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Berkeley Lab

2012 Publications

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

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


  1. Ashworth, J.; E.J. Wurtmann and N.S. Baliga (2012) Reverse engineering systems models of regulation: discovery, prediction and mechanisms. Current Opinion in Biotechnology. [doi]:10.1016/j.copbio.2011.12.005 {PMID}:22209016 PMCID:PMC3477774
  2. Bare, J.C.; and N.S. Baliga (2012) Architecture for interoperable software in biology. Briefings in Bioinformatics. [doi]:10.1093/bib/bbs074 {PMID}:23235920 PMCID:PMC4103535
  3. Borglin, S.; D. Joyner, K.M. DeAngelis, J. Khudyakov, P. D’Haeseleer, M.P. Joachimiak and T.C. Hazen (2012) Application of phenotypic microarrays to environmental microbiology. Current Opinion in Biotechnology. [doi]:10.1016/j.copbio.2011.12.006 {PMID}:22217654
  4. Brown, S.D.; M. Podar, D.M. Klingeman, C.M. Johnson, Z.K. Yang, S.M. Utturkar, M.L. Land, J.J. Mosher, R.A. Hurt Jr, T.J. Phelps, A.V. Palumbo, A.P. Arkin, T.C. Hazen and D.A. Elias (2012) Draft genome sequences for two metal-reducing Pelosinus fermentans strains isolated from a Cr(VI)-contaminated site and for type strain R7. Journal of Bacteriology. [doi]:10.1128/JB.01174-12 {PMID}:22933770 PMCID:PMC3430306
  5. Chakraborty, R.; C.H. Wu and T.C. Hazen (2012) Systems biology approach to bioremediation. Current Opinion in Biotechnology. [doi]:10.1016/j.copbio.2012.01.015 {PMID}:22342400
  6. Clark, M.E.; Z. He, A.M. Redding, M.P. Joachimiak, J.D. Keasling, J. Zhou, A.P. Arkin, A. Mukhopadhyay and M.W. Fields (2012) Transcriptomic and Proteomic Analyses of Desulfovibrio vulgaris Biofilms: Carbon and Energy Flow Contribute to the Distinct Biofilm Growth State. BioMed Central Genomics. [doi]:10.1186/1471-2164-13-138 {PMID}:22507456 PMCID:PMC3431258
  7. De León, K.B.; B.D. Ramsay and M.W. Fields (2012) Quality-score refinement of SSU rRNA gene pyrosequencing differs across gene region for environmental samples. Microbial Ecology. [doi]:10.1007/s00248-012-0043-9 {PMID}:22476815 PMCID:PMC3391548
  8. De León, K.B.; M.L. Young, L.B. Camilleri, S.D. Brown, J.M. Skerker, A.M. Deutschbauer, A.P. Arkin and M.W. Fields (2012) Draft genome sequence of Pelosinus fermentans JBW45, isolated during in situ stimulation for Cr(VI) reduction. Journal of Bacteriology. [doi]:10.1128/JB.01224-12 {PMID}:22965085 PMCID:PMC3457247
  9. Deng, Y.; Y.H. Jiang, Y. Yang, Z. He, F. Luo and J. Zhou (2012) Molecular ecological network analyses. BioMed Central Bioinformatics. [doi]:10.1186/1471-2105-13-113 {PMID}:22646978 PMCID:PMC3428680
  10. Friedman, J.; and E.J. Alm (2012) Inferring Correlation Networks from Genomic Survey Data. Public Library of Science Computational Biology. [doi]:10.1371/journal.pcbi.1002687 {PMID}:23028285 PMCID:PMC3447976
  11. Greving, M.; X. Cheng, W. Reindl, B. Bowen, K. Deng, K. Louie, M. Nyman, J. Cohen, A. Singh, B. Simmons, P.D. Adams, G. Siuzdak and T.R. Northen (2012) Acoustic deposition with NIMS as a high-throughput enzyme activity assay. Analytical and Bioanalytical Chemistry. [doi]:10.1007/s00216-012-5908-8 {PMID}:22407334
  12. Han, B.-G.; R.W. Walton, A. Song, P. Hwu, M.T. Stubbs, S.M. Yannone, P. Arbeláez, M. Dong and R.M. Glaeser (2012) Electron microscopy of biotinylated protein complexes bound to streptavidin monolayer crystals. Journal of Structural Biology. [doi]:10.1016/j.jsb.2012.04.025 {PMID}:22584152
  13. Hazen, T.C.; and S. Wuertz (2012) Environmental biotechnology. Current Opinion in Biotechnology. [doi]:10.1016/j.copbio.2012.04.004 {PMID}:22560159
  14. He, Z.; Y. Deng and J. Zhou (2012) Development of functional gene microarrays for microbial community analysis. Current Opinion in Biotechnology. [doi]:10.1016/j.copbio.2011.11.001 {PMID}:22100036
  15. He, Z.; J.D. Van Nostrand and J. Zhou (2012) Applications of functional gene microarrays for profiling microbial communities. Current Opinion in Biotechnology. [doi]:10.1016/j.copbio.2011.12.021 {PMID}:22226464
  16. Mosher, J.J.; T.J. Phelps, M. Podar, R.A. Hurt Jr, J.H. Campbell, M.M. Drake, J.G. Moberly, C.W. Schadt, S.D. Brown, T.C. Hazen, A.P. Arkin, A.V. Palumbo, B.A. Faybishenko and D.A. Elias (2012) Microbial community succession during lactate amendment and electron acceptor limitation reveals a predominance of metal-reducing Pelosinus spp. Applied and Environmental Microbiology. [doi]:10.1128/AEM.07165-11 {PMID}:22267668 PMCID:PMC3302606
  17. Novichkov, P.S.; T.S. Brettin, E.S. Novichkova, P.S. Dehal, A.P. Arkin, I. Dubchak and D.A. Rodionov (2012) RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. Nucleic Acids Research. [doi]:10.1093/nar/gks562 {PMID}:22700702 PMCID:PMC3394319
  18. Rajeev, L.; K.L. Hillesland, G.M. Zane, A. Zhou, M.P. Joachimiak, Z. He, J. Zhou, A.P. Arkin, J.D. Wall and D.A. Stahl (2012) Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription. Journal of Bacteriology. [doi]:10.1128/JB.00749-12 {PMID}:22904289 PMCID:PMC3486112
  19. Ramos, A.R.; K.L. Keller, J.D. Wall and I.A. Pereira (2012) The Membrane QmoABC Complex Interacts Directly with the Dissimilatory Adenosine 5′-Phosphosulfate Reductase in Sulfate Reducing Bacteria. Frontiers in Microbiology. [doi]:10.3389/fmicb.2012.00137 {PMID}:22536198 PMCID:PMC3333476
  20. Van Nostrand J.D.; H. Zhili and J. Zhou (2012) Applications of functional gene microarrays for profiling microbial communities. Current Opinions in Biotechnology. [doi]:10.1016/j.copbio.2011.12.021
  21. Walian, P.J.; S. Allen, M. Shatsky, L. Zeng, E.D. Szakal, H. Liu, S.C. Hall, S.J. Fisher, B.R. Lam, M.E. Singer, J.T. Geller, S.E. Brenner, J.M. Chandonia, T.C. Hazen, H.E. Witkowska, M.D. Biggin and B.K. Jap (2012) High-throughput Isolation and Characterization of Untagged Membrane Protein Complexes: Outer Membrane Complexes of Desulfovibrio vulgaris. Journal of Proteome Research. [doi]:10.1021/pr300548d {PMID}:23098413 PMCID:PMC3516867
  22. Walker, C.B.; A.M. Redding-Johanson, E.E. Baidoo, L. Rajeev, Z. He, E.L. Hendrickson, M.P. Joachimiak, S. Stolyar, A.P. Arkin, J.A. Leigh, J. Zhou, J.D. Keasling, A. Mukhopadhyay and D.A. Stahl (2012) Functional responses of methanogenic archaea to syntrophic growth. International Society for Microbial Ecology Journal. [doi]:10.1038/ismej.2012.60 {PMID}:22739494 PMCID:PMC3475374
  23. Wu, M.; and A.K. Singh (2012) Single-cell protein analysis. Current Opinion in Biotechnology. [doi]:10.1016/j.copbio.2011.11.023 {PMID}:22189001 PMCID:PMC3283030
  24. Yannone, S.M.; S. Hartung, A.L. Menon, M.W.W. Adams and J.A. Tainer (2012) Metals in biology: defining metalloproteomes. Current Opinion in Biotechnology. [doi]:10.1016/j.copbio.2011.11.005 {PMID}:22138493 PMCID:PMC3273585
  25. Yilmaz, S. and A.K. Singh (2012) Single cell genome sequencing. Current Opinion in Biotechnology. [doi]:10.1016/j.copbio.2011.11.018 {PMID}:22154471 PMCID:PMC3318999
  26. Zhou, A.; Y.I. Chen, G.M. Zane, Z. He, C.L. Hemme, M.P. Joachimiak, J.K. Baumohl, Q. He, M.W. Fields, A.P. Arkin, J.D. Wall, T.C. Hazen and J. Zhou (2012) Functional Characterization of Crp/Fnr-Type Global Transcriptional Regulators in Desulfovibrio vulgaris Hildenborough. Applied and Environmental Microbiology. [doi]:10.1128/aem.05666-11 {PMID}:22156435 PMCID:PMC3273024

  27. Books/Book Chapters

  28. Baidoo, E.E.; P.I. Benke and J.D. Keasling (2012) Mass Spectrometry-Based Microbial Metabolomics. Microbial Systems Biology: Methods and Protocols. Editor: A. Navid. [doi]:10.1007/978-1-61779-827-6_9
  29. Dong, M.; M. Choi, M.D. Biggin and J. Jin (2012) A multichannel gel electrophoresis and continuous fraction collection apparatus for high-throughput protein separation and characterization. Methods in Molecular Biology, Springer Science + Business Media. Editors: B.T. Kurien and R.H. Scofield. [doi]:10.1007/978-1-61779-821-4_30
  30. Vaccaro, B.J.; A.L. Menon, W.A. Lancaster and M.W.W. Adams (2012) Metallomics using inductively coupled Plasma mass spectrometry. Current Protocols in Chemical Biology. [doi]:10.1002/9780470559277.ch120031

  31. Legacy and Synergistic External Research

  32. Berube, P.M.; and D.A. Stahl (2012) The Divergent AmoC3 Subunit of Ammonia Monooxygenase Functions as Part of a Stress Response System in Nitrosomonas europaea. Journal of Bacteriology. [doi]:10.1128/JB.00133-12 {PMID}:22544266 PMCID:PMC3434715
  33. Bridger, S.L.; W.A. Lancaster, F.L. Poole II, G.J. Schut and M.W.W. Adams (2012) Genome sequencing of a genetically tractable Pyrococcus furiosus strain reveals a highly dynamic genome. Journal of Bacteriology. [doi]:10.1128/JB.00439-12 {PMID}:22636780 PMCID:PMC3416535
  34. Brodie, E.L.; D.C. Joyner, B. Faybishenko, M.E. Conrad, C. Rios-Velazquez, B. Mork, R. Kelley, A. Willet, S. Koenigsberg, D. Herman, M.K. Firestone, T.C. Hazen (2012) Microbial community response to addition of polylactate compounds to stimulate hexavalent chromium reduction in groundwater. Chemosphere. [doi]:10.1016/j.chemosphere.2011.07.021 {PMID}:21872904
  35. Christie, J.M.; K. Hitomi, A.S. Arvai, K.A. Hartfield, M. Mettlen, A.J. Pratt, J.A. Tainer and E.D. Getzoff (2012) Structural tuning of the fluorescent protein iLOV for improved photostability. Journal of Biological Chemistry. [doi]:10.1074/jbc.M111.318881 {PMID}:22573334 PMCID:PMC3381190
  36. He, Z.; Y. Piceno, Y. Deng, M. Xu, Z. Lu, T. Desantis, G. Andersen, S.E. Hobbie, P.B. Reich and J. Zhou (2012) The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide. International Society for Microbial Ecology Journal. [doi]:10.1038/ismej.2011.99 {PMID}:21796217 PMCID:PMC3260516
  37. Liang, Y.; J.D. Van Nostrand, L.A. N’Guessan, A.D. Peacock, Y. Deng, P.E. Long, C.T. Resch, L. Wu, Z. He, G. Li, T.C. Hazen, D.R. Lovley and J. Zhou (2012) Microbial functional gene diversity with a shift of subsurface redox conditions during In Situ uranium reduction. Applied and Environmental Microbiology. [doi]:10.1128/AEM.06528-11 {PMID}:22327592 PMCID:PMC3318829
  38. **McDonald, D.; M.N. Price, J. Goodrich, E.P. Nawrocki, T.Z. Desantis, A. Probst, G.L. Andersen, R. Knight and P. Hugenholtz (2012) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. International Society for Microbial Ecology Journal. [doi]:10.1038/ismej.2011.139 {PMID}:22134646 PMCID:PMC3280142
  39. McEvoy, A.L.; H. Hoi, M. Bates, E. Platonova, P.J. Cranfill, M.A. Baird, M.W. Davidson, H. Ewers, J. Liphardt and R.E. Campbell (2012) mMaple: A Photoconvertible Fluorescent Protein for Use in Multiple Imaging Modalities. Public Library of Science ONE. [doi]:10.1371/journal.pone.0051314 {PMID}:23240015 PMCID:PMC3519878
  40. Paszek, M.J.; C.C. DuFort, M.G. Rubashkin, M.W. Davidson, K.S. Thorn, J.T. Liphardt and V.M. Weaver (2012) Scanning angle interference microscopy reveals cell dynamics at the nanoscale. Nature Methods. [doi]:10.1038/nmeth.2077 {PMID}:22751201 PMCID:PMC3454456
  41. Van Nostrand, J.D.; Z. He and J. Zhou (2012) Use of functional gene arrays for elucidating in situ biodegradation. Frontiers in Microbiology. [doi]:10.3389/fmicb.2012.00339 {PMID}:23049526 PMCID:PMC3448134