Berkeley Lab

2012 Publications

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 23(4):598-603. Epub 2012/01/03. [doi]:1016/j.copbio.2011.12.005. {PMID}:22209016
  2. Bare, J. C. and N. S. Baliga (2012). Architecture for interoperable software in biology. Briefings in Bioinformatics 15(4):626-636. [doi]:1093/bib/bbs074. {PMID}:23235920
  3. Borglin, S; D. Joyner, K. M. DeAngelis, J. Khudyakov, P. D’Haeseleer, M. P. Joachimiak and T. Hazen (2012). Application of phenotypic microarrays to environmental microbiology. Current Opinion in Biotechnology 23(1):41-48. Epub 2012/01/06. [doi]: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 194(18):5147-5148. Epub 2012/08/31. [doi]:1128/JB.01174-12. {PMID}:22933770
  5. Chakraborty, R; C. H. Wu and T. C. Hazen (2012). Systems biology approach to bioremediation. Current Opinion in Biotechnology 23(3):483-490. Epub 2012/02/22. [doi]: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. BMC Genomics 13(1):138. Epub 2012/04/18. [doi]:1186/1471-2164-13-138. {PMID}:22507456
  7. De León, K; 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 64(2):499-508. Epub 2012/04/06. [doi]:1007/s00248-012-0043-9. {PMID}:22476815
  8. De León, K; 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 194(19):5456-5457. Epub 2012/09/12. [doi]:1128/JB.01224-12. {PMID}:22965085
  9. Deng, Y; Y. H. Jiang, Y. Yang, Z. He, F. Luo and J. Zhou (2012). Molecular ecological network analyses. BMC Bioinformatics 13:113. [doi]:1186/1471-2105-13-113. {PMID}:22646978
  10. Friedman, J. and E. J. Alm (2012). Inferring Correlation Networks from Genomic Survey Data. PLoS Computational Biology 8(9):e1002687. [doi]:1371/journal.pcbi.1002687. {PMID}:23028285
  11. Greving, M; X. Cheng, W. Reindl, B. Bowen, K. Deng, K. Louie, M. Nyman, J. Cohen, A. Singh, B. Simmons, P. Adams, G. Siuzdak and T. Northen (2012). Acoustic deposition with NIMS as a high-throughput enzyme activity assay. Analytical and Bioanalytical Chemistry 403(3):707-711. Epub 2012/03/13. [doi]: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 180(1):249-253. [doi]:1016/j.jsb.2012.04.025. {PMID}:22584152
  13. Hazen, T. C. and S. Wuertz (2012). Environmental biotechnology. Current Opinion in Biotechnology 23(3):414. Epub 2012/05/09. [doi]: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 23(1):49-55. [doi]: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 23(3):460-466. Epub 2012/01/10. [doi]: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 78(7):2082-2091. Epub 2012/01/24. [doi]:1128/AEM.07165-11. {PMID}:22267668
  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 40(Web Server issue):W604-608. Epub 2012/06/16. [doi]:1093/nar/gks562. {PMID}:22700702
  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 194(21):5783-5793. Epub 2012/08/21. [doi]:1128/JB.00749-12. {PMID}:22904289
  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 3:137. Epub 2012/04/27. [doi]:3389/fmicb.2012.00137. {PMID}:22536198
  20. 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 11(12):5720-5735. Epub 2012/10/27. [doi]:1021/pr300548d. {PMID}:23098413
  21. 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. ISME Journal 6(11):2045-2055. Epub 2012/06/29. [doi]:1038/ismej.2012.60. {PMID}:22739494
  22. Wu, M. and A. K. Singh (2012). Single-cell protein analysis. Current Opinion in Biotechnology 23(1):83-88. Epub 2011/12/23. [doi]:1016/j.copbio.2011.11.023. {PMID}:22189001
  23. Yannone, S. M; S. Hartung, A. L. Menon, M. W. Adams and J. A. Tainer (2012). Metals in biology: defining metalloproteomes. Current Opinion in Biotechnology 23(1):89-95. Epub 2011/12/06. [doi]:1016/j.copbio.2011.11.005. {PMID}:22138493
  24. Yilmaz, S. and A. K. Singh (2012). Single cell genome sequencing. Current Opinion in Biotechnology 23(3):437-443. Epub 2011/12/14. [doi]:1016/j.copbio.2011.11.018. {PMID}:22154471
  25. 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 78(4):1168-1177. Epub 2011/12/14. [doi]:1128/aem.05666-11. {PMID}:22156435

  26. Books/Book Chapters

  27. Baidoo, E. E; P. I. Benke and J. D. Keasling (2012). Mass Spectrometry-Based Microbial Metabolomics. Microbial Systems Biology: Methods and Protocols. A. Navid, Humana Press, Inc. 881:152, illus. 180 in color. [doi]:1007/978-1-61779-827-6_9
  28. 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. 869:373-384. [doi]:1007/978-1-61779-821-4_30
  29. Vaccaro, B. J; Menon, A. L; Lancaster, W. A. and Adams, M. W (2012). Metallomics using inductively coupled Plasma mass spectrometry. Current Protocols in Chemical Biology 249–274. [doi]:1002/9780470559277.ch120031

  30. Legacy and Synergistic External Research

  31. 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 194(13):3448-3456. Epub 2012/05/01. [doi]:1128/JB.00133-12. {PMID}:22544266
  32. Bridger, S. L; W. A. Lancaster, F. L. Poole, 2nd, G. J. Schut and M. W. Adams (2012). Genome sequencing of a genetically tractable Pyrococcus furiosus strain reveals a highly dynamic genome. Journal of Bacteriology 194(15):4097-4106. Epub 2012/05/29. [doi]:1128/JB.00439-12. {PMID}:22636780
  33. 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). Evaluation of sustained release polylactate electron donors for removal of hexavalent chromium from contaminated groundwater. Chemosphere 85:660-665. LBNL-4905E {PMID}:21872904
  34. 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 287(26):22295-22304. Epub 2012/05/11. [doi]:1074/jbc.M111.318881. {PMID}:22573334
  35. 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. ISME Journal 6(2):259-272. Epub 2011/07/29. [doi]:1038/ismej.2011.99. {PMID}:21796217
  36. Liang, Y; J. D. Van Nostrand, A. N’Guessan L, 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 78(8):2966-2972. Epub 2012/02/14. [doi]:1128/AEM.06528-11. {PMID}:22327592
  37. **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. ISME Journal 6(3):610-618. Epub 2011/12/03. [doi]:1038/ismej.2011.139. {PMID}:22134646
  38. 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. PLoS ONE 7(12):e51314. Epub 2012/12/15. [doi]:1371/journal.pone.0051314. {PMID}:23240015
  39. 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 9(8):825-827. [doi]:1038/nmeth.2077. {PMID}:22751201
  40. Van Nostrand, J. D; Z. He and J. Zhou (2012). Use of functional gene arrays for elucidating in situ biodegradation. Frontiers in Microbiology 3:339. Epub 2012/10/11. [doi]:3389/fmicb.2012.00339. {PMID}:23049526