Staff information

Biography

Dr. Jason McDermott, senior research scientist, has extensive research experience in molecular and structural virology and data resource design, data integration and prediction of biological networks, bridging experimental and computational biology. Currently, his research interests include data integration of high-throughput ‘omics data for biomarker discovery, developing systems biology models in a number of systems focusing on host-pathogen interactions, characterizing phylogenetic and functional relationships in complex eukaryotic microbial communities, and using network inference and topology to characterize organism-level phenotypes. He is involved in the Center for Systems Biology of EnteroPathogens (http://sysbep.pnl.gov) and the Center for Systems Virology (http://www.systemsvirology.org).

Research Interests

• Systems biology
• Network inference
• Data integration
• Biological networks
• Machine learning

Education and Credentials

• Post-doctoral, University of Washington, Bioinformatics, 2006
• Ph.D., Oregon Health & Science University, Structural Virology, 2000
• B.A. Reed College, Biology, 1993

Awards and Recognitions

• 1997 Sears Fellowship Award (OHSU)
• 1998 Tartar Fellowship Award (OHSU)
• 2008 Analytics Challenge Winner (Supercomputing 2008)

PNNL Publications

2024

• Pino J.C., J.C. Posso Escobar, S.K. Joshi, M.D. Nestor, J. Moon, J.R. Hansen, and C.M. Hutchinson, et al. 2024. "Mapping the proteogenomic landscape enables prediction of drug response in acute myeloid leukemia." Cell Reports Medicine 5, no. 1:Art. No. 101359. PNNL-SA-185276. doi:10.1016/j.xcrm.2023.101359

2023

• Chang C.H., W.C. Nelson, A.R. Jerger, A.T. Wright, R.G. Egbert, and J.E. McDermott. 2023. "Snekmer: A scalable pipeline for protein sequence fingerprinting based on amino acid recoding." Bioinformatics Advances 3, no. 1:Art. No. vbad005. PNNL-SA-169271. doi:10.1039/d2cc01517j
• Couvillion S.P., R.E. Danczak, D.T. Naylor, M.L. Smith, K.G. Stratton, V.L. Paurus, and K.J. Bloodsworth, et al. 2023. "Rapid remodeling of the soil lipidome in response to a drying-rewetting event." Microbiome 11, no. 2023:34. PNNL-SA-172149. doi:10.1186/s40168-022-01427-4
• Gabbert A.D., J.L. Mydosh, P.K. Talukdar, L.M. Gloss, J.E. McDermott, K.K. Cooper, and G. Clair, et al. 2023. "The missing pieces: the role of secretion systems in Campylobacter jejuni virulence." Biomolecules 13, no. 1:Art. No. 135. PNNL-SA-181015. doi:10.3390/biom13010135
• Gangwar A., S.S. Deodhar, S. Saldanha, O. Melander, F. Abbasi, R.W. Pearce, and T.S. Collier, et al. 2023. "Proteomic Determinants of variation in Cholesterol Efflux: Observations From the Dallas Heart Study." International Journal of Molecular Sciences 24, no. 21:Art. No. 15526. PNNL-SA-189619. doi:10.3390/ijms242115526
• Merrill N.J., W. Davidson, Y. He, I. Diaz Ludovico, S. Sarkar, M.R. Berger, and J.E. McDermott, et al. 2023. "Human cerebrospinal fluid contains diverse lipoprotein subspecies enriched in proteins implicated in central nervous system health." Science Advances 9, no. 35:Art. No. eadi5571. PNNL-SA-184855. doi:10.1126/sciadv.adi5571
• Wu R., M.R. Davison, W.C. Nelson, M.L. Smith, M.S. Lipton, J.K. Jansson, and R.S. McClure, et al. 2023. "Hi-C metagenome sequencing reveals soil phage-host interactions." Nature Communications 14. PNNL-SA-181374. doi:10.1038/s41467-023-42967-z

2022

• Gosline S., C.E. Tognon, M.D. Nestor, S.K. Joshi, R.V. Modak, A. Damnernsawad, and J.C. Posso Escobar, et al. 2022. "Proteomic and phosphoproteomic measurements enhance ability to predict ex vivo drug response in AML." Clinical Proteomics 19. PNNL-SA-163043. doi:10.1186/s12014-022-09367-9
• Wu R., C. Smith, G.W. Buchko, I.K. Blaby, A. Paez-Espino, N.C. Kyrpides, and Y. Yoshikuni, et al. 2022. "Structural characterization of a soil viral auxiliary metabolic gene product - a functional chitosanase." Nature Communications 13, no. 1:Art. No. 5485. PNNL-SA-170607. doi:10.1038/s41467-022-32993-8

2021

• 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
• Emechebe U., D. Giraud, A. Ammi, K. Scott, J.M. Jacobs, J.E. McDermott, and I. Dykan, et al. 2021. "(Phospho)Proteomic dataset of ischemia- and ultrasound- stimulated mouse cardiac endothelial cells in vitro." Data in Brief 38. PNNL-SA-166312. doi:10.1016/j.dib.2021.107343
• 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
• Hixson K.K., J.V. Marques, J.P. Wendler, J.E. McDermott, K.K. Weitz, T.R. Clauss, and M.E. Monroe, et al. 2021. "New Insights Into Lignification via Network and Multi-Omics Analyses of Arogenate Dehydratase Knock-Out Mutants in Arabidopsis thaliana." Frontiers in Plant Science 12. PNNL-SA-163837. doi:10.3389/fpls.2021.664250
• Joshi S.K., T. Nechiporuk, D. Bottomly, P.D. Piehowski, J. Reisz, J. Pittsenbarger, and A. Kaempf, et al. 2021. "The AML microenvironment catalyzes a step-wise evolution to gilteritinib resistance." Cancer Cell 39, no. 7:999-1014. PNNL-SA-161620. doi:10.1016/j.ccell.2021.06.003
• McDermott J.E., S. Feng, C.H. Chang, D.J. Schmidt, and V.G. Danna. 2021. Structural- and Functional-Informed Machine Learning for Protein Function Prediction. PNNL-32088. Richland, WA: Pacific Northwest National Laboratory. Structural- and Functional-Informed Machine Learning for Protein Function Prediction
• Wu R., M.R. Davison, W.C. Nelson, E.B. Graham, S.J. Fansler, Y. Farris, and S.L. Bell, et al. 2021. "DNA viral diversity, abundance and functional potential vary across grassland soils with a range of historical moisture regimes." mBio 12, no. 6:e02595-21. PNNL-SA-166275. doi:10.1128/mBio.02595-21
• Wu R., M.R. Davison, Y. Gao, C.D. Nicora, J.E. McDermott, K.E. Burnum-Johnson, and K.S. Hofmockel, et al. 2021. "Moisture Modulates Soil Reservoirs of Active DNA and RNA Viruses." Communications Biology 4, no. 1:992. PNNL-SA-160635. doi:10.1038/s42003-021-02514-2

2020

• McDermott J.E., and J.S. Tregoning. 2020. "Ten Simple Rules to becoming a Principal Investigator." PLoS Computational Biology 16, no. 2:e1007448. PNNL-SA-146497. doi:10.1371/journal.pcbi.1007448
• McDermott J.E., O.A. Arshad, V.A. Petyuk, Y. Fu, M.A. Gritsenko, T.R. Clauss, and R.J. Moore, et al. 2020. "Proteogenomic characterization of ovarian HGSC implicates mitotic kinases, replication stress in observed chromosomal instability." Cell Reports Medicine 1, no. 1:Article No. 100004. PNNL-SA-145681. doi:10.1016/j.xcrm.2020.100004
• Nelson W.C., L.N. Anderson, R. Wu, J.E. McDermott, S.L. Bell, A. Jumpponen, and S.J. Fansler, et al. 2020. "Terabase Metagenome Sequencing of Grassland Soil Microbiomes." Microbiology Resource Announcements 9, no. 32:Article No. e00718-20. PNNL-SA-153752. doi:10.1128/MRA.00718-20
• Sanford J.A., C.D. Nogiec, M.E. Lindholm, J.N. Adkins, D. Amar, S. Dasari, and J.K. Drugan, et al. 2020. "Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise." Cell 181, no. 7:1464-1474. PNNL-SA-155782. doi:10.1016/j.cell.2020.06.004

2019

• Arshad O.A., V.G. Danna, V.A. Petyuk, P.D. Piehowski, T. Liu, K.D. Rodland, and J.E. McDermott. 2019. "An integrative analysis of tumor proteomic and phosphoproteomic profiles to examine the relationships between kinase activity and phosphorylation." Molecular & Cellular Proteomics 18, no. 8 suppl 1:S26-S36. PNNL-SA-145629. doi:10.1074/mcp.RA119.001540
• Cuesta R., M.A. Gritsenko, V.A. Petyuk, A.K. Shukla, C. Tsai, T. Liu, and J.E. McDermott, et al. 2019. "Phosphoproteome Analysis Reveals Estrogen-ER pathway as a modulator of mTOR activity via DEPTOR." Molecular & Cellular Proteomics 18, no. 8:1607-1618. PNNL-SA-145628. doi:10.1074/mcp.RA119.001506
• McClure R.S., J.P. Wendler, J.N. Adkins, J.A. Swanstrom, R. Baric, B. Kaiser, and K.L. Oxford, et al. 2019. "Unified Feature Association Networks through Integration of Transcriptomic and Proteomic Data." PLoS Computational Biology 15, no. 9:e1007241. PNNL-SA-137420. doi:10.1371/journal.pcbi.1007241
• McDermott J.E., J.R. Cort, E.S. Nakayasu, J.N. Pruneda, C.C. Overall, and J.N. Adkins. 2019. "Prediction of Bacterial E3 Ubiquitin Ligase Effectors using Reduced Amino Acid Peptide Fingerprinting." PeerJ 7. PNNL-SA-138492. doi:10.7717/peerj.7055
• Minutoli M., M. Halappanavar, A. Kalyanaraman, A. Visweswara Sathanur, R.S. McClure, and J.E. McDermott. 2019. "Fast and Scalable Implementations of Influence Maximization Algorithms." In IEEE International Conference on Cluster Computing (CLUSTER 2019), September 23-26, 2019, Albuquerque, NM. Piscataway, New Jersey:IEEE. PNNL-SA-141177. doi:10.1109/CLUSTER.2019.8890991
• 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
• Vasaikar S., C. Huang, X. Wang, V.A. Petyuk, S. Savage, B. Wen, and Y. Dou, et al. 2019. "Proteogenomic analysis of human colon cancer reveals new therapeutic opportunities." Cell 177, no. 4:1035-1049. PNNL-SA-137631. doi:10.1016/j.cell.2019.03.030

2018

• Colby S.M., R.S. McClure, C.C. Overall, R.S. Renslow, and J.E. McDermott. 2018. "Improving network inference algorithms using resampling methods." BMC Bioinformatics 19. PNNL-SA-134995. doi:10.1186/s12859-018-2402-0
• Duhen T., R. Duhen, R. Montler, J. Moses, T. Moudgil, N.F. de Miranda, and C.P. Goodall, et al. 2018. "Co-expression of CD39 and CD103 identifies tumor-reactive CD8 T cells in human solid tumors." Nature Communications 9, no. 1:Article No. 2724. PNNL-SA-135245. doi:10.1038/s41467-018-05072-0
• Hosseini M.M., S.E. Kurtz, S. Abdelhamed, S. Mahmood, M.A. Davare, A. Kaempf, and J. Elferich, et al. 2018. "Inhibition of interleukin-1 receptor-associated kinase-1 is a therapeutic strategy for acute myeloid leukemia subtypes." Leukemia 32, no. 11:2374-2387. PNNL-SA-137772. doi:10.1038/s41375-018-0112-2
• McClure R.S., C.C. Overall, E.A. Hill, H. Song, M.A. Charania, H.C. Bernstein, and J.E. McDermott, et al. 2018. "SPECIES-SPECIFIC TRANSCRIPTOMIC NETWORK INFERENCE OF INTERSPECIES INTERACTIONS." The ISME Journal 12, no. 8:2011-2023. PNNL-SA-124736. doi:10.1038/s41396-018-0145-6
• McDermott J.E., M. Partridge, and Y. Bromberg. 2018. "Ten Simple Rules for Drawing Scientific Comics." PLoS Computational Biology 14, no. 1:Article No. e1005845. PNNL-SA-127907. doi:10.1371/journal.pcbi.1005845
• 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
• Sharpnack M.F., N. Ranbaduge, A. Srivastava, F. Cerciello, S. Codreau, D. Liebler, and C. Mascaux, et al. 2018. "Proteogenomic analysis of surgically resected lung adenocarcinoma." Journal of Thoracic Oncology 13, no. 10:1519-1529. PNNL-SA-126803. doi:10.1016/j.jtho.2018.06.025

2017

• Ardini-Poleske M.E., R.F. Clark, C.K. Ansong, J.P. Carson, R.A. Corley, G. Deutsch, and J.S. Hagood, et al. 2017. "LungMAP: The Molecular Atlas of Lung Development Program." American Journal of Physiology-Lung Cellular and Molecular Physiology 313, no. 5:L733-L740. PNNL-SA-136379. doi:10.1152/ajplung.00139.2017
• Maier T.V., M. Lucio, L.H. Lee, N. VerBerkmoes, C.J. Brislawn, J. Bernhardt, and R. Lamendella, et al. 2017. "Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome and Metabolome." mBio 8, no. 5:Article No. e01343-17. PNNL-SA-126751. doi:10.1128/mBio.01343-17
• McDermott J.E. 2017. "Working Life: Drawing Connections." Science 356, no. 6343:1202. PNNL-SA-125843. doi:10.1126/science.356.6343.1202
• Wang J., Z. Ma, S.A. Carr, P. Mertins, H. Zhang, Z. Zhang, and D.W. Chan, et al. 2017. "Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction." Molecular & Cellular Proteomics 16, no. 1:121-134. PNNL-SA-124098. doi:10.1074/mcp.M116.060301

2016

• Bernstein H.C., R.S. McClure, E.A. Hill, L.M. Markillie, W.B. Chrisler, M.F. Romine, and J.E. McDermott, et al. 2016. "Unlocking the Constraints of Cyanobacterial Productivity: Acclimations Enabling Ultrafast Growth." mBio 7, no. 4:Article No. e00949-16. PNNL-SA-112394. doi:10.1128/mBio.00949-16
• McClure R.S., C.C. Overall, J.E. McDermott, E.A. Hill, L.M. Markillie, L.A. McCue, and R.C. Taylor, et al. 2016. "Network Analysis of Transcriptomics Expands Regulatory Landscapes in Synechococcus sp. PCC 7002." Nucleic Acids Research 44, no. 18:8810-8825. PNNL-SA-113421. doi:10.1093/nar/gkw737
• 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
• Oxford K.L., J.P. Wendler, J.E. McDermott, R.A. White, J.D. Powell, J.M. Jacobs, and J.N. Adkins, et al. 2016. "The Landscape of Viral Proteomics and Its Potential to Impact Human Health." Expert Review of Proteomics 13, no. 6:579-591. PNNL-SA-116259. doi:10.1080/14789450.2016.1184091
• Shi T., M. Niepel, J.E. McDermott, Y. Gao, C.D. Nicora, W.B. Chrisler, and L.M. Markillie, et al. 2016. "Conservation of Protein Abundance Patterns Reveals the Regulatory Architecture of the of the EGFR-MAPK Pathway." Science Signaling 9, no. 436:rs6. PNNL-SA-115056. doi:10.1126/scisignal.aaf0891
• Tabb D.L., X. Wang, S.A. Carr, K. Clauser, P. Mertins, M.C. Chambers, and J.D. Holman, et al. 2016. "Reproducibility of differential proteomic technologies in CPTAC fractionated xenografts." Journal of Proteome Research 15, no. 3:691-706. PNNL-SA-113210. doi:10.1021/acs.jproteome.5b00859
• Zhang H., T. Liu, Z. Zhang, S.H. Payne, B. Zhang, J.E. McDermott, and J. Zhou, et al. 2016. "Integrated proteogenomic characterization of human high grade serous ovarian cancer." Cell 166, no. 3:755-765. PNNL-SA-107151. doi:10.1016/j.cell.2016.05.069

2015

• Li J., C.C. Overall, E.S. Nakayasu, A.S. Kidwai, M.B. Jones, R. Johnson, and N.T. Nguyen, et al. 2015. "Analysis of the Salmonella regulatory network suggests involvement of SsrB and H-NS in sE-regulated SPI-2 gene expression." Frontiers in Microbiology 6. PNNL-SA-101010. doi:10.3389/fmicb.2015.00027
• Li J., C.C. Overall, R. Johnson, M.B. Jones, J.E. McDermott, F. Heffron, and J.N. Adkins, et al. 2015. "ChIP-Seq Analysis of the s E Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response." PLoS One 10, no. 9:Article No. e0138466. PNNL-SA-115504. doi:10.1371/journal.pone.0138466
• Li J., E.S. Nakayasu, C.C. Overall, R. Johnson, A.S. Kidwai, J.E. McDermott, and C. Ansong, et al. 2015. "Global analysis of Salmonella alternative sigma factor E on protein translation." Journal of Proteome Research 14, no. 4:1716-1726. PNNL-SA-105707. doi:10.1021/pr5010423
• 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
• Webb-Robertson B.M., H.K. Wiberg, M.M. Matzke, J.N. Brown, J. Wang, J.E. McDermott, and R.D. Smith, et al. 2015. "Review, Evaluation, and Discussion of the Challenges of Missing Value Imputation for Mass Spectrometry-Based Label-Free Global Proteomics." Journal of Proteome Research 14, no. 5:1993-2001. PNWD-SA-10158. doi:10.1021/pr501138h

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
• Kang S., S.H. Kahan, J.E. McDermott, N.S. Flann, and I. Shmulevich. 2014. "Biocellion: Accelerating Computer Simulation of Multicellular Biological System Models." Bioinformatics 30, no. 21:3101-3108. PNNL-SA-99077. doi:10.1093/bioinformatics/btu498
• McDermott J.E., Y. Huang, B. Zhang, H. Xu, and Z. Zhao. 2014. "Integrative Genomics and Computational Systems Medicine." BioMed Research International 2014. PNNL-SA-105051. doi:10.1155/2014/945253
• Webb-Robertson B.M., M.M. Matzke, S. Datta, S.H. Payne, J. Kang, L.M. Bramer, and C.D. Nicora, et al. 2014. "Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements." Molecular and Cellular Proteomics 13, no. 12:3639-3646. PNNL-SA-95335. doi:10.1074/mcp.M113.030932

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
• Hafen R.P., L.J. Gosink, J.E. McDermott, K.D. Rodland, K. Kleese-Van Dam, and W.S. Cleveland. 2013. "Trelliscope: A System for Detailed Visualization in Analysis of Large Complex Data." In IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV 2013), October 13-14, 2013, Atlanta, Georgia, 105-112. Piscataway, New Jersey:IEEE. PNNL-SA-95831. doi:10.1109/LDAV.2013.6675164
• 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
• Matzke M.M., J.N. Brown, M.A. Gritsenko, T.O. Metz, J.G. Pounds, K.D. Rodland, and A.K. Shukla, et al. 2013. "A Comparative Analysis of Computational Approaches to Relative Protein Quantification Using Peptide Peak Intensities in Label-free LC-MS Proteomics Experiments." Proteomics 13, no. 3-4:493-503. PNNL-SA-88866. doi:10.1002/pmic.201200269
• 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
• Niemann G., R.N. Brown, I.T. Mushamiri, N.T. Nguyen, R. Taiwo, A. Stufkens, and R.D. Smith, et al. 2013. "RNA Type III Secretion Signals that require Hfq." Journal of Bacteriology 195, no. 10:2119-2125. PNNL-SA-90112. doi:10.1128/JB.00024-13
• Sanfilippo A.P., J.N. Haack, J.E. McDermott, S. Stevens, and M. Stenzel-Poore. 2013. "Modeling Emergence in Neuroprotective Regulatory Networks." In Complex Sciences: Second International Conference COMPLEX 2012, December 5-7, 2012, Santa Fe, New Mexico. Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering, edited by K Glass, et al, 126, 291-302. New York, New York:Springer. PNNL-SA-88379. doi:10.1007/978-3-319-03473-7_26
• Wang J., B.M. Webb-Robertson, M.M. Matzke, S.M. Varnum, J.N. Brown, R.M. Riensche, and J.N. Adkins, et al. 2013. "A Semiautomated Framework for Integrating Expert Knowledge into Disease Marker Identification." Disease Markers 35, no. 5:513-523. PNNL-SA-94068. doi:10.1155/2013/613529
• Webb-Robertson B.M., M.M. Matzke, T.O. Metz, J.E. McDermott, J. Walker, K.D. Rodland, and J.G. Pounds, et al. 2013. "Sequential Projection Pursuit Principal Component Analysis - Dealing with Missing Data Associated with New -Omics Technologies." BioTechniques 54, no. 3:165-168. PNNL-SA-87092.
• Zhang B., Y. Huang, J.E. McDermott, R.H. Posey, H. Xu, and Z. Zhao. 2013. "Interdisciplinary Dialogue for Education, Collaboration, and Innovation: Intelligent Biology and Medicine In and Beyond 2013." BMC Genomics 14, no. Suppl 8:Article No. S1. PNNL-SA-99148. doi:10.1186/1471-2164-14-S8-S1

2012

• Acquaah-Mensah G., D. Malhotra, M. Vulimiri, J.E. McDermott, S. Biswal, and S. Biswal. 2012. "Suppressed Expression of T-Box Transcription Factors is Involved in Senescence in Chronic Obstructive Pulmonary Disease." PLoS Computational Biology 8, no. 7:e1002597. PNNL-SA-86177. doi:10.1371/journal.pcbi.1002597
• Ansong C.K., B.L. Deatherage, D.R. Hyduke, B. Schmidt, J.E. McDermott, M.B. Jones, and S. Chauhan, et al. 2012. "Studying Salmonellae and Yersiniae Host-Pathogen Interactions Using Integrated ‘Omics and Modeling." In Systems Biology. Current Topics in Microbiology and Immunology, edited by M Katze. 21-41. PNNL-SA-135981. doi:10.1007/82_2012_247
• Archuleta M.N., J.E. McDermott, J.S. Edwards, and H. Resat. 2012. "An Adaptive Coarse Graining Method for Signal Transduction in Three-Dimensions." FUNDAMENTA INFORMATICAE 118, no. 4:371-384. PNWD-SA-9566. doi:10.3233/FI-2012-720
• Diamond D.L., A. Krasnoselski, K.E. Burnum, M.E. Monroe, B.M. Webb-Robertson, J.E. McDermott, and M.M. Yeh, et al. 2012. "Proteome and Computational Analyses Reveal New Insights into the Mechanisms of Hepatitis C Virus Mediated Liver Disease Posttransplantation." Hepatology 56, no. 1:28-38. PNWD-SA-9552. doi:10.1002/hep.25649
• McDermott J.E., D.L. Diamond, C.D. Corley, A. Rasmussen, M.G. Katze, and K.M. Waters. 2012. "Topological Analysis of Protein Co-Abundance Networks Identifies Novel Host Targets Important for HCV Infection and Pathogenesis." BMC Systems Biology 6, no. 1:28. PNWD-SA-9359. doi:10.1186/1752-0509-6-28
• 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
• McDermott J.E., K.D. Jarman, R.C. Taylor, M.J. Lancaster, H. Shankaran, K.B. Vartanian, and S. Stevens, et al. 2012. "Modeling Dynamic Regulatory Processes in Stroke." PLoS Computational Biology 8, no. 10:e1002722. PNNL-SA-81643. doi:10.1371/journal.pcbi.1002722

2011

• Aderem A., J.N. Adkins, C. Ansong, J. Galagan, S. Kaiser, M.J. Korth, and G.L. Law, et al. 2011. "A Systems Biology Approach to Infectious Disease Research: Innovating the Pathogen-Host Research Paradigm." mBio 2, no. 1:Article No. e00325. PNNL-SA-77026. doi:10.1128/mBio.00325-10
• Heffron F., G. Niemann, H. Yoon, A.S. Kidwai, R.N. Brown, J.E. McDermott, and R.D. Smith, et al. 2011. "Salmonella-secreted Virulence Factors." In Salmonella: From Genome to Function, edited by S Porwollik. 187-223. Norfolk:Caister Academic Press. PNNL-SA-71401.
• McDermott J.E., A.L. Corrigan, E.S. Peterson, C.S. Oehmen, G. Niemann, E. Cambronne, and D. Sharp, et al. 2011. "Computational prediction of type III and IV secreted effectors in Gram-negative bacteria." Infection and Immunity 79, no. 1:23-32. PNNL-SA-72872. doi:10.1128/IAI.00537-10
• McDermott J.E., C.S. Oehmen, L.A. McCue, E.A. Hill, D.M. Choi, J. Stockel, and M.L. Liberton, et al. 2011. "A Model of Cyclic Transcriptomic Behavior in Cyanobacterium Cyanothece sp. ATCC 51142." Molecular Biosystems 7, no. 8:2407-2418. PNNL-SA-74409. doi:10.1039/C1MB05006K
• McDermott J.E., H. Shankaran, A.J. Eisfeld, S. Belisle, G. Neumann, C. Li, and S.K. Mcweeney, et al. 2011. "Conserved Host Response to Highly Pathogenic Avian Influenza Virus Infection in Human Cell Culture, Mouse and Macaque Model Systems." BMC Systems Biology 5. PNWD-SA-9377. doi:10.1186/1752-0509-5-190
• McDermott J.E., H. Yoon, E.S. Nakayasu, T.O. Metz, D.R. Hyduke, A.S. Kidwai, and B.O. Palsson, et al. 2011. "Technologies and Approaches to Elucidate and Model the Virulence Program of Salmonella." Frontiers in Microbiology 2. PNNL-SA-78291. doi:10.3389/fmicb.2011.00121
• McDermott J.E., M.N. Archuleta, B.D. Thrall, J.N. Adkins, and K.M. Waters. 2011. "Controlling the Response: Predictive Modeling of a Highly Central, Pathogen-Targeted Core Response Module in Macrophage Activation." PLoS One 6(2). PNWD-SA-9011. doi:10.1371/journal.pone.0014673
• McDermott J.E., M.N. Costa, S. Stevens, M. Stenzel-Poore, and A.P. Sanfilippo. 2011. "DEFINING THE PLAYERS IN HIGHER-ORDER NETWORKS: PREDICTIVE MODELING FOR REVERSE ENGINEERING FUNCTIONAL INFLUENCE NETWORKS." In Biocomputing 2011: Proceedings of the Pacific Symposium on Biocomputing, January 3-7, 2011, Kohala Coast, Hawaii, edited by RB Altman, et al, 314-25. London:World Scientific. PNNL-SA-74078. doi:10.1142/9789814335058_0033
• McDermott J.E., P. Braun, R.A. Bonneau, and D.R. Hyduke. 2011. "MODELING HOST-PATHOGEN INTERACTIONS: COMPUTATIONAL BIOLOGY AND BIOINFORMATICS FOR INFECTIOUS DISEASE RESEARCH (Session introduction)." In Pacific Syposium on Biocomputing 2012, January 3-7, 2012, Honolulu, Hawaii, 17, 283-286. Stanford, California:Stanford University. PNNL-SA-83019.
• Niemann G., R.N. Brown, J.K. Gustin, A. Stufkens, A.S. Shaikh-Kidwai, J. Li, and J.E. McDermott, et al. 2011. "Discovery of Novel Secreted Virulence Factors from Salmonella enterica Serovar Typhimurium by Proteomic Analysis of Culture Supernatants." Infection and Immunity 79, no. 1:33-43. PNNL-SA-71385. doi:10.1128/IAI.00771-10
• Rasmussen A., D.L. Diamond, J.E. McDermott, X. Gao, T.O. Metz, M.M. Matzke, and V. Carter, et al. 2011. "Systems Virology Identifies a Mitochondrial Fatty Acid Oxidation Enyzme, Dodecenoyl Coenzyme A Delta Isomerase, Required for Hepatitis C Virus Replication and Likely Pathogenesis." Journal of Virology 85, no. 22:11646-11654. PNWD-SA-9324. doi:10.1128/JVI.05605-11
• Taylor R.C., A.P. Sanfilippo, J.E. McDermott, R.L. Baddeley, R.M. Riensche, R.S. Jensen, and M. Verhagen, et al. 2011. "Enriching regulatory networks by bootstrap learning using optimised GO-based gene similarity and gene links mined from PubMed abstracts." International Journal of Computational Biology and Drug Design 4, no. 1:56-82. PNNL-SA-76542. doi:10.1504/IJCBDD.2011.038657
• Yoon H., C. Ansong, J.E. McDermott, M.A. Gritsenko, R.D. Smith, F. Heffron, and J.N. Adkins. 2011. "Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella." BMC Systems Biology 5. PNNL-SA-77197. doi:10.1186/1752-0509-5-100

2010

• Buchko G.W., G. Niemann, E.S. Baker, M.E. Belov, R.D. Smith, F. Heffron, and J.N. Adkins, et al. 2010. "A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins." Molecular Biosystems 6, no. 12:2448-2458. PNNL-SA-73691. doi:10.1039/c0mb00097c
• Diamond D.L., A.J. Syder, J.M. Jacobs, C.M. Sorensen, K. Walters, S. Proll, and J.E. McDermott, et al. 2010. "Temporal Proteome and Lipidome Profiles Reveal HCV-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics." PLoS Pathogens 6, no. 1:Art. No. e1000719. PNWD-SA-8678. doi:10.1371/journal.ppat.1000719
• Lawrence P., W. Kittichotirat, J.E. McDermott, and R.E. Bumgarner. 2010. "A Three-way Comparative Genomic Analysis of Mannheimia haemolytica Isolates." BMC Genomics 11. PNNL-SA-75660. doi:10.1186/1471-2164-11-535
• Lawrence P., W. Kittichotirat, R.E. Bumgarner, J.E. McDermott, D. Herndon, D.P. Knowles, and S. Srikumaran. 2010. "Genome sequences of Mannheimia haemolytica serotype A2: ovine and bovine isolates." Journal of Bacteriology 192, no. 4:1167-1168. PNWD-SA-8800. doi:10.1128/JB.01527-09
• McDermott J.E., A.P. Sanfilippo, R.C. Taylor, R.L. Baddeley, R.M. Riensche, and R.S. Jensen. 2010. "An Integrated Approach to Predictive Genomic Analytics." In Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 390-393. New York, New York:Association for Computing Machinery. PNNL-SA-72871. doi:10.1145/1854776.1854837
• McDermott J.E., M.N. Costa, D.B. Janszen, M. Singhal, and S.C. Tilton. 2010. "Separating the Drivers from the Driven: Integrative Network and Pathway Approaches Aid Identification of Disease Biomarkers from High-Throughput Data." Disease Markers 28, no. 4:253-266. PNNL-SA-70130. doi:10.3233/DMA-2010-0695
• Taylor R.C., A.P. Sanfilippo, J.E. McDermott, R.L. Baddeley, R.M. Riensche, R.S. Jensen, and M. Verhagen. 2010. "Learning Biological Networks via Bootstrapping with Optimized GO-based Gene Similarity." In Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 515-519. New York, New York:Association for Computing Machinery. PNNL-SA-71923. doi:10.1145/1854776.1854875
• Wang J., J. Zhang, R. Li, H. Zheng, J. Li, Y. Zhang, and H. Li, et al. 2010. "Evolutionary transients in the rice transcriptome." Genomics, Proteomics & Bioinformatics 8, no. 4:211-228. PNNL-SA-58635. doi:10.1016/S1672-0229(10)60023-X

2009

• Cannon W.R., B.M. Webb-Robertson, A.R. Willse, M. Singhal, L.A. McCue, J.E. McDermott, and R.C. Taylor, et al. 2009. "An Integrative Computational Framework for Hypotheses-Driven Systems Biology Research in Proteomics and Genomics." In Computational and Systems Biology: Methods and Applications. 63-85. Trivandrum:Research Signpost. PNNL-SA-57999.
• Frazier Z., J.E. McDermott, M. Guerquin, and R. Samudrala. 2009. "Computational representation of biological systems." In Computational Systems Biology, Methods in Molecular Biology. 535-550. Totowa, New Jersey:Humana Press. PNNL-SA-56401.
• Guerquin M., J.E. McDermott, Z. Frazier, and R. Samudrala. 2009. "The Bioverse API and Web Application." In Computational Systems Biology, Methods in Molecular Biology. 511-534. Totowa, New Jersey:Humana Press. PNNL-SA-56404.
• McDermott J.E., J. Wang, J. Yu, G. Wong, and R. Samudrala. 2009. "Prediction and Annotation of Plant Protein Interaction Networks." In Plant Genomics and Bioinformatics, edited by GP Rao, C Wagner, RK Singh and ML Sharma. 207-238. Houston, Texas:Studium Press LLC. PNNL-SA-57922.
• McDermott J.E., R. Samudrala, R.E. Bumgarner, K. Montogomery, R. Ireton, and R. Ireton. 2009. Computational Systems Biology. Totowa, New Jersey:Humana Press. PNNL-SA-57221.
• McDermott J.E., R.C. Taylor, H. Yoon, and F. Heffron. 2009. "Bottlenecks and Hubs in Inferred Networks Are Important for Virulence in Salmonella typhimurium." Journal of Computational Biology 16, no. 2:169-180. PNNL-SA-61800. doi:10.1089/cmb.2008.04TT
• Rashid I., I. Rashid, J.E. McDermott, and R. Samudrala. 2009. "Inferring molecular interactions pathways from eQTL data." In Computational Systems Biology, Methods in Molecular Biology. 211-224. Totowa, New Jersey:Humana Press. PNNL-SA-56402.
• Samudrala R., F. Heffron, and J.E. McDermott. 2009. "Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems." PLoS Pathogens 5, no. 4. PNNL-SA-61526. doi:10.1371/journal.ppat.1000375
• Sanfilippo A.P., R.L. Baddeley, N. Beagley, J.E. McDermott, R.M. Riensche, R.C. Taylor, and B. Gopalan. 2009. "Using the Gene Ontology to Enrich Biological Pathways." International Journal of Computational Biology and Drug Design 2, no. 3:221-235. PNNL-SA-69383. doi:10.1504/IJCBDD.2009.030114
• Shi L., C. Ansong, H.S. Smallwood, L.M. Rommereim, J.E. McDermott, H.M. Brewer, and A.D. Norbeck, et al. 2009. "Proteome of Salmonella enterica serotype Tyhimurium Grown in Low Mg2+/pH Medium." Journal of Proteomics and Bioinformatics 2, no. 9:388-397. PNNL-SA-68770. doi:10.4172/jpb.1000099
• Shi L., C. Ansong, H.S. Smallwood, L.M. Rommereim, J.E. McDermott, H.M. Brewer, and A.D. Norbeck, et al. 2009. "Proteome of Salmonella Enterica SerotypeTyphimurium Grown in a Low Mg2+/pH Medium." Journal of Proteomics and Bioinformatics 2, no. 9:388-397. PNNL-SA-60692. doi:10.4172/jpb.1000099
• Shi L., S.M. Chowdhury, H.S. Smallwood, H. Yoon, H.M. Mottaz-Brewer, A.D. Norbeck, and J.E. McDermott, et al. 2009. "Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Infection with Salmonella enterica." Infection and Immunity 77, no. 8:3227-3233. PNNL-SA-62432. doi:10.1128/IAI.00063-09
• Taylor R.C., M. Singhal, D.S. Daly, J.M. Gilmore, W.R. Cannon, K.O. Domico, and A.M. White, et al. 2009. "An analysis pipeline for the inference of protein-protein interaction networks." International Journal of Data Mining and Bioinformatics 3, no. 4) (Sp. Iss. SI:409-430. PNNL-SA-59756. doi:10.1504/IJDMB.2009.029204
• Taylor R.C., M. Singhal, J.B. Weller, J.B. Weller, S. Khoshnevis, L. Shi, and J.E. McDermott. 2009. "A Network Inference Workflow Applied to Virulence-Related Processes in Salmonella typhimurium." In Annals of the New York Academy of Sciences. 143-158. New York, New York:PubMed. PNNL-SA-60416.
• Toepel J., J.E. McDermott, T. Summerfield, and L.A. Sherman. 2009. "Transcriptional analysis of the unicellular, diazotrophic cyanobacterium Cyanothece sp. ATCC 51142 grown under short day/night cycles." Journal of Phycology 45, no. 3:610-620. PNNL-SA-62083. doi:10.1111/j.1529-8817.2009.00674.x
• Webb-Robertson B.M., L.A. McCue, N. Beagley, J.E. McDermott, D.S. Wunschel, S.M. Varnum, and J.Z. Hu, et al. 2009. "A Bayesian Integration Model of High-Throughput Proteomics and Metabolomics Data for Improved Early Detection of Microbial Infections." In Pacific Symposium on Biocomputing, 14, 451-463. Singapore:World Scientific Publishing Co. PNNL-SA-61531.
• Wichadakul D., J.E. McDermott, and R. Samudrala. 2009. "Prediction and integration of regulatory and protein-protein interactions." In Computational Systems Biology, Methods in Molecular Biology. 101-144. Totowa, New Jersey:Humana Press. PNNL-SA-56403.
• Yoon H., J.E. McDermott, S. Porwollik, M. Mcclelland, and F. Heffron. 2009. "Coordinated Regulation of Virulence during Systemic Infection of Salmonella enterica serovar Typhimurium." PLoS Pathogens 5, no. 2:1-16. PNNL-SA-61974.

2008

• Ansong C., H. Yoon, A.D. Norbeck, J.K. Gustin, J.E. McDermott, H.M. Mottaz, and J. Rue, et al. 2008. "Proteomics Analysis of the Causative Agent of Typhoid Fever." Journal of Proteome Research 7, no. 2:546-557. PNNL-SA-56065. doi:10.1021/pr070434u
• Gorton I., C.S. Oehmen, and J.E. McDermott. 2008. "It Takes Glue to Tango: MeDICi integration framework creates data-intensive computing pipeline." Scientific Computing 25, no. 7:16-24. PNNL-SA-62541.
• McDermott J.E., and R. Samudrala. 2008. "Bioinformatic characterization of plant networks." In Proceedings of the Asia Pacific Conference on Plant Tissue Culture and Agrobiotechnology (APaCPA) 2007. Bedong:Aimst University. PNNL-SA-55710.

2007

• Taylor R.C., M. Singhal, D.S. Daly, K.O. Domico, A.M. White, D.L. Auberry, and K.J. Auberry, et al. 2007. "SEBINI-CABIN: An Analysis Pipeline for Biological Network Inference, with a Case Study in Protein-Protein Interaction Network Reconstruction." In Sixth International Conference on Machine Learning and Applications, (ICMLA 2007), 587-593. Washington Dc:IEEE Computer Society. PNNL-SA-55941. doi:10.1109/ICMLA.2007.63