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Computational Sciences & Mathematics

Staff information

Katrina Waters

Katrina Waters

Biological Sciences Division
Scientist, TL
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-18
Richland, WA 99352
509/375-3907

Biography

Dr. Katrina Waters is a Senior Research Scientist in the Computational Biology and Bioinformatics Group at the Pacific Northwest National Laboratory.

Waters has a Ph.D. in biochemistry and more than eight years of experience in microarray data analysis. Her expertise and research interests are focused around the analysis and biological interpretation of global gene and protein expression data related to mechanism of action or applied research. In addition, she has several years experience developing and carrying out molecular and biochemical assays in the laboratory to test hypotheses resulting from microarray experiments. Her previous work at Merck Research Labs was in the area of investigative toxicology, supporting the safety assessment of drug-development candidates and biomarker-discovery efforts.

Research Interests

  • Biomarker discovery for lung inflammation from nanoparticle exposure.
  • Pathway-based biomarker discovery for environmental exposure to lung toxicants, including disease susceptibility factors.
  • Network modeling of lung inflammation through macrophage and epithelial cell paracrine communication.
  • Development and integration of computational tools for integration of 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 – Board of Scientific Counselors, Environmental Protection Agency Subcommittee for Computational Toxicology
  • 2009 – Full Member, Society of Toxicology
  • 2008 – DOE Q Clearance
  • 2008 – Editorial Board: Toxicology and Applied Pharmacology
  • 2006 - Associate Member, Society for Toxicologic Pathology
  • 2005 - Member, American Society for Cell Biology
  • 2005 - External Advisory Board Member, NIDA Center on Functional Genomics and HCV-Associated Liver Disease at the University of WA
  • Journal Reviews include Endocrinology, Journal of Bone and Mineral Research, Metabolism: Clinical and Experimental, Toxicological Sciences

Awards and Recognitions

  • 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

2014

  • Tilton SC, NJ Karin, A Tolic, Y Xie, X Lai, RF Hamilton, KM Waters, A Holian, Ph.D., FA Witzmann, and G Orr. 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(5):533-548.  doi:10.3109/17435390.2013.803624
  • Webb-Robertson BJM, YM Kim, EM Zink, KA Hallaian, Q Zhang, R Madupu, KM Waters, and TO Metz. 2014. "A Statistical Analysis of the Effects of Urease Pre-Treatment on the Measurement of the Urinary Metabolome by Gas Chromatography-Mass Spectrometry." Metabolomics 1(12):, doi:10.1007/s11306-014-0642-1

2013

  • Gralinski L, A Bankhead, S Jeng, V Menachery, S Proll, S Belisle, MM Matzke, BJM Webb-Robertson, ML Luna, AK Shukla, MT Ferris, M Bolles, JH Chang, LD Aicher, KM Waters, RD Smith, TO Metz, GL Law, MG Katze, SK Mcweeney, and R Baric. 2013. "Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury." mBio 4(4):Article No. e00271-13.  doi:10.1128/mBio.00271-13
  • Knecht A, B Goodale, L Truong, M Simonich, A Swanson, MM Matzke, KA Anderson, KM Waters, and R Tanguay. 2013. "Comparative Developmental Toxicity of Environmentally Relevant Oxygenated PAHs." Toxicology and Applied Pharmacology 271(2):266-275.  doi:10.1016/j.taap.2013.05.006
  • Larkin AJ, LK Siddens, SK Krueger, SC Tilton, KM Waters, DE Williams, and WM 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(2):192-199.  doi:10.1016/j.taap.2012.12.011
  • Long JP, MS Kotur, GV Stark, RL Warren, MD Kasoji, JL Craft, R Albrecht, A Garcia-Sastre, MG Katze, KM Waters, D Vasconcelos, PJ Sabourin, HS Bresler, and CL Sabourin. 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(6):1305-22.  doi:10.1007/s00705-012-1593-3
  • Matzke MM, JN Brown, MA Gritsenko, TO Metz, JG Pounds, KD Rodland, AK Shukla, RD Smith, KM Waters, JE McDermott, and BJM Webb-Robertson. 2013. "A Comparative Analysis of Computational Approaches to Relative Protein Quantification Using Peptide Peak Intensities in Label-free LC-MS Proteomics Experiments." Proteomics 13(3-4):493-503.  doi:10.1002/pmic.201200269
  • Mitchell HD, AJ Eisfeld, A Sims, JE McDermott, MM Matzke, BJM Webb-Robertson, SC Tilton, N Tchitchek, L Josset, C Li, AL Ellis, JH Chang, RA Heegel, ML Luna, AA Schepmoes, AK Shukla, TO Metz, G Neumann, A Benecke, RD Smith, R Baric, Y Kawaoka, MG Katze, and KM Waters. 2013. "A Network Integration Approach to Predict Conserved Regulators Related to Pathogenicity of Influenza and SARS-CoV Respiratory Viruses." PLoS One 8(7):e69374.  doi:10.1371/journal.pone.0069374
  • Motorykin O, MM Matzke, KM Waters, and SL 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(7):3410-3416.  doi:10.1021/es305295d
  • Saili KS, SC Tilton, KM 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 38:89-101.  doi:10.1016/j.reprotox.2013.03.009
  • Sims AC, SC Tilton, V Menachery, L Gralinski, A Schafer, MM Matzke, BJM Webb-Robertson, JH Chang, ML Luna, C Long, AK Shukla, A Bankhead, S Burkett, G Zornester, CK Tseng, TO Metz, R Pickles, SK Mcweeney, RD Smith, MG Katze, KM Waters, and R Baric. 2013. "Release of Severe Acute Respiratory Syndrome Coronavirus Nuclear Import Block Enhances Host Transcription in Human Lung Cells." Journal of Virology 87(7):3885-902.  doi:10.1128/JVI.02520-12
  • Tchitchek N, AJ Eisfeld, J Tisoncik-Go, L Josset, L Gralinski, C Becavin, SC Tilton, BJM Webb-Robertson, MT Ferris, AL Totura, C Li, G Neumann, TO Metz, RD Smith, KM Waters, R Baric, Y Kawaoka, and MG Katze. 2013. "Specific Mutations in H5N1 Mainly Impact the Magnitude and Velocity of the Host Response in Mice." BMC Systems Biology 7:Article No. 69.  doi:10.1186/1752-0509-7-69
  • Tilton SC, KM Waters, NJ Karin, BJM Webb-Robertson, RC Zangar, MK Lee, DJ Bigelow, JG Pounds, and RA Corley. 2013. "Diet-Induced Obesity Reprograms the Inflammatory Response of the Murine Lung to Inhaled Endotoxin." Toxicology and Applied Pharmacology 262(2):137-148.  doi:10.1016/j.taap.2012.12.020
  • Tilton SC, NJ Karin, BJM Webb-Robertson, KM Waters, VB Mikheev, KM Lee, RA Corley, JG Pounds, and DJ Bigelow. 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(7):1034-1042.  doi:10.1021/tx400078b
  • Truong L, SC Tilton, T Zaikovia, E Richman, KM Waters, JE Hutchinson, and R Tanguay. 2013. "Surface Functionalities of Gold Nanoparticles Impact Embryonic Gene Expression Responses." Nanotoxicology 7(2):192-201.  doi:10.3109/17435390.2011.648225
  • Waters KM, RL Sontag, and TJ Weber. 2013. "Hepatic Leukemia Factor Promotes Resistance To Cell Death: Implications For Therapeutics and Chronotherapy." Toxicology and Applied Pharmacology 268(2):141-148.  doi:10.1016/j.taap.2013.01.031
  • Webb-Robertson BJM, MM Matzke, TO Metz, JE McDermott, J Walker, KD Rodland, JG Pounds, and KM Waters. 2013. "Sequential Projection Pursuit Principal Component Analysis – Dealing with Missing Data Associated with New -Omics Technologies." BioTechniques 54(3):165-168. 

2012

  • Matzke MM, S Allan, KA Anderson, and KM Waters. 2012. "An Approach for Calculating a Confidence Interval from a Single Aquatic Sample for Monitoring Hydrophobic Organic Contaminants." Environmental Toxicology and Chemistry 31(12):2888-2892.  doi:10.1002/etc.2014
  • McDermott JE, DL Diamond, CD Corley, A Rasmussen, MG Katze, and KM Waters. 2012. "Topological Analysis of Protein Co-Abundance Networks Identifies Novel Host Targets Important for HCV Infection and Pathogenesis ." BMC Systems Biology 6(1):28.  doi:10.1186/1752-0509-6-28
  • Chen J, C Huang, L Truong, JK La Du, SC Tilton, KM Waters, K Lin, R Tanguay, and Q Dong. 2012. "Early Life Stage Trimethyltin Exposure Induces ADP-Ribosylation Factor Expression and Perturbs the Vascular System in Zebrafish." Toxicology 302(2-3):129-139.  doi:10.1016/j.tox.2012.09.004
  • Diamond DL, A Krasnoselski, KE Burnum, ME Monroe, BJM Webb-Robertson, JE McDermott, MM Yeh, JF Golib-Dzib, N Susnow, S Strom , S Proll, S Belisle, DE Purdy, A Rasmussen, KA Walters, JM Jacobs, MA Gritsenko, DG Camp, II, R Bhattacharya, JD Perkins, RL Carithers, IW Liou, AM Larson, A Benecke, KM Waters, RD Smith, and MG Katze. 2012. "Proteome and Computational Analyses Reveal New Insights into the Mechanisms of Hepatitis C Virus Mediated Liver Disease Posttransplantation." Hepatology 53(1):28-38.  doi:10.1002/hep.25649
  • Forsberg ND, D Stone, A Harding, BL Harper, SG Harris, MM Matzke, A Cardenas, KM Waters, and K Anderson. 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(27):6899–6906.  doi:10.1021/jf300978m
  • Freiin von Neubeck CH, H Shankaran, NJ Karin, PM Kauer, WB Chrisler, X Wang, RJ Robinson, KM Waters, SC Tilton, and MB Sowa. 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(4):247–259.  doi:10.1002/em.21682
  • Goodale B, JK La Du, WH Bisson, DB Janszen, KM Waters, and R Tanguay. 2012. "AHR2 Mutant Reveals Functional Diversity of Aryl Hydrocarbon Receptors in Zebrafish." PLoS One 7(1):e29346.  doi:10.1371/journal.pone.0029346
  • Hobbie KA, ES Peterson, M Barton, KM Waters, and KA 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(4):275-83. 
  • Rutledge AC, G Fontes, MA Gritsenko, AD Norbeck, DJ Anderson, KM Waters, JN Adkins, RD Smith, V Poitout, and TO Metz. 2012. "Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics." Journal of Proteome Research 11(7):3520-32.  doi:10.1021/pr3002996
  • Shorey L, DJ Castro, WM Baird, LK Siddens, CV Lohr, MM Matzke, KM Waters, RA Corley, and DE Williams. 2012. "Transplacental Carcinogenesis with Dibenzo[def,p]chrysene (DBC): Timing of Maternal Exposures Determines Target Tissue Response in Offspring." Cancer Letters 317(1):49-55.  doi: 10.1016/j.canlet.2011.11.010
  • Siddens LK, AJ Larkin, SK Krueger, CA Bradfield, KM Waters, SC Tilton, C Pereira, CV Lohr, VM Arlt, DH Phillips, DE Williams, and WM Baird. 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(3):377-386.  doi:10.1016/j.taap.2012.08.014
  • Tal T, J Franzosa, SC Tilton, KA Philbrick, UT Iwaniec, RT Turner, KM Waters, and R Tanguay. 2012. "MicroRNAs Control Neurobehavioral Development and Function in Zebrafish." FASEB Journal 26(4):1452-1461.  doi:10.1096/fj.11-194464
  • Thomas SN, KM Waters, WF Morgan, A Yang, and JE 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(3):618-628.  doi:10.1016/j.freeradbiomed.2012.03.025
  • Thrall BD, KR Minard, JG Teeguarden, and KM Waters. 2012. Multiscale Toxicology - Building the Next Generation Tools for ToxicologyPNNL-21916, Pacific Northwest National Laboratory, Richland, WA. 
  • Tilton SC, T Tal, SM Scroggins, J Franzosa, ES Peterson, R Tanguay, and KM Waters. 2012. "Bioinformatics Resource Manager v2.3: An Integrated Software Environment for Systems Biology with microRNA and Cross-species Analysis Tools." BMC Bioinformatics 13:Article No. 311.  doi:10.1186/1471-2105-13-311
  • Varnum SM, DL Springer, ME Chaffee, KA Lien, BJM Webb-Robertson, KM Waters, and CA Sacksteder. 2012. "The Effects of Low Dose Irradiation on Inflammatory Response Proteins in a 3D Reconstituted Human Skin Tissue Model." Radiation Research 178(6):591-599.  doi:10.1667/RR2976.1
  • Waters KM, DL Stenoien, MB Sowa, CH Freiin Von Neubeck, WB Chrisler, R Tan, RL Sontag, and TJ Weber. 2012. "Annexin A2 Modulates Radiation-Sensitive Transcriptional Programming and Cell Fate." Radiation Research 179(1):56-61.  doi:10.1667/RR3056.1
  • Waters KM, T Liu, RD Quesenberry, AR Willse, S Bandyopadhyay, LE Kathmann, TJ Weber, RD Smith, HS Wiley, and BD Thrall. 2012. "Network Analysis of Epidermal Growth Factor Signaling using Integrated Genomic, Proteomic and Phosphorylation Data ." PLoS One 7(3):Article No. e34515.  doi:10.1371/journal.pone.0034515
  • Yang F, KM Waters, BJM Webb-Robertson, MB Sowa, CH Freiin von Neubeck, JT Aldrich, LM Markillie, RM Wirgau, MA Gristenko, R Zhao, DG Camp, II, RD Smith, and DL Stenoien. 2012. "Quantitative Phosphoproteomics Identifies Filaggrin and other Targets of Ionizing Radiation in a Human Skin Model." Experimental Dermatology 21(5):352–357.  doi:10.1111/j.1600-0625.2012.01470.x

2011

  • McDermott JE, H Shankaran, AJ Eisfeld, S Belisle, G Neumann, C Li, SK Mcweeney, CL Sabourin, Y Kawaoka, MG Katze, and KM Waters. 2011. "Conserved Host Response to Highly Pathogenic Avian Influenza Virus Infection in Human Cell Culture, Mouse and Macaque Model Systems." BMC Systems Biology 5:Article No. 190.  doi:10.1186/1752-0509-5-190
  • McDermott JE, MN Archuleta, BD Thrall, JN Adkins, and KM Waters. 2011. "Controlling the Response: Predictive Modeling of a Highly Central, Pathogen-Targeted Core Response Module in Macrophage Activation." PLoS One 6(2):e14673.  doi:10.1371/journal.pone.0014673
  • Ahring BK, NS Baliga, JR Frederickson, S Kaplan, HB Pakrasi, JG Pounds, I shah, S Slater, G Stacey, KJ Auberry, DR Baer, DML Brown, DE Cowley, DW Hoyt, DW Koppenaal, BE Linggi, KT Mueller, G Orr, EW Robinson, RG Teller, HS Wiley, NJ Hess, L Pasa-Tolic, KM Waters, and KD Rodland. 2011. Biological Interactions and Dynamics Science Theme Advisory Panel (BID-STAP)PNNL-20717, Pacific Northwest National Laboratory, Richland, WA. 
  • Li C, A Bankhead, AJ Eisfeld, Y Hatta, S Jeng, JH Chang, LD Aicher, S Proll, AL Ellis, GL Law, KM Waters, G Neumann, MG Katze, SK Mcweeney, and Y Kawaoka. 2011. "Host Regulatory Network Response to Infection with Highly Pathogenic H5N1 Avian Influenza Virus." Journal of Virology 85(21):10955-10967. 
  • Matzke MM, KM Waters, TO Metz, JM Jacobs, A Sims, R Baric, JG Pounds, and BJM Webb-Robertson. 2011. "Improved Quality Control Processing of Peptide-centric LC-MS Proteomics Data." Bioinformatics 27(20):2866-2872. 
  • Rasmussen A, DL Diamond, JE McDermott, X Gao, TO Metz, MM Matzke, V Carter, S Belisle, MJ Korth, KM Waters, RD Smith, and MG Katze. 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(22):11646-11654.  doi:10.1128/JVI.05605-11
  • Teeguarden JG, BJM Webb-Robertson, KM Waters, A Murray, E Kisin, SM Varnum, JM Jacobs, JG Pounds, RC Zangar, and A Shvedova. 2011. "Comparative Proteomics and Pulmonary Toxicity of Instilled Single Walled Carbon Nanotubes, Crocidolite Asbestos and Ultrafine Carbon Black in Mice." Toxicological Sciences 120(1):123-135.  doi:10.1093/toxsci/kfq363
  • Waters KM, JM Jacobs, MA Gritsenko, and NJ Karin. 2011. "Regulation of gene expression and subcellular protein distribution in MLO-Y4 osteocytic cells by lysophosphatidic acid: Relevance to dendrite outgrowth." Bone 48(6):1328-35.  doi:10.1016/j.bone.2011.02.020
  • Webb-Robertson BJM, MM Matzke, JM Jacobs, JG Pounds, and KM Waters. 2011. "A Statistical Selection Strategy for Normalization Procedures in LC-MS Proteomics Experiments through Dataset Dependent Ranking of Normalization Scaling Factors." Proteomics 11(24):4736–4741.  doi: 10.1002/pmic.201100078

2010

  • Bailey VL, SJ Fansler, S Bandyopadhyay, JL Smith, KM Waters, and H Bolton, Jr. 2010. "Direct Detection of Soil mRNAs using Targeted Microarrays for Genes Associated with Lignin Degradation." Soil Biology and Biochemistry 42:1793-1799. 
  • Diamond DL, AJ Syder, JM Jacobs, CM Sorensen, KA Walters, S Proll, JE McDermott, MA Gritsenko, Q Zhang, R Zhao, TO Metz, DG Camp, II, KM Waters, RD Smith, CM Rice, and MG Katze. 2010. "Temporal Proteome and Lipidome Profiles Reveal HCV-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics ." PLoS Pathogens 6(1):Art. No. e1000719.  doi:10.1371/journal.ppat.1000719
  • Webb-Robertson BJM, LA McCue, KM Waters, MM Matzke, JM Jacobs, TO Metz, SM Varnum, and JG Pounds. 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(11):5748-5756. 
  • Yang F, KM Waters, JH Miller, MA Gritsenko, R Zhao, X Du, EA Livesay, SO Purvine, ME Monroe, Y Wang, DG Camp, II, RD Smith, and DL Stenoien. 2010. "Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation." PLoS One 5(11):e14152.  doi:10.1371/journal.pone.0014152

2009

  • Cannon WR, BJM Webb-Robertson, AR Willse, M Singhal, LA McCue, JE McDermott, RC Taylor, KM Waters, and CS Oehmen. 2009. "An Integrative Computational Framework for Hypotheses-Driven Systems Biology Research in Proteomics and Genomics." Chapter 4 in Computational and Systems Biology: Methods and Applications, pp. 63-85.  Research Signpost, Trivandrum, India. 
  • Castro DJ, CV Lohr, KA Fischer, KM Waters, BJM Webb-Robertson, RH Dashwood, GS Bailey, and DE Williams. 2009. "Identifying Efficacious Approaches to Chemoprevention with chlorophyllin, purified chlorophylls and freeze-dried spinach in a Mouse Model of Transplacental Carcinogenesis." Carcinogenesis 30(2):315-320. 
  • Waters KM, LM Masiello, RC Zangar, BJ Tarasevich, NJ Karin, RD Quesenberry, S Bandyopadhyay, JG Teeguarden, JG Pounds, and BD Thrall. 2009. "Macrophage Responses to Silica Nanoparticles are Highly Conserved Across Particle Sizes." Toxicological Sciences 107(2):553-569. 
  • Waters KM, R Tan, LK Opresko, RD Quesenberry, S Bandyopadhyay, WB Chrisler, and TJ Weber. 2009. "Cellular Dichotomy Between Anchorage-Independent Growth Responses to bFGF and TA Reflects Molecular Switch in Commitment to Carcinogenesis." Molecular Carcinogenesis 48(11):1059-1069. 

2008

  • Jacobs JM, KM Waters, LE Kathmann, DG Camp, II, HS Wiley, RD Smith, and BD Thrall. 2008. "The Mammary Epithelial Cell Secretome and its Regulation by Signal Transduction Pathways." Journal of Proteome Research 7(2):558-569.  doi:10.1021/pr0704377
  • Ding SJ, Y Wang, JM Jacobs, W Qian, F Yang, AV Tolmachev, X Du, W Wang, RJ Moore, ME Monroe, SO Purvine, KM Waters, TH Heibeck, JN Adkins, DG Camp, II, RL Klemke, and RD Smith. 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(10):4215-24.  doi:10.1021/pr7007785
  • Rickard DJ, UT Iwaniec, G Evans, TE Hefferan, JC Hunter, KM Waters, JP Lydon, BW O'Malley, S Khosla, TC Spelsberg, and RT Turner. 2008. "Bone growth and turnover in progesterone receptor knockout mice." Endocrinology 149(5):2383-2390.  doi:10.1210/en.2007-1247
  • Rogers S, M Girolami, W Kolch, KM Waters, T Liu, BD Thrall, and HS Wiley. 2008. "Investigating the Correspondence Between Transcriptomic and Proteomic Expression Profiles Using Coupled Cluster Models." Bioinformatics 24(24):2894-2900.  doi:10.1093/bioinformatics/btn553
  • Shah AR, M Singhal, TD Gibson, C Sivaramakrishnan, KM 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, pp. 190-197.  IEEE Computer Society, Los Alamitos, CA.  doi:10.1109/eScience.2008.69
  • Webb-Robertson BJM, WR Cannon, CS Oehmen, AR Shah, V Gurumoorthi, MS Lipton, and KM Waters. 2008. "A Support Vector Machine model for the prediction of proteotypic peptides for accurate mass and time proteomics." Bioinformatics 24(13):1503-1509.  doi:10.1093/bioinformatics/btn218

2007

  • Shah AR, M Singhal, KR Klicker, EG Stephan, HS Wiley, and KM Waters. 2007. "Enabling high-throughput data management systems biology: The Bioinformatics Resource Manager." Bioinformatics 23(7):906-909.  doi:10.1093/bioinformatics/btm031
  • Waters KM, R Tan, DC Genetos, S Verma, CE Yellowley, and NJ Karin. 2007. "DNA microarray analysis reveals a role for lysophosphatidic acid in the regulation of anti-inflammatory genes in MC3T3-E1 cells." Bone 41(5):833-841.  doi:10.1016/j.bone.2007.06.029

2006

  • Waters KM, JG Pounds, and BD Thrall. 2006. "Data Merging for Integrated Microarray and Proteomic Analysis." Briefings in Functional Genomics and Proteomics 5(4):261-272.  doi:10.1093/bfgp/ell019
  • Waters KM, M Singhal, BJM Webb-Robertson, EG Stephan, and JM Gephart. 2006. "Breaking the High-Throughput Bottleneck: New tools help biologists integrate complex datasets." Scientific Computing 23(4):22-26. 

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