David Beck

David Beck

David Beck

David Beck

Research Associate Professor of Chemical Engineering

eScience Institute Director of Research

Adjunct Research Associate Professor, Environmental & Occupational Health Sciences
Adjunct Research Associate Professor, Paul G. Allen School of Computer Science & Engineering

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 DA, Carothers JM, Subramanian V, Pfaendtner J. Data science: Accelerating innovation and discovery in chemical engineering. AIChE Journal. 2016;62(5):1402-16.
  • Chu F, Beck DA, Lidstrom ME. MxaY regulates the lanthanide-mediated methanol dehydrogenase switch in Methylomicrobium buryatense. PeerJ. 2016;4:e2435.
  • Ziels R, Karlsson A, Beck DA, Ejlertsson J, Lekta S, Bjorn A, Stensel HD, Svensson, BH. Microbial community adaptation influences long-chain fatty acid conversion during anaerobic codigestion of fats, oils, and grease with municipal sludge. Water Research. 2016;103.
  • Yu Z, Krause S, Beck DA, Chistoserdova L. A synthetic ecology perspective: how well does behavior of model organisms in the laboratory predict microbial activities in natural habitats? Frontiers in Microbiology. 2016;7:946.
  • Hu B, Yang Y-M, Beck DA, Wang Q-W, Chen W-J, Yang J, Lidstrom ME, Yang S. Comprehensive molecular characterization of Methylobacterium extorquens AM1 adapted for 1-butanol tolerance. Biotechnology for biofuels. 2016;9(1):1-14.
  • Torre A, Metivier A, Chu F, Laurens LM, Beck DA, Pienkos PT, Lidstrom ME, Kalyuzhnaya MG. Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G (B1). Microbial cell factories. 2015;14(1):1.
  • Puri AW, Owen S, Chu F, Chavkin T, Beck DA, Kalyuzhnaya MG, Lidstrom ME. Genetic tools for the industrially promising methanotroph Methylomicrobium buryatense. Applied and environmental microbiology. 2015;81(5):1775-81.
  • Paik J, Pershutkina O, Meeker S, Yi J, Dowling S, Hsu C, Hajjar A, Maggio-Price L, DA B. Potential for using a hermetically-sealed, positive-pressured isocage system for studies involving germ-free mice outside a flexible-film isolator. Gut Microbes. 2015;6(4):255-65.
  • Oshkin IY, Beck DA, Lamb AE, Tchesnokova V, Benuska G, McTaggart TL, Kalyuzhnaya MG, Dedysh SN, Lidstrom ME, Chistoserdova L. Methane-fed microbial microcosms show differential community dynamics and pinpoint taxa involved in communal response. The ISME journal. 2015;9(5):1119-29. 
  • Beck DA, McTaggart TL, Setboonsarng U, Vorobev A, Goodwin L, Shapiro N, Woyke T, Kalyuzhnaya MG, Lidstrom ME, Chistoserdova L. Multiphyletic origins of methylotrophy in Alphaproteobacteria, exemplified by comparative genomics of Lake Washington isolates. Environmental microbiology. 2015;17(3):547-54.
  • Rysavy SJ, Beck DA, Daggett V. Dynameomics: Datadriven methods and models for utilizing largescale protein structure repositories for improving fragmentbased loop prediction. Protein Science. 2014;23(11):1584-95.
  • Hendrickson EL, Wang T, Beck DA, Dickinson BC, Wright CJ, J Lamont R, Hackett M. Proteomics of Fusobacterium nucleatum within a model developing oral microbial community. Microbiologyopen. 2014;3(5):729-51.
  • Kalyuzhnaya MG, Yang S, Rozova O, Smalley N, Clubb J, Lamb A, Gowda GN, Raftery D, Fu Y, Bringel F. Highly efficient methane biocatalysis revealed in a methanotrophic bacterium. Nature communications. 2013;4.