PNNL

Bobbie-Jo Webb-Robertson has 20 years of experience in the statistics and data science fields. She currently serves as the chief scientist of computational biology in the Biological Sciences Division at PNNL. Her research portfolio is largely related to the biomedical field and primarily focuses on the development and application of advanced statistical and machine learning methods to address challenges associated with large and complex omics data, as well as integration across multiple data sources. She is a highly accomplished publisher with an h-index of 30 and more than 100 publications.

Webb-Robertson also holds three joint appointments:

• Clinical Volunteer Professor, Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus
• Courtesy Assistant Professor, Department of Pathology, Immunology, and Laboratory Medicine, University of Florida
• Clinical Associate Professor, Department of Biomedical Engineering, School of Medicine, Oregon Health and Sciences University

• Mass spectrometry-based omics data analysis
• Machine learning
• Statistical data integration

• Statistics
• Machine learning
• Predictive modeling
• Feature Identification
• Bioinformatics
• Biomarker discovery 

• PhD in Engineering Systems, Rensselaer Polytechnic Institute, 2002
• ME in Statistics, Rensselaer Polytechnic Institute, 2000
• BA in Mathematics, Oregon State University, 1997

• Member, North Carolina State National Science Foundation Grant Randomized Numerical Analysis National Advisory Committee (2018-current)
• Review Editor, Frontiers in Artificial Intelligence and Frontiers in Big Data (2018-current)
• Scientific Advisory Board Member, Juvenile Diabetes Research Fund IBM Machine Learning Project (2017-current)
• Executive Editor, Journal of Proteomics and Genomics Research (2013-current)
• Member, American Statistical Association (2013-current)
• Member, International Society for Computational Biology (2009-current)
• Special Issue Editor, High-Throughput – Algorithms and Tools in Computational Proteomics (2018)
• Advisor, Global Disease Surveillance Initiative, Bill & Melinda Gates Foundation (2012-2015)
• Executive Editor, Journal of Proteomics and Genomics Research

• Chauncey and Doris Starr Graduate Fellowship, 1997
• GE Future Faculty Scholarship, 1999-2000
• National Science Foundation Program in Mathematics and Molecular Biology Fellowship, 1999-2001
• HPC Analytics challenge in biology finalist team member, 2006
• HPC Analytics challenge in biology first place team member, 2007
• "Spirit of nPOD" award from the Network for Pancreatic Organ Donors with Diabetes
• “Machine Learning for Biomarker Discover” at the Expert Meeting on AI in Drug Discovery, US Government Accountability Office, US National Academy of Medicine, Boston, MA, July 2019 (invited)
• “Machine Learning Biomarker Discovery in the Era of Big Data” at the National Academies of Science 6^th Arab-American Frontiers of Science, Engineering and Medicine Symposium, Kuwait, November 2018 (invited)
• “Plasma Protein Biomarker Discovery and Down Selection for Subsequent Validation in The Environmental Determinants of Diabetes in the Young Cohort” at the HUPO 17-th Annual World Congress, Orlando, FL, October 2018 (invited)

2021

• Anderson-Baucum E, Piñeros AR, Kulkarni A, Webb-Robertson BJ, Maier B, Anderson RM, Wu W, Tersey SA, Mastracci TL, Casimiro I, Scheuner D, Metz TO, Nakayasu ES, Evans-Molina C, Mirmira RG.Cell Metab. 2021. "Deoxyhypusine synthase promotes a pro-inflammatory macrophage phenotype." Sep 7;33(9):1883-1893.e7. doi: 10.1016/j.cmet.2021.08.003.PMID: 34496231 
• Nakayasu E.S., M.A. Gritsenko, P.D. Piehowski, Y. Gao, D.J. Orton, A.A. Schepmoes, and T.L. Fillmore, et al. 2021. "Tutorial: best practices and considerations for mass spectrometry-based protein biomarker discovery and validation." Nature Protocols 16. PNNL-SA-154632. doi:10.1038/s41596-021-00566-6
• Pomraning K.R., Z. Dai, N. Munoz Munoz, Y. Kim, Y. Gao, S. Deng, and J. Kim, et al. 2021. "Integration of proteomics and metabolomics into the Design, Build, Test, Learn cycle to improve 3-hydroxypropionic acid production in Aspergillus pseudoterreus." Frontiers in Bioengineering and Biotechnology 9. PNNL-SA-149911. doi:10.3389/fbioe.2021.603832
• Kyle J.E., K.G. Stratton, E.M. Zink, Y. Kim, K.J. Bloodsworth, M.E. Monroe, and K.M. Waters, et al. 2021. "A resource of lipidomics and metabolomics data from individuals with undiagnosed diseases." Scientific Data 8, no. 1:114. PNNL-SA-150181. doi:10.1038/s41597-021-00894-y
• Kirby J, Geiselman GM, Yaegashi J, Kim J, Zhuang X, Tran-Gyamfi MB, Prahl JP, Sundstrom ER, Gao Y, Munoz N, Burnum-Johnson KE, Benites VT, Baidoo EEK, Fuhrmann A, Seibel K, Webb-Robertson BM, Zucker J, Nicora CD, Tanjore D, Magnuson JK, Skerker JM, Gladden JM. Further engineering of R. toruloides for the production of terpenes from lignocellulosic biomass. Biotechnol Biofuels. 2021 Apr 21;14(1):101. doi: 10.1186/s13068-021-01950-w. PMID: 33883010; PMCID: PMC8058980.
• Xavier J.B., V.B. Young, J. Skufca, F. Ginty, T. Testerman, A.T. Pearson, and P. Macklin, et al. 2020. "The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View." Trends In Cancer 6, no. 3:192-204. PNNL-SA-151543. doi:10.1016/j.trecan.2020.01.004
• Khadempour L., J.E. Kyle, B.M. Webb-Robertson, C.D. Nicora, F.B. Smith, R.D. Smith, and M.S. Lipton, et al. 2021. "From plants to ants: Fungal modification of leaf lipids for nutrition and communication in the leaf-cutter ant fungal garden ecosystem." mSystems 6, no. 2:e01307-20. PNNL-SA-147384. doi:10.1128/mSystems.01307-20
• Moran A.M., S.D. Hampton, S.T. Dowson, J. Dagdelen, A. Trewartha, G. Ceder, and K.A. Persson, et al. 2021. "Online Interactive Platform for COVID-19 Literature Visual Analytics: Platform Development Study." Journal of Medical Internet Research 23, no. 7:Article No. e26995. PNNL-SA-158456. doi:10.2196/26995
• Webb-Robertson B.M. 2021. "Explainable Artificial Intelligence in Endocrinological Medical Research." Journal of Clinical Endocrinology and Metabolism 106, no. 7:e2809 - e2810. PNNL-SA-160901. doi:10.1210/clinem/dgab237
• Kyle J.E., L. Aimo, A.J. Bridge, G. Clair, M. Fedorova, J.B. Helms, and M.R. Molenaar, et al. 2021. "Interpreting the Lipidome: Bioinformatic Approaches to Embrace the Complexity." Metabolomics 17, no. 8:55. PNNL-SA-162774. doi:10.1007/s11306-021-01802-6
• Bramer L.M., J. Irvahn, P.D. Piehowski, K.D. Rodland, and B.M. Webb-Robertson. 2021. "A review of imputation strategies for isobaric labeling-based shotgun proteomics." Journal of Proteome Research 20, no. 1:1-13. PNNL-SA-149520. doi:10.1021/acs.jproteome.0c00123
• Webb-Robertson B.M., L.M. Bramer, B.A. Stanfill, S.M. Reehl, E.S. Nakayasu, T.O. Metz, and B. Frohnert, et al. 2021. "Prediction of the Development of Islet Autoantibodies through Integration of Environmental, Genetic, and Metabolic Markers." Journal of Diabetes 13, no. 2:143-153. PNNL-SA-146734. doi:10.1111/1753-0407.13093

2020

• Gao Y., T.L. Fillmore, N. Munoz Munoz, G. Bentley, C.W. Johnson, J. Kim, and J. Meadows, et al. 2020. "High-throughput large-scale targeted proteomics assays for quantifying pathway proteins in Pseudomonas putida KT2440." Frontiers in Bioengineering and Biotechnology 8. PNNL-SA-156111. doi:10.3389/fbioe.2020.603488
• Odenkirk M.T., K.G. Stratton, L.M. Bramer, B.M. Webb-Robertson, K.J. Bloodsworth, M.E. Monroe, and K.E. Burnum-Johnson, et al. 2020. "From prevention to disease perturbations: A multi-omic assessment of exercise and myocardial infarctions." Biomolecules 11, no. 1:Article No. 40. PNNL-SA-158202. doi:10.3390/biom11010040
• Odenkirk M.T., K.G. Stratton, M.A. Gritsenko, L.M. Bramer, B.M. Webb-Robertson, K.J. Bloodsworth, and K.K. Weitz, et al. 2020. "Unveiling molecular signatures of preeclampsia and gestational diabetes mellitus with multi-omics and innovative cheminformatics visualization tools." Molecular Omics 16, no. 6:521-532. PNNL-SA-152804. doi:10.1039/d0mo00074d
• Chowdhury A.S., S.M. Reehl, K. Kehn-Hall, B. Bishop, and B.M. Webb-Robertson. 2020. "Better Understanding and Prediction of Antiviral Peptides through Primary and Secondary Structure Feature Importance." Scientific Reports 10, no. 1:Article No. 19260. PNNL-SA-154696. doi:10.1038/s41598-020-76161-8
• Anderson-Baucum E., A.R. Pineros, A. Kulkarni, B.M. Webb-Robertson, B.F. Maier, R.M. Anderson, and W. Wu, et al. 2021. "Deoxyhypusine Synthase Promotes a Pro-Inflammatory Macrophage Phenotype." Cell Metabolism 33, no. 9:1883-1893.e7. PNNL-SA-162924. doi:10.1016/j.cmet.2021.08.003
• Onengut-Gumuscu S., U.D. Paila, W. Chen, A. Ratan, Z. Zhu, A.K. Steck, and B. Frohnert, et al. 2020. "Novel genetic risk factors influence progression of islet autoimmunity to type 1 diabetes." Scientific Reports 10, no. 1:Article No. 19193. PNNL-SA-151476. doi:10.1038/s41598-020-75690-6
• Webb-Robertson BJM, LM Bramer, BA Stanfill, SM Reehl, ES Nakayasu, TO Metz, BI Frohnert, JM Norris, RK Johnson, SS Rich, MJ Rewers. 2020. “Prediction of the development of islet autoantibodies through integrated environmental, genetic and metabolic markers.” Journal of Diabetes, in press.
• Kirby J., G.M. Geiselman, J. Yaegashi, J. Kim, X. Zhuang, M. Tran-Gyamfi, and J. Prahl, et al. 2021. "Further engineering of R. toruloides for the production of terpenes from lignocellulosic biomass." Biotechnology for Biofuels 14, no. 1:Article No. 101. PNNL-SA-162406. doi:10.1186/s13068-021-01950-w
• Syed F, S Tersey, JV Turatsinze, J Felton, NJ Kang, J Nelson, E Sims, M Defrance, M Bizet, F Fuks, M Cnop, M Bugliani, P Marchetti, AG Ziegler, E Bonifacio, BJM Webb-Robertson, A Balamurugan, C Evans-Molina, D Eizirik, K Mather, S Arslanian, and RG Mirmira. 2020. “Circulating unmethylated CHTOP and INS DNA fragments provide evidence of possible islet cell death in youth with obesity and diabetes.” Clinical Epigenetics, in press.
• Colli M.L., M. Ramos-Rodriquez, E.S. Nakayasu, M.I. Alvelos, M. Lopes, J.L. Hill, and J. Turatsinze, et al. 2020. "An integrated multi-omics approach identifies the landscape of interferon-a-mediated responses of human pancreatic beta cells." Nature Communications 11. PNNL-SA-144581. doi:10.1038/s41467-020-16327-0
• JB Xavier, VB Young, J Skufca, F Ginty, T Testerman, AT Pearson, P Macklin, M Mitchell, I Shmulevich, L Xie, JG Caporaso, KA Crandall, NL Simone, F Godoy-Vitorino, TJ Griffin, KL Whiteson, HH Gustafson, DJ Slade, TM Schmidt, MRS Walther-Antonio, T Korem, BJM Webb-Robertson, MP Stycynski, WE Johnson, C Jobin, JM Ridlon, AY Koh, M Yu, L Kelly, JA Wargo (2020) The Cancer Microbiome: distinguishing direct and indirect effects requires a systemic view. Trends in Cancer, 6(3): 192-204. PMID: 32101723
• Kaiser B., J.M. Jacobs, A.A. Schepmoes, H.M. Brewer, B.M. Webb-Robertson, S. Valtier, and V.S. Bebarta, et al. 2020. "Assessment of the Utility of the Oral Fluid and Plasma Proteome for Hydrocodone Usage." Journal of Medical Toxicology 16, no. 1:49-60. PNNL-SA-121218. doi:10.1007/s13181-019-00731-0
• Nakayasu E.S., F. Syed, S. Tersey, M.A. Gritsenko, H.D. Mitchell, C. Chan, and J. Turatsinze, et al. 2020. "Comprehensive proteomics analysis of stressed human islets identifies GDF15 as a target for type 1 diabetes intervention." Cell Metabolism 31, no. 2:363-374.e6. PNNL-SA-150166. doi:10.1016/j.cmet.2019.12.005
• Piehowski P.D., Y. Zhu, L.M. Bramer, K.G. Stratton, R. Zhao, D.J. Orton, and R.J. Moore, et al. 2020. "Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-µm spatial resolution." Nature Communications 11, no. 1:Article No. 8. PNNL-SA-138884. doi:10.1038/s41467-019-13858-z
• Webb-Robertson BJM, KG Stratton, JE Kyle, YM Kim, LM Bramer, KM Waters, DM Koeller, TO Metz. 2020. "Statistically-driven metabolite and lipid profiling of patients from the undiagnosed diseases network.” Analytical Chemistry, 92(2):1796-1803. PMID: 31742994
• Frohnert BI, BJM Webb-Robertson, LM Bramer, SM Reehl, K Waugh, AK Steck, JM Norris, MJ Rewers. 2020. “Predictive modeling of type 1 diabetes stages using disparate data sources.” Diabetes, 69(2):238-248. PMID: 31740441

2019

• Bramer L.M., K.G. Stratton, A.M. White, A.A. Bleeker, M.A. Kobold, K.M. Waters, and T.O. Metz, et al. 2019. "P-Mart: Interactive Analysis of Ion Abundance Global Proteomics Data." Journal of Proteome Research 18, no. 3:1426-1432. PNNL-SA-140572. doi:10.1021/acs.jproteome.8b00840
• Dickinson M., L.N. Anderson, B.M. Webb-Robertson, J.R. Hansen, R.D. Smith, A.T. Wright, and K. Hybiske. 2019. "Proximity-dependent proteomics of the Chlamydia trachomatis inclusion membrane reveals functional interactions with endoplasmic reticulum exit sites." PLoS Pathogens 15, no. 4:Article Number e1007698. PNNL-SA-132851. doi:10.1371/journal.ppat.1007698
• Romas-Rodriquez M., H. Raurell-Vila, M.L. Colli, M.I. Alvelos, M. Subirana, J.J. Mateu, and R. Norris, et al. 2019. "The impact of proinflammatory cytokines on the ß-cell regulatory landscape provides new insights into the genetics of type 1 diabetes." Nature Genetics 51, no. 11:1588-1595. PNNL-SA-141684. doi:10.1038/s41588-019-0524-6
• Stanfill B.A., S.M. Reehl, L.M. Bramer, E.S. Nakayasu, S.S. Rich, T.O. Metz, and M. Rewers, et al. 2019. "Extending Classification Algorithms to Case-Control Studies." Biomedical Engineering and Computational Biology 10. PNNL-SA-135302. doi:10.1177/1179597219858954
• Stratton K.G., B.M. Webb-Robertson, L. McCue, B.A. Stanfill, D.M. Claborne, I.G. Godinez, and T. Johansen, et al. 2019. "pmartR: Quality Control and Statistics for Mass Spectrometry-based Biological Data." Journal of Proteome Research 18, no. 3:1418-1425. PNNL-SA-138429. doi:10.1021/acs.jproteome.8b00760

2018

• Liu C., L.M. Bramer, B.M. Webb-Robertson, K. Waugh, M. Rewers, and Q. Zhang. 2018. "Temporal Expression Profiling of Plasma Proteins Reveals Oxidative Stress in Early Stages of Type 1 Diabetes Progression." Journal of Proteomics 172. PNNL-SA-125485. doi:10.1016/j.jprot.2017.10.004
• 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
• Ortega C., A. Frando, B.M. Webb-Robertson, L.N. Anderson, N. Fleck, E.L. Flannery, and M. Fishbaugher, et al. 2018. "A global survey of ATPase activity in Plasmodium falciparum asexual blood stages and gametocytes." Molecular and Cellular Proteomics 17, no. 1:111-120. PNNL-SA-121236. doi:10.1074/mcp.RA117.000088
• Sadler N.C., B.M. Webb-Robertson, T. Clauss, J.G. Pounds, R.A. Corley, and A.T. Wright. 2018. "High-fat diets alter the modulatory effects of xenobiotics on cytochrome P450 activities." Chemical Research in Toxicology 31, no. 5:308-318. PNNL-SA-126308. doi:10.1021/acs.chemrestox.8b00008
• Stanfill B.A., E.S. Nakayasu, L.M. Bramer, A.M. Thompson, C.K. Ansong, T. Clauss, and M.A. Gritsenko, et al. 2018. "Quality Control Analysis in Real-time (QC-ART): A Tool for Real-time Quality Control Assessment of Mass Spectrometry-based Proteomics Data." Molecular and Cellular Proteomics 17, no. 9:1824-1836. PNNL-SA-129934. doi:10.1074/mcp.RA118.000648

2017

• Bryant A., M.J. Aldape, C.R. Bayer, E.J. Katahira, L. Bond, C.D. Nicora, and T.L. Fillmore, et al. 2017. "Effects of delayed NSAID administration after experimental eccentric contraction injury - A cellular and proteomics study." PLoS One 12, no. 12:Article No. e0172486. PNNL-SA-112551. doi:10.1371/journal.pone.0172486
• 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
• 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
• Kerkhoven E.J., Y. Kim, S. Wei, C.D. Nicora, T.L. Fillmore, S.O. Purvine, and B.M. Webb-Robertson, et al. 2017. "Leucine biosynthesis is involved in regulating high lipid accumulation in Yarrowia lipolytica." mBio 8, no. 3:Article No. e00857-17. PNNL-SA-122829. doi:10.1128/mBio.00857-17
• Liu C., L.M. Bramer, B.M. Webb-Robertson, K. Waugh, M. Rewers, and Q. Zhang. 2017. "Temporal profiles of plasma proteome during childhood development." Journal of Proteomics 152. PNNL-SA-122850. doi:10.1016/j.jprot.2016.11.016
• Webb-Robertson B.M., L.M. Bramer, J.L. Jensen, M.A. Kobold, K.G. Stratton, A.M. White, and K.D. Rodland. 2017. "P-MartCancer-Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets." Cancer Research 77, no. 21:e47-e50. PNNL-SA-123730. doi:10.1158/0008-5472.CAN-17-0335

2016

• Khadempour L., K.E. Burnum-Johnson, E.S. Baker, C.D. Nicora, B.M. Webb-Robertson, R.A. White, and M.E. Monroe, et al. 2016. "The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates." Molecular Ecology 25, no. 22:5795-5805. PNNL-SA-113016. doi:10.1111/mec.13872
• Nakayasu E.S., C.D. Nicora, A.C. Sims, K.E. Burnum-Johnson, Y. Kim, J.E. Kyle, and M.M. Matzke, et al. 2016. "MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses." mSystems 1, no. 3:e00043-16. PNNL-SA-114737. doi:10.1128/mSystems.00043-16
• Sadler N.C., P. Nandhikonda, B.M. Webb-Robertson, C. Ansong, L.N. Anderson, J.N. Smith, and R.A. Corley, et al. 2016. "Hepatic cytochrome P450 activity, abundance, and expression throughout human development." Drug Metabolism and Disposition 44, no. 7:984-91. PNNL-SA-112422. doi:10.1124/dmd.115.068593
• Sigdel T.K., Y. Gao, J. He, A. Wang, C.D. Nicora, T.L. Fillmore, and T. Shi, et al. 2016. "Mining the Human Urine Proteome for Monitoring Renal Transplant Injury." Kidney International 89, no. 6:1244-1252. PNNL-SA-115293. doi:10.1016/j.kint.2015.12.049
• 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
• Webb-Robertson B.M., L.M. Bramer, S.M. Reehl, T.O. Metz, Q. Zhang, M. Rewers, and B. Frohnert. 2016. "ROFI - The use of Repeated Optimization for Feature Interpretation." In International Conference on Computational Science and Computational Intelligence (CSCI 2016), December 15-17, 206, Las Vegas, Nevada, edited by HR Arabnia, L Deligiannidis and M Yang. Piscataway, New Jersey:IEEE. PNWD-SA-10276. doi:10.1109/CSCI.2016.0013

2015

• Bramer L.M., S. Chatterjee, A.E. Holmes, S.M. Robinson, S.F. Bradley, and B.M. Webb-Robertson. 2015. "A Machine Learning Approach for Business Intelligence Analysis using Commercial Shipping Transaction Data." In The 11th International Conference on Data Mining (DMIN 2015), July 27-30, 2015, Las Vegas, Nevada, 162-167. Athens, Georgia:CSREA Press. PNNL-SA-110014.
• Cha J., K.E. Burnum-Johnson, A. Bartos, Y. Li, E.S. Baker, S.C. Tilton, and B.M. Webb-Robertson, et al. 2015. "Muscle segment homeobox genes direct embryonic diapause by limiting inflammation in the uterus." Journal of Biological Chemistry 290, no. 24:15337-15349. PNNL-SA-107786. doi:10.1074/jbc.M115.655001
• 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
• 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
• Suh M., A. Tovchigrechko, V. Thovari, M.A. Rolfe, M. Torralba, J. Wang, and J.N. Adkins, et al. 2015. "Quantitative Differences in the Urinary Proteome of Siblings Discordant for Type 1 Diabetes Include Lysosomal Enzymes." Journal of Proteome Research 14, no. 8:3123-3135. PNWD-SA-10457. doi:10.1021/acs.jproteome.5b00052
• Townsend P., Q. Zhang, J. Shapiro, B.M. Webb-Robertson, L.M. Bramer, A.A. Schepmoes, and K.K. Weitz, et al. 2015. "Serum Proteome Profiles in Stricturing Crohn’s Disease: A pilot study." Inflammatory Bowel Diseases 21, no. 8:1935-41. PNNL-SA-108499. doi:10.1097/MIB.0000000000000445
• 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
• Baker E.S., K.E. Burnum-Johnson, J.M. Jacobs, D.L. Diamond, R.N. Brown, Y.M. Ibrahim, and D.J. Orton, et al. 2014. "Advancing the High Throughput Identification of Liver Fibrosis Protein Signatures Using Multiplexed Ion Mobility Spectrometry." Molecular and Cellular Proteomics 13, no. 4:1119-1127. PNNL-SA-90826. doi:10.1074/mcp.M113.034595
• Bowden M.E., K.J. Alvine, J.L. Fulton, J.P. Lemmon, X. Lu, B.M. Webb-Robertson, and S.M. Heald, et al. 2014. "X-ray Absorption Measurements on Nickel Cathode of Sodium-beta Alumina batteries: Fe-Ni-CI Chemical Associations." Journal of Power Sources 247. PNNL-SA-95939. doi:10.1016/j.jpowsour.2013.08.046
• Huang E.L., F.O. Aylward, Y. Kim, B.M. Webb-Robertson, C.D. Nicora, Z. Hu, and T.O. Metz, et al. 2014. "The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation." Environmental Microbiology Reports 6, no. 4:389-95. PNNL-SA-96938. doi:10.1111/1758-2229.12163
• 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
• Webb-Robertson B.M., C.D. Corley, L.A. McCue, B.H. Clowers, C.P. Dowling, K.L. Wahl, and D.S. Wunschel, et al. 2014. "Forensic Signature Detection of Yersinia Pestis Culturing Practices Across Institutions Using a Bayesian Network." Journal of Forensic Investigation 2, no. 1:Article No. 7. PNNL-SA-96751.
• 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
• Zhang Q., M.M. Matzke, A.A. Schepmoes, R.J. Moore, B.M. Webb-Robertson, Z. Hu, and M.E. Monroe, et al. 2014. "High and Low Doses of Ionizing Radiation Induce Different Secretome Profiles in a Human Skin Model." PLoS One 9, no. 3:Article No. e92332. PNNL-SA-98075. doi:10.1371/journal.pone.0092332

2013

• 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
• Holmes A.E., L.H. Sego, B.M. Webb-Robertson, H.W. Kreuzer, R.M. Anderson, S.D. Unwin, and M.R. Weimar, et al. 2013. An Approach for Assessing the Signature Quality of Various Chemical Assays when Predicting the Culture Media Used to Grow Microorganisms. PNNL-22126. Richland, WA: Pacific Northwest National Laboratory. An Approach for Assessing the Signature Quality of Various Chemical Assays when Predicting the Culture Media Used to Grow Microorganisms
• 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
• Sego L.H., A.E. Holmes, L.J. Gosink, B.M. Webb-Robertson, H.W. Kreuzer, R.M. Anderson, and A.J. Brothers, et al. 2013. "Assessing the Quality of Bioforensic Signatures." In IEEE International Conference on Intelligence and Security Informatics (ISI 2013), June 4-7, 2013, Seattle, Washington, edited by K Glass, et al, 346-351. Piscataway, New Jersey:IEEE. PNNL-SA-95423. doi:10.1109/ISI.2013.6578856
• 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
• Taylor R.C., B.M. Webb-Robertson, L.M. Markillie, M.H. Serres, B.E. Linggi, J.T. Aldrich, and E.A. Hill, et al. 2013. "Changes in Translational Efficiency is a Dominant Regulatory Mechanism in the Environmental Response of Bacteria." Integrative Biology 5, no. 11:1393-1406. PNNL-SA-95628. doi:10.1039/C3IB40120K
• 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
• 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
• Watkins D.M., L.H. Sego, A.E. Holmes, B.M. Webb-Robertson, A.M. White, D.S. Wunschel, and H.W. Kreuzer, et al. 2013. "Assessing Performance and Tradeoffs of Bioforensic Signature Systems." In IEEE International Conference on Technologies for Homeland Security (HST 2013), November 12-14, 2013, Waltham, Massachusetts, 304-309. Piscataway, New Jersey:IEEE. PNNL-SA-96498. doi:10.1109/THS.2013.6699019
• Webb-Robertson B.M., C.D. Corley, L.A. McCue, K.L. Wahl, and H.W. Kreuzer. 2013. "Fusion of Laboratory and Textual Data for Investigative Bioforensics." Forensic Science International 226, no. 1-3:118-24. PNNL-SA-88567. doi:10.1016/j.forsciint.2012.12.016
• 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.
• Wiedner S.D., C. Ansong, B.M. Webb-Robertson, L.M. Pederson, S. Fortuin, B.A. Hofstad, and A.K. Shukla, et al. 2013. "Disparate Proteome Responses of Pathogenic and Non-pathogenic Aspergilli to Human Serum Measured by Activity-Based Protein Profiling (ABPP)." Molecular & Cellular Proteomics. MCP 12, no. 7:1791-1805. PNNL-SA-91969. doi:10.1074/mcp.M112.026534

2012

• 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
• Peterson E.S., L.A. McCue, A.C. Rutledge, J.L. Jensen, J. Walker, M.A. Kobold, and S.R. Webb, et al. 2012. "VESPA: Software to Facilitate Genomic Annotation of Prokaryotic Organisms Through Integration of Proteomic and Transcriptomic Data." BMC Genomics 13, no. 1:Article No. 131. PNNL-SA-82717. doi:10.1186/1471-2164-13-131
• Varnum S.M., B.M. Webb-Robertson, J.G. Pounds, R.J. Moore, R.D. Smith, C. Frevert, and S.J. Skerret, et al. 2012. "Proteomic analysis of bronchoalveolar lavage fluid proteins from mice infected with Francisella tularensis ssp novicida." Journal of Proteome Research 11, no. 7:3690-3703. PNNL-SA-86269.
• 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
• Webb-Robertson B.M., H.W. Kreuzer, G.L. Hart, J. Ehleringer, J.B. West, J.B. West, and G.A. Gill, et al. 2012. "Bayesian Integration of Isotope Ratios for Geographic Sourcing of Castor Beans." Journal of Biomedicine and Biotechnology 2012. PNNL-SA-83058. doi:10.1155/2012/450967
• Webb-Robertson B.M., V.L. Bailey, S.J. Fansler, M.J. Wilkins, and N.J. Hess. 2012. "Spectral Signatures for the Classification of Microbial Species using Raman Spectra." Analytical and Bioanalytical Chemistry 404, no. 2:563-572. PNNL-SA-84618. doi:10.1007/s00216-012-6152-y
• 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

• Jin H., B.M. Webb-Robertson, E.S. Peterson, R. Tan, D.J. Bigelow, M. Scholand, and J.R. Hoidal, et al. 2011. "Smoking, COPD and 3-Nitrotyrosine Levels of Plasma Proteins." Environmental Health Perspectives 119, no. 9:1314-1320. PNNL-SA-73870. doi:10.1289/ehp.1103745
• 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.
• McGrath L.R., K.O. Domico, C.D. Corley, and B.M. Webb-Robertson. 2011. "Complex Biological Event Extraction from Full Text using Signatures of Linguistic and Semantic Features." In The 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies: Proceedings of BioNLP Shared Task 2011Workshop, June 24th, Portland, Oregon, 130-137. Stroudsburg, Pennsylvania:Association for Computational Linguistics. PNNL-SA-79051.
• 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
• Varnum S.M., B.M. Webb-Robertson, N. Hessol, R.D. Smith, and R.C. Zangar. 2011. "Plasma Biomarkers for Detecting Hodgkin's Lymphoma in HIV Patients." PLoS One 6, no. 12:Article No. e29263. PNNL-SA-81553. doi:10.1371/journal.pone.0029263
• Webb-Robertson B.M., A.L. Bunn, and V.L. Bailey. 2011. "Phospholipid fatty acid biomarkers in a freshwater periphyton community exposed to uranium: discovery by non-linear statistical learning." Journal of Environmental Radioactivity 102, no. 1:67-71. PNNL-SA-72816. doi:10.1016/j.jenvrad.2010.09.005
• 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
• Zhang H., K.E. Burnum, M.L. Luna, B.O. Petritis, J. Kim, W. Qian, and R.J. Moore, et al. 2011. "Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size." Proteomics 11, no. 23:4569-4577. PNNL-SA-74159. doi:10.1002/pmic.201100037

2010

• Beagley N., K.G. Stratton, and B.M. Webb-Robertson. 2010. "VIBE 2.0: Visual Integration for Bayesian Evaluation." Bioinformatics 26, no. 2:280-282. PNNL-SA-66347.
• MCClay J.L., D.E. Adkins, N.G. Isern, T.M. O'Connell, J.B. Wooten, B.K. Zedler, and M.S. Dasika, et al. 2010. "H-1 Nuclear Magnetic Resonance Metabolomics Analysis Identifies Novel Urinary Biomarkers for Lung Function." Journal of Proteome Research 9, no. 6:3083-3090. PNNL-SA-64898.
• Oehmen C.S., and B.M. Webb-Robertson. 2010. "Evaluating the Computational Requirements of using SVM software to train Data-Intensive Problems." In Machine Learning Research Progress, Nova Science Publishers. Hauppauge, New York:Nova Science. PNNL-SA-59493.
• Shah A.R., J.N. Adkins, D.J. Baxter, W.R. Cannon, D. Chavarr�a-Miranda, S. Choudhury, and I. Gorton, et al. 2010. "Applications in Data-Intensive Computing." In Advances in Computers, edited by M Zelkowitz. 1-70. San Diego, California:Academic Press Inc. PNNL-SA-67358.
• Webb-Robertson B.M., K. Ratuiste, and C.S. Oehmen. 2010. "Physicochemical property distributions for accurate and rapid pairwise protein homology detection." BMC Bioinformatics 11. PNWD-SA-8719. doi:10.1186/1471-2105-11-145
• 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.

2009

• Bystroff C., and B.M. Webb-Robertson. 2009. "Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure." BMC Bioinformatics 9, no. 429:10 pages. PNNL-SA-58982. doi:10.1186/1471-2105-9-429
• 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.
• Miracle A.L., V.L. Bailey, S.E. Baker, A.L. Bunn, J.K. Magnuson, and B.M. Webb-Robertson. 2009. "Integration of ‘omics technologies for characterization of complex microbial ecosystems - 8119." In Waste Management Symposium 2008, 832-841. Tucson, Arizona:WM Symposia. PNNL-SA-58003.
• Webb-Robertson B.M. 2009. "Support Vector Machines for Improved Peptide Identification from Tandem Mass Spectrometry Database Search." In Mass Spectrometry of Proteins and peptides: Methods in Molecular Biology Vol 146. New York, New York:Humana Press. PNNL-SA-51841.
• 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.
• Webb-Robertson B.M., M.M. Matzke, and C.S. Oehmen. 2009. "Dimension Reduction via Unsupervised Learning Yields Significant Computational Improvements for Support Vector Machine Based Protein Family Classification." In The Seventh International Conference on Machine Learning and Applications, 457-462. Los Alamitos, California:IEEE Computer Society. PNNL-SA-60288.
• Wunschel D.S., B.M. Webb-Robertson, C.W. Frevert, S.J. Skerret, S.J. Skerret, N. Beagley, and A.R. Willse, et al. 2009. "Differentiation of Gram-Negative Bacterial Aerosol Exposure Using Detected Markers in Bronchial-Alveolar Lavage Fluid." PLoS One 4, no. 9:e7047. PNNL-SA-64283. doi:10.1371/journal.pone.0007047

2008

• Ferris K.F., B.M. Webb-Robertson, D.V. Jordan, and D.M. Jones. 2008. "Data-driven exploration of the ionization-phonon partitioning in scintillating radiation detector materials." In IEEE Transactions on Nuclear Science, 55, 1042-1048. Piscataway, New Jersey:Institute of Electrical Electronics Engineers. PNNL-SA-56260.
• Shah A.R., C.S. Oehmen, and B.M. Webb-Robertson. 2008. "SVM-Hustle - An iterative semi-supervised machine learning approach for pairwise protein remote homology detection." Bioinformatics 24, no. 6:783-790. PNNL-SA-56589.
• Valentine N.B., M.G. Butcher, Y. Su, K.H. Jarman, M.M. Matzke, B.M. Webb-Robertson, and E.A. Panisko, et al. 2008. "Evaluation of Sampling Tools for Environmental Sampling of Bacterial Endospores from Porous and Non-porous Surfaces." Journal of Applied Microbiology 105, no. 4:1107-1113. PNNL-SA-60777.
• Webb-Robertson B.M., C.S. Oehmen, and A.R. Shah. 2008. "A Feature Vector Integration Approach for a Generalized Support Vector Machine Pairwise Homology Algorithm." Computational Biology and Chemistry 32, no. 6:458-461. PNWD-SA-8160. doi:10.1016/j.compbiolchem.2008.07.017
• Webb-Robertson B.M., K.F. Ferris, and D.M. Jones. 2008. "Design Rules for Ce-activated scintillating radiation detection materials: Compromises between Luminosity and stopping power." IEEE Transactions on Nuclear Science 55, no. 3 pt 2:1210-1215. PNNL-SA-56001.
• Webb-Robertson B.M., L.A. McCue, and C.E. Lawrence. 2008. "Measuring Global Credibility with Application to Local Sequence Alignment." PLoS Computational Biology 4, no. 5:Art. No e1000077. PNWD-SA-8141. doi:10.1371/journal.pcbi.1000077
• 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

• Cannon W.R., and B.M. Webb-Robertson. 2007. "Computational Proteomics: High-throughput Analysis for Systems Biology." In Biocomputing 2007. Proceedings of the Pacific Symposium, Maui, Hawaii, USA, 3 - 7 January 2007, edited by RB Altman, AK Dunker, L Hunter, T Murray & TE Klein, 403-408. Singapore:World Scientific Publishing Company. PNNL-SA-51602. Computational Proteomics: High-throughput Analysis for Systems Biology
• Ferris K.F., B.M. Webb-Robertson, and D.M. Jones. 2007. "Materials Discovery: Informatic Strategies for Optical Materials." In Proceedings of the SPIE: Laser-Induced Damage in Optical Material, edited by Gregory J. Exarhos, et al, 6403, Art No. 64032A. Bellingham, Washington:SPIE. PNNL-SA-56258. doi:10.1117/12.719514
• Shah A.R., C.S. Oehmen, J.K. Harper, and B.M. Webb-Robertson. 2007. "Integrating Subcellular Location for Improving Machine Learning Models of Remote Homology Detection in Eukaryotic Organisms." Computational Biology and Chemistry 31, no. 2:138-142. PNNL-SA-48402. doi:10.1016/j.compbiolchem.2007.02.012
• Webb-Robertson B.M., and W.R. Cannon. 2007. "Current Trends in Computational Inference from Mass Spectrometry-based Proteomics." Briefings in Bioinformatics 8, no. 5:304-317. PNNL-SA-55170. doi:10.1093/bib/bbm023
• Webb-Robertson B.M., C.S. Oehmen, and W.R. Cannon. 2007. "Support Vector Machine Classification of Probability Models and Peptide Features for Improved Peptide Identification from Shotgun Proteomics." In The Sixth International Conference on Machine Learning and Applications (ICMLA ’07), 500-505. Washington Dc:IEEE Computer Society. PNNL-SA-58675. doi:10.1109/ICMLA.2007.17
• Webb-Robertson B.M., E.S. Peterson, M. Singhal, K.R. Klicker, C.S. Oehmen, J.N. Adkins, and S.L. Havre. 2007. "PQuad - A visual analysis platform for proteomic data exploration of microbial organism." Bioinformatics 23, no. 13:1705-1707. PNNL-SA-52772. doi:10.1093/bioinformatics/btm132

2006

• Callister S.J., R.C. Barry, J.N. Adkins, E.T. Johnson, W. Qian, B.M. Webb-Robertson, and R.D. Smith, et al. 2006. "Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics." Journal of Proteome Research 5, no. 2:277-286. PNNL-SA-46453. doi:10.1021/pr050300l
• Ferris K.F., B.M. Webb-Robertson, and D.M. Jones. 2006. "Information-Based Development of New Radiation Detectors." In Materials Research Society Symposium Proceedings: Combinatorial Methods and Informatics in Materials Science, edited by MJ Fasolka, et al, 894. Warrendale, Pennsylvania:Materials Research Society. PNNL-SA-47703.
• Havre S.L., A. Shah, C. Posse, and B.M. Webb-Robertson. 2006. "Diverse Information Integration and Visualization." In Visualization and Data Analysis 2006, 15-19 January 2006, San Jose, California, USA. Proceedings of SPIE, edited by R.F. Erbacher, J.C. Roberts, M.T. Gröhn, K. Börner, 6060. Bellingham, Washington:SPIE The International Society for Optical Engineering. PNNL-SA-44998.
• Oehmen C.S., T. Straatsma, G.A. Anderson, G. Orr, B.M. Webb-Robertson, R.C. Taylor, and R.W. Mooney, et al. 2006. "New Challenges Facing Integrative Biological Science in the Post-Genomic Era." Journal of Biological Systems 14, no. 2:275-293. PNNL-SA-45428.
• 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.
• Webb-Robertson B.M., W.R. Cannon, J.N. Adkins, and D.K. Gracio. 2006. "The Challenge of Proteomic Data from Molecular Signals to Biological Networks and Disease." In Pacific Symposium On Biocomputing 2006, edited by R.B. Altman, et al, 212-218. Singapore:World Scientific. PNNL-SA-47364. doi:10.1142/9789812701626_0020

2005

• Cannon W.R., K.H. Jarman, B.M. Webb-Robertson, D.J. Baxter, C.S. Oehmen, K.D. Jarman, and A. Heredia-Langner, et al. 2005. "A Comparison of Probability and Likelihood Models for Peptide Identification from Tandem Mass Spectrometry Data." Journal of Proteome Research 4, no. 5:1687-1698. PNNL-SA-45622.
• Havre S.L., B.M. Webb-Robertson, A. Shah, C. Posse, B. Gopalan, and F.J. Brockman. 2005. "Bioinformatic Insights from Metagenomics through Visualization." In Proceedings of the IEEE Computational Systems Bioinformatics Conference (CSB 2005). August 8-11, 2005, 341-350. Los Alamitos, California:IEEE Computer Society. PNNL-SA-44583. doi:10.1109/CSB.2005.19
• Havre S.L., M. Singhal, D.A. Payne, M.S. Lipton, and B.M. Webb-Robertson. 2005. "Enabling Proteomics Discovery Through Visual Analysis." IEEE Engineering in Medicine and Biology Magazine 24, no. 3:50-57. PNNL-SA-41942.
• Webb-Robertson B.M., C.S. Oehmen, and M.M. Matzke. 2005. "SVM-BALSA: Remote Homology Detection based on Bayesian Sequence Alignment." Computational Biology and Chemistry 29, no. 6:440-3. PNNL-SA-45823.
• Webb-Robertson B.M., D.F. Lowry, K.H. Jarman, S.J. Harbo, Q. Meng, A.F. Fuciarelli, and J.G. Pounds, et al. 2005. "A Study of Spectral Integration and Normalization in NMR-based Metabonomic Analyses." Journal of Pharmaceutical and Biomedical Analysis 39, no. 3-4:830-836. PNWD-SA-6799.
• Webb-Robertson B.M., K.H. Jarman, S.D. Harvey, C. Posse, and B.W. Wright. 2005. "An improved optimization algorithm and Bayes factor termination criterion for sequential projection pursuit." Chemometrics and Intelligent Laboratory Systems 77, no. 1-2:149-160. PNNL-SA-41907.
• Webb-Robertson B.M., S.L. Havre, and D.A. Payne. 2005. "A Bayesian Framework for SNP Identification." In Pacific Symposium on Biocomputing, Hawaii, USA, 4-8 January 2005, 421-432. Singapore:World Scientific Publishing Co. Pte. Ltd. PNNL-SA-46031.

2004

• Havre S.L., M. Singhal, B. Gopalan, D.A. Payne, K.R. Klicker, G.R. Kiebel, and K.J. Auberry, et al. 2004. "Integrating Evolving Tools for Proteomics Research." In Proceedings of The 2004 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, edited by Valafar, Faramarz and Homayoun Valafar, 2004, 307-313. Las Vegas, Nevada:CSREA Press. PNNL-SA-40933.
• Havre S.L., M. Singhal, D.A. Payne, and B.M. Webb-Robertson. 2004. "PQuad: Visualization of Predicted Peptides and Proteins." In Proceedings of IEEE Visualization Conference (Vis 2004), 473-480. Los Alamitos, California:IEEE Computer Society Press. PNNL-SA-41292.
• Webb-Robertson B.M., and S.L. Havre. 2004. "Effective Dimension Reduction Using Sequential Projection Pursuit On Gene Expression Data for Cancer Classification." In Proceedings of The International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'04), edited by Faramarz Valafar & Homayoun Valafar, 345-351. Las Vegas, Nevada:CSREA Press. PNNL-SA-41412.