Faculty & Research

David Beck

David Beck


David Beck

Research Assistant Professor of Chemical Engineering

eScience Institute Director of Research — Life Sciences

Office: Benjamin Hall IRB, Room 440
Phone: 206-221-0709
Fax: 206-543-3778
E-mail: dacb@uw.edu


  • B.S., Drexel University, Computer Science, (2000)
  • Ph.D., University of Washington, Medicinal Chemistry, Biomolecular Structure & Design, 2006.

Research Interests 

  • Systems biology of microbial cultures and communities
    • Pathway reconstruction and analysis of bacterial communities from *omics datasets with relevance to biogeochemical cycles, biofuels, and human health
    • Development of techniques for analysis, comparison, and unification of transcriptomics and proteomics datasets
  • Biophysical chemistry software, methods and applications
    • Author of in lucem Molecular Mechanics (ilmm, Beck, D.A.C., Alonso, D.O.V., & Daggett, V)
    • Development of an XML schema for molecular mechanics parameter library: MMPL
    • Methods and software development for in silico drug and protein design in high-performance computing (HPC) environments
    • Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations
      • All atom, explicit solvent native and thermal unfolding simulations for hundreds of target proteins whose folds represent about 80% of the known protein domains
      • For more information, see our website: http://www.dynameomics.org
  • eScience
    • Workflow design and engineering for data-intensive analytics in biology and chemistry
    • Data mining, management and sharing strategies for large biological datasets

Selected Publications

  • Beck, D.A.C., Ojala, D.S., Kalyuzhnaya, M.G., Chistoserdova, L. Ultra-short read based metatranscriptomics using a reference metagenome: a case study. In preparation for submission to BMC Genomics.
  • Xia, Q., Beck, D.A.C., Wang, T., Leigh, J.A., Hackett, M. Quantitative local false discovery rates, deep sampling and protein abundance change detection for Methanococcus maripaludis. Proteomics, submitted.
  • Toofanny, R.D., Simms, A., Beck, D.A.C., Daggett, V. Implementation of3D spatial hashing in a large-scale molecular dynamics simulation database for rapid atomic contact detection. BMC Bioinformatics, 2011, 12:334.
  • Beck, D.A.C., Hendrickson, E.L., Vorobev, A., Wang, T., Lim, S., Kalyuzhnaya, M.G., Lidstrom, M.E., Hackett, M., Chistoserdova, L. An integrated proteomics/transcriptomics approach points to oxygen as the main electron sink for methanol metabolism in Methylotenera mobilis. J Bacteriol, 2011, Jul 15.
  • Lapidus A., Clum A., Labutti K., Kaluzhnaya M.G., Lim S., Beck D.A.C., Glavina Del Rio T., Nolan M., Mavromatis K., Huntemann M., Lucas S., Lidstrom M.E., Ivanova N., Chistoserdova L. Genomes of three methylotrophs from a single niche reveal the genetic and metabolic divergence of the methylophilaceae. J Bacteriol 2011, 193(15), pp. 3757-64.
  • Kalyuzhnaya, M.G., Beck, D.A.C., Chistoserdova, L. Functional metagenomics of methylotrophs. Methods in Enzymology 2011, 495, pp. 81-98, 2011.
  • Ojala, D.S., Beck, D.A.C., Kalyuzhnaya, M.G. Genetic tools for moderately halo(alkali)philic bacteria of the genus Methylomicrobium. Methods in Enzymology 2011, 495, pp. 99-118.
  • Barga, R., Howe, B., Beck, D.A.C., Bowers, S., Dobyns, W., Haynes, W., Higdon, R., Howard, C., Roth, C., Stewart, E., Welch, D., Kolker, E. Bioinformatics and Data-Intensive Scientific Discovery. OMICS 2011, 15(4).
  • McCully M.E., Beck D.A.C., Fersht A.R., Daggett, V. Refolding the Engrailed Homeodomain: Structural Basis for the Accumulation of a Folding Intermediate. Biophysical Journal 2010, 99, pp. 1628-1636.
  • Van der Kamp, M.W., Schaeffer, R.D., Jonsson, A.L., Scouras, A.D., Simms, A.M., Toofanny, R.D., Benson, N.C., Anderson, P.C., Merkley, E.D., Rysavy, S., Bromley, D., Beck, D.A.C., Daggett, V. Dynameomics: A Comprehensive Database of Protein Dynamics. Structure 2010, 18, pp. 423-435. [DOI] [Cover Image]