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Berkeley Lab

2016 Publications

(Paper highlighted as: Impact factor >8.0, ** of outstanding interest, partial funding)

Jump to: Books/Book Chapters | Legacy and Synergistic External Research

  1. de Raad, M.; C.R. Fischer and T.R. Northen (2016) High-throughput platforms for metabolomics. Current Opinions in Chemical Biology. [doi]:10.1016/j.cbpa.2015.10.012 {PMID}:26544850
  2. Fischer, C.R.; O. Ruebel and B.P. Bowen (2016) An accessible, scalable ecosystem for enabling and sharing diverse mass spectrometry imaging analyses. Archives of Biochemistry and Biophysics. [doi]:10.1016/ {PMID}:26365033
  3. Gao, J.; M. de Raad, B.P. Bowen, R.N. Zuckerman and T.R. Northen (2016) Application of Black Silicon for Nanostructure-Initiator Mass Spectrometry. Analytical Chemistry. [doi]:10.1021/acs.analchem.5b03452 {PMID}:26741735
  4. Hemme, C.L.; S.J. Green, L. Rishishwar, O. Prakash, A. Pettenato, R. Chakraborty, A.M. Deutschbauer, J.D. Van Nostrand, L. Wu, Z. He, I.K. Jordan, T.C. Hazen, A.P. Arkin, J.E. Kostka and J. Zhou (2016) Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community. mBio. [doi]:10.1128/mBio.02234-15 {PMID}:27048805 PMCID:PMC4817265 
  5. Kosina, S.M.; M.A. Danielewicz, M. Mohammed, J. Ray, Y. Suh, S. Yilmaz, A.K. Singh, A.P. Arkin, A.M. Deutschbauer and T.R. Northen (2016) Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism. American Chemical Society Synthetic Biology. [doi]:10.1021/acssynbio.5b00236 {PMID}:26885935
  6. Kurczy, M.E.; E.M. Forsberg, M.P. Thorgerson, F.L. Poole II, H.P. Benton, J. Ivanisevic, M.L. Tran, J.D. Wall, D.A. Elias, M.W.W. Adams and G. Siuzdak (2016) Global Isotope Metabolomics Reveals Adaptive Strategies for Nitrogen Assimilation. American Chemical Society Chemical Biology. [doi]:10.1021/acschembio.6b00082 {PMID}:27045776 PMCID:PMC5730404 
  7. Lindemann, S.R.; H.C. Bernstein, H.-S. Song, M.W. Fields, W. Shou, D. Johnson, J.K. Fredrickson and A.S. Beliaev (2016) Engineering microbial consortia for controllable outputs. International Society for Microbial Ecology Journal. [doi]:10.1038/ismej.2016.26 {PMID}:26967105 PMCID:PMC4989317 
  8. Louie, K.B.; B.P. Bowen, R.K. Lau and T.R. Northen (2016) Localizing metabolic synthesis in microbial cultures with kinetic mass spectrometry imaging (kMSI). bioRxiv. [doi]:10.1101/050658
  9. Montenegro-Burke, J.R.; T. Phommavongsay, A.E. Aisporna, T. Huan, D. Rinehart, F.L. Poole, M.P. Thorgersen, M.W.W. Adams, G. Krantz, M.W. Fields, P.D. Robbins, L.J. Niedernhofer, H.P. Benton and G. Siuzdak (2016) Smartphone Analytics: Mobilizing the Lab into the Cloud for Omic-Scale Analyses. Analytical Chemistry. [doi]:10.1021/acs.analchem.6b02676 {PMID}:27560777 PMCID:PMC5054939
  10. Olesen, S.; S. Vora, S. Techtmann, J.L. Fortney, J.R. Bastidas-Oyanedel, J. Rodriguez, T.C. Hazen and E.J. Alm (2016) A novel analysis method for paired-sample microbial ecology experiments. Public Library of Science ONE. [doi]:10.1371/journal.pone.0154804 {PMID}:27152415 PMCID:PMC4859510
  11. Price, M.N.; K.M. Wetmore, R.J. Waters, M. Callaghan, J. Ray, J.V. Kuehl, R.A. Melnyk, J.S. Lamson, Y. Suh, Z. Esquivel, H. Sadeeshkumar, R. Chakraborty, B.E. Rubin, J. Bristow, M.J. Blow, A.P. Arkin and A.M. Deutschbauer (2016) Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes. bioRxiv. [doi]:10.1101/072470
  12. Price, M.N.; K.M. Wetmore, A.M. Deutschbauer and A.P. Arkin (2016) A Comparison of the Costs and Benefits of Bacterial Gene Expression. Public Library of Science ONE. [doi]:10.1371/journal.pone.0164314 {PMID}:27711251 PMCID:PMC5053530
  13. Price, M.N.; and A.P. Arkin (2016) Weakly deleterious mutations and low rates of recombination limit the impact of natural selection on bacterial genomes. mBio. [doi]:10.1128/mBio.01302-15 {PMID}:26670382 PMCID:PMC4701828
  14. Price, M.N.; and A.P. Arkin (2016) A Theoretical Lower Bound for Selection on the Expression Levels of Proteins. Genome Biology and Evolution. [doi]:10.1093/gbe/evw126 {PMID}:27289091 PMCID:PMC4943197
  15. Rhee, M.; Y.K. Light, R.J. Meagher and A.K. Singh (2016) Digital Droplet Multiple Displacement Amplification (ddMDA) for whole genome sequencing of limited DNA samples. Public Library of Science ONE. [doi]:10.1371/journal.pone.0153699 {PMID}:27144304 PMCID:PMC4856258 
  16. Rocha, A.M.; Q. Yuan, D. Close, K.B. O’dell, J. Fortney, J. Wu and T.C. Hazen (2016) Rapid Detection of Microbial Cell Abundance in Aquatic Systems. Biosensors and Bioelectronics. [doi]:10.1016/j.bios.2016.05.098 {PMID}:27315516
  17. Shatsky, M.; M. Dong, H. Liu, L.L. Yang, M. Choi, M.E. Singer, J.T. Geller, S.J. Fisher, S.C. Hall, T.C. Hazen, S.E. Brenner, G.P. Butland, J. Jin, H.E. Witkowska, J.-M. Chandonia and M.D. Biggin (2016) Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions. Molecular & Cellular Proteomics. [doi]:10.1074/mcp.M115.057117 {PMID}27099342 PMCID:PMC5083090
  18. Shatsky, M.; S. Allen, B.L. Gold, N.L. Liu, T.R. Juba, S.A. Reveco, D.A. Elias, R. Prathapam, J. He, W. Yang, E.D. Szakal, H. Liu, M.E. Singer, J.T. Geller, B.R. Lam, A. Saini, V.V. Trotter, S.C. Hall, S.J. Fisher, S.E. Brenner, S.R. Chhabra, T.C. Hazen, J.D. Wall, H.E. Witkowska, M.D. Biggin, J.-M. Chandonia and G. Butland (2016) Bacterial interactomes: interacting protein partners share similar function and are validated in independent assays more frequently than previously reported. Molecular and Cellular Proteomics. [doi]:10.1074/mcp.M115.054692 {PMID}:26873250 PMCID:PMC4858938
  19. Spencer, S.J.; M.V. Tamminen, S.P. Preheim, M.T. Guo, A.W. Briggs, I.L. Brito, D.A. Weitz, L.K. Pitkanen, F. Vigneault, M.P. Virta and E.J. Alm (2016) Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers. International Society for Microbial Ecology Journal. [doi]:10.1038/ismej.2015.124 {PMID}:26394010 PMCID:PMC4737934
  20. Thorgersen, M.P.; and M.W.W. Adams (2016) Nitrite Reduction Assay for Whole Pseudomonas Cells. Bio-protocol. [doi]:10.21769/BioProtoc.1818
  21. Vaccaro, B.J.; M.P. Thorgersen, W.A. Lancaster, M.N. Price, K.M. Wetmore, F.L. Poole, A.M. Deutschbauer, A.P. Arkin and M.W.W. Adams (2016) Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses. Applied and Environmental Microbiology. [doi]:10.1128/Aem.02602-15 {PMID}:26452555 PMCID:PMC4702625
  22. Vaccaro, B.J.; W.A. Lancaster, M.P. Thorgersen, G.M. Zane, A.D. Younkin, A.E. Kazakov, K.M. Wetmore, A.M. Deutschbauer, A.P. Arkin, P.S. Novichkov, J.D. Wall and M.W.W. Adams (2016) Novel metal cation resistance systems from mutant fitness analysis of denitrifying Pseudomonas stutzeri. Applied and Environmental Microbiology. [doi]:10.1128/AEM.01845-16 {PMID}:27474723 PMCID:PMC5038046

  23. Books/Book Chapters

  24. Hazen, T.C. and G.S. Sayler (2016) Environmental Systems Microbiology of Contaminated Environments. Manual of Environmental Microbiology, 4th Edition. Editors: M. Yates, C. Nakatsu, R. Miller and S. Pillai. [doi]:10.1128/9781555818821.ch5.1.6
  25. Lubbe, A.; and T.R. Northen (2016) Exometabolomics for Linking Soil Carbon Dynamics to Microbial Communities. Microbial Metabolomics: Applications in Clinical, Environmental, and Industrial Microbiology. Editors: D. Beale, K. Kouremenos and E. Palombo. [doi]:10.1007/978-3-319-46326-1_5

  26. Legacy and Synergistic External Research

  27. Blaser, M.J.; Z.G. Cardon, M.K. Cho, J.L. Dangl, T.J. Donohue, J.L. Green, R. Knight, M.E. Maxon, T.R. Northen, K.S. Pollard and E.L. Brodie (2016) Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges. mBio. [doi]:10.1128/mBio.00714-16 {PMID}:27178263 PMCID:PMC4895116
  28. Bouskill, N.J.; T.E. Wood, R. Baran, Z. Ye, B.P. Bowen, H. Lim, J. Zhou, J.D. Nostrand, P. Nico, T.R. Northen, W.L. Silver and E.L. Brodie (2016) Belowground Response to Drought in a Tropical Forest Soil. I. Changes in Microbial Functional Potential and Metabolism. Frontiers in Microbiology. [doi]:10.3389/fmicb.2016.00525 {PMID}:27148214 PMCID:PMC4837414
  29. Bouskill, N.J.; T.E. Wood, R. Baran, Z. Hao, Z. Ye, B.P. Bowen, H.C. Lim, P.S. Nico, H.Y. Holman, B. Gilbert, W.L. Silver, T.R. Northen and E.L. Brodie (2016) Belowground Response to Drought in a Tropical Forest Soil. II. Change in Microbial Function Impacts Carbon Composition. Frontiers in Microbiology. [doi]:10.3389/fmicb.2016.00323 {PMID}:27014243 PMCID:PMC4791749
  30. Paradis, C.J.; S. Jagadamma, D.B. Watson, L.D. McKay, T.C. Hazen, M. Park and J.D. Istok (2016) In situ mobility of uranium in the presence of nitrate following sulfate-reducing conditions. Journal of Contaminant Hydrology. [doi]:10.1016/j.jconhyd.2016.02.002 {PMID}:26897652