Chief Scientist
Chief Scientist

Biography

Bill Cannon is author of more than 60 technical publications in physics, statistical thermodynamics, modeling and simulation, and statistical analysis applied to biological processes. His graduate work in statistical mechanics was done in the laboratory of J. Andrew McCammon, where he studied molecular recognition proteins using molecular dynamics and Monte Carlo methods. His graduate work in experimental and computational enzymology was done in the laboratory of Steven J. Benkovic. Before joining Pacific Northwest National Laboratory (PNNL), Cannon spent time at Monsanto working on high-throughput transcriptome statistical analysis, machine learning, and network inference. Since joining PNNL, 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.

View Cannon’s Google Scholar page.

Research Interest

  • Biochemistry and proteomics
  • Computational physics
  • High-performance computing
  • Modeling and simulation including deterministic and stochastic simulation of metabolism
  • Microbial metabolism
  • Simulations of state
  • Statistical analysis
  • Statistical mechanics
  • Statistical proteomics data analysis

Disciplines and Skills

  • Biophysics
  • Chemical thermodynamics
  • Computational systems biology
  • Enzyme activity
  • Enzyme kinetics
  • Metabolism
  • Statistical mechanics
  • Theoretical and computational chemistry
  • Theoretical biology

Education

  • PhD in biophysics, University of Houston
  • BS in chemistry, University of California, Santa Cruz

Affiliations and Professional Service

  • American Chemical Society
  • American Physical Society
  • Associate Editor, Frontiers in Physics
  • Frequent Guest Editor, PLoS Computational Biology
  • Biophysical Society
  • Adjunct Professor, Department of Mathematics, University of California, Riverside
  • International Union of Pure and Applied Chemistry/International Union of Biochemistry and Molecular Biology Committee on Chemical and Biochemical Thermodynamics
  • Member, various National Institutes of Health (NIH) study sections
  • Steering Committee, NIH-National Science Foundation (NSF)-Department of Energy (DOE) Interagency Multiscale Modeling Consortium
  • Session Organizer, American Physical Society, 2023
  • Session Organizer, American Physical Society, 2022
  • Session Organizer, American Association for the Advancement of Science Annual Meeting, 2021
  • Session Organizer, Society for Mathematical Biology, 2021
  • Session Organizer, Western Sectional Meeting, American Mathematical Society, 2019
  • Session Organizer, NIH Workshop on Scientific Machine Learning, 2019
  • Lead for Theory and Methods, NIH-NSF-DOE Interagency Multiscale Modeling Consortium, 2018 – 2023
  • Editorial Board, Nature Scientific Reports, 2016 – 2020
  • Program Committee, Conference on Computational Systems Bioinformatics, 2009
  • Session Organizer, Pacific Symposium on Biocomputing, 2006
  • Session Organizer, Pacific Symposium on Biocomputing, 2007

Awards and Recognitions

  • Outstanding Performance Award, Computational and Information Sciences Directorate, PNNL, 2013
  • Outstanding Performance Award, Computational and Information Sciences Directorate, PNNL, 2007
  • Outstanding Performance Award, Fundamental Sciences Directorate, PNNL, 2004
  • Outstanding Performance Award, Fundamental Sciences Directorate, PNNL, 2003
  • Outstanding Performance Award, Monsanto, 2000
  • Postdoctoral National Research Service Award in Biophysical Chemistry, NIH, 1995
  • Predoctoral National Research Service Award in Biophysics, NIH, 1992
  • Welch Foundation Graduate Award, University of Houston, 1990
  • Honors in Chemistry, University of California, 1985

Patents

  • Jarman, K. D., K. H. Jarman, A. Heredia-Langner, and B. Cannon. 2011. Peptide Identification, US Patent 7,979,214.

Publications

2023

  • King E., J.T. Holzer, J.A. North, and W.R. Cannon. 2023. "An Approach to Learn Regulation to Maximize Growth and Entropy Production Rates in Metabolism." Frontiers in Systems Biology 3. PNNL-SA-170735. doi:10.3389/fsysb.2023.981866
  • Palmer B.J., A. Almgren, C. Johnson, A.T. Myers, and W.R. Cannon. 2023. "BMX: Biological Modelling and Interface Exchange." Scientific Reports 13. PNNL-SA-189605. doi:10.1038/s41598-023-39150-1

2021

  • Cannon W.R., and L.M. Raff. 2021. "The Formulation of Chemical Potentials and Free Energy Changes in Biochemical Reactions." Physical Chemistry Chemical Physics 23, no. 27:14783-14795. PNNL-SA-163521. doi:10.1039/D1CP02045E
  • Peng G.C., M. Alber, A. Buganza Tepole, W.R. Cannon, S. De, S. Dura-Bernal, and K. Garikipati, et al. 2021. "Multiscale Modeling Meets Machine Learning: What Can We Learn?." Archives of Computatiional Methods of Engineering 28, no. 3:1017-1037. PNNL-SA-156360. doi:10.1007/s11831-020-09405-5

2020

  • Britton S.R., M. Alber, and W.R. Cannon. 2020. "Enzyme Activities Predicted by Metabolite Concentrations and Solvent Capacity in the Cell." Journal of the Royal Society Interface 17, no. 171:20200656. PNNL-SA-152952. doi:10.1098/rsif.2020.0656
  • North J.A., A.B. Narrowe, W. Xiong, K. Byerly, G. Zhao, S.J. Young, and S. Murali, et al. 2020. "A nitrogenase-like enzyme system catalyzes methionine, ethylene, and methane biogenesis." Science 369, no. 6507:1094-1098. PNNL-SA-153010. doi:10.1126/science.abb6310

2019

  • Alber M., A. Buganza Tepole, W.R. Cannon, S. De, S. Dura-Bernal, K. Garikipati, and G.E. Karniadakis, et al. 2019. "Integrating Machine Learning and Multiscale Modeling: Perspectives, Challenges, and Opportunities in the Biological, Biomedical, and Behavioral Sciences." npj Digital Medicine 2, no. 115. PNNL-SA-147139. doi:10.1038/s41746-019-0193-y
  • Raff L.M., and W.R. Cannon. 2019. "On the Reunification of Chemical and Biochemical Thermodynamics: A Simple Example for Classroom Use." Journal of Chemical Education 96, no. 2:274-284. PNNL-SA-138991. doi:10.1021/acs.jchemed.8b00795

2018

  • Cannon W.R., J.D. Zucker, D.J. Baxter, N. Kumar, S.E. Baker, J. Hurley, and J.C. Dunlap. 2018. "Prediction of Metabolite Concentrations, Rate Constants and Post-Translational Regulation using Maximum Entropy-based Simulations with Application to Central Metabolism of Neurospora crassa." Processes 6, no. 6:Article No. 63. PNNL-SA-134563. doi:10.3390/pr6060063
  • Hurley J.M., M.S. Jankowski, H. De Los Santos, A.M. Crowell, S. Fordyce, J.D. Zucker, and N. Kumar, et al. 2018. "Circadian proteomic analysis uncovers mechanisms of post-transcriptional regulation in metabolic pathways." Cell Systems 7, no. 6:613-626. PNNL-SA-138421. doi:10.1016/j.cels.2018.10.014

2017

  • Cannon W.R., and S.E. Baker. 2017. "Non-Steady State Mass Action Dynamics Without Rate Constants: Dynamics of Coupled Reactions using Chemical Potentials." Physical Biology 14, no. 5:Article No. 055003. PNNL-SA-114146. doi:10.1088/1478-3975/aa7d80

2016

  • Clancy C.E., G. An, W.R. Cannon, Y. Liu, E.E. May, P. Ortoleva, and A. Popel, et al. 2016. "Multiscale Modeling in the Clinic: Drug Design and Development." Annals of Biomedical Engineering 44, no. 9:2591-2610. PNNL-SA-114540. doi:10.1007/s10439-016-1563-0

2014

  • Cannon W.R. 2014. "Concepts, Challenges and Successes in Modeling Thermodynamics of Metabolism." Frontiers in Bioengineering and Biotechnology 2. PNNL-SA-105724. doi:10.3389/fbioe.2014.00053
  • Cannon W.R. 2014. "Simulating Metabolism with Statistical Thermodynamics." PLoS One 9, no. 8:Article No. e103582. PNNL-SA-98000. doi:10.1371/journal.pone.0103582
  • Song H., W.R. Cannon, A.S. Beliaev, and A. Konopka. 2014. "Mathematical Modeling of Microbial Community Dynamics: A Methodological Review." Processes 2, no. 4:711-752. PNNL-SA-104609. doi:10.3390/pr2040711
  • Thomas D.G., S.I. Jaramillo Riveri, D.J. Baxter, and W.R. 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, no. 51:14745-14760. PNNL-SA-100020. doi:10.1021/jp5075913

2012

  • Cannon W.R., and D.J. 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, Illinois:Argonne National Laboratory. PNNL-SA-80570.
  • Hugo A.E., D.J. Baxter, W.R. Cannon, A. Kalyanaraman, G.R. Kulkarni, and S.J. 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, 17, 225-234. Palo Alto, California:Stanford University. PNNL-SA-80000.
  • 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
  • Wu C., A. Kalyanaraman, and W.R. Cannon. 2012. "pGraph: Efficient Parallel Construction of Large-Scale Protein Sequence Homology Graphs." IEEE Transactions on Parallel and Distributed Systems 23, no. 10:1923-1933. PNNL-SA-77189. doi:10.1109/TPDS.2012.19

2011

  • Cannon W.R., M.M. Rawlins, D.J. Baxter, S.J. Callister, M.S. Lipton, and D.A. Bryant. 2011. "Large Improvements in MS/MS Based Peptide Identification Rates using a Hybrid Analysis." Journal of Proteome Research 10, no. 5:2306-2317. PNNL-SA-73911. doi:10.1021/pr101130b
  • Kalyanaraman A., W.R. Cannon, B.K. Latt, and D.J. Baxter. 2011. "MapReduce Implementation of a Hybrid Spectral Library-Database Search Method for Large-Scale Peptide Identification." Bioinformatics 27, no. 21:3072-3073. PNNL-SA-83443. doi:10.1093/bioinformatics/btr523

2010

  • Cannon W.R., and M.M. Rawlins. 2010. "Physicochemical/Thermodynamic Framework for the Interpretation of Peptide Tandem Mass Spectra." Journal of Physical Chemistry C 114, no. 12:5360-5366. PNNL-SA-66352. doi:10.1021/jp905049d
  • Shah A.R., J.N. Adkins, D.J. Baxter, W.R. Cannon, D. Chavarría-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.
  • Wu C., A. Kalyanaraman, and W.R. 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, 333-342. Los Alamitos, California:IEEE Computer Society. PNNL-SA-76029. doi:10.1109/ICPP.2010.41

2009

  • Cannon W.R., B.M. Webb-Robertson, A.R. Willse, M. Singhal, L.A. McCue, J.E. McDermott, and R.C. Taylor, et al. 2009. "An Integrative Computational Framework for Hypotheses-Driven Systems Biology Research in Proteomics and Genomics." In Computational and Systems Biology: Methods and Applications. 63-85. Trivandrum:Research Signpost. PNNL-SA-57999.
  • Sharp J.L., J.J. Borkowski, D.A. Schmoyer, D.S. Daly, S.O. Purvine, W.R. Cannon, and G.B. Hurst. 2009. "Statistically Appraising Process Quality of Affinity Isolation Experiments." Computational Statistics & Data Analysis 53, no. 5:1720-1726 (special issue). PNNL-SA-59018.
  • Taylor R.C., M. Singhal, D.S. Daly, J.M. Gilmore, W.R. Cannon, K.O. Domico, and A.M. White, et al. 2009. "An analysis pipeline for the inference of protein-protein interaction networks." International Journal of Data Mining and Bioinformatics 3, no. 4) (Sp. Iss. SI:409-430. PNNL-SA-59756. doi:10.1504/IJDMB.2009.029204

2008

  • Oehmen C.S., and W.R. Cannon. 2008. "Bringing high performance computing to the biologist’s workbench: approaches, applications and challenges." In SciDAC 2008: Journal of Physics: Conference Series, 125, 012052. Bristol:IOP Publishing Ltd. PNNL-SA-61076. doi:10.1088/1742-6596/125/1/012052
  • Pelletier D.A., G.B. Hurst, L.J. Foote, P.K. Lankford, C.K. McKeown, T.S. Lu, and D.D. Schmoyer, et al. 2008. "A general system for studying protein-protein interactions in gram-negative bacteria." Journal of Proteome Research 7, no. 8:3319-3328. PNNL-SA-58778. doi:10.1021/pr8001832
  • 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
  • Cannon W.R., D.J. Taasevigen, D.J. 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, no. 9:1625-1637. PNNL-SA-54583. doi:10.1016/j.jasms.2007.06.005
  • Samatova N.F., A. Gorin, E. Uberbacher, T.V. Karpinets, B. Park, C. Pan, and T. Straatsma, et al. 2007. "Data driven computing for Biological Systems." SciDAC Review 5, no. Fall 2007:10-25. PNNL-SA-55247.
  • Sharp J.L., K.K. Anderson, D.S. Daly, D.L. Auberry, J.J. Borkowski, and W.R. 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, 5 pages. Alexandria, Virginia:American Statistical Association. PNNL-SA-49349.
  • Sharp J.L., K.K. Anderson, G.B. Hurst, D.S. Daly, D.A. Pelletier, W.R. Cannon, and D.L. Auberry, et al. 2007. "Statistically Inferring Protein-Protein Asociations with Affinity Isolation LC-MS/MS Assays." Journal of Proteome Research 6, no. 9:3788-3795. PNNL-SA-57329. doi:10.1021/pr0701106
  • Taylor R.C., M. Singhal, D.S. Daly, K.O. Domico, A.M. White, D.L. Auberry, and K.J. Auberry, et al. 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), 587-593. Washington Dc:IEEE Computer Society. PNNL-SA-55941. doi:10.1109/ICMLA.2007.63
  • 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

2006

  • 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.
  • Malard J.M., A. Heredia-Langner, W.R. Cannon, R.W. Mooney, and D.J. Baxter. 2005. "Peptide identification via constrained multi-objective optimization: Pareto-based genetic algorithms." Concurrency and Computation. Practice & Experience 17, no. 14:1687-1704. PNNL-SA-42966.

2004

  • Heredia-Langner A., W.R. Cannon, K.D. Jarman, and K.H. 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), edited by Faramarz Valafar & Homayoun Valafar, 113-117. Las Vegas, Nevada:CSREA Press. PNNL-SA-41413.
  • Heredia-Langner A., W.R. Cannon, K.D. Jarman, and K.H. Jarman. 2004. "Sequence optimization as an alternative to de novo analysis of tandem mass spectrometry data." Bioinformatics 20, no. 14:2296-2304. PNNL-SA-37724.
  • Malard J.M., A. Heredia-Langner, D.J. Baxter, K.H. Jarman, and W.R. Cannon. 2004. "Constrained De-Novo Peptide Identification via Multi-objective Optimization." In Proceedings of the 18th International Parallel and Distributed Processing Symposium, 191-199. Piscataway, New Jersey:Institute of Electrical and Electronics Engineers. PNNL-SA-44532.

2003

  • Cannon W.R. 2003. "Whipple's disease, genomics, and drug therapy." The Lancet 361, no. 9372:1961. PNWD-SA-6165.
  • Cannon W.R., and K.D. Jarman. 2003. "Improved peptide sequencing using isotope information inherent in tandem mass spectra." Rapid Communications in Mass Spectrometry 17, no. 15:1793-1801. PNNL-SA-36888.
  • Jarman K.D., W.R. Cannon, K.H. 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, 206-213. Los Alamitos, California:IEEE Computer Society. PNNL-SA-39306.

Prior Publications

  • Cannon W.R., and S.J. Benkovic. 1998. “Solvation, Reorganization Energy and Biological Catalysis.” J. Biol. Chem. 273:26257-26260. doi:10.1074/jbc.273.41.26257
  • Cannon W.R., B.J. Garrison, and S.J. Benkovic. 1997. “Consideration of the pH-dependent inhibition of dihydrofolate  reductase by methotrexate.” J. Molec. Biol. 271:656-668. doi:10.1006/jmbi.1997.1173
  • Cannon W.R., B.J. Garrison, and S.J. Benkovic. 1997. “Electrostatic characterization of enzyme complexes: Evaluation of the mechanism of catalysis of dihydrofolate reductase.” J. Am. Chem. Soc. 119:2386-2395. doi:10.1021/ja962621r
  • Cannon, W., S. Singleton, and S. Benkovic. 1996. “A perspective on biological catalysis.” Nat Struct Mol Biol 3, 821–833. doi:10.1038/nsb1096-821
  • Cannon, W.R., J.M. Briggs, J. Shen, J.A. McCammon, and F.A. Quiocho. 1995. “Conservative and nonconservative mutations in proteins: anomalous mutations in a transport receptor analyzed by free energy and quantum chemical calculations.” Protein science : a publication of the Protein Society, 4(3), 387–393. doi:10.1002/pro.5560040305
  • Cannon W.R., B.M. Pettitt, and J.A. McCammon. 1994. “Sulfate anion in water: Model structural, thermodynamic and dynamic properties.” J. Phys. Chem. 98:6225. doi: 10.1021/j100075a027
  • Cannon W.R., J.D. Madura, R.A. Thummel, and J.A. McCammon. 1993. “Molecular recognition: effect of rotational isomers on host-guest binding.” J. Amer. Chem. Soc. 115:879. doi:10.1021/ja00056a009