Staff information

Biography

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

Research Interests

• Network inference from high-throughput data
• Network topology

Education and Credentials

• B.S. - Molecular Biology, Brigham Young University
• Ph.D. - Molecular Biology, Mayo Graduate School

Awards and Recognitions

• 2013 - Award winner, SBV IMPROVER challenge

PNNL Publications

2024

• Fu J., B. McKinley, B. James, W.B. Chrisler, L. Markillie, M.J. Gaffrey, and H.D. Mitchell, et al. 2024. "Cell-type-specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems." The Plant Journal 118, no. 5:1668-1688. PNNL-SA-201514. doi:10.1111/tpj.16690
• Yang Y., T.A. Chaffin, Y. Saho, V. Balasubramanian, L. Markillie, H.D. Mitchell, and M.M. Rubio-Wilhelmi, et al. 2024. "Novel synthetic inducible promoters controlling gene expression during water-deficit stress with green tissue specificity in transgenic poplar." Plant Biotechnology Journal 22, no. 6:1596-1609. PNNL-SA-189970. doi:10.1111/pbi.14289

2023

• Fulcher J.M., L. Markillie, H.D. Mitchell, S.M. Williams, K.M. Engbrecht, R.J. Moore, and W.B. Chrisler, et al. 2023. Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting. PNNL-34730. Richland, WA: Pacific Northwest National Laboratory. Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting
• Kinmonth-Schultz H.A., S. Walker, A.K. Bingol, D.W. Hoyt, Y. Kim, L. Markillie, and H.D. Mitchell, et al. 2023. "Oligosaccharide production and signaling correlate with delayed flowering in an Arabidopsis genotype grown and selected in high [CO2]." PLoS One 18, no. 12:Art. No. e0287943. PNNL-SA-187156. doi:10.1371/journal.pone.0287943
• Wang B., X. Zhou, A.N. Kettenbach, H.D. Mitchell, L. Markillie, J.J. Loros, and J.C. Dunlap. 2023. "A crucial role for dynamic expression of components encoding the negative arm of the circadian clock." Nature Communications 14. PNNL-SA-176537. doi:10.1038/s41467-023-38817-7

2022

• Anderson C.E., J. Zhang, L. Markillie, H.D. Mitchell, W.B. Chrisler, M.J. Gaffrey, and G. Orr, et al. 2022. "Capturing an Early Gene Induction Event during Wood Decay by the Brown Rot Fungus Rhodonia placenta." Applied and Environmental Microbiology 88, no. 8:Art. No. e00188-22. PNNL-SA-172027. doi:10.1128/aem.00188-22
• Lee J., H.D. Mitchell, M.C. Burnet, R. Wu, S.C. Jenson, E.D. Merkley, and E.S. Nakayasu, et al. 2022. "Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics." Journal of Proteome Research 21, no. 8:2023-2035. PNNL-SA-138497. doi:10.1021/acs.jproteome.2c00334
• Mitchell H.D., J.E. Kyle, K.M. Engbrecht, and A.C. Sims. 2022. Defining Lipidomic Responses to Coronavirus Infection. PNNL-33440. Richland, WA: Pacific Northwest National Laboratory. Defining Lipidomic Responses to Coronavirus Infection
• Novikova I.V., J.E. Evans, L. Markillie, and H.D. Mitchell. 2022. Validation and functional characterization of transcription factors in wheat using cell-free protein expression and high-throughput sequencing technologies. PNNL-33703. Richland, WA: Pacific Northwest National Laboratory. Validation and functional characterization of transcription factors in wheat using cell-free protein expression and high-throughput sequencing technologies
• Zhang J., L. Markillie, H.D. Mitchell, M.J. Gaffrey, G. Orr, and J.S. Schilling. 2022. "Distinctive carbon repression effects in the carbohydrate-selective wood decay fungus Rhodonia placenta." Fungal Genetics and Biology : FG & B 159. PNNL-SA-170453. doi:10.1016/j.fgb.2022.103673

2021

• Boiteau R.M., L. Markillie, D.W. Hoyt, D. Hu, R.K. Chu, H.D. Mitchell, and L. Pasa-Tolic, et al. 2021. "Metabolic interactions between Brachypodium and Pseudomonas fluorescens under 1 controlled iron-limited conditions." mSystems 6, no. 1:e00580-20. PNNL-SA-159673. doi:10.1128/mSystems.00580-20
• Chroumpi T., M. Peng, L. Markillie, H.D. Mitchell, C.D. Nicora, C.M. Hutchinson, and V.L. Paurus, et al. 2021. "Re-routing of sugar catabolism provides a better insight into fungal flexibility in using plant biomass-derived monomers as substrates." Frontiers in Bioengineering and Biotechnology 9. PNNL-SA-158642. doi:10.3389/fbioe.2021.644216
• Danna V.G., H.D. Mitchell, L.N. Anderson, I.G. Godinez, S. Gosline, J.G. Teeguarden, and J.E. McDermott. 2021. "leapR: An R Package for MultiOmic Pathway Analysis." Journal of Proteome Research 20, no. 4:2116-2121. PNNL-SA-159351. doi:10.1021/acs.jproteome.0c00963
• Del Cerro C., E. Erickson, T. Dong, A.R. Wong, E. Eder, S.O. Purvine, and H.D. Mitchell, et al. 2021. "Intracellular pathways for lignin catabolism in white-rot fungi." Proceedings of the National Academy of Sciences (PNAS) 118, no. 9:e2017381118. PNNL-SA-155713. doi:10.1073/pnas.2017381118
• Feng S., E. Heath, B.A. Jefferson, C.A. Joslyn, H.J. Kvinge, H.D. Mitchell, and B.L. Praggastis, et al. 2021. "Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response." BMC Bioinformatics 22, no. 1:287. PNNL-SA-155930. doi:10.1186/s12859-021-04197-2
• Sims A.C., H.D. Mitchell, L. Gralinski, J.E. Kyle, K.E. Burnum-Johnson, M. Lam, and L.M. Fulcher, et al. 2021. "Unfolded Protein Response Inhibition Reduces Middle East Respiratory Syndrome Coronavirus-Induced Acute Lung Injury." mBio 12, no. 4:e01572-21. PNNL-SA-162254. doi:10.1128/mBio.01572-21

2020

• 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
• Mensch A.C., H.D. Mitchell, L. Markillie, E. Laudadio, J. Orbeck, A. Dohnalkova, and M.P. Schwartz, et al. 2020. "Subtoxic dose of lithium cobalt oxide nanosheets impacts critical molecular pathways in trout gill epithelial cells." Environmental Science: Nano 7, no. 11:3419-3430. PNNL-SA-152612. doi:10.1039/D0EN00844C
• Metz T.O., A.C. Sims, L.M. Bramer, and H.D. Mitchell. 2020. Multi-omics Characterization of the Host Response to COVID-19. PNNL-30763. Richland, WA: Pacific Northwest National Laboratory. Multi-omics Characterization of the Host Response to COVID-19
• 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

2019

• 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, no. 6:1941-1953. PNNL-SA-147546. doi:10.1007/s00425-019-03273-5
• 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. PNNL-SA-142134. doi:10.1007/s00425-019-03273-5
• 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
• 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
• Mitchell H.D., and J.E. Kyle. 2019. Full Integration of Lipidomics Data into Multi-OMIC Functional Enrichment. PNNL-29388. Richland, WA: Pacific Northwest National Laboratory. Full Integration of Lipidomics Data into Multi-OMIC Functional Enrichment

2018

• 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 (PNAS) 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

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 lignolyticusSCF1 during growth in lignin-amended medium." PLoS One 12, no. 10:e0186440. PNNL-SA-131719. doi:10.1371/journal.pone.0186440

2016

• 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

2015

• 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

2014

• 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.

2013

• 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
• 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

2012

• 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