Berkeley Lab

2017 Publications

Jump to: Preprint (not peer-reviewed) | Legacy and Synergistic External Research

    1. Baran R, Lau R, Bowen BP, Diamond S, Jose N, Garcia-Pichel F, Northen TR. Extensive Turnover of Compatible Solutes in Cyanobacteria Revealed by Deuterium Oxide (D(2)O) Stable Isotope Probing. ACS Chem Biol. 2017 Mar 17;12(3):674-681. doi: 10.1021/acschembio.6b00890. Epub 2017 Jan 18. PubMed PMID: 28068058.
    2. Chakraborty, R; H. Woo, P. Dehal, R. Walker, M. Zemla, M. Auer, L.A. Goodwin, A. Kazakov, P. Novichkov, A.P. Arkin, and T.C. Hazen. (2017). Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site. Standards in Genomic Sciences, 12, 23. [doi]:1186/s40793-017-0233-7 {PMID}:28194258
    3. de Raad, M; T. de Rond, O. Rübel, J.D. Keasling, T.R. Northen, B.P. Bowen. (2017) OpenMSI Arrayed Analysis Toolkit: Analyzing spatially defined samples using mass spectrometry imaging. Analytical Chemistry. [doi]:1021/acs.analchem.6b05004
    4. Erbilgin, O.; B.P. Bowen, S. Jenkins, S.M. Kosina, R.K. Lau, T.R. Northen (2017) Dynamic substrate preferences and predicted metabolic properties of a simple microbial consortium. BMC Bioinformatics. [doi]:1186/s12859-017-1478-2 {PMID}:28114881
    5. Huan, T., E.M. Forsberg, D. Rinehart, C.H. Johnson, J. Ivanisevic, H.P. Benton, M. Fang, A. Aisporna, B. Hilmers, F.L. Poole, M.P. Thorgersen, M.W.W. Adams, G. Krantz, M.W. Fields, P.D. Robbins, L.J. Niedernhofer, T. Ideker, E.L. Majumder, J.D. Wall, N.J.W. Rattray, R. Goodacre, L.L. Lairson, and G. Siuzdak. (2017) Systems biology guided by XCMS Online metabolomics. Nat Meth. 14(5): p. 461-462. [doi]:1038/nmeth.4260
    6. Jenkins, S., T.L. Swenson, R. Lau, A. Rocha, A. Aaring, T.C. Hazen, R. Chakraborty, and T.R. Northen. (2017) Construction of soil defined media using quantitative exometabolomic analysis of soil metabolites. Frontiers in Microbiology. [doi]: 1101/151282.
    7. King, A.J; S.P. Preheim, K.L. Bailey, M.S. Robeson II, T. Roy Chowdhury, B.R. Crable, R.A. Hurt Jr., T. Mehlhorn, K.A. Lowe, T.J. Phelps, A.V. Palumbo, C.C. Brandt, S.D. Brown, M. Podar, P. Zhang, W.A. Lancaster, F. Poole, D.B. Watson, M.W. Fields, J.M. Chandonia, E.J. Alm, J. Zhou, M.W.W. Adams, T.C. Hazen, A.P. Arkin, and D.A. Elias. (2017)  Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation.  Environmental Science & Technology. 51 (5), pp 2879–2889 [doi]:1021/acs.est.6b04751 {PMID}:28112946
    8. Majumder, E.L-W; J.D. Wall. (2017). Uranium Bio-transformations: Chemical or Biological Processes? Open Journal of Inorganic Chemistry: Actinide Special Issue. [doi]:4236/ojic.2017.72003
    9. Paradis, C. J., L. D. McKay, E. Perfect, J. D. Istok, and T. C. Hazen. (2017) Push-pull tests for estimating effective porosity: expanded analytical solution and in situ application. Hydrogeology Journal. [doi]:
    10. Sagawa S, Price MN, Deutschbauer AM, Arkin AP (2017) Validating regulatory predictions from diverse bacteria with mutant fitness data. PLoS ONE 12(5): e0178258. [doi]:1371/journal.pone.0178258
    11. Thompson, A.W., S. Turkarslan, C.E. Arens, A. López García de Lomana, A.V. Raman, D.A. Stahl, and N.S. Baliga. (2017) Robustness of a model microbial community emerges from population structure among single cells of a clonal population. Environmental Microbiology. [doi]:1111/1462-2920.13764. {PMID}:28419704
    12. Thorgersen, M.P; W.A. Lancaster, X. Ge, G. Zane, K.M. Wetmore, B.J. Vaccaro, F.L. Poole, A.M. Deutschbauer, A.P. Arkin, J.D. Wall and M.W.W. Adams (2017) “Mechanisms of Uranium and Chromium Toxicity in Pseudomonas stutzeri RCH2 Grown Under Anaerobic Nitrate-Reducing Conditions” Environmental Microbiology. [doi]:10.3389/fmicb.2017.01529
    13. Thorgersen, M. P., Lancaster, W. A., Rajeev, L., Ge, X., Vaccaro, B. J., Poole, F. P., Arkin, A. P., Mukhopadhyay, A. and Adams, M. W. W. (2017) “A highly expressed high molecular weight S-layer complex of Pelosinus strain UFO1 binds uranium” Applied and Environmental Microbiology 83(4). pii: e03044-16.[doi]:1128/AEM.03044-16. {PMID}:27913415 {PMID}:28848534
    14. Turkarslan, S., A.V. Raman, A.W. Thompson, C.E. Arens, M.A. Gillespie, F. von Netzer, K.L. Hillesland, S. Stolyar, A. López García de Lomana, D.J. Reiss, D. Gorman-Lewis, G.M. Zane, J.A. Ranish, J.D. Wall, D.A. Stahl, and N.S. Baliga. (2017) Mechanism for microbial population collapse in a fluctuating resource environment. Molecular Systems Biology. 13(3): p. 919[doi]:15252/msb.20167058. {PMID}:28320772
    15. Warth B.; N. Levin, D. Rinehart, H.P. Benton, J. Teijaro, and G. Siuzdak (2017) Metabolizing Data in the Cloud. Trends in Biotechnology. [doi]:1016/j.tibtech.2016.12.010 {PMID}:28117091
    16. Wu, X; A.M. Deutschbauer, A.E. Kazakov, K.M. Wetmore, B.A. Cwick, R.M. Walker, P.S. Novichkov, A.P. Arkin, R. Chakraborty. (2017) Draft Genome Sequences of Two Janthinobacterium strains, Isolated from Pristine Groundwater Collected from Oak Ridge Field Research Center. Genome Announcements. 5:e00582-17; [doi]:1128/genomeA.00582-17
    17. Zhang, P.; Z. He, J.D. Van Nostrand, Y. Qin, Y. Deng, L. Wu, Q. Tu, J. Wang, C.W. Schadt, M.W. Fields, T.C. Hazen, A.P. Arkin, D.A. Stahl, and J. Zhou. (2017) Dynamic succession of groundwater sulfate-reducing communities during prolonged reduction of uranium in a contaminated aquifer. Environmental Science and Technology. [doi]:1021/acs.est.6b02980 {PMID}:28300407
    18. Zeng, L; E. Wooton, D.A. Stahl, P.J. Walian. (2017) Identification and Characterization of the Major Porin of Desulfovibrio vulgaris Hildenborough. Journal of Bacteriology. [doi]:10.1128/JB.00286-17
    19. Zhou J., Ning D. (2017) Stochastic Community Assembly: Does It Matter in Microbial Ecology? Microbiology and Molecular Biology Reviews. [doi]:10.1128/MMBR.00002-17 {PMID}: 29021219


Preprint (not peer-reviewed)

  1. Jenkins, S.; T.L. Swenson, R. Lau, A.M. Rocha, A. Aaring, T.C. Hazen, R. Chakraborty, T.R. Northen (2017) Construction of soil defined media using quantitative metabolomics analysis of soil metabolites. bioRxiv. [doi]:10.1101/151282
  2. Kothari, A. Y-W. Wu, M. Charrier, L. Rajeev, A.M. Rocha, T.C. Hazen, S.W. Singer, and A. Mukhopadhyay.(2017)  Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive presence of metal resistance genes.  bioRxiv.
  3. Price M. N.; and A. P. Arkin (2017) PaperBLAST: Text-mining papers for information about homologs. bioRxiv. [doi]:1101/133041
  4. Price,M.N; K.M. Wetmore, R.J. Waters, R.A. Melnyk, M. Callaghan, J. Ray, J.V. Kuehl, J.S. Lamson, Y. Suh, Z. Esquivel, R. Chakraborty, M.J. Blow, J. Bristow, A.P. Arkin, A.M. Deutschbauer. (2017) Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes. bioRxiv. [doi]:10.1101/072470
  5. Ray, J; M. N. Price, A. T. Iavarone, H. K. Carlson, E. M. Ryan, R. R. Malmstrom, A. P. Arkin, A. M. Deutschbauer (2017) An Oxidative Pathway of Deoxyribose Catabolism. bioRxiv. [doi]:10.1101/205583


Legacy and Synergistic External Research

  1. Rand, JM.; Pisithkul, T.; Clark, R.L.; Thiede, J. M.; Mehrer, C.R.; Agnew, D.E.; Campbell, C.E.; Markley, A. L.; Price, M. N.; Ray, J.; Wetmore, K. M.; Suh, Y.; Arkin, A.P.; Deutschbauer, A.M.; Amador-Noguez, D.; and Pfleger, B.F. (2017) A metabolic pathway for catabolizing levulinic acid in bacteria. Nature Microbiology, 2017. 2(12): p. 1624-1634