Publications

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Not always up to date list of citations:

  • Kalyuzhnaya, M.G., Yang, S., Rozova, O.N., Smalley, N.E., Clubb, J., Lamb A., Nagana Gowda G.A., Raftery, D., Fu, Y., Bringel F., Vuilleumier, S., Beck, D.A.C., Trotsenko, Y.A., Khmelenina, V.N., and Lidstrom, M.E. (2013) Highly Efficient Methane Biocatalysis Revealed in a Methanotrophic Bacterium. Nature Comm. In press.
  • Beck D.A.C., Kalyuzhnaya M.G., Malfatti S., Tringe S., Glavina del Rio T., Ivanova N., Lidstrom M. E., Chistoserdova L. (2013) A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae. PeerJ 1:e23.
  • Khmelenina V. N., Beck D.A.C., Munk C., et al. (2013) Draft Genome Sequence of Methylomicrobium buryatense Strain 5G, a Haloalkaline-Tolerant Methanotrophic Bacterium. Genome Announc. Jul-Aug; 1(4): e00053-13.
  • Vorobev A., Beck D.A.C., Kalyuzhnaya M.G., Lidstrom M. E., Chistoserdova L. (2013) Comparative transcriptomics in three Methylophilaceae species uncover different strategies for environmental adaptation. PeerJ 1:e115.
  • Krumholz LR, Wang L, Beck D.A.C., Wang T, Hackett M, Mooney B, Juba TR, McInerney MJ, Meyer B, Wall JD, Stahl DA. Membrane protein complex of APS reductase and Qmo is present in Desulfovibrio vulgaris and Desulfovibrio alaskensis. Microbiology. 2013 Oct;159(Pt 10):2162-8. doi: 10.1099/mic.0.063818-0.
  • Yang S., Matsen J.B., Konopka M., Green-Saxena A., Clubb J., Sadilek M., Orphan V.J., Beck, D.A.C., and M.G. Kalyuzhnaya. Global molecular analyses of methane metabolism in methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part II. metabolomics and 13C-labeling study. Front. Microbiol., 03 April 2013.
  • Matsen J.B., Yang S., Stein L.Y., Beck, D.A.C., and M.G. Kalyuzhnaya. Global molecular analyses of methane metabolism in methanotrophic alphaproteobacterium, Methylosinus trichosporium OB3b. Part I: transcriptomic study. Front. Microbiol., 03 April 2013.
  • McCully M.E., Beck D.A.C., Daggett V. Multimolecule test-tube simulations of protein unfolding and aggregation. Proceedings of the National Academy of Sciences USA, 109:17851-17856 2012. [DOI]
  • McCully M.E., Beck D.A.C., Daggett V. Promiscuous contacts and heightened dynamics increase thermostability in an engineered variant of the engrailed homeodomain. Protein Engineering & Selection, Online: 2012. [DOI]
  • Hirano T.*, Beck D.A.C.*, Wright C.J., Demuth D.R., Hackett M., Lamont R.J. Regulon controlled by the GppX hybrid two component system in Porphyromonas gingivalis. Mol Oral Microbiol., Sep 20, Epub, 2012. *Contributed equally.
  • Hirano T.*, Beck D.A.C.*, Demuth D.R., Hackett M., Lamont R.J. Deep Sequencing of Porphyromonas gingivalis and Comparative Transcriptome Analysis of a LuxS Mutant. Front Cell Infect Microbiol., 2:79, 2012. *Contributed equally.
  • Toofanny, R.D., Simms, A., Beck, D.A.C., and V. Daggett. Implementation of3D spatial hashing in a large-scale molecular dynamics simulation database for rapid atomic contact detection. BMC Bioinformatics, 12:334, 2011. [DOI]
  • 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.
  • Kittichotirat W, Good NM, Hall R, Bringel F, Lajus A, Médigue C, Smalley NE, Beck D, Bumgarner R, Vuilleumier S, Kalyuzhnaya MG. Genome sequence of Methyloversatilis universalis FAM5T, a methylotrophic representative of the order Rhodocyclales. J. Bacteriol. 193(17):4541-2, 2011.
  • 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. 193(15):3757-64, 2011.
  • Kalyuzhnaya, M.G., Beck, D.A.C., and L. Chistoserdova. Functional metagenomics of methylotrophs. Methods in Enzymology, 495:81-98, 2011.
  • Ojala, D.S., Beck, D.A.C., and M.G. Kalyuzhnaya. Genetic tools for moderately halo(alkali)philic bacteria of the genus Methylomicrobium. Methods in Enzymology, 495:99- 118, 2011.
  • Barga, R., Howe, B., Beck, D.A.C., Bowers, S., Dobyns, W., Haynes, W., Higdon, R., Howard, C., Roth, C., Stewart, E., Welch, D., and Kolker, E. Bioinformatics and Data-Intensive Scientific Discovery. OMICS, 15(4), 2011.
  • McCully M.E., Beck D.A.C., Fersht A.R., and Daggett V. Refolding the Engrailed Homeodomain: Structural Basis for the Accumulation of a Folding Intermediate. Biophysical Journal 99:1628-1636, 2010. [DOI]
  • 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., and Daggett V. Dynameomics: A Comprehensive Database of Protein Dynamics. Structure 18:423-435, 2010. [DOI] [Cover Image]
    • Research Highlight on this paper in Nature Methods. [DOI]
  • Hendrickson E.L., Beck D.A.C., Wang T., Lidstrom M. E., Hackett. M., and L. Chistoserdova. The expressed genome of Methylobacillus flagellatus defined through proteogenomics and new insights into methylotrophy. Journal of Bacteriology, 192: 4859-4867, 2010.[DOI]
  • Kalyuzhnaya, M.G., Beck, D.A.C., Suciu, D., Pozhitkov, A., Lidstrom M.E., and L. Chistoserdova. Functioning in situ: gene expression in Methylotenera mobilis in its native environment as assessed via transcriptomics. ISME Journal, 4: 388-398, 2009.
  • Beck D.A.C., Alonso D.O.V., Inoyama D., and Daggett V. The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins. Proceedings of the National Academy of Sciences USA 105: 12259-12264, 2008. [DOI]
  • McCully M.E., Beck D.A.C., and Daggett V. Microscopic Reversibility of Protein Folding in Molecular Dynamics Simulations of the Engrailed Homeodomain. Biochemistry 47: 7079-7089, 2008. [DOI]
  • Smolin N., Li B., Beck D.A.C., and Daggett V. Side-chain dynamics are critical for water permeation through aquaporin-1. Biophysical Journal 95:1089-1098, 2008. [DOI]
  • Beck, D.A.C., Jonsson, A.L., Schaeffer, R.D., Scott, K.A., Day, R., Toofanny, R.D., Alonso, D.O.V., and V. Daggett. Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations. Protein Engineering Design & Selection, 21, 353-368, 2008. [DOI]
  • Beck, D.A.C. and V. Daggett. A One-Dimensional Reaction Coordinate for Identification of Transition States from Explicit Solvent Pfold-Like Calculations. Biophysical Journal, 93, 8832-3391, 2007. [HTML] [PDF]
  • Beck, D.A.C., Bennion, B.J., Alonso, D.O.V and V. Daggett. Simulations of macromolecules in protective and denaturing osmolytes: properties of mixed solvent systems and their effects on water and protein structure and dynamics. Methods in Enzymology, 428, 373-396, 2007. [DOI]
  • Beck, D.A.C., White, G.W.N., and V. Daggett, Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations. Journal of Structural Biology, 157, 514-523, 2007. [DOI]
  • Beck, D.A.C., Armen, R.S. and V. Daggett, Cutoff size need not strongly influence molecular dynamics results on solvated polypeptides. Biochemistry, 44, 609-616, 2005. [DOI] (#12 most cited paper for Biochemistry in 2005)
  • Beck, D.A.C. and V. Daggett, Methods for Molecular Dynamics Simulations of Protein Folding/Unfolding in Solution, Methods, 34, 112-120, 2004. [DOI]
  • Day, R., Beck, D.A.C., Armen, R. and V. Daggett, A Consensus View of Fold Space: Combining SCOP, CATH, and the Dali Domain Dictionary, Protein Science, 12, 2150-2160, 2003. [DOI]
  • Beck, D.A.C., Alonso, D.O.V. and V. Daggett. A microscopic view of peptide and protein solvation. Biophysical Chemistry 100, 221-237, 2003. [DOI]