Berkeley Lab

2012 Publications

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

Bare C., N.S. Baliga. (2012) Architecture for Interoperable Software in Biology. Briefings in Bioinformatics

Borglin, S. E., D. C. 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 23:41-48

De León, K., B.D. Ramsay, and M.W. Fields. (2012) Quality-score refinement of SSU rRNA gene pyrosequencing differs across gene region for in situ samples. Microbial Ecol. (DOI 10.1007/s00248-012-0043-9)

De León K., M.L. Young, LB. Camilleri, S.D. Brown, J.M. Skerker, A.M. Deutschbauer, A.P. Arkin, and M.W. Fields J. (2012) Draft Genome Sequence of Pelosinus fermentans JBW45, Isolated during In Situ Stimulation for Cr(VI) Reduction. Journal of Bacteriol. October 2012 194:5456-5457; doi:10.1128/JB.01224-12

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, 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

Chakraborty, R. Wu, C. H. Hazen, T. C. (2012) Systems Biology approach to bioremediation. Current Opinion in Biotechnology. (DOI:10.1016/j.copbio.2012.01.015.) PMID: 22342400

Clark, M.E., Z. He, A.M. Redding, M.F. 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 uniqueness of the biofilm growth state. BMC Genomics 13 :138

Deng, Y., Y. Jiang, Y. Yang, Z. He, F. Luo, and J.-Z. Zhou. (2012) Molecular Ecological Network Analyses. BMC Bioinformatics 13: 113

Friedman J, Alm EJ. (2012 Inferring correlation networks from genomic survey data. PLoS Comput Biol. 8(9):e1002687

Greving M., Cheng X., Reindl W., Bowen B., Deng K., Louie K., Nyman M., Cohen J., Singh A., Simmons B., Adams P., Siuzdak G., Northen T. (2012) Acoustic deposition with NIMS as high throughput enzyme activity assay. Analytical and Bioanalytical Chemistry. 403(3):707-711

Hazen, TC., Rocha, AM., Techtmann, SM. (2012) Advances in monitoring environmental microbes. Current Opinion in Biotechnology. DOI:10.1016/j.copbio.2012.10.020

Hazen, T. C. and S. Wuertz. (2012) Environmental Biotechnology: Editorial Overview. Curr. Opin. Biotech. 23:1

He Z., J.D. Van Nostrand, and J. Zhou. (2012) Applications of functional gene microarrays for profiling microbial communities. Current Opinions in Biotechnolnology 23:49-55.

He Z, Deng Y, Zhou J. (2012) Development of functional gene microarrays for microbial community analysis. Current Opinion in Biotechnology. 2012;23(1):49-55. (DOI: 10.1016/j.copbio.2011.11.001. PMID: 22100036

Mosher J. J., T. J. Phelps,M. Podar, R.A. Hurt, 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, D. A. Elias. (2012) Microbial community succession during lactate amendment of chromium contaminated groundwater reveals a predominance of Pelosinus spp. Appl. Environ. Microbiol. 78:2082-2091. doi:10.1128/AEM.05666-11

Novichkov, P. S., T. S. Brettin, et al. (2012). “RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.” Nucleic Acids Res 40(Web Server issue): W604-608

Rajeev L., Hillesland K.L., Zane G.M., Zhou A., Joachimiak M.P., He Z, Zhou J, Arkin A.P., Wall J.D. and Stahl D.A. (2012) Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription. Journal of Bacteriology. 194(21):5783. DOI: 10.1128/JB.00749-12

Ramos, AR, Keller KL, Wall JD, Pereira IA (2012) The membrane QmoABC complex interacts directly with the dissimilatory adenosine 5’-phosphosulfate reductase in sulfate reducing bacteria. Front. Microbiol. 3:137 Epub 2012 Apr 23. PMID:22536198

Vaccaro, B. J., Menon, A. L., Lancaster, W. A. and Adams, M. W. W. (2012) “Metallomics using inductively coupled Plasma mass spectrometry” Current Protocols in Chemical Biology. 249–274. DOI: 10.1002/9780470559277.ch120031

Walian, S. Allen, M. Shatsky, L. Zeng, E. Szakal, H. Liu, S. C. Hall, S. J. Fisher, B. Lam, M. E. Singer, J. T. Geller, T. C. Hazen, S. E. Brenner, J.-M. Chandonia, H. E. Witkowska, M. D. Biggin, B. K. Jap (2012) High-throughput Isolation and Characterization of Untagged Membrane Protein Complexes – Outer Membrane Complexes of Desulfovibrio vulgaris. Journal of Proteome Research

Walker C.B., A.M. Redding-Johanson, 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 J

Wang L., X. Wang, A.P. Arkin and M. Samoilov, (2012) Inference of gene regulatory networks from genome-wide knockout fitness data. BIOINFORMATICS Vol. 00 no. 00 2012 Pages 1–10

Wu M, Singh AK. (2012) Single-cell protein analysis. Current Opinion in Biotechnology. 23(1):83-8

Zhou A., Y. Chen, G. Zane, Z. He, C. Hemme, M.P. Joachimiak, J. Baumohl, Q. He, M. 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):1168-77. Epub 2011/12/14. doi: 10.1128/aem.05666-11. PMID: 22156435

Books/Book Chapters

Baidoo EEK, Benke PI, Keasling JD (2012) Mass spectrometry-based Microbial Metabolomics (Chapter 3). Microbial Systems Biology: Methods and Protocols. Vol. 881, 692 p. 152 illus., 80 in color. Humana Press Inc, Ali Navid Editor

Dong M., Choi M., Biggin M.D., Jin J. (2012) A multichannel gel electrophoresis and continuous fraction collection apparatus for high-throughput protein separation and characterization. Protein Electrophoresis: Methods Molecular Biology. Volume 869, 373-384, DOI: 10.1007/978-1-61779-821-4_30 Springer Science + Business Media

Legacy and Synergistic External Research

Berube, M.P. and D.A. Stahl. (2012) The divergent Amoc3 subunit of ammonia monooxygenase functions as part of the stress response system of Nitrosomonas europaea. Journal of Bacteriology. 194(13):3448-3456

Bridger, S. L., Lancaster, W. A., Poole, F. L., Schut, G. J. and Adams, M. W. W. (2012) “Genome sequencing of a genetically-tractable Pyrococcus furiosus strain reveals a highly dynamic genome” J. Bacteriol. 194:4097-4106

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, and 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

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.-Z. Zhou. (2012) Microbial Functional Gene Diversity with a Shift of Subsurface Redox Conditions during in situ Uranium Reduction. Applied and Environmental Microbiology 78: 2966-2972

Van Nostrand, JD, Z He, and J Zhou. (2012) Use of functional gene arrays for elucidating in situ biodegradation. Front. Microbio. 3:339. doi: 10.3389/fmicb.2012.00339