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Fundamental and Computational Sciences Directorate

Staff information

Katrina

Katrina Waters

Earth & Biological Sciences
Lab Fellow, Team Lead, Biomedical Sci
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-18
Richland, WA 99352

Biography

Dr. Katrina Waters is the division director for Biological Sciences at the Pacific Northwest National Laboratory.

Waters has a Ph.D. in biochemistry and more than 15 years of experience in microarray and proteomics data analysis. Her research interests are focused on the integration of genomics, proteomics, metabolomics and high-throughput screening data to enable predictive mechanistic modeling of disease and toxicity pathways. Her current programs include dose-response modeling of toxicant exposures, mechanistic understanding of PAH mixtures bioactivity, and network modeling of host-pathogen interactions during lethal human viral infections. She leads the Computational Modeling Core for the University of Wisconsin Center for Predictive Modeling of Infectious Diseases, led by Dr. Yoshihiro Kawaoka, the Biostatistics and Modeling Core for the Oregon State University NIEHS Superfund program, led by Dr. Robert Tanguay, and a Department of Homeland Security program for Predictive Modeling of Viral Infections.

Research Interests

  • Pathway-based biomarker discovery for environmental exposure to toxicants, including disease susceptibility factors.
  • High-throughput screening approaches for hazard assessment and mechanism-based risk assessment.
  • Predictive modeling of lethal human viral infections, including influenza, SARS, Ebola and West Nile Virus.
  • Development of computational tools for integration of genomics, proteomics, metabolomics and high-throughput data.

Education and Credentials

  • Ph.D., Biochemistry, University of Wisconsin, 1996
  • A.B., Chemistry, Ripon College, 1992
  • NRSA Postdoctoral Fellowship with Thomas C. Spelsberg, Mayo Graduate School of Medicine, Rochester, MN.
  • Postdoctoral Fellowship with Kevin Gaido, CIIT Centers for Health Research - Research Triangle Park, NC.

Affiliations and Professional Service

  • 2009 - Full Member, Society of Toxicology
  • 2008 - DOE Q Clearance
  • 2013 Scientific Advisory Panel on Methods for Prioritizing Endocrine Disrupting Chemicals using Computational Toxicology Tools, Environmental Protection Agency
  • 2013 - Scientific Advisory Board for Center for Genome Research and Biocomputing at Oregon State University
  • 2013 - 2016 Scientific Advisory Board for Food and Drug Administration National Center for Toxicological Research
  • 2014 - 2015 National Academy of Science Committee on Predictive Toxicology Approaches for Military Assessments of Acute Exposures
  • 2014 - 2015 PNNL Representative on Department of Energy Ebola Task Force, participating in Biomedical Advanced Research and Development Authority (BARDA) Modeling meetings
  • 2015 - Member & Chair, EPA’s Board of Scientific Counselors Subcommittee on Chemical Safety for Sustainability
  • 2015 - National Academy of Science Committee on Endocrine-Related Low Dose Toxicity, commissioned to evaluate the Environmental Protection Agency’s current regulatory toxicity testing strategy for low dose exposures
  • 2016 - 2019 Science Advisory Board for the National Toxicology Program of the National Institutes of Environmental Health Sciences for the Secretary of Health & Human Services
  • 2009 - 2012 Board of Scientific Counselors, Environmental Protection Agency Subcommittee for Computational Toxicology
  • 2008 - 2012 Editorial Board: Toxicology and Applied Pharmacology
  • 2006 - 2011 Associate Member, Society for Toxicologic Pathology

Awards and Recognitions

  • Secretary of Energy Appreciation Award for the National Laboratory Ebola Task Force Team, January 2017
  • Oregon State University James and Mildred Oldfield/E.R. Jackman Team Award: OSU/PNNL Superfund Research Program: “PAHs: New Technologies and Emerging Health Threats”, September 2015.
  • Best Presentation in Mixtures, Awarded by the SOT Mixtures Specialty Section, March 2012
  • Outstanding Poster Travel Award, Gordon Conference on Toxicogenomics, June 2007
  • Outstanding Performance Award, Pacific Northwest National Laboratory, October 2006
  • Plenary Poster Award, American Society for Bone and Mineral Research, June 1998
  • National Research Service Award, NCI Postdoctoral Fellowship, 1997-1999

PNNL Publications

2018

  • Haggard D.E., P.D. Noyes, K.M. Waters, and R. Tanguay. 2018. "Transcriptomic and phenotypic profiling in developing zebrafish exposed to thyroid hormone receptor agonists." Reproductive Toxicology 77. PNNL-SA-122324. doi:10.1016/j.reprotox.2018.02.006
  • 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

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
  • Davie-Martin C.L., K.G. Stratton, J.G. Teeguarden, K.M. Waters, and S.L. Massey Simonich. 2017. "Implications of bioremediation of polycyclic aromatic hydrocarbon-contaminated soils for human health and cancer risk." Environmental Science & Technology 51, no. 17:9458-9468. PNNL-SA-122323. doi:10.1021/acs.est.7b02956
  • 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
  • Madeen E.P., C.V. Lohr, H. You, L.E. Siddens, S.K. Krueger, R.H. Dashwood, and F.J. Gonzalez, et al. 2017. "Dibenzo[def,p]chrysene transplacental carcinogenesis in wild-type, Cyp1b1 knockout, and CYP1B1 humanized mice." Molecular Carcinogenesis 56, no. 1:163-171. PNWD-SA-10523. doi:10.1002/mc.22480
  • 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
  • Powell J.D., and K.M. Waters. 2017. "Influenza-omics and the host response: recent advances and future prospects." Pathogens 6, no. 2:25. PNNL-SA-126286. doi:10.3390/pathogens6020025

2016

  • Haggard D.E., P.D. Noyes, K.M. Waters, and R. Tanguay. 2016. "Phenotypically anchored transcriptome profiling of developmental exposure to the antimicrobial agent, triclosan, reveals hepatotoxicity in embryonic zebrafish." Toxicology and Applied Pharmacology 308. PNWD-SA-10549. doi:10.1016/j.taap.2016.08.013
  • 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
  • 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
  • Teeguarden J.G., Y. Tan, S. Edwards, J.A. Leonard, K. Anderson, R.A. Corley, and M.L. Kile, et al. 2016. "Expanding on Successful Concepts, Models, and Organization." Environmental Science & Technology 50, no. 17:8921-8922. PNNL-SA-119240. doi:10.1021/acs.est.6b03027
  • Teeguarden J.G., Y. Tan, Y. Tan, S. Edwards, J.A. Leonard, K.A. Anderson, and R.A. Corley, et al. 2016. "Completing the Link between Exposure Science and Toxicology for Improved Environmental Health Decision Making: The Aggregate Exposure Pathway Framework." Environmental Science & Technology 50, no. 9:4579-4586. PNNL-SA-114098. doi:10.1021/acs.est.5b05311
  • 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
  • Wittwehr C., H. Aladjov, G.T. Ankley, H.J. Byrne, J. de Knecht, E. Heinzle, and G. Klambauer, et al. 2016. "How Adverse Outcome Pathways Can Aid the Development and Use of Computational Prediction Models for Regulatory Toxicology." Toxicological Sciences 155, no. 2:326-336. PNNL-SA-117451. doi:10.1093/toxsci/kfw207

2015

  • Goodale B., J.K. La Du, S.C. Tilton, C.M. Sullivan, W.H. Bisson, K.M. Waters, and R. Tanguay. 2015. "Ligand-specific transcriptional mechanisms underlie aryl hydrocarbon receptor-mediated developmental toxicity of oxygenated PAHs." Toxicological Sciences 147, no. 2:397-411. PNWD-SA-10474. doi:10.1093/toxsci/kfv139
  • Hu J.Z., X. Wang, J. Feng, B.M. Webb-Robertson, K.M. Waters, S.C. Tilton, and J.G. Pounds, et al. 2015. "Metabolite Signatures in Hydrophilic Extracts of Mouse Lungs Exposed to Cigarette Smoke Revealed By 1H NMR Metabolomics Investigation." Metabolomics 5, no. 2:Article No. 143. PNNL-SA-102290. doi:10.4172/2153-0769.1000143
  • Kebaabetswe L.P., A.K. Haick, M.A. Gritsenko, T.L. Fillmore, R.K. Chu, S.O. Purvine, and B.M. Webb-Robertson, et al. 2015. "Proteomic Analysis Reveals Down-Regulation of Surfactant Protein B in Murine Type II Pneumocytes Infected with Influenza A Virus." Virology 438. PNWD-SA-10439. doi:10.1016/j.virol.2015.03.045
  • Lafontaine S., J. Schrlau, J. Butler, Y. Jia, B.L. Harper, S.G. Harris, and L.M. Bramer, et al. 2015. "RELATIVE INFLUENCE OF TRANS-PACIFIC AND REGIONAL ATMOSPHERIC TRANSPORT OF PAHS IN THE PACIFIC NORTHWEST, U.S." Environmental Science & Technology 49, no. 23:13807-13816. PNWD-SA-10478. doi:10.1021/acs.est.5b00800
  • 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
  • Rohlman D., L. Syron, K. Hobbie, K. Anderson, C. Scaffidi, D. Sudakin, and E.S. Peterson, et al. 2015. "A Community-Based Approach to Developing a Mobile Device for Measuring Ambient Air Exposure, Location and Respiratory Health." Environmental Justice 8, no. 4:126-134. PNWD-SA-10454. doi:10.1089/env.2015.0001
  • Siddens L.K., K.L. Bunde, T.A. Harper Jr., T.J. McQuistan, C.V. Lohr, L.M. Bramer, and K.M. Waters, et al. 2015. "Cytochrome P450 1b1 in Polycyclic Aromatic Hydrocarbon (PAH)-Induced Skin Carcinogenesis: Tumorigenicity of Individual PAHs and Coal-Tar Extract, DNA Adduction and Expression of Select Genes in the Cyp1b1 Knockout Mouse Toxicology and Applied Pharmacology." Toxicology and Applied Pharmacology 287, no. 2:149-160. PNWD-SA-10455. doi:10.1016/j.taap.2015.05.019
  • Tilton S.C., L.K. Siddens, S.K. Krueger, A.J. Larkin, C.V. Lohr, D.E. Williams, and W.M. Baird, et al. 2015. "Mechanism-based Classification of PAH Mixtures to Predict Carcinogenic Potential." Toxicological Sciences 146, no. 1:135-45. PNWD-SA-10456. doi:10.1093/toxsci/kfv080
  • Tilton S.C., M.M. Matzke, M.B. Sowa, D.L. Stenoien, T.J. Weber, W.F. Morgan, and K.M. Waters. 2015. "Data Integration Reveals Key Homeostatic Mechanisms Following Low Dose Radiation Exposure." Toxicology and Applied Pharmacology 285, no. 2:1-11. PNNL-SA-102570. doi:10.1016/j.taap.2015.01.019
  • 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
  • Baulch J.E., U. Aypar, K.M. Waters, A. Yang, and W.F. Morgan. 2014. "Genetic and Epigenetic Changes in Chromosomally Stable and Unstable Progeny of Irradiated Cells." PLoS One 9, no. 9:e107722. PNNL-SA-103002. doi:10.1371/journal.pone.0107722
  • Govey P.M., J.M. Jacobs, S.C. Tilton, A.E. Loiselle, Y. Zhang, W.M. Freeman, and K.M. Waters, et al. 2014. "Integrative Transcriptomic and Proteomic Analysis of Osteocytic Cells Exposed to Fluid Flow Reveals Novel Mechano-Sensitive Signaling Pathways." Journal of Biomechanics 47, no. 8:1838-1845. PNWD-SA-10062. doi:10.1016/j.jbiomech.2014.03.022
  • Hengel S., J.T. Aldrich, K.M. Waters, L. Pasa-Tolic, and D.L. Stenoien. 2014. "Quantitative Proteomic Profiling of Low Dose Ionizing Radiation Effects in a Human Skin Model." Proteomes 2, no. 3:382-398. PNNL-SA-102010. doi:10.3390/proteomes2030382
  • Menachery V., A.J. Eisfeld, A. Schafer, L. Josset, A.C. Sims, S. Proll, and S. Fan, et al. 2014. "Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches to Control Interferon-Stimulated Gene Responses." mBio 5, no. 3:Article No. e01174-14. PNWD-SA-9990. doi:10.1128/mBio.01174-14
  • Teeguarden J.G., V.B. Mikheev, K.R. Minard, W.C. Forsythe, W. Wang, G. Sharma, and N.J. Karin, et al. 2014. "Comparative Iron Oxide Nanoparticle Cellular Dosimetry and Response in Mice by the Inhalation and Liquid Cell Culture Exposure Routes." Particle and Fibre Toxicology 11. PNNL-SA-101188. doi:10.1186/s12989-014-0046-4
  • Tilton S.C., N.J. Karin, A. Tolic, Y. Xie, X. Lai, R.F. Hamilton, and K.M. Waters, et al. 2014. "Three Human Cell Types Respond to Multi-Walled Carbon Nanotubes and Titanium Dioxide Nanobelts with Cell-Specific Transcriptomic and Proteomic Expression Patterns." Nanotoxicology 8, no. 5:533-548. PNNL-SA-94058. doi:10.3109/17435390.2013.803624
  • Waters K.M., B.S. Cummings, H. Shankaran, N.E. Scholpa, and T.J. Weber. 2014. "ERK Oscillation-Dependent Gene Expression Patterns and Deregulation by Stress-Response." Chemical Research in Toxicology 27, no. 9:1496-1503. PNNL-SA-101628. doi:10.1021/tx500085u
  • 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
  • Webb-Robertson B.M., Y. Kim, E.M. Zink, K.A. Hallaian, Q. Zhang, R. Madupu, and K.M. Waters, et al. 2014. "A Statistical Analysis of the Effects of Urease Pre-Treatment on the Measurement of the Urinary Metabolome by Gas Chromatography-Mass Spectrometry." Metabolomics 10, no. 5:897-908. PNWD-SA-10204. doi:10.1007/s11306-014-0642-1

2013

  • Franzosa J., S. Bugel, T. Tal, J.K. La Du, S.C. Tilton, K.M. Waters, and R. Tanguay. 2013. "Retinoic Acid-Dependent Regulation of miR-19 Expression Elicits Vertebrate Axis Defects." FASEB Journal 27, no. 12:4866-76. PNWD-SA-9975. doi:10.1096/fj.12-225524
  • Goodale B., S.C. Tilton, M.M. Corvi, G.V. Wilson, D.B. Janszen, K.A. Anderson, and K.M. Waters, et al. 2013. "Structurally Distinct Polycyclic Aromatic Hydrocarbons Induce Differential Transcriptional Responses in Developing Zebrafish." Toxicology and Applied Pharmacology 272, no. 3:656-670. PNNL-SA-93495. doi:10.1016/j.taap.2013.04.024
  • Gralinski L., A. Bankhead, S. Jeng, V. Menachery, S. Proll, S. Belisle, and M.M. Matzke, et al. 2013. "Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury." mBio 4, no. 4:Article No. e00271-13. PNWD-SA-9804. doi:10.1128/mBio.00271-13
  • Knecht A., B. Goodale, L. Truong, M. Simonich, A. Swanson, M.M. Matzke, and K.A. Anderson, et al. 2013. "Comparative Developmental Toxicity of Environmentally Relevant Oxygenated PAHs." Toxicology and Applied Pharmacology 271, no. 2:266-275. PNNL-SA-91217. doi:10.1016/j.taap.2013.05.006
  • Larkin A.J., L.K. Siddens, S.K. Krueger, S.C. Tilton, K.M. Waters, D.E. Williams, and W.M. Baird. 2013. "Application of a Fuzzy Neural Network Model in Predicting Polycyclic Aromatic Hydrocarbon-Mediated Perturbations of the Cyp1b1 Transcriptional Regulatory Network in Mouse Skin." Toxicology and Applied Pharmacology 267, no. 2:192-199. PNWD-SA-9877. doi:10.1016/j.taap.2012.12.011
  • Long J.P., M.S. Kotur, G.V. Stark, R.L. Warren, M.D. Kasoji, J.L. Craft, and R. Albrecht, et al. 2013. "Accumulation of CD11b+GR-1+ Cells in the Lung, Blood and Bone Marrow of Mice Infected with Highly Pathogenic H5N1 and H1N1 Influenza Viruses." Archives of Virology 158, no. 6:1305-22. PNWD-SA-9467. doi:10.1007/s00705-012-1593-3
  • 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
  • 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
  • Motorykin O., M.M. Matzke, K.M. Waters, and S.L. Massey Simonich. 2013. "Association of Carcinogenic Polycyclic Aromatic Hydrocarbon Emissions and Smoking with Lung Cancer Mortality Rates on a Global Scale." Environmental Science & Technology 47, no. 7:3410-3416. PNWD-SA-9831. doi:10.1021/es305295d
  • Saili K.S., S.C. Tilton, K.M. Waters, and R. Tanguay. 2013. "Global Gene Expression Analysis Reveals Pathway Differences Between Teratogenic and Non-Teratogenic Exposure Concentrations of Bisphenol A and 17ß-Estradiol in Embryonic Zebrafish." Reproductive Toxicology 38. PNWD-SA-9894. doi:10.1016/j.reprotox.2013.03.009
  • Sims A.C., S.C. Tilton, V. Menachery, L. Gralinski, A. Schafer, M.M. Matzke, and B.M. Webb-Robertson, et al. 2013. "Release of Severe Acute Respiratory Syndrome Coronavirus Nuclear Import Block Enhances Host Transcription in Human Lung Cells." Journal of Virology 87, no. 7:3885-902. PNWD-SA-9741. doi:10.1128/JVI.02520-12
  • Tchitchek N., A.J. Eisfeld, J. Tisoncik-Go, L. Josset, L. Gralinski, C. Becavin, and S.C. Tilton, et al. 2013. "Specific Mutations in H5N1 Mainly Impact the Magnitude and Velocity of the Host Response in Mice." BMC Systems Biology 7. PNNL-SA-94011. doi:10.1186/1752-0509-7-69
  • Tilton S.C., K.M. Waters, N.J. Karin, B.M. Webb-Robertson, R.C. Zangar, M.K. Lee, and D.J. Bigelow, et al. 2013. "Diet-Induced Obesity Reprograms the Inflammatory Response of the Murine Lung to Inhaled Endotoxin." Toxicology and Applied Pharmacology 262, no. 2:137-148. PNNL-SA-89403. doi:10.1016/j.taap.2012.12.020
  • Tilton S.C., N.J. Karin, B.M. Webb-Robertson, K.M. Waters, V.B. Mikheev, K.M. Lee, and R.A. Corley, et al. 2013. "Impaired Transcriptional Response of the Murine Heart to Cigarette Smoke in the Setting of High Fat Diet and Obesity." Chemical Research in Toxicology 26, no. 7:1034-1042. PNNL-SA-90838. doi:10.1021/tx400078b
  • Truong L., S.C. Tilton, T. Zaikovia, E. Richman, K.M. Waters, J.E. Hutchinson, and R. Tanguay. 2013. "Surface Functionalities of Gold Nanoparticles Impact Embryonic Gene Expression Responses." Nanotoxicology 7, no. 2:192-201. PNWD-SA-9547. doi:10.3109/17435390.2011.648225
  • Waters K.M., R.L. Sontag, and T.J. Weber. 2013. "Hepatic Leukemia Factor Promotes Resistance To Cell Death: Implications For Therapeutics and Chronotherapy." Toxicology and Applied Pharmacology 268, no. 2:141-148. PNNL-SA-93319. doi:10.1016/j.taap.2013.01.031
  • 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.

2012

  • Chen J., C. Huang, L. Truong, J.K. La Du, S.C. Tilton, K.M. Waters, and K. Lin, et al. 2012. "Early Life Stage Trimethyltin Exposure Induces ADP-Ribosylation Factor Expression and Perturbs the Vascular System in Zebrafish." Toxicology 302, no. 2-3:129-139. PNWD-SA-9327. doi:10.1016/j.tox.2012.09.004
  • 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
  • Forsberg N.D., D. Stone, A. Harding, B.L. Harper, S.G. Harris, M.M. Matzke, and A. Cardenas, et al. 2012. "Effect of Native American Fish Smoking Methods on Dietary Exposure to Polycyclic Aromatic Hydrocarbons and Possible Risks to Human Health." Journal of Agricultural and Food Chemistry 60, no. 27:6899-6906. PNWD-SA-9736. doi:10.1021/jf300978m
  • Freiin von Neubeck C.H., H. Shankaran, N.J. Karin, P.M. Kauer, W.B. Chrisler, X. Wang, and R.J. Robinson, et al. 2012. "Cell Type-dependent Gene Transcription Profile in Three Dimensional Human Skin Tissue Model Exposed to Low Doses of Ionizing Radiation: Implications for Medical Exposures." Environmental and Molecular Mutagenesis 53, no. 4:247-259. PNNL-SA-79289. doi:10.1002/em.21682
  • Goodale B., J.K. La Du, W.H. Bisson, D.B. Janszen, K.M. Waters, and R. Tanguay. 2012. "AHR2 Mutant Reveals Functional Diversity of Aryl Hydrocarbon Receptors in Zebrafish." PLoS One 7, no. 1:e29346. PNWD-SA-9525. doi:10.1371/journal.pone.0029346
  • Hobbie K.A., E.S. Peterson, M. Barton, K.M. Waters, and K.A. Anderson. 2012. "Integration of Data Systems and Technology Improves Research and Collaboration for a Superfund Research Center." JALA. Journal of the Association for Laboratory Automation 17, no. 4:275-83. PNWD-SA-9755.
  • Matzke M.M., S. Allan, K.A. Anderson, and K.M. Waters. 2012. "An Approach for Calculating a Confidence Interval from a Single Aquatic Sample for Monitoring Hydrophobic Organic Contaminants." Environmental Toxicology and Chemistry 31, no. 12:2888-2892. PNWD-SA-9693. doi:10.1002/etc.2014
  • 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
  • Rutledge A.C., G. Fontes, M.A. Gritsenko, A.D. Norbeck, D.J. Anderson, K.M. Waters, and J.N. Adkins, et al. 2012. "Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics." Journal of Proteome Research 11, no. 7:3520-32. PNNL-SA-77193. doi:10.1021/pr3002996
  • Shorey L., D.J. Castro, W.M. Baird, L.K. Siddens, C.V. Lohr, M.M. Matzke, and K.M. Waters, et al. 2012. "Transplacental Carcinogenesis with Dibenzo[def,p]chrysene (DBC): Timing of Maternal Exposures Determines Target Tissue Response in Offspring." Cancer Letters 317, no. 1:49-55. PNWD-SA-9570. doi:10.1016/j.canlet.2011.11.010
  • Siddens L.K., A.J. Larkin, S.K. Krueger, C.A. Bradfield, K.M. Waters, S.C. Tilton, and C. Pereira, et al. 2012. "Polycyclic Aromatic Hydrocarbons as Skin Carcinogens: Comparison of Benzo[a]pyrene, Dibenzo[def,p]chrysene and Three Environmental Mixtures in the FVB/N Mouse." Toxicology and Applied Pharmacology 264, no. 3:377-386. PNWD-SA-9832. doi:10.1016/j.taap.2012.08.014
  • Tal T., J. Franzosa, S.C. Tilton, K.A. Philbrick, U.T. Iwaniec, U.T. Iwaniec, and R.T. Turner, et al. 2012. "MicroRNAs Control Neurobehavioral Development and Function in Zebrafish." FASEB Journal 26, no. 4:1452-1461. PNWD-SA-9473. doi:10.1096/fj.11-194464
  • Thomas S.N., K.M. Waters, W.F. Morgan, A. Yang, and J.E. Baulch. 2012. "Quantitative Proteomic Analysis of Mitochondrial Proteins Reveals Pro-Survival Mechanisms in the Perpetuation of Radiation-Induced Genomic Instability." Free Radical Biology & Medicine 53, no. 3:618-628. PNNL-SA-86050. doi:10.1016/j.freeradbiomed.2012.03.025
  • Thrall B.D., K.R. Minard, J.G. Teeguarden, and K.M. Waters. 2012. Multiscale Toxicology - Building the Next Generation Tools for Toxicology. PNNL-21916. Richland, WA: Pacific Northwest National Laboratory.
  • Tilton S.C., T. Tal, S.M. Scroggins, J. Franzosa, E.S. Peterson, R. Tanguay, and K.M. Waters. 2012. "Bioinformatics Resource Manager v2.3: An Integrated Software Environment for Systems Biology with microRNA and Cross-species Analysis Tools." BMC Bioinformatics 13. PNWD-SA-9777. doi:10.1186/1471-2105-13-311
  • Varnum S.M., D.L. Springer, M.E. Chaffee, K.A. Lien, B.M. Webb-Robertson, K.M. Waters, and C.A. Sacksteder. 2012. "The Effects of Low Dose Irradiation on Inflammatory Response Proteins in a 3D Reconstituted Human Skin Tissue Model." Radiation Research 178, no. 6:591-599. PNNL-SA-86146. doi:10.1667/RR2976.1
  • Waters K.M., D.L. Stenoien, M.B. Sowa, C.H. Freiin Von Neubeck, W.B. Chrisler, R. Tan, and R.L. Sontag, et al. 2012. "Annexin A2 Modulates Radiation-Sensitive Transcriptional Programming and Cell Fate." Radiation Research 179, no. 1:56-61. PNNL-SA-84443. doi:10.1667/RR3056.1
  • Waters K.M., T. Liu, R.D. Quesenberry, A.R. Willse, S. Bandyopadhyay, L.E. Kathmann, and T.J. Weber, et al. 2012. "Network Analysis of Epidermal Growth Factor Signaling using Integrated Genomic, Proteomic and Phosphorylation Data." PLoS One 7, no. 3:Article No. e34515. PNNL-SA-85737. doi:10.1371/journal.pone.0034515
  • Yang F., K.M. Waters, B.M. Webb-Robertson, M.B. Sowa, C.H. Freiin von Neubeck, J.T. Aldrich, and L.M. Markillie, et al. 2012. "Quantitative Phosphoproteomics Identifies Filaggrin and other Targets of Ionizing Radiation in a Human Skin Model." Experimental Dermatology 21, no. 5:352-357. PNNL-SA-79030. doi:10.1111/j.1600-0625.2012.01470.x

2011

  • Ahring B.K., N.S. Baliga, J.R. Frederickson, S. Kaplan, H.B. Pakrasi, J.G. Pounds, and I. shah, et al. 2011. Biological Interactions and Dynamics Science Theme Advisory Panel (BID-STAP). PNNL-20717. Richland, WA: Pacific Northwest National Laboratory.
  • Li C., A. Bankhead, A.J. Eisfeld, Y. Hatta, S. Jeng, J.H. Chang, and L.D. Aicher, et al. 2011. "Host Regulatory Network Response to Infection with Highly Pathogenic H5N1 Avian Influenza Virus." Journal of Virology 85, no. 21:10955-10967. PNWD-SA-9325.
  • Matzke M.M., K.M. Waters, T.O. Metz, J.M. Jacobs, A. Sims, R. Baric, and J.G. Pounds, et al. 2011. "Improved Quality Control Processing of Peptide-centric LC-MS Proteomics Data." Bioinformatics 27, no. 20:2866-2872. PNNL-SA-76540.
  • 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., 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
  • 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
  • Teeguarden J.G., B.M. Webb-Robertson, K.M. Waters, A. Murray, E. Kisin, S.M. Varnum, and J.M. Jacobs, et al. 2011. "Comparative Proteomics and Pulmonary Toxicity of Instilled Single Walled Carbon Nanotubes, Crocidolite Asbestos and Ultrafine Carbon Black in Mice." Toxicological Sciences 120, no. 1:123-135. PNNL-SA-74369. doi:10.1093/toxsci/kfq363
  • Waters K.M., J.M. Jacobs, M.A. Gritsenko, and N.J. Karin. 2011. "Regulation of gene expression and subcellular protein distribution in MLO-Y4 osteocytic cells by lysophosphatidic acid: Relevance to dendrite outgrowth." Bone 48, no. 6:1328-35. PNNL-SA-74808. doi:10.1016/j.bone.2011.02.020
  • Webb-Robertson B.M., M.M. Matzke, J.M. Jacobs, J.G. Pounds, and K.M. Waters. 2011. "A Statistical Selection Strategy for Normalization Procedures in LC-MS Proteomics Experiments through Dataset Dependent Ranking of Normalization Scaling Factors." Proteomics 11, no. 24:4736-4741. PNNL-SA-78392. doi:10.1002/pmic.201100078

2010

  • Bailey V.L., S.J. Fansler, S. Bandyopadhyay, J.L. Smith, K.M. Waters, and H. Bolton. 2010. "Direct Detection of Soil mRNAs using Targeted Microarrays for Genes Associated with Lignin Degradation." Soil Biology and Biochemistry 42. PNNL-SA-63713.
  • 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
  • Webb-Robertson B.M., L.A. McCue, K.M. Waters, M.M. Matzke, J.M. Jacobs, T.O. Metz, and S.M. Varnum, et al. 2010. "Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-based Proteomics Data." Journal of Proteome Research 9, no. 11:5748-5756. PNNL-SA-72886.
  • Yang F., K.M. Waters, J.H. Miller, M.A. Gritsenko, R. Zhao, X. Du, and E.A. Livesay, et al. 2010. "Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation." PLoS One 5, no. 11:e14152. PNNL-SA-73768. doi:10.1371/journal.pone.0014152

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.
  • Castro D.J., C.V. Lohr, K.A. Fischer, K.M. Waters, B.M. Webb-Robertson, R.H. Dashwood, and G.S. Bailey, et al. 2009. "Identifying Efficacious Approaches to Chemoprevention with chlorophyllin, purified chlorophylls and freeze-dried spinach in a Mouse Model of Transplacental Carcinogenesis." Carcinogenesis 30, no. 2:315-320. PNNL-SA-60493.
  • Waters K.M., L.M. Masiello, R.C. Zangar, B.J. Tarasevich, N.J. Karin, R.D. Quesenberry, and S. Bandyopadhyay, et al. 2009. "Macrophage Responses to Silica Nanoparticles are Highly Conserved Across Particle Sizes." Toxicological Sciences 107, no. 2:553-569. PNNL-SA-62659.
  • Waters K.M., R. Tan, L.K. Opresko, R.D. Quesenberry, S. Bandyopadhyay, W.B. Chrisler, and T.J. Weber. 2009. "Cellular Dichotomy Between Anchorage-Independent Growth Responses to bFGF and TA Reflects Molecular Switch in Commitment to Carcinogenesis." Molecular Carcinogenesis 48, no. 11:1059-1069. PNNL-SA-57090.

2008

  • Ding S., Y. Wang, J.M. Jacobs, W. Qian, F. Yang, A.V. Tolmachev, and X. Du, et al. 2008. "Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis applying Dual-step 18O Labeling Coupled with Immobilized Metal-ion Affinity Chromatography." Journal of Proteome Research 7, no. 10:4215-24. PNNL-SA-52241. doi:10.1021/pr7007785
  • Jacobs J.M., K.M. Waters, L.E. Kathmann, D.G. Camp, H.S. Wiley, R.D. Smith, and B.D. Thrall. 2008. "The Mammary Epithelial Cell Secretome and its Regulation by Signal Transduction Pathways." Journal of Proteome Research 7, no. 2:558-569. PNNL-SA-56310. doi:10.1021/pr0704377
  • Rickard D.J., U.T. Iwaniec, U.T. Iwaniec, G. Evans, T.E. Hefferan, T.E. Hefferan, and J.C. Hunter, et al. 2008. "Bone growth and turnover in progesterone receptor knockout mice." Endocrinology 149, no. 5:2383-2390. PNNL-SA-57031. doi:10.1210/en.2007-1247
  • Rogers S., M. Girolami, M. Girolami, W. Kolch, K.M. Waters, T. Liu, and B.D. Thrall, et al. 2008. "Investigating the Correspondence Between Transcriptomic and Proteomic Expression Profiles Using Coupled Cluster Models." Bioinformatics 24, no. 24:2894-2900. PNNL-SA-61286. doi:10.1093/bioinformatics/btn553
  • Shah A.R., M. Singhal, T.D. Gibson, C. Sivaramakrishnan, K.M. Waters, and I. Gorton. 2008. "An extensible, scalable architecture for managing bioinformatics data and analysis." In IEEE 4th International Conference on e-Science, December 7-12, 2008, Indianapolis, Indiana, 190-197. Los Alamitos, California:IEEE Computer Society. PNWD-SA-8283. doi:10.1109/eScience.2008.69
  • Webb-Robertson B.M., W.R. Cannon, C.S. Oehmen, A.R. Shah, V. Gurumoorthi, M.S. Lipton, and K.M. Waters. 2008. "A Support Vector Machine model for the prediction of proteotypic peptides for accurate mass and time proteomics." Bioinformatics 24, no. 13:1503-1509. PNNL-SA-60074. doi:10.1093/bioinformatics/btn218

2007

  • Shah A.R., M. Singhal, K.R. Klicker, E.G. Stephan, H.S. Wiley, and K.M. Waters. 2007. "Enabling high-throughput data management systems biology: The Bioinformatics Resource Manager." Bioinformatics 23, no. 7:906-909. PNNL-SA-49327. doi:10.1093/bioinformatics/btm031
  • Waters K.M., R. Tan, D.C. Genetos, S. Verma, C.E. Yellowley, and N.J. Karin. 2007. "DNA microarray analysis reveals a role for lysophosphatidic acid in the regulation of anti-inflammatory genes in MC3T3-E1 cells." Bone 41, no. 5:833-841. PNNL-SA-55566. doi:10.1016/j.bone.2007.06.029

2006

  • Waters K.M., J.G. Pounds, and B.D. Thrall. 2006. "Data Merging for Integrated Microarray and Proteomic Analysis." Briefings in Functional Genomics and Proteomics 5, no. 4:261-272. PNNL-SA-47947. doi:10.1093/bfgp/ell019
  • Waters K.M., M. Singhal, B.M. Webb-Robertson, E.G. Stephan, and J.M. Gephart. 2006. "Breaking the High-Throughput Bottleneck: New tools help biologists integrate complex datasets." Scientific Computing 23, no. 4:22-26. PNNL-SA-48217.

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