-1166. PNNL-SA-150305. doi:10.1111/1462-2920.14907.
  • Nakayasu E.S., F. Syed, S. Tersey, M.A. Gritsenko, H.D. Mitchell, C. Chan, and J. Turatsinze, et al. 2020. "Comprehensive proteomics analysis of stressed human islets identifies GDF15 as a target for type 1 diabetes intervention." Cell Metabolism 31, no. 2:363-374.e6. PNNL-SA-150166. doi:10.1016/j.cmet.2019.12.005.
  • Piehowski P.D., Y. Zhu, L.M. Bramer, K.G. Stratton, R. Zhao, D.J. Orton, and R.J. Moore, et al. 2020. "Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-µm spatial resolution." Nature Communications 11, no. 1: Article No. 8. PNNL-SA-138884. doi:10.1038/s41467-019-13858-z.


  • Dalcin-Martins P., J. Frank, H.D. Mitchell, L. Markillie, and M.J. Wilkins. 2019. "Wetland Sediments Host Diverse Microbial Taxa Capable of Cycling Alcohols." Applied and Environmental Microbiology 8, no. 12. PNNL-SA-147002. doi:10.1128/AEM.00189-19.
  • Zhang J., H.D. Mitchell, L.M. Markillie, M.J. Gaffrey, G. Orr, and J. Schilling. 2019. “Reference genes for accurate normalization of gene expression in wood-decomposing fungi.” Fungal Genetics and Biology 123, February 2019:33-40. PNNL-SA-152387 doi:10.1016/j.fgb.2018.11.005. 
  • Dai Y., H.A. Ogilvie, Y. Liu, M. Huang, L. Markillie, H.D. Mitchell, and E.J. Borrego, et al. 2019. "Rosette Core Fungal Resistance in Arabidopsis thaliana." Planta 250. PNNL-SA-142134. doi:10.1007/s00425-019-03273-5.
  • Mitchell H.D., A.J. Eisfeld, K.G. Stratton, N.C. Heller, L.M. Bramer, J. Wen, and J.E. McDermott, et al. 2019. "The Role of EGFR in Influenza Pathogenicity: Multiple Network-based Approaches To Identify a Key Regulator of Non-Lethal Infections." Frontiers in Cell and Developmental Biology 7. PNNL-SA-142083. doi:10.3389/fcell.2019.00200.


  • Menachery V.D., A. Schafer, K.E. Burnum-Johnson, H.D. Mitchell, A.J. Eisfeld-Fenney, K.B. Walters, and C.D. Nicora, et al. 2018. "MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape." Proceedings of the National Academy of Sciences of the United States of America 115, no. 5:E1012-E1021. PNNL-SA-126254. doi:10.1073/pnas.1706928115.
  • Menachery V.D., L. Gralinski, H.D. Mitchell, K. Dinnon III, S.R. Leist, B. Yount, and E. Mcanarney, et al. 2018. "Combination attenuation offers strategy for live-attenuated coronavirus vaccines." Journal of Virology 92, no. 17:e00710-18. PNNL-SA-134212. doi:10.1128/JVI.00710-18.
  • Moghieb A.M., G. Clair, H.D. Mitchell, J. Kitzmiller, E.M. Zink, Y. Kim, and V.A. Petyuk, et al. 2018. "Time-resolved Proteome Profiling of Normal Lung Development." American Journal of Physiology-Lung Cellular and Molecular Physiology 315, no. 1:L11-L24. PNNL-SA-127218. doi:10.1152/ajplung.00316.2017.


  • Menachery V.D., H.D. Mitchell, A. Cockrell, L. Gralinski, B. Yount, R.L. Graham, and E. Mcanarney, et al. 2017. "MERS-CoV Accessory ORFs play key role for infection and pathogenesis." mBio 8, no. 4: Article No. e00665-17. PNNL-SA-126255. doi:10.1128/mBio.00665-17.
  • Menachery V.D., L. Gralinski, H.D. Mitchell, K. Dinnon III, S.R. Leist, B. Yount, and R.L. Graham, et al. 2017. "Middle East Respiratory Syndrome Coronavirus Nonstructural Protein 16 is Necessary for Interferon Resistance and Viral Pathogenesis." mSphere 2, no. 6: Article No. e00346-17. PNNL-SA-128149. doi:10.1128/mSphere.00346-17.
  • Orellana R., G. Chaput, L. Markillie, H.D. Mitchell, M.J. Gaffrey, G. Orr, and K.M. Deangelis. 2017. "Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium." PLoS One 12, no. 10:e0186440. PNNL-SA-131719. doi:10.1371/journal.pone.0186440.


  • McDermott J.E., H.D. Mitchell, L. Gralinski, A.J. Eisfeld, L. Josset, A. Bankhead, and G. Neumann, et al. 2016. "The Effect of inhibition of PP1 and TNFa signaling on pathogenesis of SARS coronavirus." BMC Systems Biology 10, no. 1:93. PNNL-SA-118784. doi:10.1186/s12918-016-0336-6
  • Mitchell H.D., L. Markillie, W.B. Chrisler, M.J. Gaffrey, D. Hu, C.J. Szymanski, and Y. Xie, et al. 2016. "Cells Respond to Distinct Nanoparticle Properties with Multiple Strategies as Revealed by Single-Cell RNA-Seq." ACS Nano 10, no. 11:10173-10185. PNNL-SA-121323. doi:10.1021/acsnano.6b05452
  • Vartanian K.B., H.D. Mitchell, S. Stevens, V.K. Conrad, J.E. McDermott, and M. Stenzel-Poore. 2015. "CpG preconditioning regulates miRNA expression that modulates genomic reprogramming associated with neuroprotection against ischemic injury." Journal of Cerebral Blood Flow and Metabolism 35, no. 2:257-266. PNWD-SA-10412. doi:10.1038/jcbfm.2014.193.


  • Aevermann B., B.E. Pickett, S. Kumar, E.B. Klem, S. Agnihothram, P.S. Askovich, and A. Bankhead, et al. 2014. "A Comprehensive Collection of Systems Biology Data Characterizing the Host Response to Viral Infection." Scientific Data 1. PNNL-SA-101269. doi:10.1038/sdata.2014.33
  • Eraso J.M., L.M. Markillie, H.D. Mitchell, R.C. Taylor, G. Orr, and W. Margolin. 2014. "The highly conserved MraZ protein is a transcriptional regulator in Escherichia coli." Journal of Bacteriology 196, no. 11:2053-2066. PNNL-SA-98128. doi:10.1128/JB.01370-13
  • Welkie D.G., X. Zhang, L.M. Markillie, R.C. Taylor, G. Orr, J.M. Jacobs, and K. Bhide, et al. 2014. "Transcriptomic and proteomic dynamics in the metabolism of a diazotrophic cyanobacterium, Cyanothece sp. PCC 7822 during a diurnal light-dark cycle." BMC Genomics 15. PNNL-SA-104956.


  • Kim Y., B. Schmidt, A.S. Kidwai, M.B. Jones, B.L. Deatherage, H.M. Brewer, and H.D. Mitchell, et al. 2013. "Salmonella Modulates Metabolism During Growth under Conditions that Induce Expression of Virulence Genes." Molecular Biosystems 9, no. 6:1522-1534. PNNL-SA-89810. doi:10.1039/C3MB25598K
  • McDermott J.E., J. Wang, H.D. Mitchell, B.M. Webb-Robertson, R.P. Hafen, J.A. Ramey, and K.D. Rodland. 2013. "Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data." Expert Opinion on Medical Diagnostics 7, no. 1:37-51. PNNL-SA-86517. doi:10.1517/17530059.2012.718329
  • Mitchell H.D., A.J. Eisfeld, A. Sims, J.E. McDermott, M.M. Matzke, B.M. Webb-Robertson, and S.C. Tilton, et al. 2013. "A Network Integration Approach to Predict Conserved Regulators Related to Pathogenicity of Influenza and SARS-CoV Respiratory Viruses." PLoS One 8, no. 7:e69374. PNNL-SA-92748. doi:10.1371/journal.pone.0069374
  • Ansong C., A.C. Rutledge, H.D. Mitchell, S. Chauhan, M.B. Jones, Y. Kim, and K. Mcateer, et al. 2013. "A multi-omic systems approach to elucidating Yersinia virulence mechanisms." Molecular Biosystems 9, no. 1:44-54. PNNL-SA-89164. doi:10.1039/C2MB25287B


  • McDermott J.E., K.B. Vartanian, H.D. Mitchell, S. Stevens, A.P. Sanfilippo, and M. Stenzel-Poore. 2012. "Identification and Validation of Ifit1 as an Important Innate Immune Bottleneck." PLoS One 7, no. 6:e36465. PNNL-SA-82946. doi:10.1371/journal.pone.0036465