Staff information

Research Interests

• Lipidomics - in the environment and human systems
• Mass Spectrometry

Education and Credentials

• 2010 - 2012 NASA Postdoctoral Fellow, NASA Ames and Portland State University, USA
• 2009 Ph.D. in Geology (specialized in geobiology), University of Toronto, Canada

Awards and Recognitions

• 2015 PNNL Software Development Award
• 2014 - 2015 Outstanding Performance Award, Pacific Northwest National Laboratory
• 2010 - 2012 NASA Astrobiology Institute Postdoctoral Fellow

PNNL Publications

2023

• Uehara Y., Y. Tanaka, S. Zhao, N.M. Nikolaidis, L.B. Pitstick, H. Wu, and J.J. Yu, et al. 2023. "Insights into pulmonary phosphate homeostasis and osteoclastogenesis emerge from the study of pulmonary alveolar microlithiasis." Nature Communications 14. PNNL-SA-182417. doi:10.1038/s41467-023-36810-8

2022

• Cruz-Morales P., K. Yin, A. Landera, J.R. Cort, R.P. Young, J.E. Kyle, and R. Bertrand, et al. 2022. "Biosynthesis of polycyclopropanated high energy biofuels." Joule 6, no. 7:1590-1605. PNNL-SA-170223. doi:10.1016/j.joule.2022.05.011
• Farley S.E., J.E. Kyle, H.C. Leier, L.M. Bramer, J.B. Weinstein, T.A. Bates, and J. Lee, et al. 2022. "A global lipid map reveals host dependency factors conserved across SARS-CoV-2 variants." Nature Communications 13. PNNL-SA-165174. doi:10.1038/s41467-022-31097-7
• Lukowski J.K., H.M. Olson, M. Velickovic, J. Wang, J.E. Kyle, Y. Kim, and S.M. Williams, et al. 2022. "An optimized approach and inflation media for obtaining complimentary mass spectrometry-based omics data from human lung tissue." Frontiers in Molecular Biosciences 9. PNNL-SA-170826. doi:10.3389/fmolb.2022.1022775

2021

• Barklis E.W., A. Alfadhli, J.E. Kyle, L.M. Bramer, K.J. Bloodsworth, R. Lid Barklis, and H.C. Leier, et al. 2021. "Ceramide Synthase 2 Deletion Decreases the Infectivity of HIV-1." Journal of Biological Chemistry 296. PNNL-SA-156982. doi:10.1016/j.jbc.2021.100340
• Khadempour L., J.E. Kyle, B.M. Webb-Robertson, C.D. Nicora, F.B. Smith, R.D. Smith, and M.S. Lipton, et al. 2021. "From plants to ants: Fungal modification of leaf lipids for nutrition and communication in the leaf-cutter ant fungal garden ecosystem." mSystems 6, no. 2:e01307-20. PNNL-SA-147384. doi:10.1128/mSystems.01307-20
• Kyle J.E. 2021. "How lipidomics can transform our understanding of virus infections." Expert Review of Proteomics 18, no. 5:329-332. PNNL-SA-160917. doi:10.1080/14789450.2021.1929177
• Kyle J.E., K.G. Stratton, E.M. Zink, Y. Kim, K.J. Bloodsworth, M.E. Monroe, and K.M. Waters, et al. 2021. "A resource of lipidomics and metabolomics data from individuals with undiagnosed diseases." Scientific Data 8, no. 1:114. PNNL-SA-150181. doi:10.1038/s41597-021-00894-y
• Kyle J.E., L. Aimo, A.J. Bridge, G. Clair, M. Fedorova, J.B. Helms, and M.R. Molenaar, et al. 2021. "Interpreting the Lipidome: Bioinformatic Approaches to Embrace the Complexity." Metabolomics 17, no. 8:55. PNNL-SA-162774. doi:10.1007/s11306-021-01802-6
• Neurath R., J. Pett-Ridge, I. Jacoby, D. Herman, T. Whitman, P.S. Nico, and A.S. Lipton, et al. 2021. "Root carbon interation with soil minerals is dynamic, leaving a legacy of microbially derived residues." Environmental Science & Technology 55, no. 19:13345-13355. PNNL-SA-158887. doi:10.1021/acs.est.1c00300
• 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
• Velickovic D., R.K. Chu, C. Henkel, A. Nyhuis, N. Tao, J.E. Kyle, and J.N. Adkins, et al. 2021. "Preserved and variable spatial-chemical changes of lipids across tomato leaves in response to central vein wounding reveals potential origin of linolenic acid in signal transduction cascade." Plant-Environment Interactions 2, no. 1:28-35. PNNL-SA-158820. doi:10.1002/pei3.10038
• Wang L., A. Karpova, M.A. Gritsenko, J.E. Kyle, S. Cao, Y. Li, and D. Rykunov, et al. 2021. "Proteogenomic and Metabolomic Characterization of Human Glioblastoma." Cancer Cell 39, no. 4:509-528.e20. PNNL-SA-151124. doi:10.1016/j.ccell.2021.01.006
• Wilson R.M., M.M. Tfaily, M. Kolton, E.R. Johnston, C. Petro, C.A. Zalman, and P.J. Hanson, et al. 2021. "Soil metabolome response to whole-ecosystem warming at the Spruce and Peatland Responses under Changing Environments experiment." Proceedings of the National Academy of Sciences (PNAS) 118, no. 25:e2004192118. PNNL-SA-152358. doi:10.1073/pnas.2004192118
• Zamith-Miranda D., H.M. Heyman, M.C. Burnet, S.P. Couvillion, X. Zheng, N. Munoz Munoz, and W.C. Nelson, et al. 2021. "A Histoplasma capsulatum lipid metabolic map identifies antifungal targets." mBio 12, no. 6:e02972-21. PNNL-SA-152496. doi:10.1128/mBio.02972-21

2020

• Blanco-Sanchez B., A. Clément, S.J. Stednitz, J.E. Kyle, J.L. Peirce, M. McFadden, and J. Wegner, et al. 2020. "yippee like 3 (ypel3) is a novel gene required for myelinating and perineurial glia development." PLoS Genetics 16, no. 6:Article No. e1008841. PNNL-SA-147624. doi:10.1371/journal.pgen.1008841
• Kyle J.E. 2020. "Extracting Biological Insight from Untargeted Lipidomics Data." In Computation Methods and Data Analysis for Metabolomics. Methods in Molecular Biology, edited by S. Li. 121-137. New York, New York:Humana. PNNL-SA-142580. doi:10.1007/978-1-0716-0239-3_7
• Leier H.C., J.B. Weinstein, J.E. Kyle, J. Lee, L.M. Bramer, K.G. Stratton, and D. Kempthorne, et al. 2020. "A global lipid map defines a network essential for Zika virus replication." Nature Communications 11, no. 3652. PNNL-SA-139745. doi:10.1038/s41467-020-17433-9
• Leier H.C., J.B. Weinstein, J.E. Kyle, J. Lee, L.M. Bramer, K.G. Stratton, and D. Kempthorne, et al. 2020. "A global lipid map defines a network essential for Zika virus replication." Nature Communications 11. PNNL-SA-148085. doi:10.1038/s41467-020-17433-9
• Nicora C.D., A. Sims, K.J. Bloodsworth, Y. Kim, R.J. Moore, J.E. Kyle, and E.S. Nakayasu, et al. 2020. "Metabolite, Protein, and Lipid Extraction (MPLEx): a method that simultaneously inactivates Middle East respiratory syndrome coronavirus and allows analysis of multiple host cell components following infection." In MERS Coronavirus: Methods and Protocols, edited by R. Vijay. 173-194. New York, New York:Humana. PNNL-SA-142077. doi:10.1007/978-1-0716-0211-9_14
• Webb-Robertson B.M., K.G. Stratton, J.E. Kyle, Y. Kim, L.M. Bramer, K.M. Waters, and D. Koeller, et al. 2020. "Statistically Driven Metabolite and Lipid Profiling of Patients from the Undiagnosed Diseases Network." Analytical Chemistry 92, no. 2:1796-1803. PNNL-SA-145014. doi:10.1021/acs.analchem.9b03522

2019

• Angerer T.B., D. Velickovic, C.D. Nicora, J.E. Kyle, D.J. Graham, C.R. Anderton, and L.J. Gamble. 2019. "Exploiting the Semidestructive Nature of Gas Cluster Ion Beam Time-of-Flight Secondary Ion Mass Spectrometry Imaging for Simultaneous Localization and Confident Lipid Annotations." Analytical Chemistry 91, no. 23:15073-15080. PNNL-SA-150104. doi:10.1021/acs.analchem.9b03763
• Clair G., S.M. Reehl, K.G. Stratton, M.E. Monroe, M. Tfaily, C.K. Ansong, and J.E. Kyle. 2019. "Lipid Mini-On: Mining and ontology tool for enrichment analysis of lipidomic data." Bioinformatics 35, no. 21:4507-4508. PNNL-SA-142630. doi:10.1093/bioinformatics/btz250
• Coelho C., L. Brown, M. Maryam, R. Vij, D.F. Smith, M.C. Burnet, and J.E. Kyle, et al. 2019. "Listeria monocytogenes Virulence Factors, including listeriolysin O, are Secreted in Biologically Active Extracellular Vesicles." Journal of Biological Chemistry 294, no. 4:1202-1217. PNNL-SA-128462. doi:10.1074/jbc.RA118.006472
• Fudyma J.D., J.E. Lyon, R. Aminitabrizi, H. Gieschen, R.K. Chu, D.W. Hoyt, and J.E. Kyle, et al. 2019. "Untargeted metabolomic profiling of Sphagnum fallax reveals novel antimicrobial metabolites." Plant Direct 3, no. 11:Article No. e00179. PNNL-SA-146621. doi:10.1002/pld3.179
• Kyle J.E., K.E. Burnum-Johnson, J.P. Wendler, A.J. Eisfeld, P.J. Halfmann, T. Watanabe, and F. Sahr, et al. 2019. "Plasma lipidome reveals critical illness and recovery from human Ebola virus disease." Proceedings of the National Academy of Sciences (PNAS) 116, no. 9:3919-3928. PNNL-SA-136689. doi:10.1073/pnas.1815356116
• Tfaily M., R.M. Wilson, H.M. Brewer, R.K. Chu, H.M. Heyman, D.W. Hoyt, and J.E. Kyle, et al. 2019. "Single-throughput complementary high-resolution analytical techniques for characterizing complex natural organic matter mixtures." Journal of Visualized Experiments. PNNL-SA-138197. doi:10.3791/59035

2018

• Cole J.K., B.R. Morton, H.C. Cardamone, H.R. Lake, A. Dohnalkova, Y. Kim, and J.E. Kyle, et al. 2018. "Salinivirga fredricksonii gen. nov. , sp. nov., a heterotrophic halophile isolated from photosynthetic mat of a novel lineage (Salinivirgaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinivirgaceae." International Journal of Systematic and Evolutionary Microbiology 68, no. 5:1591-1598. PNNL-SA-118460. doi:10.1099/ijsem.0.002715
• Kyle J.E., G. Clair, G. Bandyopadhyay, R. Misra, E.M. Zink, K.J. Bloodsworth, and A.K. Shukla, et al. 2018. "Cell type-resolved human lung lipidome reveals cellular cooperation in lung function." Scientific Reports 8, no. 1:Article No. 13455. PNNL-SA-132404. doi:10.1038/s41598-018-31640-x
• Kyle J.E., N.A. Aly, X. Zheng, K.E. Burnum-Johnson, R.D. Smith, and E.M. Baker. 2018. "Evaluating lipid mediator structural complexity using ion mobility spectrometry combined with mass spectrometry." Bioanalysis 10, no. 5:279-289. PNNL-SA-130733. doi:10.4155/bio-2017-0245
• Nicora C.D., K.E. Burnum-Johnson, E.S. Nakayasu, C.P. Casey, R.A. White, T. Roy Chowdhury, and J.E. Kyle, et al. 2018. "The MPLEx Protocol for Multi-Omic Analyses of Soil Samples." Journal of Visualized Experiments e57343, no. 135. PNNL-SA-129344. doi:10.3791/57343
• Yin R., J.E. Kyle, K.E. Burnum-Johnson, K.J. Bloodsworth, L. Sussel, C.K. Ansong, and J. Laskin. 2018. "High Spatial Resolution Imaging of Mouse Pancreatic Islets Using Nanospray Desorption Electrospray Ionization Mass Spectrometry." Analytical Chemistry 90, no. 11:6548-6555. PNNL-SA-162133. doi:10.1021/acs.analchem.8b00161

2017

• Burnum-Johnson K.E., J.E. Kyle, A.J. Eisfeld, C.P. Casey, K.G. Stratton, J.F. Gonzalez, and F. Habyarimana, et al. 2017. "MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling." Analyst 142, no. 3:442-448. PNNL-SA-116063. doi:10.1039/c6an02486f
• Dautel S.E., J.E. Kyle, G. Clair, R.L. Sontag, K.K. Weitz, A.K. Shukla, and S.N. Nguyen, et al. 2017. "Lipidomics reveals dramatic lipid compositional changes in the maturing postnatal lung." Scientific Reports 7. PNNL-SA-121148. doi:10.1038/srep40555
• Eisfeld A.J., P. Halfmann, J.P. Wendler, J.E. Kyle, K.E. Burnum-Johnson, Z. Peralta, and T. Maemura, et al. 2017. "Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis." Cell Host & Microbe 22, no. 6:817-829. PNNL-SA-120881. doi:10.1016/j.chom.2017.10.011
• Kyle J.E., C.P. Casey, K.G. Stratton, E.M. Zink, Y. Kim, X. Zheng, and M.E. Monroe, et al. 2017. "Comparing Identified and Statistically Significant Lipids and Metabolites in 15-Year Old Serum and Dried Blood Spot Samples for Longitudinal Studies." Rapid Communications in Mass Spectrometry 31, no. 5:447-456. PNNL-SA-121197. doi:10.1002/rcm.7808
• Kyle J.E., K.L. Crowell, C.P. Casey, G.M. Fujimoto, S. Kim, S.E. Dautel, and R.D. Smith, et al. 2017. "LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data." Bioinformatics 33, no. 11:1744-1746. PNNL-SA-118436. doi:10.1093/bioinformatics/btx046
• Qafoku N., A.R. Lawter, D.H. Bacon, L. Zheng, J.E. Kyle, and C.F. Brown. 2017. "Review of the Impacts of Leaking CO2 Gas and Brine on Groundwater Quality"." Earth - Science Reviews 169. PNNL-SA-119041. doi:10.1016/j.earscirev.2017.04.010
• Tang X., J.M. Snowball, Y. Xu, C. Na, T.E. Weaver, G. Clair, and J.E. Kyle, et al. 2017. "EMC3 coordinates surfactant protein and lipid homeostasis required for respiration." Journal of Clinical Investigation 127, no. 12:4314-4325. PNNL-SA-127808. doi:10.1172/JCI94152

2016

• Kyle J.E., X. Zhang, K.K. Weitz, M.E. Monroe, Y.M. Ibrahim, R.J. Moore, and J. Cha, et al. 2016. "Uncovering Biologically Significant Lipid Isomers with Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry." Analyst 141, no. 5:1649-1659. PNNL-SA-111991. doi:10.1039/C5AN02062J
• Lanekoff I., J. Cha, J.E. Kyle, S.K. Dey, J. Laskin, and K.E. Burnum-Johnson. 2016. "Trp53 deficient mice predisposed to preterm birth display region-specific lipid alterations at the embryo implantation site." Scientific Reports 6. PNNL-SA-116850. doi:10.1038/srep33023
• Nakayasu E.S., C.D. Nicora, A.C. Sims, K.E. Burnum-Johnson, Y. Kim, J.E. Kyle, and M.M. Matzke, et al. 2016. "MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses." mSystems 1, no. 3:e00043-16. PNNL-SA-114737. doi:10.1128/mSystems.00043-16
• Rivas Ubach A., J.A. Hodar, J. Sardans, J.E. Kyle, Y. Kim, M. Oravec, and O. Urban, et al. 2016. "Are the metabolomic responses to folivory of closely related plant species linked to macroevolutionary and plant-folivore coevolutionary processes?." Ecology and Evolution 6, no. 13:4372-4386. PNNL-SA-116150. doi:10.1002/ece3.2206
• Tisoncik-Go J., D.J. Gasper, J.E. Kyle, A.J. Eisfeld, C. Selinger, M. Hatta, and J. Morrison, et al. 2016. "Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism." Cell Host & Microbe 19, no. 2:254-66. PNWD-SA-10483. doi:10.1016/j.chom.2016.01.002
• Wang M., J.J. Carver, V.V. Phelan, L.M. Sanchez, N. Garg, Y. Peng, and D. Nguyen, et al. 2016. "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking." Nature Biotechnology 34, no. 8:828-837. PNWD-SA-10551. doi:10.1038/nbt.3597

2015

• Lovelace E.S., J. Wagoner, J. MacDonald, T. Bammler, J. Bruckner, J. Brownell, and R. Beyer, et al. 2015. "Silymarin Suppresses Cellular Inflammation By Inducing Reparative Stress Signaling." Journal of Natural Products 78, no. 8:1990-2000. PNNL-SA-109357. doi:10.1021/acs.jnatprod.5b00288
• Touchette M.H., G.R. Bommineni, R.J. Delle Bovi, J. Gadbery, C.D. Nicora, A.K. Shukla, and J.E. Kyle, et al. 2015. "Diacyltransferase Activity and Chain Length Specificity of Mycobacterium tuberculosis PapA5 in the Synthesis of Alkyl ß-Diol Lipids." Biochemistry 54, no. 35:5457-5468. PNNL-SA-108635. doi:10.1021/acs.biochem.5b00455
• Zhang X., Y.M. Ibrahim, T. Chen, J.E. Kyle, R.V. Norheim, M.E. Monroe, and R.D. Smith, et al. 2015. "Enhancing Biological Analyses with Three Dimensional Field Asymmetric Ion Mobility, Low Field Drift Time Ion Mobility and Mass Spectrometry (µFAIMS/IMS-MS) Separations." Analyst 140. PNNL-SA-110080. doi:10.1039/c5an00897b