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Fundamental and Computational Sciences Directorate

Staff information


Bobbie-Jo Webb-Robertson

Computing & Analytics Div
Pacific Northwest National Laboratory
PO Box 999
MSIN: K7-20
Richland, WA 99352


Dr. Webb-Robertson is currently the technical group manager of the Applied Statistics and Computational Modeling group, as well as leading a body of research in the development and application of advanced statistical methods for MS-based omics analyses. Her research interests includes the development of statistical inference models, largely machine learning, with application to diverse biomarker discovery problems.

Research Interests

  • MS-based Omics Data Analysis
  • Machine Learning
  • Statistical Data Integration

Education and Credentials

  • Ph.D., Decision Sciences and Engineering Systems, Rensselaer Polytechnic Institute, 2002
  • M.E., Operations Research and Statistics, Rensselaer Polytechnic Institute, 2000
  • B.A., Mathematics, Eastern Oregon University, 1997

PNNL Publications


  • Menachery VD, A Schafer, KE Burnum-Johnson, HD Mitchell, AJ Eisfeld-Fenney, KB Walters, CD Nicora, SO Purvine, CP Casey, ME Monroe, KK Weitz, KG Stratton, BJM Webb-Robertson, L Gralinski, TO Metz, RD Smith, KM Waters, AC Sims, Y Kawaoka, and R Baric. 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(5):E1012-E1021.  doi:10.1073/pnas.1706928115
  • Ortega C, A Frando, BJM Webb-Robertson, LN Anderson, N Fleck, EL Flannery, M Fishbaugher, TA Murphree, JR Hansen, RD Smith, SH Kappe, AT Wright, and C Grunder. 2018. "A global survey of ATPase activity in Plasmodium falciparum asexual blood stages and gametocytes." Molecular and Cellular Proteomics 17(1):111-120.  doi:10.1074/mcp.RA117.000088


  • Burnum-Johnson KE, JE Kyle, AJ Eisfeld, CP Casey, KG Stratton, JF Gonzalez, F Habyarimana, NM Negretti, AC Sims, S Chauhan, LB Thackray, P Halfmann, KB Walters, YM Kim, EM Zink, CD Nicora, KK Weitz, BJM Webb-Robertson, ES Nakayasu, B Ahmer, M Konkel, VL Motin, R Baric, MS Diamond, Y Kawaoka, KM Waters, RD Smith, and TO Metz. 2017. "MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling." Analyst 142(3):442-448.  doi:10.1039/c6an02486f
  • Bryant A, MJ Aldape, CR Bayer, EJ Katahira, L Bond, CD Nicora, TL Fillmore, TRW Clauss, TO Metz, BJM Webb-Robertson, and DL Stevens. 2017. "Effects of delayed NSAID administration after experimental eccentric contraction injury - A cellular and proteomics study." PLoS One 12(12):Article No. e0172486.  doi:10.1371/journal.pone.0172486
  • Eisfeld AJ, P Halfmann, JP Wendler, JE Kyle, KE Burnum-Johnson, Z Peralta, T Maemura, KB Walters, T Watanabe, S Fukuyama, M Yamashita, JM Jacobs, YM Kim, CP Casey, KG Stratton, BJM Webb-Robertson, MA Gritsenko, ME Monroe, KK Weitz, AK Shukla, M Tian, G Neumann, JL Reed, H van Bakel, TO Metz, RD Smith, KM Waters, A N'jai, F Sahr, and Y Kawaoka. 2017. "Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis." Cell Host & Microbe 22(6):817-829.  doi:10.1016/j.chom.2017.10.011
  • Kerkhoven EJ, YM Kim, S Wei, CD Nicora, TL Fillmore, SO Purvine, BJM Webb-Robertson, RD Smith, SE Baker, TO Metz, and JB Nielsen. 2017. "Leucine biosynthesis is involved in regulating high lipid accumulation in Yarrowia lipolytica." mBio 8(3):Article No. e00857-17.  doi:10.1128/mBio.00857-17
  • Liu CW, LM Bramer, BJM Webb-Robertson, K Waugh, M Rewers, and Q Zhang. 2017. "Temporal profiles of plasma proteome during childhood development." Journal of Proteomics 152:321-328.  doi:10.1016/j.jprot.2016.11.016
  • Webb-Robertson BJM, LM Bramer, JL Jensen, MA Kobold, KG Stratton, AM White, and KD Rodland. 2017. "P-MartCancer-Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets." Cancer Research 77(21):e47-e50.  doi:10.1158/0008-5472.CAN-17-0335


  • Khadempour L, KE Burnum-Johnson, ES Baker, CD Nicora, BJM Webb-Robertson, RA White, III, ME Monroe, EL Huang, RD Smith, and CR Currie. 2016. "The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates." Molecular Ecology 25(22):5795-5805.  doi:10.1111/mec.13872
  • Nakayasu ES, CD Nicora, AC Sims, KE Burnum-Johnson, YM Kim, JE Kyle, MM Matzke, AK Shukla, RK Chu, AA Schepmoes, JM Jacobs, R Baric, BJM Webb-Robertson, RD Smith, and TO Metz. 2016. "MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses." mSystems 1(3):e00043-16.  doi:10.1128/mSystems.00043-16
  • Sadler NC, P Nandhikonda, BJM Webb-Robertson, C Ansong, LN Anderson, JN Smith, RA Corley, and AT Wright. 2016. "Hepatic cytochrome P450 activity, abundance, and expression throughout human development." Drug Metabolism and Disposition 44(7):984-91.  doi:10.1124/dmd.115.068593
  • Sigdel TK, Y Gao, J He, A Wang, CD Nicora, TL Fillmore, T Shi, BJM Webb-Robertson, RD Smith, W Qian, O Salvatierra, DG Camp, II, and M Sarwal. 2016. "Mining the Human Urine Proteome for Monitoring Renal Transplant Injury ." Kidney International 89(6):1244-1252.  doi:10.1016/j.kint.2015.12.049
  • Tisoncik-Go J, DJ Gasper, JE Kyle, AJ Eisfeld, C Selinger, M Hatta, J Morrison, MJ Korth, EM Zink, YM Kim, AA Schepmoes, CD Nicora, SO Purvine, KK Weitz, X Peng, R Green, SC Tilton, BJM Webb-Robertson, KM Waters, TO Metz, RD Smith, Y Kawaoka, M Suresh, L Josset, and MG Katze. 2016. "Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism." Cell Host & Microbe 19(2):254-66.  doi:10.1016/j.chom.2016.01.002
  • Webb-Robertson BJM, LM Bramer, SM Reehl, TO 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, ed. HR Arabnia, L Deligiannidis and M Yang.  IEEE, PISCATAWAY, NJ.  doi:10.1109/CSCI.2016.0013


  • Bramer LM, S Chatterjee, AE Holmes, SM Robinson, SF Bradley, and BJM 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, pp. 162-167.  CSREA Press, ATHENS, GA. 
  • Cha J, KE Burnum-Johnson, A Bartos, Y Li, ES Baker, SC Tilton, BJM Webb-Robertson, PD Piehowski, ME Monroe, A Jegga, S Murata, Y Hirota, and SK Dey. 2015. "Muscle segment homeobox genes direct embryonic diapause by limiting inflammation in the uterus." Journal of Biological Chemistry 290(24):15337-15349.  doi:10.1074/jbc.M115.655001
  • Hu JZ, X Wang, J Feng, BJM Webb-Robertson, KM Waters, SC Tilton, JG Pounds, RA Corley, M Liu, and MY Hu. 2015. "Metabolite Signatures in Hydrophilic Extracts of Mouse Lungs Exposed to Cigarette Smoke Revealed By 1H NMR Metabolomics Investigation." Metabolomics 5(2):Article No. 143.  doi:10.4172/2153-0769.1000143
  • Kebaabetswe LP, AK Haick, MA Gritsenko, TL Fillmore, RK Chu, SO Purvine, BJM Webb-Robertson, MM Matzke, RD Smith, KM Waters, TO Metz, and TA Miura. 2015. "Proteomic Analysis Reveals Down-Regulation of Surfactant Protein B in Murine Type II Pneumocytes Infected with Influenza A Virus." Virology 438:96-107.  doi:10.1016/j.virol.2015.03.045
  • Lovelace ES, J Wagoner, J MacDonald, T Bammler, J Bruckner, J Brownell, R Beyer, EM Zink, YM Kim, JE Kyle, BJM Webb-Robertson, KM Waters, TO Metz, F Farin, NH Oberlies, and S Polyak. 2015. "Silymarin Suppresses Cellular Inflammation By Inducing Reparative Stress Signaling." Journal of Natural Products 78(8):1990-2000.  doi:10.1021/acs.jnatprod.5b00288
  • Suh MJ, A Tovchigrechko, V Thovari, MA Rolfe, M Torralba, J Wang, JN Adkins, BJM Webb-Robertson, W Osborne, F Cogen, P Kaplowitz, TO Metz, KE Nelson, R Madupu, and R Pieper. 2015. "Quantitative Differences in the Urinary Proteome of Siblings Discordant for Type 1 Diabetes Include Lysosomal Enzymes." Journal of Proteome Research 14(8):3123-3135.  doi:10.1021/acs.jproteome.5b00052
  • Townsend P, Q Zhang, J Shapiro, BJM Webb-Robertson, LM Bramer, AA Schepmoes, KK Weitz, M Mallette, H Moniz, R Bright, M Merrick, SA Shah, BE Sands, and N Leleiko. 2015. "Serum Proteome Profiles in Stricturing Crohn’s Disease: A pilot study." Inflammatory Bowel Diseases 21(8):1935-41.  doi:10.1097/MIB.0000000000000445
  • Webb-Robertson BJM, HK Wiberg, MM Matzke, JN Brown, J Wang, JE McDermott, RD Smith, KD Rodland, TO Metz, JG Pounds, and KM Waters. 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(5):1993-2001.  doi:10.1021/pr501138h


  • Aevermann B, BE Pickett, S Kumar, EB Klem, S Agnihothram, PS Askovich, A Bankhead, M Bolles, V Carter, JH Chang, TRW Clauss, P Dash, AH Diercks, AJ Eisfeld, AL Ellis, S Fan, MT Ferris, L Gralinski, R Green, MA Gritsenko, M Hatta, RA Heegel, JM Jacobs, S Jeng, L Josset, SM Kaiser, S Kelly, GL Law, C Li, J Li, C Long, ML Luna, MM Matzke, JE McDermott, V Menachery, TO Metz, HD Mitchell, ME Monroe, G Navarro, G Neumann, RL Podyminogin, SO Purvine, C Rosenberger, CJ Sanders, AA Schepmoes, AK Shukla, A Sims, P Sova, VC Tam, N Tchitchek, PG Thomas, SC Tilton, AL Totura, J Wang, BJM Webb-Robertson, J Wen, JM Weiss, F Yang, B Yount, Q Zhang, SK Mcweeney, RD Smith, KM Waters, Y Kawaoka, R Baric, A Aderem, MG Katze, and RH Scheuermann. 2014. "A Comprehensive Collection of Systems Biology Data Characterizing the Host Response to Viral Infection." Scientific Data 1:Article No. 140033.  doi:10.1038/sdata.2014.33
  • Baker ES, KE Burnum-Johnson, JM Jacobs, DL Diamond, RN Brown, YM Ibrahim, DJ Orton, PD Piehowski, DE Purdy, RJ Moore, WF Danielson, III, ME Monroe, KL Crowell, GW Slysz, MA Gritsenko, JD Sandoval, BL Lamarche, MM Matzke, BJM Webb-Robertson, BC Simons, BJ McMahon, R Bhattacharya, JD Perkins, RL Carithers, S Strom, S Self, MG Katze, GA Anderson, and RD Smith. 2014. "Advancing the High Throughput Identification of Liver Fibrosis Protein Signatures Using Multiplexed Ion Mobility Spectrometry." Molecular and Cellular Proteomics 13(4):1119-1127.  doi:10.1074/mcp.M113.034595
  • Bowden ME, KJ Alvine, JL Fulton, JP Lemmon, X Lu, BJM Webb-Robertson, SM Heald, M Balasubramanian, DR Mortensen, GT Seidler, and NJ Hess. 2014. "X-ray Absorption Measurements on Nickel Cathode of Sodium-beta Alumina batteries: Fe-Ni-CI Chemical Associations." Journal of Power Sources 247:517-526.  doi:10.1016/j.jpowsour.2013.08.046
  • Huang EL, FO Aylward, YM Kim, BJM Webb-Robertson, CD Nicora, Z Hu, TO Metz, MS Lipton, RD Smith, CR Currie, and KE Burnum-Johnson. 2014. "The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation." Environmental Microbiology Reports 6(4):389-95.  doi:10.1111/1758-2229.12163
  • Menachery V, AJ Eisfeld, A Schafer, L Josset, AC Sims, S Proll, S Fan, C Li, G Neumann, SC Tilton, JH Chang, L Gralinski, C Long, R Green, CM Williams, JM Weiss, MM Matzke, BJM Webb-Robertson, AA Schepmoes, AK Shukla, TO Metz, RD Smith, KM Waters, MG Katze, Y Kawaoka, and R Baric. 2014. "Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches to Control Interferon-Stimulated Gene Responses." mBio 5(3):Article No. e01174-14.  doi:10.1128/mBio.01174-14
  • Webb-Robertson BJM, CD Corley, LA McCue, BH Clowers, CP Dowling, KL Wahl, DS Wunschel, and HW Kreuzer. 2014. "Forensic Signature Detection of Yersinia Pestis Culturing Practices Across Institutions Using a Bayesian Network." Journal of Forensic Investigation 2(1):Article No. 7. 
  • Webb-Robertson BJM, MM Matzke, S Datta, SH Payne, J Kang, LM Bramer, CD Nicora, AK Shukla, TO Metz, KD Rodland, RD Smith, MF Tardiff, JE McDermott, JG Pounds, and KM Waters. 2014. "Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements." Molecular and Cellular Proteomics 13(12):3639-3646.  doi:10.1074/mcp.M113.030932
  • 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 10(5):897-908.  doi:10.1007/s11306-014-0642-1
  • Zhang Q, MM Matzke, AA Schepmoes, RJ Moore, BJM Webb-Robertson, Z Hu, ME Monroe, W Qian, RD Smith, and WF Morgan. 2014. "High and Low Doses of Ionizing Radiation Induce Different Secretome Profiles in a Human Skin Model." PLoS One 9(3):Article No. e92332.  doi:10.1371/journal.pone.0092332


  • 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
  • Holmes AE, LH Sego, BJM Webb-Robertson, HW Kreuzer, RM Anderson, SD Unwin, MR Weimar, MF Tardiff, and CD Corley. 2013. An Approach for Assessing the Signature Quality of Various Chemical Assays when Predicting the Culture Media Used to Grow MicroorganismsPNNL-22126, Pacific Northwest National Laboratory, Richland, WA. 
  • 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
  • McDermott JE, J Wang, HD Mitchell, BJM Webb-Robertson, RP Hafen, JA Ramey, II, and KD Rodland. 2013. "Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data." Expert Opinion on Medical Diagnostics 7(1):37-51.  doi:10.1517/17530059.2012.718329
  • 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
  • Sego LH, AE Holmes, LJ Gosink, BJM Webb-Robertson, HW Kreuzer, RM Anderson, AJ Brothers, CD Corley, and MF Tardiff. 2013. "Assessing the Quality of Bioforensic Signatures." In IEEE International Conference on Intelligence and Security Informatics (ISI 2013), June 4-7, 2013, Seattle, Washington, ed. K Glass, et al, pp. 346-351.  IEEE, Piscataway, NJ.  doi:10.1109/ISI.2013.6578856
  • 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
  • Taylor RC, BJM Webb-Robertson, LM Markillie, MH Serres, BE Linggi, JT Aldrich, EA Hill, MF Romine, MS Lipton, and HS Wiley. 2013. "Changes in Translational Efficiency is a Dominant Regulatory Mechanism in the Environmental Response of Bacteria." Integrative Biology 5(11):1393-1406.  doi:10.1039/C3IB40120K
  • 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
  • Wang J, BJM Webb-Robertson, MM Matzke, SM Varnum, JN Brown, RM Riensche, JN Adkins, JM Jacobs, JR Hoidal, MB Scholand, JG Pounds, MR Blackburn, KD Rodland, and JE McDermott. 2013. "A Semiautomated Framework for Integrating Expert Knowledge into Disease Marker Identification." Disease Markers 35(5):513-523.  doi:10.1155/2013/613529
  • Watkins DM, LH Sego, AE Holmes, BJM Webb-Robertson, AM White, DS Wunschel, HW Kreuzer, CD Corley, and MF Tardiff. 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, pp. 304-309.  IEEE, Piscataway, NJ.  doi:10.1109/THS.2013.6699019
  • Webb-Robertson BJM, CD Corley, LA McCue, KL Wahl, and HW Kreuzer. 2013. "Fusion of Laboratory and Textual Data for Investigative Bioforensics." Forensic Science International 226(1-3):118-24.  doi:10.1016/j.forsciint.2012.12.016
  • 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. 
  • Wiedner SD, C Ansong, BJM Webb-Robertson, LM Pederson, S Fortuin, BA Hofstad, AK Shukla, EA Panisko, RD Smith, and AT Wright. 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(7):1791-1805.  doi:10.1074/mcp.M112.026534


  • Varnum SM, BJM Webb-Robertson, JG Pounds, RJ Moore, RD Smith, C Frevert, SJ Skerret, and DS Wunschel. 2012. "Proteomic analysis of bronchoalveolar lavage fluid proteins from mice infected with Francisella tularensis ssp novicida." Journal of Proteome Research 11(7):3690-3703. 
  • 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
  • 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 56(1):28-38.  doi:10.1002/hep.25649
  • Peterson ES, LA McCue, AC Rutledge, JL Jensen, J Walker, MA Kobold, SR Webb, SH Payne, C Ansong, JN Adkins, WR Cannon, and BJM Webb-Robertson. 2012. "VESPA: Software to Facilitate Genomic Annotation of Prokaryotic Organisms Through Integration of Proteomic and Transcriptomic Data." BMC Genomics 13(1):Article No. 131.  doi:10.1186/1471-2164-13-131
  • Webb-Robertson BJM, HW Kreuzer, GL Hart, J Ehleringer, JB West, GA Gill, and DC Duckworth. 2012. "Bayesian Integration of Isotope Ratios for Geographic Sourcing of Castor Beans." Journal of Biomedicine and Biotechnology 2012:Article No. 450967.  doi:10.1155/2012/450967
  • Webb-Robertson BJM, VL Bailey, SJ Fansler, MJ Wilkins, and NJ Hess. 2012. "Spectral Signatures for the Classification of Microbial Species using Raman Spectra." Analytical and Bioanalytical Chemistry 404(2):563-572.  doi:10.1007/s00216-012-6152-y
  • 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


  • Varnum SM, BJM Webb-Robertson, N Hessol, RD Smith, and RC Zangar. 2011. "Plasma Biomarkers for Detecting Hodgkin's Lymphoma in HIV Patients." PLoS One 6(12):Article No. e29263.  doi:10.1371/journal.pone.0029263
  • Jin H, BJM Webb-Robertson, ES Peterson, R Tan, DJ Bigelow, MB Scholand, JR Hoidal, JG Pounds, and RC Zangar. 2011. "Smoking, COPD and 3-Nitrotyrosine Levels of Plasma Proteins." Environmental Health Perspectives 119(9):1314-1320.  doi:10.1289/ehp.1103745
  • 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. 
  • McGrath LR, KO Domico, CD Corley, and BJM 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, pp. 130-137.  Association for Computational Linguistics, Stroudsburg, PA. 
  • 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
  • Webb-Robertson BJM, AL Bunn, and VL 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(1):67-71.  doi:10.1016/j.jenvrad.2010.09.005
  • 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
  • Zhang H, KE Burnum, ML Luna, BO Petritis, JS Kim, W Qian, RJ Moore, A Heredia-Langner, BJM Webb-Robertson, BD Thrall, DG Camp, II, RD Smith, JG Pounds, and T Liu. 2011. "Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size." Proteomics 11(23):4569-4577.  doi:10.1002/pmic.201100037


  • Beagley N, KG Stratton, and BJM Webb-Robertson. 2010. "VIBE 2.0: Visual Integration for Bayesian Evaluation." Bioinformatics 26(2):280-282. 
  • MCClay JL, DE Adkins, NG Isern, TM O'Connell, JB Wooten, BK Zedler, MS Dasika, BT Webb, BJM Webb-Robertson, JG Pounds, EL Murrelle, MF Leppert, and EJ van den Oord. 2010. "H-1 Nuclear Magnetic Resonance Metabolomics Analysis Identifies Novel Urinary Biomarkers for Lung Function." Journal of Proteome Research 9(6):3083-3090. 
  • Oehmen CS, and BJM Webb-Robertson. 2010. "Evaluating the Computational Requirements of using SVM software to train Data-Intensive Problems." In Machine Learning Research Progress, Nova Science Publishers.  Nova Science, Hauppauge, NY. 
  • Shah AR, JN Adkins, DJ Baxter, WR Cannon, D Chavarrķa-Miranda, S Choudhury, I Gorton, DK Gracio, TD Halter, N Jaitly, JR Johnson, RT Kouzes, MC Macduff, A Marquez, ME Monroe, CS Oehmen, WA Pike, C Scherrer, O Villa, BJM Webb-Robertson, PD Whitney, and N Zuljevic. 2010. "Applications in Data-Intensive Computing." In Advances in Computers, vol. 79, ed. M Zelkowitz, pp. 1-70.  Academic Press Inc., San Diego, CA. 
  • Webb-Robertson BJM, K Ratuiste, and CS Oehmen. 2010. "Physicochemical property distributions for accurate and rapid pairwise protein homology detection." BMC Bioinformatics 11:Article No. 145.  doi:10.1186/1471-2105-11-145
  • 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. 


  • Bystroff C, and BJM Webb-Robertson. 2009. "Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure." BMC Bioinformatics 9(429):10 pages.  doi:10.1186/1471-2105-9-429
  • 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. 
  • Miracle AL, VL Bailey, SE Baker, AL Bunn, JK Magnuson, and BJM Webb-Robertson. 2009. "Integration of ‘omics technologies for characterization of complex microbial ecosystems - 8119." In Waste Management Symposium 2008, pp. 832-841.  WM Symposia, Tucson, AZ. 
  • Webb-Robertson BJM, LA McCue, N Beagley, JE McDermott, DS Wunschel, SM Varnum, JZ Hu, NG Isern, GW Buchko, K Mcateer, JG Pounds, SJ Skerret, D Liggitt, and CW Frevert. 2009. "A Bayesian Integration Model of High-Throughput Proteomics and Metabolomics Data for Improved Early Detection of Microbial Infections." In Pacific Symposium on Biocomputing, vol. 14, pp. 451-463.  World Scientific Publishing Co., Singapore, Singapore. 
  • Webb-Robertson BJM, MM Matzke, and CS 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 , pp. 457-462.  IEEE Computer Society, Los Alamitos, CA. 
  • Webb-Robertson BJM. 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.  Humana Press, New York, NY. 
  • Wunschel DS, BJM Webb-Robertson, CW Frevert, SJ Skerret, N Beagley, AR Willse, HA Colburn, and KC Antolick. 2009. "Differentiation of Gram-Negative Bacterial Aerosol Exposure Using Detected Markers in Bronchial-Alveolar Lavage Fluid." PLoS One 4(9):e7047.  doi:10.1371/journal.pone.0007047


  • Ferris KF, BJM Webb-Robertson, DV Jordan, and DM Jones. 2008. "Data-driven exploration of the ionization-phonon partitioning in scintillating radiation detector materials." In IEEE Transactions on Nuclear Science, vol. 55, no. 3 Pt.2, pp. 1042-1048.  Institute of Electrical Electronics Engineers, Piscataway, NJ. 
  • Shah AR, CS Oehmen, and BJM Webb-Robertson. 2008. "SVM-Hustle - An iterative semi-supervised machine learning approach for pairwise protein remote homology detection." Bioinformatics 24(6):783-790. 
  • Valentine NB, MG Butcher, YF Su, KH Jarman, MM Matzke, BJM Webb-Robertson, EA Panisko, BAB Seiders, and KL Wahl. 2008. "Evaluation of Sampling Tools for Environmental Sampling of Bacterial Endospores from Porous and Non-porous Surfaces." Journal of Applied Microbiology 105 (4):1107-1113. 
  • Webb-Robertson BJM, KF Ferris, and DM Jones. 2008. "Design Rules for Ce-activated scintillating radiation detection materials: Compromises between Luminosity and stopping power." IEEE Transactions on Nuclear Science 55(3 pt 2):1210-1215. 
  • Webb-Robertson BJM, CS Oehmen, and AR Shah. 2008. "A Feature Vector Integration Approach for a Generalized Support Vector Machine Pairwise Homology Algorithm." Computational Biology and Chemistry 32(6):458-461.  doi:10.1016/j.compbiolchem.2008.07.017
  • Webb-Robertson BJM, LA McCue, and CE Lawrence. 2008. "Measuring Global Credibility with Application to Local Sequence Alignment." PLoS Computational Biology 4(5):Art. No e1000077.  doi:10.1371/journal.pcbi.1000077
  • 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


  • Cannon WR, and BJM 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, ed. RB Altman, AK Dunker, L Hunter, T Murray & TE Klein, pp. 403-408.  World Scientific Publishing Company, Singapore, Singapore. 
  • Ferris KF, BJM Webb-Robertson, and DM Jones. 2007. "Materials Discovery: Informatic Strategies for Optical Materials." In Proceedings of the SPIE: Laser-Induced Damage in Optical Material, vol. 6403, ed. Gregory J. Exarhos, et al, p. Art No. 64032A.  SPIE , Bellingham, WA.  doi:10.1117/12.719514
  • Shah AR, CS Oehmen, JK Harper, and BJM Webb-Robertson. 2007. "Integrating Subcellular Location for Improving Machine Learning Models of Remote Homology Detection in Eukaryotic Organisms." Computational Biology and Chemistry 31(2):138-142.  doi:10.1016/j.compbiolchem.2007.02.012
  • Webb-Robertson BJM, ES Peterson, M Singhal, KR Klicker, CS Oehmen, JN Adkins, and SL Havre. 2007. "PQuad - A visual analysis platform for proteomic data exploration of microbial organism." Bioinformatics 23(13):1705-1707.  doi:10.1093/bioinformatics/btm132
  • Webb-Robertson BJM, and WR Cannon. 2007. "Current Trends in Computational Inference from Mass Spectrometry-based Proteomics." Briefings in Bioinformatics 8(5):304-317.  doi:10.1093/bib/bbm023
  • Webb-Robertson BJM, CS Oehmen, and WR 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), pp. 500-505.  IEEE Computer Society, Washington DC.  doi:10.1109/ICMLA.2007.17


  • Ferris KF, BJM Webb-Robertson, and DM Jones. 2006. "Information-Based Development of New Radiation Detectors." In Materials Research Society Symposium Proceedings: Combinatorial Methods and Informatics in Materials Science, vol. 894, no. Paper No. 0894-LL09-02, ed. MJ Fasolka, et al.  Materials Research Society, Warrendale, PA. 
  • Callister SJ, RC Barry, JN Adkins, ET Johnson, W Qian, BJM Webb-Robertson, RD Smith, and MS Lipton. 2006. "Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics." Journal of Proteome Research 5(2):277-286.  doi:10.1021/pr050300l
  • Havre SL, A Shah, C Posse, and BJM 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 , vol. 6060, ed. R.F. Erbacher, J.C. Roberts, M.T. Gröhn, K. Börner.  SPIE The International Society for Optical Engineering, Bellingham, WA. 
  • Oehmen CS, TP Straatsma, GA Anderson, G Orr, BJM Webb-Robertson, RC Taylor, RW Mooney, DJ Baxter, DR Jones, and DA Dixon. 2006. "New Challenges Facing Integrative Biological Science in the Post-Genomic Era." Journal of Biological Systems 14(2):275-293. 
  • 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. 
  • Webb-Robertson BJM, WR Cannon, JN Adkins, and DK Gracio. 2006. "The Challenge of Proteomic Data from Molecular Signals to Biological Networks and Disease." In Pacific Symposium On Biocomputing 2006, pp. 212-218.  World Scientific, , Singapore. 


  • Cannon WR, KH Jarman, BJM Webb-Robertson, DJ Baxter, CS Oehmen, KD Jarman, A Heredia-Langner, KJ Auberry, and GA Anderson. 2005. "A Comparison of Probability and Likelihood Models for Peptide Identification from Tandem Mass Spectrometry Data." Journal of Proteome Research 4(5):1687-1698. 
  • Havre SL, BJM Webb-Robertson, A Shah, C Posse, B Gopalan, and FJ Brockman. 2005. "Bioinformatic Insights from Metagenomics through Visualization ." In Proceedings of the IEEE Computational Systems Bioinformatics Conference (CSB 2005). August 8-11, 2005, pp. 341-350.  IEEE Computer Society, Los Alamitos, CA.  doi:10.1109/CSB.2005.19
  • Havre SL, M Singhal, DA Payne, MS Lipton, and BJM Webb-Robertson. 2005. "Enabling Proteomics Discovery Through Visual Analysis." IEEE Engineering in Medicine and Biology Magazine 24(3):50-57. 
  • Webb-Robertson BJM, CS Oehmen, and MM Matzke. 2005. "SVM-BALSA: Remote Homology Detection based on Bayesian Sequence Alignment." Computational Biology and Chemistry 29(6):440-3. 
  • Webb-Robertson BJM, DF Lowry, KH Jarman, SJ Harbo, Q Meng, AF Fuciarelli, JG Pounds, and MT Lee. 2005. "A Study of Spectral Integration and Normalization in NMR-based Metabonomic Analyses ." Journal of Pharmaceutical and Biomedical Analysis 39(3-4):830-836. 
  • Webb-Robertson BJM, KH Jarman, SD Harvey, C Posse, and BW Wright. 2005. "An improved optimization algorithm and Bayes factor termination criterion for sequential projection pursuit." Chemometrics and Intelligent Laboratory Systems 77(1-2):149-160. 
  • Webb-Robertson BJM, SL Havre, and DA Payne. 2005. "A Bayesian Framework for SNP Identification ." In Pacific Symposium on Biocomputing, Hawaii, USA, 4-8 January 2005 , pp. 421-432.  World Scientific Publishing Co. Pte. Ltd., Singapore, Singapore. 


  • Havre SL, M Singhal, DA Payne, and BJM Webb-Robertson. 2004. "PQuad: Visualization of Predicted Peptides and Proteins." In Proceedings of IEEE Visualization Conference (Vis 2004), pp. 473-480.  IEEE Computer Society Press, Los Alamitos, CA. 
  • Havre SL, M Singhal, B Gopalan, DA Payne, KR Klicker, GR Kiebel, KJ Auberry, EG Stephan, BJM Webb-Robertson, and DK Gracio. 2004. "Integrating Evolving Tools for Proteomics Research." In Proceedings of The 2004 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, vol. 2004, ed. Valafar, Faramarz and Homayoun Valafar, pp. 307-313.  CSREA Press, Las Vegas, NV. 
  • Webb-Robertson BJM, and SL 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), ed. Faramarz Valafar & Homayoun Valafar, pp. 345-351.  CSREA Press, Las Vegas, NV. 

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