U.S. Department of Energy

Pacific Northwest National Laboratory

Bill Cannon

Bill Cannon
Professional Title: 

Dr. Cannon is author of more than 50 technical publications in modeling and simulation, data analysis and proteomics. His graduate work was in statistical thermodynamics in the laboratory of J. Andrew McCammon studying molecular recognition proteins using molecular dynamics and Monte Carlo methods. His graduate work was in the laboratory of Steven J. Benkovic where he worked in both experimental and computational enzymology. Before joining PNNL, Dr. Cannon spent time at Monsanto working on high-throughput transcriptome data analysis and network inference. Since joining PNNL, Dr. Cannon has worked on statistical methods for integrating proteomics data with models, the use of supercomputers to maximize the identification of peptides and proteins from high throughput mass spectrometry assays, and the modeling and simulation of metabolic pathways.

  • Bachelor of Arts, Chemistry, University of California, Santa Cruz
  • Doctorate, Biochemistry and Biophysics, University of Houston
  • Post-doctoral Scholar, Enzymology, Pennsylvania State University
  • Academic Tree
  • 2013 Computational and Information Sciences Directorate Outstanding Performance Award
  • 2007 Computational and Information Sciences Directorate Outstanding Performance Award
  • 2003 FSD Outstanding Performance Award
  • 2004 FSD Outstanding Performance Award
  • 2000 Monsanto Outstanding Performance Award
  • 1995 NIH Post-doctoral National Research Service Award in Biophysical Chemistry
  • 1992 NIH Pre-doctoral National Research Service Award in Biophysics
  • 1990 Welch Foundation Graduate Award 1990, University of Houston
  • 1985 Honors in Chemistry, University of California


Research Interests: 
  • Computational biophysics, biochemistry and proteomics; Modeling and simulation including deterministic and stochastic simulation of metabolism; simulations of state; microbial metabolism; statistics, statistical mechanics and statistical proteomics data analysis; Cloud computing and high performance computing.


  • Cannon WR, Zucker JD, Baxter DJ, Kumar N, Baker SE, Hurley JM, Dunlap JC. "Prediction of Metabolite Concentrations, Rate Constants and Post-Translational Regulation using Maximum Entropy-based Simulations with Application to Central Metabolism of Neurospora crassa." http://www.preprints.org/manuscript/201804.0280/v1.


  • Cannon WR and Baker SE. 2017. "Non-Steady State Mass Action Dynamics Without Rate Constants: Dynamics of Coupled Reactions Using Chemical Potentials." Phys. Biol. 14(5):055003.  10.1088/1478-3975/aa7d80


  • Clancy CE, G An, WR Cannon, Y Liu, EE May, P Ortoleva, A Popel, JP Sluka, J Su, P Vicini , X Zhou, and DM Eckmann. 2016. "Multiscale Modeling in the Clinic: Drug Design and Development." Annals of Biomedical Engineering 44(9):2591-2610.  doi:10.1007/s10439-016-1563-0


  • Cannon WR. 2014. "Concepts, Challenges and Successes in Modeling Thermodynamics of Metabolism." Frontiers in Bioengineering and Biotechnology 2:Article No. 53. doi:10.3389/fbioe.2014.00053 
  • Cannon WR. 2014. "Simulating Metabolism with Statistical Thermodynamics." PLoS One 9(8):Article No. e103582.  doi:10.1371/journal.pone.0103582
  • Song HS, WR Cannon, AS Beliaev, and A Konopka. 2014. "Mathematical Modeling of Microbial Community Dynamics: A Methodological Review." Processes 2(4):711-752. doi:10.3390/pr2040711
  • Thomas DG, SI Jaramillo Riveri, DJ Baxter, and WR Cannon. 2014. "Comparison of Optimal Thermodynamic Models of the Tricarboxylic Acid Cycle from Heterotrophs, Cyanobacteria, and Green Sulfur Bacteria." Journal of Physical Chemistry B 118(51):14745-14760. doi:10.1021/jp5075913


  • Cannon WR, and DJ Baxter. 2012. "Analyzing Data for Systems Biology: Working at the Intersection of Thermodynamics and Data Analytics." In Proceedings of SciDAC 2011, July 10-14, 2011. Denver, Colorado.  Argonne National Laboratory, Argonne, IL. 
  • Hugo AE, DJ Baxter, WR Cannon, A Kalyanaraman, GR Kulkarni, and SJ Callister. 2012. "Proteotyping of Microbial Communities by Optimization of Tandem Mass Spectrometry Data Interpretation." In Pacific Symposium in BioComputing 2012, January 2-7, 2012, Hawaii, vol. 17, pp. 225-234.  Stanford University, Palo Alto, CA. 
  • 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
  • Wu C, A Kalyanaraman, and WR Cannon. 2012. "pGraph: Efficient Parallel Construction of Large-Scale Protein Sequence Homology Graphs." IEEE Transactions on Parallel and Distributed Systems 23(10):1923-1933.  doi:10.1109/TPDS.2012.19


  • Cannon WR, MM Rawlins, DJ Baxter, SJ Callister, MS Lipton, and DA Bryant. 2011. "Large Improvements in MS/MS Based Peptide Identification Rates using a Hybrid Analysis." Journal of Proteome Research 10(5):2306-2317.  doi:10.1021/pr101130b
  • Kalyanaraman A, WR Cannon, BK Latt, and DJ Baxter. 2011. "MapReduce Implementation of a Hybrid Spectral Library-Database Search Method for Large-Scale Peptide Identification." Bioinformatics 27(21):3072-3073.  doi:10.1093/bioinformatics/btr523


  • Cannon WR, and MM Rawlins. 2010. "Physicochemical/Thermodynamic Framework for the Interpretation of Peptide Tandem Mass Spectra." Journal of Physical Chemistry C 114(12):5360-5366.  doi:10.1021/jp905049d
  • Shah AR, JN Adkins, DJ Baxter, WR Cannon, D Chavarr�a-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. 
  • Wu C, A Kalyanaraman, and WR Cannon. 2010. "A Scalable Parallel Algorithm for Large-Scale Protein Sequence Homology Detection." In 39th International Conference on Parallel Processing (ICPP2010), September 13-16, 2010, San Diego, California, pp. 333-342.  IEEE Computer Society, Los Alamitos, CA.  doi:10.1109/ICPP.2010.41


  • 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. 
  • Sharp JL, JJ Borkowski, DA Schmoyer, DS Daly, SO Purvine, WR Cannon, and GB Hurst. 2009. "Statistically Appraising Process Quality of Affinity Isolation Experiments ." Computational Statistics & Data Analysis 53(5):1720-1726 (special issue). 
  • Taylor RC, M Singhal, DS Daly, JM Gilmore, WR Cannon, KO Domico, AM White, DL Auberry, KJ Auberry, BS Hooker, GB Hurst, JE McDermott, WH McDonald, DA Pelletier, DA Schmoyer, and HS Wiley. 2009. "An analysis pipeline for the inference of protein-protein interaction networks." International Journal of Data Mining and Bioinformatics 3(4) (Sp. Iss. SI):409-430. 


  • Oehmen CS, and WR Cannon. 2008. "Bringing high performance computing to the biologist’s workbench: approaches, applications and challenges." In SciDAC 2008: Journal of Physics: Conference Series, vol. 125, p. 012052.  IOP Publishing Ltd., Bristol, United Kingdom.  doi:10.1088/1742-6596/125/1/012052
  • Pelletier DA, GB Hurst, LJ Foote, PK Lankford, CK McKeown, TYS Lu, DD Schmoyer, MB Shah, WJ Hervey IV, WH McDonald, BS Hooker, WR Cannon, DS Daly, JM Gilmore, HS Wiley, DL Auberry, Y Wang, F Larimer, SJ Kennel, MJ Doktycz, J Morrell-Falvey, ET Owens, and MV Buchanan. 2008. "A general system for studying protein-protein interactions in gram-negative bacteria." Journal of Proteome Research 7(8):3319-3328.  doi:10.1021/pr8001832
  • 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. 
  • Cannon WR, DJ Taasevigen, DJ Baxter, and J Laskin. 2007. "Evaluation of the Influence of Amino Acid Composition on the Propensity for Collision-Induced Dissociation of Model Peptides Using Molecular Dynamics Simulations." Journal of the American Society for Mass Spectrometry 18(9):1625-1637.  doi:10.1016/j.jasms.2007.06.005
  • Samatova NF, A Gorin, E Uberbacher, TV Karpinets, BH Park, C Pan, TP Straatsma, WR Cannon, H Resat, RD Lins, and CS Oehmen. 2007. "Data driven computing for Biological Systems." SciDAC Review 5(Fall 2007):10-25. 
  • Sharp JL, KK Anderson, DS Daly, DL Auberry, JJ Borkowski, and WR Cannon. 2007. "Inferring Protein Associations Using Protein Pulldown Assays." In 2006 Joint Statistical Meetings: Statistics for an Uncertain World: Meeting Global Challenges, August 6-10, Seattle, WA, p. 5 pages.  American Statistical Association, Alexandria, VA. 
  • Sharp JL, KK Anderson, GB Hurst, DS Daly, DA Pelletier, WR Cannon, DL Auberry, DD Schmoyer, WH McDonald, AM White, BS Hooker, KD Victry, MV Buchanan, V Kery, and HS Wiley. 2007. "Statistically Inferring Protein-Protein Asociations with Affinity Isolation LC-MS/MS Assays." Journal of Proteome Research 6(9):3788-3795.  doi:10.1021/pr0701106
  • Taylor RC, M Singhal, DS Daly, KO Domico, AM White, DL Auberry, KJ Auberry, BS Hooker, GB Hurst, JE McDermott, WH McDonald, DA Pelletier, DD Schmoyer, and WR Cannon. 2007. "SEBINI-CABIN: An Analysis Pipeline for Biological Network Inference, with a Case Study in Protein-Protein Interaction Network Reconstruction ." In Sixth International Conference on Machine Learning and Applications, (ICMLA 2007) , pp. 587-593.  IEEE Computer Society, Washington DC.  doi:10.1109/ICMLA.2007.63
  • 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


  • 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. 
  • Malard JM, A Heredia-Langner, WR Cannon, RW Mooney, and DJ Baxter. 2005. "Peptide identification via constrained multi-objective optimization: Pareto-based genetic algorithms ." Concurrency and Computation. Practice & Experience 17(14):1687-1704. 


  • Heredia-Langner A, WR Cannon, KD Jarman, and KH Jarman. 2004. "De Novo Analysis of Tandem Mass Spectrometry Data as a Non-Deterministic Optimization Problem." In Proceedings of The International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'04), ed. Faramarz Valafar & Homayoun Valafar, pp. 113-117.  CSREA Press, Las Vegas, NV. 
  • Heredia-Langner A, WR Cannon, KD Jarman, and KH Jarman. 2004. "Sequence optimization as an alternative to de novo analysis of tandem mass spectrometry data." Bioinformatics 20(14):2296-2304. 
  • Malard JM, A Heredia-Langner, DJ Baxter, KH Jarman, and WR Cannon. 2004. "Constrained De-Novo Peptide Identification via Multi-objective Optimization." In Proceedings of the 18th International Parallel and Distributed Processing Symposium, pp. 191-199.  Institute of Electrical and Electronics Engineers, Piscataway, NJ. 


  • Cannon WR. 2003. "Whipple's disease, genomics, and drug therapy." The Lancet 361(9372):1961. 
  • Jarman KD, WR Cannon, KH Jarman, and A Heredia-Langner. 2003. "A model of random sequences for de novo peptide sequencing." In Proceedings of the 3rd IEEE International Symposium on Bioinformatics and Bioengineering, pp. 206-213.  IEEE Computer Society, Los Alamitos, CA. 
  • Cannon WR, and KD Jarman. 2003. "Improved peptide sequencing using isotope information inherent in tandem mass spectra ." Rapid Communications in Mass Spectrometry 17(15):1793-1801. 
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