Berkeley Lab
Bringing Science Solutions to the World
Berkeley Lab

2013 Publications

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

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

  1. Baran, R.; B.P. Bowen, M.N. Price, A.P. Arkin, A.M. Deutschbauer and T.R. Northen (2013) Metabolic Footprinting of Mutant Libraries to Map Metabolite Utilization to Genotype. American Chemical Society Chemical Biology. [doi]:10.1021/cb300477w {PMID}:23082955
  2. Baran, R.; and T.R. Northen (2013) RAMSI: Robust Automated Mass Spectra Interpretation and Chemical Formula Calculation Using Mixed Integer Linear Programming. Analytical Chemistry. [doi]:10.1021/ac402180c {PMID}:24032353
  3. Brileya, K.A.; J.M. Connolly, C. Downey, R. Gerlach and M.W. Fields (2013) Taxis toward hydrogen gas by Methanococcus maripaludis. Scientific Reports. [doi]:10.1038/srep03140 {PMID}:24189441 PMCID:PMC3817446
  4. Brown, S.D.; S.M. Utturkar, A.P. Arkin, A.M. Deutschbauer, D.A. Elias, T.C. Hazen and R. Chakraborty (2013) Draft Genome Sequence for Desulfovibrio africanus Strain PCS. Genome Announcements. [doi]:10.1128/genomeA.00144-13 {PMID}:23580709 PMCID:PMC3624683
  5. Chivian, D.; P.S. Dehal, K. Keller and A.P. Arkin (2013) MetaMicrobesOnline: phylogenomic analysis of microbial communities. Nucleic Acids Research. [doi]:10.1093/nar/gks1202 {PMID}:23203984 PMCID:PMC3531168  
  6. Cipriano, M.J.; P.N. Novichkov, A.E. Kazakov, D.A. Rodionov, A.P. Arkin, M.S. Gelfand and I. Dubchak (2013) RegTransBase–a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. BioMed Central Genomics. [doi]:10.1186/1471-2164-14-213 {PMID}:23547897 PMCID:PMC3639892
  7. Costa, K.C.; S.H. Yoon, M. Pan, J.A. Burn, N.S. Baliga and J.A. Leigh (2013) Effects of H2 and formate on growth yield and regulation of methanogenesis in Methanococcus maripaludis. Journal of Bacteriology. [doi]:10.1128/JB.02141-12 {PMID}:23335420 PMCID:PMC3624518
  8. Fels, S.R.; G.M. Zane, S.M. Blake and J.D. Wall (2013) Rapid transposon liquid enrichment sequencing (TnLE-seq) for gene fitness evaluation in underdeveloped bacterial systems. Applied and Environmental Microbiology. [doi]:10.1128/AEM.02051-13 {PMID}:24077707 PMCID:PMC3837734
  9. Hazen, T.C. (2013) Opinion: The SuperChip for Microbial Community Structure, and Function from all Environments. Microbial Biotechnology. [doi]:10.1111/1751-7915.12045 {PMID}:23464831 PMCID:PMC3918150
  10. Hazen, T.C.; A.M. Rocha and S.M. Techtmann (2013) Advances in monitoring environmental microbes. Current Opinion in Biotechnology. [doi]:10.1016/j.copbio.2012.10.020 {PMID}:23183250
  11. Kazakov, A.E.; L. Rajeev, E.G. Luning, G.M. Zane, K. Siddartha, D.A. Rodionov, I. Dubchak, A.P. Arkin, J.D. Wall, A. Mukhopadhyay and P.S. Novichkov (2013) New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria. Journal of Bacteriology. [doi]:10.1128/jb.00679-13 {PMID}:23913324 PMCID:PMC3807478
  12. Kazakov, A.E.; D.A. Rodionov, M.N. Price, A.P. Arkin, I. Dubchak and P. Novichkov (2013) Transcription factor family-based reconstruction of singleton regulons: Study of the Crp/Fnr, ArsR and GntR families in Desulfovibrionales genomes. Journal of Bacteriology. [doi]:10.1128/JB.01977-12 {PMID}:23086211 PMCID:PMC3536172
  13. Keller, K.L.; B.J. Rapp-Giles, E.S. Semkiw, I. Porat, S.D. Brown and J.D. Wall (2013) New model for electron flow for sulfate reduction in Desulfovibrio alaskensis G20. Applied and Environmental Microbiology. [doi]:10.1128/AEM.02963-13 {PMID}:24242254 PMCID:PMC3911205
  14. Krumholz, L.R.; L. Wang, D.A.C. Beck, T. Wang, M. Hackett, B. Mooney, T.R. Juba, M.J. McInerney, B. Meyer, J.D. Wall and D.A. Stahl (2013) Membrane protein complex of APS reductase and Qmo is present in Desulfovibrio vulgaris and Desulfovibrio alaskensis. Microbiology Society. [doi]:10.1099/mic.0.063818-0 {PMID}:23842468
  15. Louie, K.B.; B.P. Bowen, X. Cheng, J.E. Berleman, R. Chakraborty, A.M. Deutschbauer, A.P. Arkin and T.R. Northen (2013) “Replica-Extraction-Transfer” Nanostructure-Initiator Mass Spectrometry Imaging of Acoustically Printed Bacteria. Analytical Chemistry. [doi]:10.1021/ac402240q {PMID}:24111681
  16. Meyer, B.; J.V. Kuehl, A.M. Deutschbauer, M.N. Price, A.P. Arkin and D.A. Stahl (2013) Variation among Desulfovibrio Species in Electron Transfer Systems Used for Syntrophic Growth. Journal of Bacteriology. [doi]:10.1128/JB.01959-12 {PMID}:23264581 PMCID:PMC3571329
  17. Meyer, B.; J.V. Kuehl, A.M. Deutschbauer, A.P. Arkin and D.A. Stahl (2013) Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes. Journal of Bacteriology. [doi]:10.1128/JB.00504-13 {PMID}:23974031 PMCID:PMC3807489
  18. Momeni, B.; K.A. Brileya, M.W. Fields and W. Shou (2013) Strong inter-population cooperation leads to partner intermixing in microbial communities. eLife. [doi]:10.7554/eLife.00230 {PMID}:23359860 PMCID:PMC3552619
  19. Novichkov, P.S.; A.E. Kazakov, D.A. Ravcheev, S.A. Leyn, G.Y. Kovaleva, R.A. Sutormin, M.D. Kazanov, W. Riehl, A.P. Arkin, I. Dubchak and D.A. Rodionov (2013) RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria. BioMed Central Genomics. [doi]:10.1186/1471-2164-14-745 {PMID}:24175918 PMCID:PMC3840689
  20. Novichkov, P.S.; X. Li, J.V. Kuehl, A.M. Deutschbauer, A.P. Arkin, M.N. Price and D.A. Rodionov (2013) Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria. Environmental Microbiology. [doi]:10.1111/1462-2920.12273 {PMID}:24118949
  21. Orellana, M.V.; W.L. Pang, P.M. Durand, K. Whitehead and N.S. Baliga (2013) A Role for Programmed Cell Death in the Microbial Loop. Public Library of Science ONE. [doi]:10.1371/journal.pone.0062595 {PMID}:23667496 PMCID:PMC3648572
  22. Pang, W.L.; A. Kaur, A.V. Ratushny, A. Cvetkovic, S. Kumar, M. Pan, A.P. Arkin, J.D. Aitchison, M.W.W. Adams and N.S. Baliga (2013) Metallochaperones Regulate Intracellular Copper Levels. Public Library of Science Computational Biology. [doi]:10.1371/journal.pcbi.1002880 {PMID}:23349626 PMCID:PMC3551603
  23. Preheim, S.P.; A.R. Perrotta, A.M. Martin-Platero, A. Gupta and E.J. Alm (2013) Distribution-Based Clustering: Using Ecology to Refine the Operational Taxonomic Unit. Applied and Environmental Microbiology. [doi]:10.1128/aem.00342-13 {PMID}:23974136 PMCID:PMC3811501
  24. Price, M.N.; A.M. Deutschbauer, J.M. Skerker, K.M. Wetmore, T. Ruths, J.S. Mar, J.V. Kuehl, W. Shao and A.P. Arkin (2013) Indirect and suboptimal control of gene expression is widespread in bacteria. Molecular Systems Biology. [doi]:10.1038/msb.2013.16 {PMID}:23591776 PMCID:PMC3658271
  25. Radivojac, P.; W.T. Clark, T.R. Oron, A.M. Schnoes, T. Wittkop, A. Sokolov, K. Graim, C. Funk, K. Verspoor, A. Ben-Hur, G. Pandey, J.M. Yunes, A.S. Talwalkar, S. Repo, M.L. Souza, D. Piovesan, R. Casadio, Z. Wang, J. Cheng, H. Fang, J. Gough, P. Koskinen, P. Toronen, J. Nokso-Koivisto, L. Holm, D. Cozzetto, D.W.A. Buchan, K. Bryson, D.T. Jones, B. Limaye, H. Inamdar, A. Datta, S.K. Manjari, R. Joshi, M. Chitale, D. Kihara, A.M. Lisewski, S. Erdin, E. Venner, O. Lichtarge, R. Rentzsch, H. Yang, A.E. Romero, P. Bhat, A. Paccanaro, T. Hamp, R. Kaszner, S. Seemayer, E. Vicedo, C. Schaefer, D. Achten, F. Auer, A. Boehm, T. Braun, M. Hecht, M. Heron, P. Honigschmid, T.A. Hopf, S. Kaufmann, M. Kiening, D. Krompass, C. Landerer, Y. Mahlich, M. Roos, J. Bjorne, T. Salakoski, A. Wong, H. Shatkay, F. Gatzmann, I. Sommer, M.N. Wass, M.J.E. Sternberg, N. Skunca, F. Supek, M. Bosnjak, P. Panov, S. Dzeroski, T. Smuc, Y.A.I. Kourmpetis, A.D.J. van Dijk, C.J.F. ter Braak, Y. Zhou, Q. Gong, X. Dong, W. Tian, M. Falda, P. Fontana, E. Lavezzo, B. Di Camillo, S. Toppo, L. Lan, N. Djuric, Y. Guo, S. Vucetic, A. Bairoch, M. Linial, P.C. Babbitt, S.E. Brenner, C. Orengo, B. Rost, S.D. Mooney and I. Friedberg (2013) A large-scale evaluation of computational protein function prediction. Nature Methods. [doi]:10.1038/nmeth.2340 {PMID}:23353650 PMCID:PMC3584181
  26. Rübel, O.; A. Greiner, S. Cholia, K. Louie, E.W. Bethel, T.R. Northen and B.P. Bowen (2013) OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging. Analytical Chemistry. [doi]:10.1021/ac402540a {PMID}:24087878
  27. Shatsky, M.; P. Arbelaez, R.M. Glaeser and S.E. Brenner (2013) Optimal and fast rotational alignment of volumes with missing data in Fourier space. Journal of Structural Biology. [doi]:10.1016/j.jsb.2013.08.006 {PMID}:23994045
  28. Somenahally, A.C.; J.J. Mosher, T. Yuan, M. Podar, T.J. Phelps, S.D. Brown, Z.K. Yang, T.C. Hazen, A.P. Arkin, A.V. Palumbo, J.D. Van Nostrand, J. Zhou and D.A. Elias (2013) Hexavalent chromium reduction under fermentative conditions with lactate stimulated native microbial communities. Public Library of Science ONE. [doi]:10.1371/journal.pone.0083909 {PMID}:24376771 PMCID:PMC3871698
  29. Tu, Q.; Z. He, Y. Deng and J. Zhou (2013) Strain/Species-specific probe design for microbial identification microarrays. Applied and Environmental Microbiology. [doi]:10.1128/AEM.01124-13 {PMID}:23747703 PMCID:PMC3754697
  30. Turkarslan, S.; E.J. Wurtmann, W.-J. Wu, N. Jiang, J.C. Bare, K. Foley, D.J. Reiss, P. Novichkov and N.S. Baliga (2013) Network portal: a database for storage, analysis and visualization of biological networks. Nucleic Acids Research. [doi]:10.1093/nar/gkt1190 {PMID}:24271392 PMCID:PMC3964938
  31. Wang, L.; X. Wang, A.P. Arkin and M.S. Samoilov (2013) Inference of gene regulatory networks from genome-wide knockout fitness data. Bioinformatics. [doi]:10.1093/bioinformatics/bts634 {PMID}:23271269 PMCID:PMC3562072
  32. Yoon, S.H.; S. Turkarslan, D.J. Reiss, M. Pan, J.A. Burn, K.C. Costa, T.J. Lie, J. Slagel, R.L. Moritz, M. Hackett, J.A. Leigh and N.S. Baliga (2013) A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen. Genome Research. [doi]:10.1101/gr.153916.112 {PMID}:24089473 PMCID:PMC3814884
  33. Zhou, A.; E. Baidoo, Z. He, A. Mukhopadhyay, J.K. Baumohl, P. Benke, M.P. Joachimiak, M. Xie, R. Song, A.P. Arkin, T.C. Hazen, J.D. Keasling, J.D. Wall, D.A. Stahl and J. Zhou (2013) Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. International Society for Microbial Ecology Journal. [doi]:10.1038/ismej.2013.60 {PMID}:23575373 PMCID:PMC3749499
  34. Zhou, A.; Z. He, Y. Qin, Z. Lu, Y. Deng, Q. Tu, C.L. Hemme, J.D. Van Nostrand, L. Wu, T.C. Hazen, A.P. Arkin and J. Zhou (2013) StressChip as a High-Throughput Tool for Assessing Microbial Community Responses to Environmental Stresses. Environmental Science & Technology. [doi]:10.1021/es4018656 {PMID}:23889170
  35. Zhou, J.; W. Liu, Y. Deng, Y.-H. Jiang, K. Xue, Z. He, J.D. Van Nostrand, L. Wu, Y. Yang and A. Wang (2013) Stochastic assembly leads to alternative communities with distinct functions in a bioreactor microbial community. mBio. [doi]:10.1128/mBio.00584-12 {PMID}:23462114 PMCID:PMC3585448
  36. Zhou, J.; Y.-H. Jiang, Y. Deng, Z. Shi, B.Y. Zhou, K. Xue, L. Wu, Z. He and Y. Yang (2013) Random sampling process leads to overestimation of β-diversity of microbial communities. mBio. [doi]:10.1128/mBio.00324-13 {PMID}:23760464 PMCID:PMC3684833

  37. Books/Book Chapters

  38. He, Z.; J.D. Van Nostrand and J. Zhou (2013) GeoChip-based metagenomics technologies for analyzing microbial community functional structure and activities. Encyclopedia of Metagenomics. Editor: K.E. Nelson. [doi]:10.1007/978-1-4614-6418-1_760-4
  39. Northen, T.R. (2013) Biofuels and biomaterials from microbes. Fundamentals of Materials for Energy and Environmental Sustainability. Editor: D. Ginley and D. Cahen. [doi]:10.1017/CBO9780511718786.029
  40. Preheim, S.P.; A.R. Perrotta, J. Friedman, C. Smilie, I.L. Brito, M.B. Smith and E.J. Alm (2013) Computational methods for high-throughput comparative analyses of natural microbial communities. Methods in Enzymology. Editor: E.F. DeLong. [doi]:10.1016/B978-0-12-407863-5.00018-6 {PMID}:24060130
  41. Stahl, D.A.; J.J. Flowers, M. Hullar and S. Davidson (2013) Structure and function of microbial communities. The Prokaryotes, 4th Edition. Editors: E. Rosenberg, E.F. DeLong, F. Thompson, S. Lory, and E. Stackebrandt. [doi]:10.1007/978-3-642-30123-0_34
  42. Van Nostrand, J.D.; T.J. Gentry and J. Zhou (2013) Microarray-Based Microbial Identification and Characterization. Advanced Techniques in Diagnostic Microbiology, 2nd ed. Editors: Y.-W. Tang and C.W. Stratton. [doi]:10.1007/0-387-32892-0_17

  43. Legacy and Synergistic External Research

  44. De León, K.B.; R. Gerlach, B.M. Peyton and M.W. Fields (2013) Archaeal and bacterial communities in three alkaline hot springs in Heart Lake Geyser Basin, Yellowstone National Park. Frontiers in Microbiology. [doi]:10.3389/fmicb.2013.00330 {PMID}:24282404 PMCID:PMC3824361
  45. Figueiredo, M.C.O.; S.A.L. Lobo, S.H. Sousa, F.P. Pereira, J.D. Wall, L.S. Nobre and L.M. Saraiva (2013) Hybrid cluster proteins and flavodiiron proteins afford protection to Desulfovibrio vulgaris upon macrophage infection. Journal of Bacteriology. [doi]:10.1128/JB.00074-13 {PMID}:23564166 PMCID:PMC3676046 
  46. Fischer, C.R.; B.P. Bowen, C. Pan, T.R. Northen and J.F. Banfield (2013) Stable-Isotope Probing Reveals That Hydrogen Isotope Fractionation in Proteins and Lipids in a Microbial Community Are Different and Species-Specific. American Chemical Society Chemical Biology. [doi]:10.1021/cb400210q {PMID}:23713674
  47. Ivanisevic, J.; Z.-J. Zhu, L. Plate, R. Tautenhahn, S. Chen, P.J. O’Brien, C.H. Johnson, M.A. Marletta, G.J. Patti and G. Siuzdak (2013) Toward ‘omic scale metabolite profiling: a dual separation-mass spectrometry approach for coverage of lipid and central carbon metabolism. Analytical Chemistry. [doi]:10.1021/ac401140h {PMID}:23781873 PMCID:PMC3761963
  48. Kang, S.; J.D. Van Nostrand, H.L. Gough, Z. He, T.C. Hazen, D.A. Stahl and J. Zhou (2013) Functional gene array-based analysis of microbial communities in heavy metals-contaminated lake sediments. Federation of European Microbiological Society Microbiology Ecology. [doi]:10.1111/1574-6941.12152 {PMID}:23710534
  49. Patti, G.J.; R. Tautenhahn, D. Rinehart, K. Cho, L.P Shriver, M. Manchester, I. Nikolskiy, C.H. Johnson, N.G. Mahieu and G. Siuzdak (2013) A view from above: cloud plots to visualize global metabolomic data. Analytical Chemistry. [doi]:10.1021/ac3029745 {PMID}:23206250 PMCID:PMC3716252
  50. Rübel, O.; A. Greiner, S. Cholia, K.B. Louie, E.W. Bethel, T.R. Northen and B.P. Bowen (2013) OpenMSI: High-performance web-based visualization, analysis and management of mass spectrometry imaging data. Analytical Chemistry. [doi]:10.1021/ac402540a {PMID}:24087878
  51. Sim, M.S.; D.T. Wang, G.M. Zane, J.D. Wall, T. Bosak and S. Ono (2013) Fractionation of sulfur isotopes by Desulfovibrio vulgaris mutants lacking hydrogenases or type I tetraheme cytochrome c 3. Frontiers in Microbiology. [doi]:10.3389/fmicb.2013.00171 {PMID}:23805134 PMCID:PMC3691511
  52. Sun, E.I.; S.A. Leyn, M.D. Kazanov, M.H. Saier Jr., P.S. Novichkov and D.A. Rodionov (2013) Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. BioMed Central Genomics. [doi]:10.1186/1471-2164-14-597 {PMID}:24060102 PMCID:PMC3766115
  53. Zhu, Z.-J.; A.W. Schultz, J. Wang, C.H. Johnson, S.M. Yannone, G.J. Patti and G. Siuzdak (2013) Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database. Nature Protocols. [doi]:10.1038/nprot.2013.004 {PMID}:23391889 PMCID:PMC3666335