2024

1. 1. Biggs, B.W.; M.N. Price, D. Lai, J. Escobedo, L. Fortanel, Y.Y. Huang, K. Kim, V.V. Trotter, J.V. Kuehl, L.M. Lui, R. Chakraborty, A.M. Deutschbauer and A.P. Arkin (2024) High-throughput protein characterization by complementation using DNA barcoded fragment libraries. Molecular Systems Biology. [DOI]:10.1038/s44320-024-00068-z OSTI: 2466271
  2. Chen, M.; V.V. Trotter, P.J. Walian, Y. Chen, R. Lopez, L.M. Lui, T.N. Nielsen, R.G. Malana, M.P. Thorgersen, A.J. Hendrickson, H. Carion, A.M. Deutschbauer, C.J. Petzold, H.J. Smith, A.P. Arkin, M.W.W. Adams, M.W. Fields, R. Chakraborty (2024) Molecular mechanisms and environmental adaptations of flagellar loss and biofilm growth of Rhodanobacter under environmental stress. The ISME Journal. [DOI]: 10.1093/ismejo/wrae151 OSTI:2460472
  3. Fan, Y.; D. Wan, J.X. Yang, D. Ning, Z. He, P. Zhang, A.M. Rocha, J.D. Van Nostrand, J.P. Michael, D.C. Joyner, M.W.W. Adams, M.W. Fields, E.J. Alm, T.C. Hazen, D.A. Stahl, P.D. Adams, A.P. Arkin, C. Pan, J-Z. Zhou (2024) Modest functional diversity decline and pronounced composition shifts of microbial communities in a uranium-polluted aquifer. Water Research. Submitted
  4. Goff, J.L.; E.G. Szink, K.L. Durrence, L.M. Lui, T.N. Nielsen, J.V. Kuehl, K.A. Hunt, J.-M. Chandonia, J. Huang, M.P. Thorgersen, F.L. Poole, D.A. Stahl, R. Chakraborty, A.M. Deutschbauer, A.P. Arkin and M.W.W. Adams (2024) Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface. Environmental Microbiome. [DOI]:10.1186/s40793-024-00570-9 OSTI:2341350
  5. Goff, J.L.; L.M. Lui, T.N. Nielsen, F.L. Poole, H.J. Smith, K.F. Walker, T.C. Hazen, M.W. Fields, A.P. Arkin and M.W.W. Adams (2024) Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes. ISME Communications. [DOI]:10.1093/ismeco/ycae064 {PMID}:38800128 PMCID:PMC11128244 OSTI: 2367243 Supplemental data KBase narrative [DOI]:10.25982/160429.7/2203457 OSTI:2203457
  6. Hunt, K. A.; A.V. Carr, A.E. Otwell, J.J. Valenzuela, K.S. Walker, E.R. Dixon, L.M. Lui, T.N. Nielsen, S. Bowman, F. von Netzer, J.-W. Moon, C.W. Schadt, M. Rodriguez, K. Lowe, D. Joyner, K.J. Davis, X. Wu, R. Chakraborty, M.W. Fields, J. Zhou, T.C. Hazen, A.P. Arkin, S.D. Wankel, N.S. Baliga, D.A. Stahl (2024) Contribution of Microorganisms with the Clade II Nitrous Oxide Reductase to Suppression of Surface Emissions of Nitrous Oxide. Environmental Science & Technology. [DOI]: 10.1021/acs.est.3c07972 OSTI: 2426897
  7. Lui, L.M; T.N. Nielsen, H.J. Smith, J-M. Chandonia, J. Kuehl, F. Song, A. Sczesnak, A. Hendrickson, T.C. Haze, M.W. Fields, A.P. Arkin (2024) Sediment and Groundwater Metagenomes from Subsurface Microbial Communities from the Oak Ridge National Laboratory Field Research Center, Oak Ridge, TN, USA. Research Square. [doi]:10.21203/rs.3.rs-3401657/v1
  8. Michael, J.P.; A.D. Putt, Y. Yang, B.G. Adams, K.R. McBride, Y. Fan, K.A. Lowe, D. Ning, S. Jagadamma, J.W. Moon, D.M. Klingeman, P. Zhang, Y. Fu, T.C. Hazen and J. Zhou (2024) Reproducible responses of geochemical and microbial successional patterns in the subsurface to carbon source amendment. Water Research. [DOI]:10.1016/j.watres.2024.121460 OSTI:2326252
  9. Ning, D.; Y. Wang, Y. Fan, J. Wang, J.D. Van Nostrand, L. Wu, P. Zhang, D.J. Curtis, R. Tian, L. Lui, T.C. Hazen, E.J. Alm, M.W. Fields, F. Poole, M.W.W. Adams, R. Chakraborty, D.A. Stahl, P.D. Adams, A.P. Arkin, Z. He, J. Zhou (2024) Environmental stress mediates groundwater microbial community assembly. Nat. Microbiol. [DOI]: 10.1038/s41564-023-01573-x OSTI: 2281000
  10. Price M.N.; A.P. Arkin (2024) A fast comparative genome browser for diverse bacteria and archaea. PLoS One. [DOI]:10.1371/journal.pone.0301871 OSTI: 2335832
  11. Price, M.N.; A.M. Deutschbauer and A.P. Arkin (2024) Many Families of Lids for TonB-dependent Transporters in Bacteroides. bioRxiv. [doi]:10.1101/2023.03.17.533168
  12. Shi, Z.J.; N. Xiao, D. Ning, R. Tian, P. Zhang, D. Curtis, J.D. Van Nostrand, L. Wu, T.C. Hazen, A.M. Rocha, Z. He, A.P. Arkin, M.K. Firestone, J. Zhou (2024) EcoFun-MAP: An Ecological Function Oriented Metagenomic Analysis Pipeline. bioRxiv [doi]:10.1101/2022.04.05.481366 /mLife in revision.
  13. Thorgersen, M.P.; J.L. Goff, V.V. Trotter, F.L. Poole, A.P. Arkin, A.M. Deutschbauer and M.W.W. Adams (2024) Fitness factors impacting survival of a subsurface bacterium in contaminated groundwater. The ISME Journal. [DOI]:10.1093/ismejo/wrae176 {PMID}:39259908 OSTI:2447947
  14. Valenzuela, J.J.; S.R. Christinal Immanuel, J. Wilson, S. Turkarslan, M. Ruiz, S.M. Gibbons, K.A. Hunt, M. Auer, M. Zemla, D.A. Stahl and N.S. Baliga (2024) Origin of biogeographically distinct ecotypes during laboratory evolution. Nature Communications. [DOI]:10.1038/s41467-024-51759-y OSTI:2438359
  15. Wang, Y.; N.R. Saichek, S.M. Kosina, B.P. Bowen, R. Chakraborty, and T.R. Northen (2024) Conservation of isolate substrate preferences in mixed communities revealed through ribosomal marker protein profiling. bioRxiv. [doi]:10.1101/2021.05.12.443848.
  16. Zhou, J-Z.; N. Xiao, D. Ning, Q. He, M.A. Leibold, A. Hastings (2024) Microbial Interactions: Can They Be Inferred from Species Abundance Data? mLife. Submitted

Syngergistic Tool Development

1. 1. Day L.A.; H.K. Carlson, D.R. Fonseca, A.P. Arkin, M.N. Price, A.M. Deutschbauer, K.C. Costa. (2024) High-throughput genetics enables identification of nutrient utilization and accessory energy metabolism genes in a model methanogen. MBio. [DOI]: 10.1128/mbio.00781-24
  2. Huang, Y.Y., M.N. Price, A. Hung, O. Gal-Oz, S. Tripathi, C.W. Smith, D. Ho, H. Carion, A.M. Deutschbauer and A.P. Arkin (2024) Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance. Nature Communications. [DOI]:10.1038/s41467-024-50124-3 {PMID}:39103350 PMCID:PMC11300592 OSTI:2426698
  3. Joachimiak, M.P.; C. Tuglus, R. Salamzade, M. van der Laan, A.P. Arkin (2024) Deep surveys of transcriptional modules with Massive Associative K-biclustering (MAK). bioRxiv [doi]:10.1101/2022.08.26.505372 PLoS Computational Biology. Submitted
  4. Lim, J.J.; C. Diener, J. Wilson, J.J. Valenzuela, N.S. Baliga, S. M. Gibbons (2024) Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes. Nature Communications. [DOI]:10.1038/s41467-023-41424-1 OSTI: 2281214

2023

1. 1. Adler, B.A.; K. Chamakura, H. Carion, J. Krog, A.M. Deutschbauer, R. Young, V.K. Mutalik and A.P. Arkin (2023) Multicopy suppressor screens reveal convergent evolution of single-gene lysis proteins. Nature Chemical Biology [DOI]:1038/s41589-023-01269-7 OSTI:1960236
  2. Carlson, H.K.; D. Piya, M.L. Moore, R.T. Magar, N.H. Elisabeth, A.M. Deutschbauer, A.P. Arkin and V.K. Mutalik (2023) Geochemical constraints on bacteriophage infectivity in terrestrial environments. ISME communications. [DOI]:1038/s43705-023-00297-7, PMID:37596312, PMCID: PMC10439110 OSTI:1995856
  3. Chen, Y.; J. W. Gin, Y. Wang, M. de Raad, S. Tan, N. J. Hillson, T. R. Northen, P. D. Adams, C. J. Petzold (2023) Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format. Public Library of Science ONE. [DOI]:10.1371/journal.pone.0288102 {PMID}:37418444 PMCID:PMC10328223 OSTI: 1988658
  4. Davenport, R.; B.P. Bowen, L.M. Lynch, S.M. Kosina, I. Shabtai, T.R. Northen and J. Lehmann (2023) Decomposition decreases molecular diversity and ecosystem similarity of soil organic matter. Proceedings of the National Academy of Sciences of the United States of America. [DOI]:10.1073/pnas.2303335120 {PMID}:37307452 OSTI: 1984703
  5. Garber, M.E.; V. Frank, A.E. Kazakov, M.R. Incha, A.A. Nava, H. Zhang, L.E. Valencia, J.D. Keasling, L. Rajeev and A. Mukhopadhyay (2023) REC protein family expansion by the emergence of a new signaling pathway. mBio. [DOI]:10.1128/mbio.02622-23 {PMID}:37991384 OSTI:2221817
  6. Harwood, T.; D.G.C. Treen, M. Wang, W. de Jong, T.R. Northen and B.P. Bowen (2023) BLINK: Ultrafast tandem mass spectrometry cosine similarity scoring. Scientific Reports. [DOI]:10.1038/s41598-023-40496-9 PMCID:PMC10439109 OSTI:2205517
  7. Piya, D.; N. Nolan, M.L. Moore, L.A. Ramirez Hernandez, B.F. Cress, R. Young, A.P. Arkin, V.K. Mutalik (2023) Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages. PLoS Biology. [DOI]: 10.1371/journal.pbio.3002416 OSTI:2228323
  8. Qin, Y.; L. Wu, Q. Zhang, C. Wen, J.D. Van Nostrand, D. Ning, L. Raskin, A. Pinto, and J.-Z. Zhou (2023) Effects of error, chimera, bias, and GC content on the accuracy of amplicon sequencing. mSystems. [DOI]:10.1128/msystems.01025-23 {PMID}:38038441 PMCID:PMC10734440 OSTI:2228371
  9. Thorgersen, M.P.; J.L. Goff, F.L. Poole II, K.F. Walker, A.D. Putt, L.M. Lui, T.C. Hazen, A.P. Arkin, and M.W.W. Adams (2023) Mixed Nitrate and Metal Contamination Influences Operational Speciation of Toxic and Essential Elements. Environmental Pollution. [DOI]:10.1016/j.envpol.2023.122674 {PMID}:37793542 OSTI:2007162
  10. Trotter, V.V.; M. Shatsky, M.N. Price, T.R. Juba, G.M. Zane, K.B. De León, E.L. Majumder, Qin Gui, R. Ali, K.M. Wetmore, J.V. Kuehl, A.P. Arkin, J.D. Wall, A.M. Deutschbauer, J-M. Chandonia and G.P. Butland (2022) Large-scale Genetic Characterization of a Model Sulfate-Reducing Bacterium. Frontiers in Microbiology. 2023 Mar 31; [DOI]:10.3389/fmicb.2023.1095191 OSTI:1777971
  11. Wang D.; K.A. Hunt, P. Candry, X. Tao, N.Q. Wofford, J. Zhou, M.J. McInerney, D.A. Stahl, R.S. Tanner, A. Zhou, M. Winkler, C. Pan (2023) Cross-feedings, competitions, positive and negative synergies in a four-species synthetic community for anaerobic degradation of cellulose to methane. mBio. [DOI]:10.1128/mbio.03189-22 OSTI:1958886
  12. Wu, L.; Y. Yang, D. Ning, Q. Gao, H. Yin, N. Xiao, B.Y. Zhou, S. Chen, Q. He and J-Z. Zhou (2023) A Process Models-Based Quantitative Framework For Assessing Community Assembly Mechanisms. mLife. [DOI]:10.1002/mlf2.12076 OSTI:2205081
  13. Wu, X.; S. Gushgari-Doyle, L.M. Lui, A.J. Hendrickson, Y. Liu, S. Jagadamma, T.N. Nielsen, N.B. Justice, T. Simmons, N.J. Hess, D.C. Joyner, T.C. Hazen, A.P. Arkin and R. Chakraborty (2023) Distinct Depth-Discrete Profiles of Microbial Communities and Geochemical Insights in the Subsurface Critical Zone. Applied and Environmental Microbiology. [DOI]:10.1128/aem.00500-23 {PMID}:37272792 OSTI: 1984328

Synergistic Collaboration/Tool Development

1. 1. Ascensao, J.A.; K.M. Wetmore, B.H. Good, A.P. Arkin and O. Hallatschek (2023) Quantifying the local adaptive landscape of a nascent bacterial community. Nature Communications. [DOI]: 1038/s41467-022-35677-5 {PMID}:36646697 PMCID:PMC9842643 OSTI:1909251
  2. Bernstein, D.B.; B. Akkas, M.N. Price and A.P. Arkin (2023) Evaluating E. coli genome-scale metabolic model accuracy with high-throughput mutant fitness data. Molecular Systems Biology. [DOI]:15252/msb.202311566 {PMID}:37888487 OSTI: 2203993
  3. Ramoneda, J.; T.B.N. Jensen, M.N. Price, E.O. Casamayor and N. Fierer (2023) Taxonomic and environmental distribution of bacterial amino acid auxotrophies. Nature Communications. [DOI]:10.1038/s41467-023-43435-4 {PMID}:37993466 PMCID:PMC10665431 OSTI: 2217635

2022

1. 1. Cabugao K.G., Gushgari-Doyle S., Chacon S.S., Wu X., Bhattacharyya A., Bouskill N.J., Chakraborty R. (2022) Characterizing natural organic matter transformations by microbial communities in terrestrial subsurface ecosystems: A critical review of analytical techniques and challenges. Frontiers in Microbiology. [DOI]:10.3389/fmicb.2022.864895 OSTI: 1866292
  2. de Raad, Y.V. Li, J.V. Kuehl, P.F. Andeer, S.M. Kosina, A. Hendrickson, N.R. Saichek, A.N. Golini, L.Z. Han, Y. Wang, B.P. Bowen, A.M. Deutschbauer, A.P. Arkin, R. Chakraborty and T.R. Northen (2022) A defined medium for cultivation and exometabolite profiling of soil bacteria. Frontiers in microbiology. [DOI]:10.3389/fmicb.2022.855331 OSTI:1825687
  3. Garber ME, Fregoso R, Lake J, Kakouridis A, Mukhopadhyay A*. (2022) Pseudomonas response regulators produced in an E. coli heterologous expression host exhibit host-derived post-translational phosphorylation. npj Scientific Reports [DOI]:10.1038/s41598-022-13525-2 OSTI:1889195
  4. Goff JL, Chen Y, Thorgersen MP, Hoang LT, Szink EG, Poole FL II, Siuzdak G, Petzold CJ, Adams MWW. (2023) Mixed Heavy Metals Stress Induces Global Iron Starvation as Revealed by System Level Multi-Omic Analyses. ISME J. [DOI]:1038/s41396-022-01351-3 OSTI:1922819
  5. Goff, J.L.; L.M. Lui, T.N. Nielsen, M.P. Thorgersen, E.G. Szink, J-M. Chandonia, F.L. Poole II, J. Zhou, T.C. Hazen, A.P. Arkin, and M. W.W. Adams (2022) Complete Genome Sequence of Bacillus cereus strain CPT56D-587-MTF Isolated from a Nitrate and Metals Contaminated Subsurface Environment. Microbiology Resource Announcements. [DOI]:10.1128/mra.00145-22 OSTI: 1868751
  6. Goff, J.L.; E.G. Szink, M.P. Thorgersen, A.D. Putt, K.A. Hunt, Y. Fan, L.M. Lui, T.N. Nielsen, J.P. Michael, Y. Wang, D. Ning, Y. Fu, F.L. Poole II, T.C. Hazen, D.A. Stahl, J. Zhou, A.P. Arkin, and M.W.W. Adams (2022) Ecophysiological and genomic analyses of a highly abundant Bacillus cereus strain reveal niche adaptation to a mixed waste contaminated subsurface environment. Environmental Microbiology [DOI]:10.1111/1462-2920.16173 [doi]:https://kbase.us/n/112150/61/ OSTI:1889254
  7. Gushgari-Doyle, S; L.M. Lui, T.N. Nielsen, X. Wu, R.G. Malana, F.L. Poole II, M.W.W. Adams, A.P. Arkin, R. Chakraborty (2022) Genotype to ecotype in niche environments: Adaptation of Arthrobacter to carbon availability and environmental conditions. ISME Comm. [DOI]:10.1038/s43705-022-00113-8 OSTI:1860268
  8. Hunt KA, von Netzer F, Gorman-Lewis D, Stahl DA. (2022) Microbial maintenance energy quantified and modeled with microcalorimetry. Biotechnol Bioeng. 2022 Jun 9; [DOI]:10.1002/bit.28155 {PMID}: 35680566 OSTI:1874049
  9. Novichkov, PS*; Chandonia, J-M*; Arkin, AP. (2022) CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis. GigaScience [DOI]:10.1093/gigascience/giac089 OSTI: 1888047
  10. Peng, M.; D. Wang, L.M. Lui, T. Nielsen, R. Tian, M.L. Kempher, X. Tao, C. Pan, R. Chakraborty, A.M. Deutschbauer, M.W.W Adams, M.W. Fields, T.C. Hazen, A.P. Arkin, A. Zhou, J-Z. Zhou (2022) Genomic features and pervasive negative selection in Rhodanobacter strains isolated from nitrate and heavy metal contaminated aquifer. Microbiology Spectrum [DOI]: 10.1128/spectrum.02591-21 PMID: 35107332 OSTI: 1843281
  11. Price, M.N.; and A.P. Arkin (2022) Interactive analysis of functional residues in protein families. mSystems. [doi]:10.1128/msystems.00705-22 {PMID}:36374048 PMCID:PMC9765024 OSTI:1898172
  12. Price, M.N.; (2022) Erroneous Predictions of Auxotrophies by CarveMe. Nature Ecology and Evolution. [DOI]:10.1038/s41559-022-01936-3 OSTI:1901792
  13. Price M.N.; AM. Deutschbauer and A.P. Arkin (2022) Filling Gaps in Bacterial Catabolic Pathways with Computation and High-throughput Genetics. PLoS Genetics [DOI]:10.1371/journal.pgen.1010156 {PMID}:35417463 OSTI:1862968
  14. Putt, A.; E. Kelly, K. Lowe, M. Rodriguez, T. C. Hazen (2022) Effects of Cone Penetrometer Testing on Shallow Hydrogeology at a Contaminated Site. Frontiers in Environmental Science [DOI]:10.3389/fenvs.2021.821882 OSTI: 1839769
  15. Tao, X.; A. Zhou, M. Kempher, J. Liu, M. Peng, Y. Li, J.P. Michael, R. Chakraborty, A.M. Deutschbauer, A.P. Arkin and J-Z. Zhou (2022) Development of a Markerless Deletion Mutagenesis System in Nitrate-Reducing Bacterium Rhodanabacter denitrificans. Appl. Environ. Microbiol. [DOI]:10.1128/aem.00401-22 OSTI:1889276
  16. Treen, D.G.C.; M. Wang, S. Xing, K.B. Louie, T. Huan, P.C. Dorrestein, T.R. Northen and B.P. Bowen (2022) SIMILE enables alignment of tandem mass spectra with statistical significance. Nature Communications. [doi]:10.1038/s41467-022-30118-9 {PMID}:35523965 PMCID:PMC9076661 OSTI: 1866627
  17. Wang, Y.; Wilhelm, R. C.; Swenson, T. L.; Silver, A.; Andeer, P.; Golini, A.; Kosina, S. M.; Bowen, B. P.; Buckley, D. H.; Northen, T. R. (2022) Substrate Utilization and Competitive Interactions Among Soil Bacteria Vary With Life-History Strategies. Front. Microbiol. [DOI]3389/fmicb.2022.914472 OSTI:1889858
Synergistic Collaboration/Tool Development
1. 1. Adler BA, Kazakov AE, Zhong C, Liu H, Kutter E, Lui LM, Nielsen TN, Carion H, Deutschbauer AM, Mutalik VK, Arkin AP (2022) The genetic basis of phage susceptibility, cross-resistance and host-range in Salmonella. Microbiology (Reading, Engl). 2021 Dec; 167(12) [DOI]:1099/mic.0.001126, [PMID]:34910616, PMCID: PMC8744999 OSTI:1863787
  2. Aisporna A, Benton HP, Chen A, Derks RJE, Galano JM, Giera M, Siuzdak G (2022) Neutral loss mass spectral data enhances molecular similarity analysis in METLIN. J Am Soc Mass Spectrom. 2022 Feb 17. [DOI]: 10.1021/jasms.1c00343 [PMID]:35174708 OSTI:1959342
  3. Giera M, Yanes O, Siuzdak G (2022) Metabolite discovery: Biochemistry’s scientific driver. Cell Metab. 2022 Jan 04; 34(1) 21-34. [DOI]:10.1016/j.cmet.2021.11.005 {PMID}:34986335 OSTI:1959336
  4. McCausland HC.; Wetmore KM, Arkin AP, Komeili A (2022) Global Analysis of Biomineralization Genes in Magnetospirillum magneticum AMB-1. mSystems. 2022 Jan 25; e0103721 [DOI]: 10.1128/msystems.01037-21, PMID: 35076272 OSTI:1844424
  5. Schweitzer, H.D.; H.J. Smith, E.P. Barnhart, L.J. McKay, R. Gerlach, A.B. Cunningham, R.R. Malmstrom, D. Goudeau and M.W. Fields (2022) Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics. npj Biofilms and Microbiomes. [DOI]:1038/s41522-022-00267-2 {PMID}:35177633 PMCID:PMC8854433 OSTI:1865082
  6. West CG, Honic SE, Lui LM, Rashcke L. (2022) Integration of authentic STEM practices in real-world education and research environments: Lessons from the PDP. In S. Seagroves, A. Barnes, L. Hunter, A. Metevier, & J. Porter (Eds.), Impact through inquiry: Twenty years of preparing leaders in effective and inclusive education at the Institute for Scientist & Engineer Educators. UC Santa Cruz: Institute for Scientist & Engineer Educators. https://escholarship.org/uc/item/13c3x5vb
  7. Xiao, N.; A. Zhou, M.L. Kempher, B. Zhou, Z. Shi, M. Yuan, X. Guo, L. Wu, D. Ning, J. Van Nostrand, M.K. Firestone, J. Zhou (2022) Disentangling Direct from Indirect Relationships in Association Networks. Proceedings of the National Academy of Sciences of the United States of America. [DOI]:1073/pnas.2109995119 {PMID}:34992138 OSTI:1844610
  8. Zheng, W.; S. Zhao, Y. Yin, H. Zhang, D.M. Needham, E.D. Evans, C.L. Dai, P.J. Lu, E.J. Alm, D.A. Weitz (2022) High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome. Science. 2022 Jun 3;376(6597):eabm1483. [DOI]:1126/science.abm1483 {PMID}:35653470 OSTI:1959222
  2021
  1. Carim, Sean.; AL. Azadeh, AE. Kazakov, MN. Price, P. Walian, LM. Lui, TN. Nielsen, R Chakraborty, AM. Deutschbauer, VK. Mutalik, AP. Arkin (2021) Systematic discovery of Pseudomonad genetic factors involved in sensitivity to tailocins. ISME Journal [DOI]:10.1038/s41396-021-00921-1 OSTI:1773739
  2. Hunt, K.A.; J. Forbes, F. Taub, N. Elliott, J. Hardwicke, R. Petersen, N. Stopnisek, D.A.C. Beck, and D.A. Stahl (2021) An automated multiplexed turbidometric and data collection system for measuring growth kinetics of anaerobes dependent on gaseous substrates. Journal of Microbiological Methods. [DOI]:1016/j.mimet.2021.106294 {PMID}:34333046 OSTI: 1828000
  3. Kosina, S.M; P. Rademacher*, K.M. Wetmore, M. de Raad, M. Zemla, G.M. Zane, J.J. Zulovich, R. Chakraborty, B.P. Bowen, J.D. Wall, M. Auer, A.P. Arkin, A.M. Deutschbauer, T.R. Northen (2021) Biofilm Interaction Mapping and Analysis (BIMA) of interspecific interactions in Pseudomonas co-culture biofilms. Frontiers in Microbiology [DOI]:10.3389/fmicb.2021.757856 {PMID}: 34956122 {PMCID}: PMC8696352
  4. Kothari, Ankita.; S. Roux, H. Zhang, A. Prieto, J-M Chandonia, S. Spencer, X. Wu, A M. Deutschbauer, A. P. Arkin, E J. Alm, R. Chakraborty, A Mukhopadhyay (2021) Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance. mSystems [DOI]:1128/mSystems.00537-21{PMID}:34184913 PMCID: PMC8269241 OSTI:1807913
  5. Lui, Lauren M.; E. L. Majumder, H.J. Smith, H.K. Carlson, N.S. Baliga, F. von Netzer, M.W. Fields, D.A. Stahl, J-Z. Zhou, T.C. Hazen, P.D. Adams, A.P. Arkin (2021) Mechanism across scales a holistic modeling framework integrating laboratory and field studies for microbial ecology. Frontiers in Microbiology. [DOI]:3389/fmicb.2021.642422OSTI:1773742
  6. Lui, Lauren M.; T.N. Nielsen, A.P. Arkin (2021) A method for achieving complete microbial genomes and better-quality bins from metagenomics data. PloS Computational Biology [DOI]:1371/journal.pcbi.1008972 OSTI:1788019
  7. Majumder, Erica L.; E.O. Billings, H. P. Benton, A. Palermo, R. L. Martin, C. Guijas, M. M. Rinschen, X. Domingo-Almenara, J. R. Montenegro-Burke, G. Siuzdak* (2021) Cognitive Analysis of Metabolomics Data for Systems Biology. Nature Protocols. [DOI]: 10.1038/s41596-020-00455-4 OSTI:1774918
  8. Paradis, C.J.; J. I. Miller, J-W. Moon, S.J. Spencer, L.M. Lui, J.D. Van Nostrand, D. Ning, A.D. Steen, L.D. McKay, A.P. Arkin, J-Z. Zhou, E.J. Alm, T.C. Hazen (2021) In situ demonstration of sustained adaptation of a natural microbial community to remove nitrate from groundwater. Ground Water [DOI]: 1111/gwat.13132{PMID}:34490626 OSTI:1807518
  9. Price Morgan N.; Adam M. Deutschbauer and A.P. Arkin (2021) Four families of folate-independent methionine synthases. PLoS Genetics. [DOI]:1371/journal.pgen.1009342OSTI:1773746
  10. Otwell, A.E.; A.V. Carr, E.L.W Majumder, M. Ruiz, R.L. Wilpiszeski, L.T. Hoang, B. Webb, S. Turkarslan, S.M. Gibbons, D.A. Elias, G. Siuzdak, D.A. Stahl, N.S. Baliga (2021) Sulfur metabolites play key system-level roles in modulating denitrification. mSystems. 6:e01025-20. [DOI]:10.1128/mSystems.01025-20. OSTI:1767862
  11. Shi, W.L.; Q. Ma, F.Y. Pan, Y.P. Fan, M.L. Kempher, D.L. Ning, J.D. Wall, A.F. Zhou, J-Z. Zhou (2021) Genetic basis of chromate stress tolerance revealed by experimental evolution of genetically diverse sulfate reducing bacterium Desulfovibrio vulgaris mSystems [DOI]:10.1128/mSystems.00493-21 {PMID}:34061571 OSTI:1785270
  12. Song, F.; J.V. Kuehl, A. Chandran, A.P. Arkin (2021) A cheap, simple and automation-friendly direct PCR approach for bacterial community analysis. mSystems [DOI]:1128/mSystems.00224-21 OSTI:1822977
  13. Thorgersen, M.P.; J. Xue, E.L.W. Majumder, V.V. Trotter, X. Ge, F.L. Poole II, T.K. Owens, L.M. Lui, T.N. Nielsen, A.P. Arkin, A.M. Deutschbauer, G. Siuzdak, and M.W.W. Adams (2021) Deciphering Microbial Metal Toxicity Defense Mechanisms using RB-TnSeq and Activity-Based Metabolomics. Appl. Environ. Microbiol. AEM0103721. [DOI]:1128/AEM.01037-21 {PMID}:34432491 OSTI:1825256
  14. Turkarslan, Serdar; N. Stopnisek, A.W Thompson, C.E Arens, J.J Valenzuela, J. Wilson, K.A Hunt, J. Hardwicke, S. Lim, Y.M Seah, Y. Fu, L. Wu, J-Z Zhou, K.L Hillesland, D.A Stahl, N.S Baliga (2021) Synergistic epistasis enhances cooperativity of mutualistic interspecies interactions. ISME Journal [DOI]: 10.1038/s41396-021-00919-9 OSTI:1773759
  15. Wall, J.D.; G.M. Zane, T.R. Juba, J.V. Kuehl, J. Ray, S. R. Chhabra, V.V. Trotter, M. Shatsky, K.B. De León, K. Keller, K.S. Bender, G.P. Butland A.M. Deutschbauer (2021) Deletion Mutants, Archived Transposon Library, and Tagged Protein Constructs of the Model Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough. Microbiology Resource Announcements. [DOI]:1128/MRA.00072-21 {PMID}:33737356 OSTI:1771247
  16. Wu, X.; A.E. Kazakov, S. Gushgari-Doyle, X. Yu, V.V. Trotter, R.K. Stuart, R. Chakraborty (2021) Comparative Genomics Reveals Insights into Induction of Violacein Biosynthesis and Adaptive Evolution in Janthinobacterium. Microbiology Spectrum [DOI]:1128/Spectrum.01414-21
Synergistic Collaboration/Tool Development
1. 1. Ha, N; M. de Raad, L.Z. Han, A. Golini, C.J. Petzold, T.R. Northen (2021) Faster, Better, and Cheaper: Harnessing Microfluidics and Mass Spectrometry for Biotechnology. RSC Chemical Biology. [DOI]:1039/D1CB00112D OSTI: 1809121
  2. McKay LJ, HJ Smith, E Barnhart, H Schweitzer, RR Malmstrom, D Goudeau, MW Fields (2021) Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane. ISME Journal [DOI]:1038/s41396-021-01139-x PMID: 34689183
  3. Xue, J; R. J. E. Derks, B. Webb, E. M. Billings, A. Aisporna, M. Giera, and G. Siuzdak (2021) Single quadrupole multiple fragment ion monitoring quantitative mass spectrometry. Analytical Chemistry 93 (31), 10879-10889 [DOI]:10.1021/acs.analchem.1c01246
    
    2020
  4. Carlson, H. K.; L.M. Lui, M. N. Price, A. E. Kazakov, A.V. Carr, J. V. Kuehl, T.K. Owens, T. Nielsen, A.P. Arkin, A.M. Deutschbauer (2020) Selective carbon sources influence the end-products of microbial nitrate respiration. ISME Journal [doi]:1038/s41396-020-0666-7 OSTI:1638903o
  5. Ge, X; M.P. Thorgersen, F.L. Poole II, A.M. Deutschbauer, J-M Chandonia, P.S. Novichkov, S. Gushgari-Doyle, L.M. Lui, T. Nielsen, R. Chakraborty, P.D. Adams, A.P. Arkin, T.C. Hazen, M. W.W. Adams. (2020). Characterization of a Metal-Resistant Bacillus Strain with a High Molybdate Affinity ModA from Contaminated Sediments at the Oak Ridge Reservation. Frontiers in Microbiology, 11:2543. https://doi.org/10.3389/fmicb.2020.587127 OSTI:1678736
  6. Ge, X; M.P. Thorgersen, F.L. Poole II, A.M. Deutschbauer, J-M Chandonia, P.S. Novichkov, P.D. Adams, A.P. Arkin, T.C. Hazen, M. W.W. Adams. (2020). Draft Genome Sequence of Bacillus sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment. Microbiology Resource Announcements, 9:e01149-20. https://doi.org/10.1128/MRA.01149-20. OSTI:1690317
  7. Kempher, M.L; X. Tao, R. Song, B. Wu, D. A. Stahl, J. D. Wall, A. P. Arkin, A. Zhou, J. Zhou (2020) Effects of genetic and physiological divergence on the evolution of a sulfate-reducing bacterium under conditions of elevated temperature. mBio 11, e00569-00520 [doi]:10.1128/mBio.00569-20 OSTI:1647684
  8. Moon J-W.; C.J. Paradis, D.C. Joyner , F. von Netzer, E.L. Majumder, E. Dixon, M. Podar, X. Ge, P.J. Walian, H.J. Smith, X. Wu, G.M. Zane, K.S. Walker, M.P. Thorgersen, F.L. Poole II, L.M. Lui , B.G. Adams, K.B. De León, S.S. Brewer, D.E. Williams, K.A. Lowe, M. Rodriguez, Jr., T.L. Mehlhorn, S.M. Pfiffner, R. Chakraborty, A.P. Arkin, J.D. Wall, M.W. Fields, M.W.W. Adams, D.A. Stahl, D.A. Elias a and T. C. Hazen* (2020) Integrated characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer. Chemosphere. [doi]:10.1016/j.chemosphere.2020.126951 OSTI:1617965
  9. Mutalik, V.K.; B.A. Adler, H.S. Rishi, D. Piya, C. Zhong, B. Koskella, E.M. Kutter, R. Calendar, P.S. Novichkov, M.N. Price, A.M. Deutschbauer, A.P. Arkin (2020) High-throughput mapping of the phage resistance landscape in E. coli. PLoS Biology [doi]:10.1371/journal.pbio.3000877 OSTI:1714384
  10. Ning, D.; M. Yuan, L. Wu, Y. Zhang, X. Guo, X. Zhou, Y. Yang, A. P. Arkin, M. K. Firestone, and J-Z. Zhou (2020) A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming. Nature Communications 11, 4717 [doi]:10.1038/s41467-020-18560-z OSTI:1766124
  11. Price M.N.; A.M. Deutschbauer, and A.P. Arkin (2020) GapMind: Automated annotation of amino acid biosynthesis. mSystems. [doi]:10.1128/mSystems.00291-20 OSTI:1721648
  12. Rajeev, L.; M.E. Garber, A.Mukhopadhyay (2020) Tools to map target genes of bacterial two-component system response regulators. Environmental Microbiology Reports. [doi]: 10.1111/1758-2229.12838 OSTI:1617064
  13. Tian, R; D. Ning, Z. He, P. Zhang, S.J. Spencer, S. Gao, W. Shi, L. Wu, Y. Zhang, Y. Yang, B. G. Adams, A.M. Rocha, B.L. Detienne, K.A. Lowe, D.C. Joyner, D.M. Klingeman, A.P. Arkin, M.W. Fields, T.C. Hazen, D.A. Stahl, E.J. Alm, J. Zhou (2020) Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity. Microbiome 8, 51 [doi]:1186/s40168-020-00825-w OSTI:1651273
  14. Wilpiszeski, R.L.; C.M. Gionfriddo, A.M. Wymore J.W. Moon, K.A. Lowe, M. Podar, S.R. Elorfi, D.C. Joyner, A.V. Palumbo, M.W. Fields, T.C. Hazen, M.W.W. Adams, F. Poole III, R. Chakraborty, Y. Fan, J.D. Van Nostrand, J-Z. Zhou, A.P. Arkin, D.A. Elias (2020) Using in-field bioreactors to monitor microbial community dynamic shifts with geochemical perturbations. PLoS [doi]:10.1371/journal.pone.0232437 OSTI:1638903
  15. Wu, B; F. Liu, A. Zhou, J. Li, L. Shu, M. L. Kempher, X. Yang, D. Ning, F. Pan, G. Zane, J. D. Wall, J. D. Van Nostrand, P. Juneau, S. Chen, Q. Yan, Z. He, and J. Zhou (2020) Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris. ISME J 14, 2862-2876 [doi]: 10.1038/s41396-020-00753-5 OSTI:1778206
  16. Wu, X.; S.J. Spencer, S. Gushgari-Doyle, M.O. Yee, J. Voriskova, Y. li, E.J. Alm, R. Chakraborty (2020) Culturing of ‘Unculturable’ Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria from Groundwater. Front. Microbiol [doi]:10.3389/fmicb.2020.610001 OSTI:1756120
  17. Xue, J.; C. Guijas, H.P. Benton, B. Warth, G. Siuzdak. (2020) METLIN MS2 molecular standards database: a broad chemical and biological resource. Nat Methods. [doi]: 10.1038/s41592-020-0942-5
  18. Zane GM, Wall JD, De León KB. (2020) Novel Mode of Molybdate Inhibition of Desulfovibrio vulgaris Hildenborough. Front Microbiol. [doi]: 10.3389/fmicb.2020.610455 {PMID}:33391236; PMCID: PMC7774982 OSTI:1734583
Books/Books Chapters
1. 1. Louie, K.B; S.M. Kosina, Y. Hu, H. Otani, M. de Raad, A.N. Kuftin, N.J. Mouncey, B.P. Bowen and T.R. Northen. (2020) Mass spectrometry for natural product discovery. Comprehensive Natural Products III: Chemistry and Biology. Elsevier [ISBN]: 978-0-08-102691-5

Synergistic Collaboration/Tool Development

1. 1. De Vrieze, J.; T. De Mulder, S. Matassa, J. Zhou, L. T. Angenent, N. Boon, W. Verstraete (2020) Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals. Microbial Biotechnology 13, 829-843 [doi]:10.1111/1751-7915.13575. OSTI:1721650
  2. Nayfach, S., S. Roux, R. Seshadri, D. Udwary, N. Varghese, F. Schulz, D. Wu, D. Paez-Espino, I-M. Chen, M. Huntemann, K. Palaniappan, J. Ladau, S. Mukherjee, T.B.K. Reddy, T. Nielsen, E. Kirton, J. P. Faria, J. N. Edirisinghe, C. S. Henry, S. P. Jungbluth, D. Chivian, P. Dehal, E. M. Wood-Charlson, A. P. Arkin, S. Tringe, A. Visel, IMG/M Data Consortium, T. Woyke, N. J. Mouncey, N. N. Ivanova, N. C. Kyrpides, E. A. Eloe-Fadrosh. (2020) A Genomic Catalogue of Earth’s Microbiomes. Nature Biotechnology [doi]:10.1038/s41587-020-0718-6 PMID: 33169036 OSTI:1735390.
  3. Xue, J.; Guijas, C.; Benton, H.P.; Warth, B.; Siuzdak, G. (2020) METLIN MS2 molecular standards database: a broad chemical and biological resource. Nature Methods. [doi]: 10.1038/s41592-020-0942-5
    {PMID}: 32839599 PMCID: PMC8802982
    
    2019
  4. Couradeau, E.; J. Sasse, D. Goudeau, N. Nath, R. Chakraborty, T.C. Hazen, B.P. Bowen, R.R. Malmstrom and T.R. Northen (2019) Probing the active fraction of soil microbiomes using BONCAT-FACS. Nature Communications. [doi]:10.1038/s41467-019-10542-0 {PMID}:31235780 PMCID:PMC6591230 OSTI:1545190
  5. Day, L.A.; K.B. De León, M.L. Kempher, J. Zhou and J.D. Wall (2019) Complete Genome Sequence of Desulfovibrio desulfuricans IC1, a Sulfonate-Respiring Anaerobe. Microbiology Resource Announcements. [doi]:10.1128/MRA.00456-19 {PMID}:31371536 PMCID:PMC6675984 OSTI:1545902
  6. Domingo-Almenara, X.; J.R. Montenegro-Burke, C. Guijas, E.L.-W. Majumder, H.P. Benton and G. Siuzdak (2019) Autonomous METLIN-Guided In-Source Fragment Annotation for Untargeted Metabolomics. American Chemical Society Analytical Chemistry. [doi]:10.1021/acs.analchem.8b03126 {PMID}:30681830 PMCID:PMC6637741 OSTI:1777377
  7. Erbilgin, O.; O. Rübel, K.B. Louie, M. Trinh, M. de Raad, T. Wildish, D. Udwary, C. Hoover, S. Deutsch, T.R. Northen and B.P. Bowen (2019) MAGI: A Method for Metabolite Annotation and Gene Integration. American Chemical Society Analytical Chemistry. [doi]:10.1021/acschembio.8b01107 {PMID}:30896917 OSTI:1545148
  8. Kothari, A.; Y.-W. Wu, M. Charrier, L. Rajeev, A.M. Rocha, C.J. Paradis, T.C. Hazen, S.W. Singer and A. Mukhopadhyay (2019) Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes. mBio. [doi]:10.1128/mBio.02899-18 {PMID}:30808697 PMCID:PMC6391923 OSTI:1496501
  9. Kothari, A.; D. Soneja, A. Tang, H. Carlson, A.M. Deutschbauer and A. Mukhopadhyay (2019) Native plasmid-encoded mercury resistance genes are functional and demonstrate natural transformation in environmental bacterial isolates. mSystems. [doi]:10.1128/mSystems.00588-19 {PMID}:31848306 PMCID:PMC6918032 OSTI:1591854
  10. Krantz, G.P.; K. Lucas, E.L.-W. Majumder, L.T Hoang, R. Avci, G. Siuzdak and M.W. Fields (2019) Bulk phase resource ratio alters carbon steel corrosion rates and endogenously produced extracellular electron transfer mediators in a sulfate-reducing biofilm. Biofouling. [doi]:10.1080/08927014.2019.1646731 {PMID}:31402749
  11. Mutalik, V.K.; P.S. Novichkov, M.N. Price, T.K. Owens, M. Callaghan, S. Carim, A.M. Deutschbauer and A.P. Arkin (2019) Dub-seq: dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria. Nature Communications. [doi]:10.1038/s41467-018-08177-8 {PMID}:30659179 PMCID:PMC6338753 OSTI:1508060
  12. Ning, D.; Y. Deng, J.M. Tiedje and J. Zhou (2019) A General Framework for Quantitatively Assessing Ecological Stochasticity. Proceedings of the National Academy of Sciences of the United States of America. [doi]:10.1073/pnas.1904623116 {PMID}:31391302 PMCID:PMC6708315 OSTI:1580904
  13. Price, M.N.; J. Ray, A.T. Iavarone, H.K. Carlson, E.M. Ryan, R.R. Malmstrom, A.P. Arkin and A.M. Deutschbauer (2019) Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism. mSystems. [doi]:10.1128/mSystems.00297-18 {PMID}:30746495 PMCID:PMC6365646 OSTI:1493373
  14. Price, M.N.; and A.P. Arkin (2019) Curated BLAST for Genomes. mSystems. [doi]:10.1128/mSystems.00072-19 {PMID}:30944879 PMCID:PMC6435814 OSTI:1504291
  15. Rajeev, L.; E.G. Luning, G.M. Zane, T.R. Juba, A.E. Kazakov, P. Novichkoc, J.D. Wall and A. Mukhopadhyay (2019) LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species. Public Library of Science ONE. [doi]:10.1371/journal.pone.0214960 {PMID}:30964892 PMCID:PMC6456213 OSTI:1545315
  16. Shi, Z.; H. Yin, J.D. Van Nostrand, J.W. Voordeckers, Q. Tu, Y. Deng, M. Yuan, A. Zhou, P. Zhang, N. Xiao, D. Ning, Z. He, L. Wu and J. Zhou (2019) Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities. International Society for Microbial Ecology Journal. [doi]:10.1128/mSystems.00296-19 {PMID}:31213523 PMCID:PMC6581690 OSTI:1580884
  17. Thorgersen, M.P.; X. Ge, F.L. Poole II, M.N. Price, A.P. Arkin and M.W.W. Adams (2019) Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation. Applied and Environmental Microbiology. [doi]:10.1128/AEM.00896-19 {PMID}:31253673 PMCID:PMC6696972 OSTI:1650072
  18. Vuono, D.C.; R.W. Read, J. Hemp, B.W. Sullivan, J.A. Arnone, I. Neveux, R.R. Blank, E. Loney, D. Miceli, M.-K.H. Winkler, R. Chakraborty, D.A. Stahl and J.J. Grzymski (2019) Resource concentration modulates the fate of dissimilated nitrogen in a dual-pathway Actinobacterium. Frontiers in Microbiology. [doi]:10.3389/fmicb.2019.00003 {PMID}:30723459 PMCID:PMC6349771 OSTI:1560586
  19. Zelaya, A.; A. Parker, K.L. Bailey, P. Zhang, J. Van Nostrand, D. Ning, D.A. Elias, J. Zhou, T.C Hazen, A.P Arkin and M.W. Fields (2019) High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer. Water Research. [doi]:10.1016/j.watres.2019.114917 {PMID}:31387058 OSTI:1607016
Synergistic Collaboration/Tool Development
1. 1. Rinschen, M.M.; Ivanisevic, J.; Giera, M.; Siuzdak, G. (2019). Identification of bioactive metabolites using activity metabolomics. Nature Reviews. Molecular Cell Biology. [doi]: 10.1038/s41580-019-0108-4
  2. McKay, L.J.; M. Dlakić, M.W. Fields, T.O. Delmont, A.M. Eren, Z.J. Jay, K.B. Klingelsmith, D. Rusch and W.P. Inskeep (2019) Co-occurring genomic capacity for anaerobic methane metabolism and dissimilatory sulfur metabolisms discovered in the Korarchaeota. Nature Microbiology. [doi]:10.1038/s41564-019-0362-4 {PMID}:30833730 OSTI: 1779059
    
    2018
  3. Carlson, H.K.; M.N. Price, M. Callaghan, A. Aaring, R. Chakraborty, H. Liu, A.P. Arkin and A.M. Deutschbauer (2018) The selective pressures on the microbial community in a metal-contaminated aquifer. International Society for Microbial Ecology Journal. [doi]:10.1038/s41396-018-0328-1 {PMID}:30523276 PMCID:PMC6461962 OSTI:1619784
  4. Christensen, G.A.; J.W. Moon, A.M. Veach, J.J. Mosher, A.M. Wymore, J.D. van Nostrand, J. Zhou, T.C. Hazen, A.P. Arkin and D.A. Elias (2018) Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition. Public Library of Science ONE. [doi]:10.1371/journal.pone.0194663 {PMID}:29558522 PMCID:PMC5860781 OSTI:1427332
  5. De León, K.B.; G.M. Zane, V.V. Trotter, G.P. Krantz, A.P. Arkin, G.P. Butland, P.J. Walian, M.W. Fields and J.D. Wall (2018) Unintended laboratory-driven evolution reveals genetic requirements for biofilm formation by Desulfovibrio vulgaris Hildenborough. mBio. [doi]:10.1128/mBio.01696-17 {PMID}:29042504 PMCID:PMC5646257 OSTI:1417607
  6. Duncombe, T.A.; M. De Raad, B.P. Bowen, A.K. Singh and T.R. Northen (2018) Insulator Nanostructure Desorption Ionization Mass Spectrometry. Analytical Chemistry. [doi]:10.1021/acs.analchem.8b01989 {PMID}:30063326 OSTI:1779086
  7. Flowers, J.; M. Richards, B. Meyer, N.S. Baliga and D.A. Stahl (2018) Constraint-Based Modeling Captures the Metabolic Versatility of Desulfovibrio vulgaris. Environmental Microbiology and Environmental Microbiology Reports. [doi]:10.1111/1758-2229.12619 {PMID}:29377633 OSTI:1777375
  8. Forsberg, E.M.; Huan, T.; Rinehart, D.; Benton, H.P.; Warth, B.; Hilmers, B.; Siuzdak, G. (2018) Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online. Nature Protocols. [doi]: 10.1038/nprot.2017.151 {PMID}: 29494574
  9. Franco, L.; S. Steinbeisser, G. Zane, J.D. Wall and M.W. Fields (2018) Cr(VI) reduction and physiological toxicity are impacted by resource ratio in Desulfovibrio vulgaris. Applied Microbiology and Biotechnology. [doi]:10.1007/s00253-017-8724-4 {PMID}:29429007 PMCID:PMC5847207 OSTI:1420176
  10. Garber, M.E.; L. Rajeev, A.E. Kazakov, J. Trinh, D. Masuno, M.G. Thompson, N. Kaplan, J. Luk, P.S. Novichkov and A. Mukhopadhyay (2018) Multiple signaling systems target a core set of transition metal homeostasis genes using similar binding motifs. Molecular Microbiology. [doi]:10.1111/mmi.13909 {PMID}:29341298
  11. Ge, X.; B.J. Vaccaro, M.P. Thorgersen, F.L. Poole, E.L. Majumder, G.M. Zane, K.B. De Leon, A.L. Lancaster, J. Moon, K.A. Lowe, C.J. Paradis, D.C. Joyner, F. von Netzer, D.A. Stahl, P.D. Adams, A.P. Arkin, J.D. Wall, T.C. Hazen and M.W.W. Adams (2018) Iron- and Aluminum-Induced Depletion of Molybdenum in Acidic Environments Impedes the Nitrogen Cycle. Environmental Microbiology. [doi]:10.1111/1462-2920.14435 {PMID}:30289197 OSTI:1528691
  12. He, Z.; P. Zhang, L. Wu, A.M. Rocha, Q. Tu, Z. Shi, B. Wu, Y. Qin, J. Wang, Q. Yan, D. Curtis, D. Ning, J.D. Van Nostrand, L. Wu, Y. Yang, D.A. Elias, D.B. Watson, M.W.W. Adams, M.W. Fields, E.J. Alm, T.C. Hazen, P.D. Adams, A.P. Arkin and J. Zhou (2018) Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning. mBio. [doi]:10.1128/mBio.02435-17 {PMID}:29463661 PMCID:PMC5821090 OSTI:1422377
  13. Justice, N.B.; A. Sczesnak, T.C. Hazen and A.P. Arkin (2018) Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing. Applied and Environmental Microbiology. [doi]:10.1128/AEM.01253-17 {PMID}:28778896 PMCID:PMC5626985 OSTI:1421797
  14. Kosina, S.M.; A.M. Greiner (NERSC), R.K. Lau, S. Jenkins, R. Baran, B.P. Bowen and T.R. Northen (2018) Web of Microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes. BioMed Central Microbiology. [doi]:10.1186/s12866-018-1256-y OSTI:1618595
  15. Liu, H.; and A.M. Deutschbauer (2018) Rapidly moving new bacteria to model-organism status. Current Opinion in Biotechnology. [doi]:10.1016/j.copbio.2017.12.006 {PMID}:29316481 OSTI:1548819
  16. Liu, H.; M.N. Price, R.J. Waters, J. Ray, H.K. Carlson, J.S. Lamson, R. Chakraborty and A.P. Arkin, A.M. Deutschbauer (2018) Magic pools: parallel assessment of transposon delivery vectors in bacteria. mSystems. [doi]:10.1128/mSystems.00143-17 {PMID}:29359196 PMCID:PMC5768790 OSTI:1434009
  17. Otwell, A.E.; A.L. García de Lomana, S.M. Gibbons, M.V. Orellana and N.S. Baliga (2018) Systems biology approaches towards predictive microbial ecology. Environmental Microbiology. [doi]:10.1111/1462-2920.14378 {PMID}:30106224 OSTI:1478266
  18. Paradis, C.J.; R. Dixon, L.M. Lui, A.P. Arkin, J.C. Parker, J.D. Istok, E. Perfect, L.D. McKay and T.C. Hazen (2018) Improved method for estimating reaction rates during push-pull tests. Ground Water. [doi]:10.1111/gwat.12770 {PMID}:29656383 OSTI:1435400
  19. Paradis, C.J.; J. Moon, D.A. Elias, L.D. McKay and T.C. Hazen (2018) In situ decay of polyfluorinated benzoic acids under anaerobic conditions. Journal of Contaminant Hydrology. [doi]:10.1016/j.jconhyd.2018.08.009 {PMID}:30201555 OSTI:1468668
  20. Price, M.N.; G.M. Zane, J.V. Kuehl, R.A. Melnyk, J.D. Wall, A.M. Deutschbauer and A.P. Arkin (2018) Filling Gaps in Bacterial Amino Acid Biosynthesis Pathways with High-throughput Genetics. Public Library of Science Genetics. [doi]:10.1371/journal.pgen.1007147 Erratum in: [doi]:10.1371/journal.pgen.1008106 {PMID}:30943208 PMCID:PMC6447180 OSTI:1580829/1416648
  21. Price, M.N.; K.M. Wetmore, R.J. Waters, M. Callaghan, J. Ray, H. Liu, J.V. Kuehl, R.A. Melnyk, J.S. Lamson, Y. Suh, H.K. Carlson, Z. Esquivel, H. Sadeeshkumar, R. Chakraborty, G.M. Zane, B.E. Rubin, J.D. Wall, A. Visel, J. Bristow, M.J. Blow, A.P. Arkin and A.M. Deutschbauer (2018) Mutant Phenotypes for Thousands of Bacterial Genes of Unknown Function. Nature. [doi]:10.1038/s41586-018-0124-0 {PMID}:29769716 OSTI:1457011 Highly Cited!
  22. Rajeev, L.; M.E. Garber, G.M. Zane, M.N. Price, I. Dubchak, J.D. Wall, P.S. Novichkov, A. Mukhopadhyay and A.E. Kazakov (2018) A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport. Environmental Microbiology. [doi]:10.1111/1462-2920.14500 {PMID}:30536693 OSTI:1490210
  23. Smith H.J.; A.J. Zelaya, K.B. De León, R. Chakraborty, D.A. Elias, T.C. Hazen, A.P. Arkin, A.B. Cunningham and M.W. Fields (2018) Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments. Federation of European Microbial Societies Microbiology Ecology. [doi]:10.1093/femsec/fiy191 {PMID}:30265315 PMCID:PMC6192502 OSTI:1493269
  24. Wu,X.; L. Wu, Y. Liu, P. Zhang, Q. Li, J. Zhou, N.J. Hess, T.C. Hazen, W. Yang and R. Chakraborty (2018) Microbial interactions with dissolved organic matter drive carbon dynamics and community succession. Frontiers in Microbiology. [doi]:10.3389/fmicb.2018.01234 {PMID}:29937762 PMCID:PMC6002664 OSTI:1460341
  25. Zhou, A.; R. Lau, R. Baran, J. Ma, F. von Netzer, W. Shi, D. Gorman-Lewis, M.L. Kempher, Z. He, Y. Qin, Z. Shi, G.M. Zane, L. Wu, B.P. Bowen, T.R. Northen, K.L. Hillesland, D.A. Stahl, J.D. Wall, A.P. Arkin and J. Zhou (2018) Key metabolites and mechanistic changes for salt tolerance in an experimentally evolved sulfate-reducing bacterium, Desulfovibrio vulgaris. mBio. [doi]:10.1128/mBio.01780-17 {PMID}:29138306 PMCID:PMC5686539 OSTI:1432221
  26. de Raad M, Northen TR, Bowen BP (2018) Analysis and interpretation of mass spectrometry imaging datasets. Book chapter in CAC Vol 82: Data Analysis for Omic Sciences: Methods and Applications. [doi]:10.1016/bs.coac.2018.06.006
  27. Hazen, T.C. (2018) Cometabolic Bioremediation. Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation, Handbook of Hydrocarbon and Lipid Microbiology. Springer International Publishing AG, part of Springer Nature 2018. R. Steffan (ed). [doi]:10.1007/978-3-319-44535-9_5-1
  28. Hazen, T.C. (2018) In Situ: Groundwater Bioremediation. Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation, Handbook of Hydrocarbon and Lipid Microbiology. Springer International Publishing AG, part of Springer Nature. R. Steffan (ed). [doi]: 10.1007/978-3-319-44535-9_11-1
    
    2017
  29. Baran, R.; R. Lau, B.P. Bowen, S. Diamond, N. Jose, F. Garcia-Pichel and T.R. Northen (2017) Extensive Turnover of Compatible Solutes in Cyanobacteria Revealed by Deuterium Oxide (D(2)O) Stable Isotope Probing. American Chemical Society Chemical Biology. [doi]:10.1021/acschembio.6b00890 {PMID}:28068058 OSTI:1347258
  30. Chakraborty, R.; H. Woo, P. Dehal, R. Walker, M. Zemla, M. Auer, L.A. Goodwin, A. Kazakov, P. Novichkov, A.P. Arkin and T.C. Hazen (2017) Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site. Standards in Genomic Sciences. [doi]:10.1186/s40793-017-0233-7 {PMID}:28194258 PMCID:PMC5299692 OSTI:161896
  31. de Raad, M.; T. de Rond, O. Rübel, J.D. Keasling, T.R. Northen and B.P. Bowen (2017) OpenMSI Arrayed Analysis Toolkit: Analyzing spatially defined samples using mass spectrometry imaging. Analytical Chemistry. [doi]:10.1021/acs.analchem.6b05004 {PMID}:28467051
  32. Erbilgin, O.; B.P. Bowen, S. Jenkins, S.M. Kosina, R.K. Lau and T.R. Northen (2017) Dynamic substrate preferences predict metabolic properties of a simple microbial consortium. BioMed Central Bioinformatics. [doi]:10.1186/s12859-017-1478-2 {PMID}:28114881 OSTI:1618529
  33. Huan, T.; E.M. Forsberg, D. Rinehart, C.H. Johnson, J. Ivanisevic, H.P. Benton, M. Fang, A. Aisporna, B. Hilmers, F.L. Poole, M.P. Thorgersen, M.W.W. Adams, G. Krantz, M.W. Fields, P.D. Robbins, L.J. Niedernhofer, T. Ideker, E.L. Majumder, J.D. Wall, N.J.W. Rattray, R. Goodacre, L.L. Lairson and G. Siuzdak (2017) Systems biology guided by XCMS Online metabolomics. Nature Methods. [doi]:10.1038/nmeth.4260 {PMID}:28448069 PMCID:PMC5933448 OSTI: 1779087
  34. Jenkins, S.; T.L. Swenson, R. Lau, A.M. Rocha, A. Aaring, T.C. Hazen, R. Chakraborty and T.R. Northen (2017) Construction of viable soil defined media using quantitative metabolomics analysis of soil metabolites. Frontiers in Microbiology. [doi]:10.3389/fmicb.2017.02618 {PMID}:29312276 PMCID:PMC5744445 OSTI:1432237
  35. King, A.J.; S.P. Preheim, K.L. Bailey, M.S. Robeson II, T. Roy Chowdhury, B.R. Crable, R.A. Hurt Jr., T. Mehlhorn, K.A. Lowe, T.J. Phelps, A.V. Palumbo, C.C. Brandt, S.D. Brown, M. Podar, P. Zhang, W.A. Lancaster, F. Poole, D.B. Watson, M.W. Fields, J.-M. Chandonia, E.J. Alm, J. Zhou, M.W.W. Adams, T.C. Hazen, A.P. Arkin and D.A. Elias (2017) Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation. Environmental Science & Technology. [doi]:10.1021/acs.est.6b04751 {PMID}:28112946 OSTI:1348330
  36. Majumder, E.L.-W.; and J.D. Wall (2017) Uranium Bio-transformations: Chemical or Biological Processes? Open Journal of Inorganic Chemistry: Actinide Special Issue. [doi]:10.4236/ojic.2017.72003 OSTI: 1779085
  37. Paradis, C.J.; L.D. McKay, E. Perfect, J.D. Istok and T.C. Hazen (2017) Push-pull tests for estimating effective porosity: expanded analytical solution and in situ application. Hydrogeology Journal. [doi]:10.1007/s10040-017-1672-3 OSTI:1435399
  38. Price M.N.; and A.P. Arkin (2017) PaperBLAST: Text-mining papers for information about homologs. mSystems. [doi]:10.1128/mSystems.00039-17 OSTI:1616214
  39. Sagawa, S.; M.N. Price, A.M. Deutschbauer and A.P. Arkin (2017) Validating regulatory predictions from diverse bacteria with mutant fitness data. Public Library of Science ONE. [doi]:10.1371/journal.pone.0178258 {PMID}:28542589 PMCID:PMC5443562 OSTI:1358532
  40. Thompson, A.W.; S. Turkarslan, C.E. Arens, A. López García de Lomana, A.V. Raman, D.A. Stahl and N.S. Baliga (2017) Robustness of a model microbial community emerges from population structure among single cells of a clonal population. Environmental Microbiology. [doi]:10.1111/1462-2920.13764 {PMID}:28419704 OSTI:1375466
  41. Thorgersen, M.P.; W.A. Lancaster, X. Ge, G. Zane, K.M. Wetmore, B.J. Vaccaro, F.L. Poole, A.M. Deutschbauer, A.P. Arkin, J.D. Wall and M.W.W. Adams (2017) Mechanisms of Chromium and Uranium Toxicity in Pseudomonas stutzeri RCH2 Grown Under Anaerobic Nitrate-Reducing Conditions. Environmental Microbiology. [doi]:10.3389/fmicb.2017.01529 {PMID}:28848534 PMCID:PMC5554334 OSTI:1476524
  42. Thorgersen, M.P.; W.A. Lancaster, L. Rajeev, X. Ge, B.J. Vaccaro, F.P. Poole, A.P. Arkin, A. Mukhopadhyay and M.W.W. Adams (2017) A Highly Expressed High-Molecular-Weight S-Layer Complex of Pelosinus sp. Strain UFO1 Binds Uranium. Applied and Environmental Microbiology. [doi]:10.1128/AEM.03044-16 {PMID}:27913415 PMCID:PMC5288816 OSTI:1393106
  43. Turkarslan, S.; A.V. Raman, A.W. Thompson, C.E. Arens, M.A. Gillespie, F. von Netzer, K.L. Hillesland, S. Stolyar, A. López García de Lomana, D.J. Reiss, D. Gorman-Lewis, G.M. Zane, J.A. Ranish, J.D. Wall, D.A. Stahl and N.S. Baliga (2017) Mechanism for microbial population collapse in a fluctuating resource environment. Molecular Systems Biology. [doi]:10.15252/msb.20167058 {PMID}:28320772 PMCID:PMC5371734 OSTI:1546850
  44. Warth B.; N. Levin, D. Rinehart, H.P. Benton, J. Teijaro and G. Siuzdak (2017) Metabolizing Data in the Cloud. Trends in Biotechnology. [doi]:10.1016/j.tibtech.2016.12.010 {PMID}:28117091 OSTI: 1413800
  45. Wu, X.; A.M. Deutschbauer, A.E. Kazakov, K.M. Wetmore, B.A. Cwick, R.M. Walker, P.S. Novichkov, A.P. Arkin and R. Chakraborty (2017) Draft Genome Sequences of Two Janthinobacterium lividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center. Genome Announcements. [doi]:10.1128/genomeA.00582-17 {PMID}:28663297 PMCID:PMC5638281 OSTI:1608714
  46. Zeng, L.; E. Wooton, D.A. Stahl and P.J. Walian (2017) Identification and Characterization of the Major Porin of Desulfovibrio vulgaris Hildenborough. Journal of Bacteriology. [doi]:10.1128/JB.00286-17 {PMID}:28874410 PMCID:PMC5686591 OSTI:1766617
  47. Zhang, P.; Z. He, J.D. Van Nostrand, Y. Qin, Y. Deng, L. Wu, Q. Tu, J. Wang, C.W. Schadt, M.W. Fields, T.C. Hazen, A.P. Arkin, D.A. Stahl and J. Zhou (2017) Dynamic succession of groundwater sulfate-reducing communities during prolonged reduction of uranium in a contaminated aquifer. Environmental Science and Technology. [doi]:10.1021/acs.est.6b02980 {PMID}:28300407 OSTI:1394592
  48. Zhou, A.; R. Lau, R. Baran, J. Ma, F. von Netzer, W. Shi, D. Gorman-Lewis, M.L. Kempher, Z. He, Y. Qin, Z. Shi, G.M. Zane, L. Wu, B.P. Bowen, T.R. Northen, K.L. Hillesland, D.A. Stahl, J.D. Wall, A.P. Arkin and J. Zhou (2017) Key metabolites and mechanistic changes for salt tolerance in an experimentally evolved sulfate-reducing bacterium, Desulfovibrio vulgaris. mBio. [doi]:10.1128/mBio.01780-17 {PMID}:29138306 PMCID:PMC5686539 OSTI:1432221
  49. **Zhou, J.; and D. Ning (2017) Stochastic Community Assembly: Does It Matter in Microbial Ecology? Microbiology and Molecular Biology Reviews. [doi]:10.1128/MMBR.00002-17 {PMID}:29021219 PMCID:PMC5706748 OSTI:1561877 **Highly cited

Synergistic Collaboration/Tool Development

1. 1. Bosak T, Schubotz F, de Santiago-Torio A, Kuehl JV, Carlson HK, Watson N, et al. (2017) System-Wide Adaptations of Desulfovibrio alaskensis G20 to Phosphate-Limited Conditions. PLoS ONE 11(12): e0168719. https://doi.org/10.1371/journal.pone.0168719 OSTI:1338432
  2. McKay, L.J.; R. Hatzenpichler, W.P. Inskeep and M.W. Fields (2017) Occurrence and expression of novel methyl-coenzyme M reductase gene (mcrA) variants in hot spring sediments. Nature Scientific Reports. [doi]:10.1038/s41598-017-07354-x OSTI:1624317
  3. Rand, J.M.; T. Pisithkul, R.L. Clark, J.M. Thiede, C.R. Mehrer, D.E. Agnew, C.E. Campbell, A.L. Markley, M.N. Price, J. Ray, K.M. Wetmore, Y. Suh, A.P. Arkin, A.M. Deutschbauer, D. Amador-Noguez and B.F. Pfleger (2017) A metabolic pathway for catabolizing levulinic acid in bacteria. Nature Microbiology. [doi]:10.1038/s41564-017-0028-z OSTI:1399002
    
    2016
  4. 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/j.abb.2015.08.021 {PMID}:26365033
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  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

Books/Book Chapters

1. 1. 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
  2. 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

Synergistic Collaboration/Tool Development

1. 1. 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
  2. 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
  3. 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
  4. de Raad, M.; Fischer, C.R; Northen, T.R. (2016) High-throughput platforms for metabolomics. Current Opinion in Chemical Biology. [doi]: 10.1016/j.cbpa.2015.10.012 {PMID}: 26544850
  5. 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 OSTI:1399002
    
    2015
  6. Baran, R.; E.L. Brodie, J. Mayberry-Lewis, E. Hummel, U.N. Da Rocha, R. Chakraborty, B.P. Bowen, U. Karaoz, H. Cadillo-Quiroz, F. Garcia-Pichel and T.R. Northen (2015) Exometabolite niche partitioning among sympatric soil bacteria. Nature Communications. [doi]:10.1038/ncomms9289 {PMID}:26392107 PMCID:PMC4595634
  7. Barnhart, E.P.; M.A. McClure, K. Johnson, S. Cleveland, K.A. Hunt and M.W. Fields (2015) Potential Role of Acetyl-CoA Synthetase (acs) and Malate Dehydrogenase (mae) in the Evolution of the Acetate Switch in Bacteria and Archaea. Scientific Reports. [doi]:10.1038/srep12498 {PMID}:26235787 PMCID:PMC4522649
  8. Brewer, B.; S.M. Techtmann, N. Mahmoudi, D. Niang, S. Pfiffner and T.C. Hazen (2015) Co-extraction of DNA and PLFA from Soil Samples. Journal of Microbiological Methods. [doi]:10.1016/j.mimet.2015.05.018 {PMID}:26027542
  9. Carlson, H.K.; J.V. Kuehl, A.B. Hazra, N.B. Justice, M.K. Stoeva, A. Sczesnak, M.R. Mullan, A.T. Iavarone, A. Engelbrektson, M.N. Price, A.M. Deutschbauer, A.P. Arkin and J.D. Coates (2015) Mechanisms of direct inhibition of the respiratory sulfate-reduction pathway by (per)chlorate and nitrate. International Society for Microbial Ecology Journal. [doi]:10.1038/ismej.2014.216 {PMID}:25405978 PMCID:PMC4438318
  10. Christensen, G.A.; G.M. Zane, A.E. Kazakov, X. Li, D.A. Rodionov, P.S. Novichkov, I. Dubchak, A.P. Arkin and J.D. Wall (2015) Rex (encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough is a repressor of sulfate adenylyl transferase and is regulated by NADH. Journal of Bacteriology. [doi]:10.1128/JB.02083-14 {PMID}:25313388 PMCID:PMC4288696
  11. De León, K.B.; S.M. Utturkar, L.B. Camilleri, D.A. Elias, A.P. Arkin, M.W. Fields, S.D. Brown and J.D. Wall (2015) Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum. Genome Announcements. [doi]:10.1128/genomeA.01090-15 {PMID}:26404608 PMCID:PMC4582584
  12. Deng, Y.; P. Zhang, Y. Qin, Q. Tu, Y. Yang, Z. He, C.W. Schadt and J. Zhou (2015) Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation. Environmental Microbiology. [doi]:10.1111/1462-2920.12981 {PMID}:26177312 Highly Cited!
  13. Hemme, C.L.; Q. Tu, Z. Shi, Y. Qin, W. Gao, Y. Deng, J.D. Van Nostrand, L. Wu, Z. He, P.S.G. Chain, S.G. Tringe, M.W. Fields, E. Rubin, J.M. Tiedje, T.C. Hazen, A.P. Arkin and J.-Z. Zhou (2015) Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Frontiers in Microbiology. [doi]:10.3389/fmicb.2015.01205 {PMID}:26583008 PMCID:PMC4628106
  14. Hwang, C.; A. Copeland, S. Lucas, A. Lapidus, K. Barry, T. Glavina Del Rio, E. Dalin, H. Tice, S. Pitluck, D. Sims, T. Brettin, D.C. Bruce, J.C. Detter, C.S. Han, J. Schmutz, F.W. Larimer, M.L. Land, L.J. Hauser, N. Kyrpides, A. Lykidis, P. Richardson, A. Belieav, R.A. Sanford, F.E. Loeffler and M.W. Fields (2015) Complete Genome Sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment. Genome Announcements. [doi]:10.1128/genomeA.01449-14 {PMID}:25614562 PMCID:PMC4319575
  15. Kazakov, A.E.; L. Rajeev, A. Chenn, E.G. Luning, I. Dubchak, A. Mukhopadhyay and P.S. Novichkov (2015) σ54-dependent Regulome in Desulfovibrio vulgaris Hildenborough. BioMed Central Genomics. [doi]:10.1186/s12864-015-2176-y {PMID}:26555820 PMCID:PMC4641369
  16. Korte, H.L.; A. Saini, V.V. Trotter, G.P. Butland, A.P. Arkin and J.D. Wall (2015) Independence of Nitrate and Nitrite Inhibition of Desulfovibrio vulgaris Hildenborough and Use of Nitrite as a Substrate for Growth. Environmental Science & Technology. [doi]:10.1021/es504484m {PMID}:25534748
  17. Kurczy, M.; T.R. Northen, S. Trauger and G. Siuzdak (2015) Nanostructure Imaging Mass Spectrometry: The Role of Fluorocarbons in Metabolite Analysis and Yoctomole Level Sensitivity. Methods in Molecular Biology. [doi]:10.1007/978-1-4939-1357-2_14 {PMID}:25361674 PMCID:PMC4755109
  18. Melnyk, R.A.; M.D. Youngblut, I.C. Clark, H.K. Carlson, K.M. Wetmore, M.N. Price, A.T. Iavarone, A.M. Deutschbauer, A.P. Arkin and J.D. Coates (2015) Novel Mechanism for Scavenging of Hypochlorite Involving a Periplasmic Methionine-Rich Peptide and Methionine Sulfoxide Reductase. mBio. [doi]:10.1128/mBio.00233-15 {PMID}:25968643 PMCID:PMC4436054
  19. Rajeev, L.; A. Chen, A.E. Kazakov, E.G. Luning, G.M. Zane, P.S. Novichkov, J.D. Wall and A. Mukhopadhyay (2015) Regulation of nitrite stress response in Desulfovibrio vulgaris Hildenborough, a model sulfate-reducing bacterium. Journal of Bacteriology. [doi]:10.1128/jb.00319-15 {PMID}:26283774 PMCID:PMC4621071
  20. Raman, A.V.; and N.S. Baliga (2015) The universe under a microscope. Environmental Microbiology Reports. [doi]:10.1111/1758-2229.12225 {PMID}:25721591
  21. Ramos, A.R.; F. Grein, G.P. Oliveira, S.S. Venceslau, K.L. Keller, J.D. Wall and I.A. Pereira (2015) The FlxABCD-HdrABC proteins correspond to a novel NADH dehydrogenase/heterodisulfide reductase widespread in anaerobic bacteria and involved in ethanol metabolism in Desulfovibrio vulgaris Hildenborough. Environmental Microbiology. [doi]:10.1111/1462-2920.12689 {PMID}:25367508
  22. Ramsay, B.D.; C. Hwang, H.L. Woo, S.L. Carroll, S. Lucas, J. Han, A.L. Lapidus, J.-F. Cheng, L.A. Goodwin, S. Pitluck, L. Peters, O. Chertkov, B. Held, J.C. Detter, C.S. Han, R. Tapia, M.L. Land, L.J. Hauser, N.C. Kyrpides, N.N. Ivanova, N. Mikhailova, I. Pagani, T. Woyke, A.P. Arkin, P. Dehal, D. Chivian, C.S. Criddle, W. Wu, R. Chakraborty, T.C. Hazen and M.W. Fields (2015) High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater. Genome Announcements. [doi]:10.1128/genomeA.00092-15 {PMID}:25767232 PMCID:PMC4357754
  23. Ray, J.; R.J. Waters, J.M. Skerker, J.V. Kuehl, M.N. Price, J. Huang, R. Chakraborty, A.P. Arkin and A.M. Deutschbauer (2015) Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site. Genome Announcements. [doi]:10.1128/genomeA.00322-15 {PMID}:25977418 PMCID:PMC4432324
  24. Reiss, D.J.; C.L. Plaisier, W.-J. Wu and N.S. Baliga (2015) cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism. Nucleic Acids Research. [doi]:10.1093/nar/gkv300 {PMID}:25873626 PMCID:PMC4513845
  25. Sahraeian, S.M.; K.R. Luo and S.E. Brenner (2015) SIFTER search: a web server for accurate phylogeny-based protein function prediction. Nucleic Acids Research. [doi]:10.1093/nar/gkv461 {PMID}:25979264 PMCID:PMC4489292
  26. Smith, M.B.; A.M. Rocha, C.S. Smillie, S.W. Olesen, C. Paradis, L. Wu, J.H. Campbell, J.L. Fortney, T.L. Mehlhorn, K.A. Lowe, J.E. Earles, J. Phillips, S.M. Techtmann, D.C. Joyner, D.A. Elias, K.L. Bailey, R.A. Hurt Jr., S.P. Preheim, M.C. Sanders, J. Yang, M.A. Mueller, S. Brooks, D.B. Watson, P. Zhang, Z. He, E.A. Dubinsky, P.D. Adams, A.P. Arkin, M.W. Fields, J. Zhou, E.J. Alm and T.C. Hazen (2015) Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors. mBio. [doi]:10.1128/mBio.00326-15 {PMID}:25968645 PMCID:PMC4436078
  27. Swenson, T.L.; S. Jenkins, B.P. Bowen and T.R. Northen (2015) Untargeted soil metabolomics methods for analysis of extractable organic matter. Soil Biology & Biochemistry. [doi]:10.1016/j.soilbio.2014.10.007
  28. Thompson, A.W.; M.J. Crow, B. Wadey, C. Arens, S. Turkarslan, S. Stolyar, N. Elliott, T.W. Petersen, G. van den Engh, D.A. Stahl and N.S. Baliga (2015) A method to analyze, sort, and retain viability of obligate anaerobic microorganisms from complex microbial communities. Journal of Microbiological Methods. [doi]:10.1016/j.mimet.2015.07.009 {PMID}:26187776
  29. Thorgersen, M.P.; W.A. Lancaster, B.J. Vaccaro, F.L. Poole, A.M. Rocha, T. Mehlhorn, A. Pettenato, J. Ray, R.J. Waters, R.A. Melnyk, R. Chakraborty, T.C. Hazen, A.M. Deutschbauer, A.P. Arkin and M.W.W. Adams (2015) Molybdenum Availability is Key to Nitrate Removal in Contaminated Groundwater Environments. Applied and Environmental Microbiology. [doi]:10.1128/AEM.00917-15 {PMID}:25979890 PMCID:PMC4495186
  30. Wetmore, K.M.; M.N. Price, R.J. Waters, J.S. Lamson, J. He, C.A. Hoover, M.J. Blow, J. Bristow, G. Butland, A.P. Arkin and A.M. Deutschbauer (2015) Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons. mBio. [doi]:10.1128/mBio.00306-15 {PMID}:25968644 PMCID:PMC4436071
  31. Yao, Y.; T. Sun, T. Wang, O. Ruebel, T.R. Northen and B.P. Bowen (2015) Analysis of Metabolomics Datasets with High-Performance Computing and Metabolite Atlases. Metabolites. [doi]:10.3390/metabo5030431 {PMID}:26287255 PMCID:PMC4588804
  32. Zhang, P.; J.D. Van Nostrand, Z. He, R. Chakraborty, Y. Deng, D. Curtis, M.W. Fields, T.C. Hazen, A.P. Arkin and J. Zhou (2015) A Slow-Release Substrate Stimulates Groundwater Microbial Communities for Long-Term in Situ Cr(VI) Reduction. Environmental Science & Technology. [doi]:10.1021/acs.est.5b00024 {PMID}:25835088
  33. Zhang, P.; W.-M. Wu, J.D. Van Nostrand, Y. Deng, Z. He, T. Gihring, G. Zhang, C.W. Schadt, D. Watson, P. Jardine, C.S. Criddle, S. Brooks, T.L. Marsh, J.M. Tiedje, A.P. Arkin and J. Zhou (2015) Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction. Applied and Environmental Microbiology. [doi]:10.1128/aem.00043-15 {PMID}:25862231 PMCID:PMC4524159
  34. Zhou, A.; K.L. Hillesland, Z. He, W. Schackwitz, Q. Tu, G.M. Zane, Q. Ma, Y. Qu, D.A. Stahl, J.D. Wall, T.C. Hazen, M.W. Fields, A.P. Arkin and J. Zhou (2015) Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris. International Society for Microbial Ecology Journal. [doi]:10.1038/ismej.2015.45 {PMID}:25848870 PMCID:PMC4611501
  35. Zhou, J.; Z. He, Y. Yang, Y. Deng, S.G. Tringe and L. Alvarez-Cohen (2015) High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. mBio. [doi]:10.1128/mBio.02288-14 {PMID}:25626903 PMCID:PMC4324309 Highly Cited!

Books/Book Chapters

1. 1. Rabus, R.; S.S. Venceslau, L. Wöhlbrand, G. Voordouw, J.D. Wall and I.A.C. Pereira (2015) A post-genomic view of the ecophysiology, catabolism and biotechnological relevance of sulfate-reducing prokaryotes. Advances in Microbial Physiology. Editor: R.K. Poole. [doi]:10.1016/bs.ampbs.2015.05.002 {PMID}:26210106
  2. Fels, S.R. (2015) Development of genome-wide genetic assays in Desulfovibrio vulgaris Hildenborough. Ph.D. thesis, University of Missouri, Columbia, MO.
    https://hdl.handle.net/10355/46854
  3. Korte, H.L. (2015) Nitrate and nitrite growth inhibition of Desulfovibrio strains. Ph.D. thesis. University of Missouri, Columbia, MO. https://mospace.umsystem.edu/xmlui/handle/10355/48213

Synergistic Collaboration/Tool Development

1. 1. Silva, L.; and T.R. Northen (2015) Exometabolomics and MSI: Deconstructing How Cells Interact to Transform Their Small Molecule Environment. Current Opinions in Biotechnology. [doi]:10.1016/j.copbio.2015.03.015 {PMID}:25855407 OSTI:1399002

2014

1. 1. Beer, K.D.; E.J. Wurtmann, N. Pinel and N.S. Baliga (2014) Model organisms retain an “ecological memory” of complex ecologically relevant environmental variation. Applied and Environmental Microbiology. [doi]:10.1128/AEM.03280-13 {PMID}:24413600 PMCID:PMC3957629
  2. Brileya, K.A.; L.B. Camilleri, G.M. Zane, J.D. Wall and M.W. Fields (2014) Biofilm growth mode promotes maximum carrying capacity and community stability during product inhibition syntrophy. Frontiers in Microbiology. [doi]:10.3389/fmicb.2014.00693 {PMID}:25566209 PMCID:PMC4266047
  3. Brileya, K.A.; J.M. Connolly, C. Downey, R. Gerlach and M.W. Fields (2014) Taxis toward hydrogen gas by Methanococcus maripaludis. Scientific Reports. [doi]:10.1038/srep03140 {PMID}:24189441 PMCID:PMC3817446
  4. Brooks, A.N.; D.J. Reiss, A. Allard, W.-J. Wu, D.M. Salvanha, C.L. Plaisier, S. Chandrasekaran, M. Pan, A. Kaur and N.S. Baliga (2014) A system-level model for the microbial regulatory genome. Molecular Systems Biology. [doi]:10.15252/msb.20145160 {PMID}:25028489 PMCID:PMC4299497
  5. Brown, S.D.; S.M. Utturkar, T.S. Magnuson, A.E. Ray, F.L. Poole, W.A. Lancaster, M.P. Thorgersen, M.W.W. Adams and D.A. Elias (2014) Complete Genome Sequence of Pelosinus sp. Strain UFO1 Assembled Using Single-Molecule Real-Time DNA Sequencing Technology. Genome Announcements. [doi]:10.1128/genomeA.00881-14 {PMID}:25189589 PMCID:PMC4155594
  6. Butland, G.; A. Saini, V. Trotter, M.N. Price, J. He, J.V. Kuehl, K. Wetmore, N. Liu, G. Zane, S. Fels, T. Juba, M. Shatsky, A.P. Arkin, J.-M. Chandonia, J. Wall and A.M. Deutschbauer (2014) Novel aspects of iron sulfur cluster biosynthesis in sulfate reducing bacteria (768.17). The Federation of American Societies for Experimental Biology Journal.
  7. Deutschbauer, A.M.; M.N. Price, K.M. Wetmore, D.R. Tarjan, Z. Xu, W. Shao, D. Leon, A.P. Arkin and J.M. Skerker (2014) Towards an informative mutant phenotype for every bacterial gene. Journal of Bacteriology. [doi]:10.1128/jb.01836-14 {PMID}:25112473 PMCID:PMC4187699
  8. Figueiredo, M.C.O.; S.A.L. Lobo, S.H. Sousa, F.P. Pereira, J.D. Wall, L.S. Nobre and L.M. Saraiva (2014) 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
  9. Hillesland, K.L.; S. Lim, J.J. Flowers, S. Turkarslan, N. Pinel, G.M. Zane, N. Elliott, Y. Qin, L. Wu, N.S. Baliga, J. Zhou, J.D. Wall and D.A. Stahl (2014) Erosion of functional independence early in the evolution of a microbial mutualism. Proceedings of the National Academy of Sciences. [doi]:10.1073/pnas.1407986111 {PMID}:25267659 PMCID:PMC4205623
  10. Hurt Jr., R.A.; M.S. Robeson Ⅱ, M. Shakya, J.G. Moberly, T.A. Vishnivetskaya, B. Gu and D.A. Elias (2014) Improved yield of high molecular weight DNA coincides with increased microbial diversity access from iron oxide cemented sub-surface clay environments. Public Library of Science ONE. [doi]:10.1371/journal.pone.0102826 {PMID}:25033199 PMCID:PMC4102596
  11. Keller, K.L.; B.J. Rapp-Giles, E.S. Semkiw, I. Porat, S.D. Brown and J.D. Wall (2014) 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
  12. Korte, H.L.; S.R. Fels, G.A. Christensen, M.N. Price, J.V. Kuehl, G.M. Zane, A.M. Deutschbauer, A.P. Arkin and J.D. Wall (2014) Genetic basis for nitrate resistance in Desulfovibrio strains. Frontiers in Microbiology. [doi]:10.3389/fmicb.2014.00153 {PMID}:24795702 PMCID:PMC4001038
  13. Kuehl, J.V.; M.N. Price, J. Ray, K.M. Wetmore, Z. Esquivel, A.E. Kazakov, M. Nguyen, R. Kuehn, R.W. Davis, T.C. Hazen, A.P. Arkin and A.M. Deutschbauer (2014) Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20. mBio. [doi]:10.1128/mBio.01041-14 {PMID}:24865553 PMCID:PMC4045070
  14. Lancaster, W.A.; A.L. Menon, I. Scott, F.L. Poole, B.J. Vaccaro, M.P. Thorgersen, J. Geller, T.C. Hazen, R.A. Hurt Jr., S.D. Brown, D.A. Elias and M.W.W. Adams (2014) Metallomics of two microorganisms relevant to heavy metal bioremediation reveal fundamental differences in metal assimilation and utilization. Metallomics. [doi]:10.1039/c4mt00050a {PMID}:24706256
  15. Meyer, B.; J.V. Kuehl, M.N. Price, J. Ray, A.M. Deutschbauer, A.P. Arkin and D.A. Stahl (2014) The energy-conserving electron transfer system used by Desulfovibrio alaskensis strain G20 during pyruvate fermentation involves reduction of endogenously formed fumarate and cytoplasmic and membrane-bound complexes, Hdr-Flox and Rnf. Environmental Microbiology. [doi]:10.1111/1462-2920.12405 {PMID}:24447568
  16. Muller, E.E.L.; N. Pinel, C.C. Laczny, M.R. Hoopmann, S. Narayanasamy, L.A. Lebrun, H. Roume, J. Lin, P. May, N.D. Hicks, A. Heintz-Buschart, L. Wampach, C.M. Liu, L.B. Price, J.D. Gillece, C. Guignard, J.M. Schupp, N. Vlassis, N.S. Baliga, R.L. Moritz, P.S. Keim and P. Wilmes (2014) Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage. Nature Communications. [doi]:10.1038/ncomms6603 {PMID}:25424998 PMCID:PMC4263124
  17. Novichkov, P.S.; X. Li, J.V. Kuehl, A.M. Deutschbauer, A.P. Arkin, M.N. Price and D.A. Rodionov (2014) Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria. Environmental Microbiology. [doi]:10.1111/1462-2920.12273 {PMID}:24118949
  18. Pedersen, K.; A. Bengtsson, J. Edlund, L. Rabe, T.C. Hazen, R. Chakraborty, L. Goodwin and N. Shapiro (2014) Complete Genome Sequence of the Subsurface, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio aespoeensis Aspo-2. Genome Announcements. [doi]:10.1128/genomeA.00509-14 {PMID}:24874683 PMCID:PMC4038888
  19. Plaisier, C.L.; F.-Y. Lo, J. Ashworth, A.N. Brooks, K.D. Beer, A. Kaur, M. Pan, D.J. Reiss, M.T. Facciotti and N.S. Baliga (2014) Evolution of context dependent regulation by expansion of feast/famine regulatory proteins. BioMed Central System Biology. [doi]:10.1186/s12918-014-0122-2 {PMID}:25394904 PMCID:PMC4236453
  20. Price, M.N.; J. Ray, K.M. Wetmore, J.V. Kuehl, S. Bauer, A.M. Deutschbauer and A.P. Arkin (2014) The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20. Frontiers in Microbiology. [doi]:10.3389/fmicb.2014.00577 {PMID}:25400629 PMCID:PMC4215793
  21. Rajeev, L.; E.G. Luning, S. Altenburg, G.M. Zane, E.E. Baidoo, M. Catena, J.D. Keasling, J.D. Wall, M.W. Fields and A. Mukhopadhyay (2014) Identification of a cyclic-di-GMP-modulating response regulator that impacts biofilm formation in a model sulfate reducing bacterium. Frontiers in Microbiology. [doi]:10.3389/fmicb.2014.00382 {PMID}:25120537 PMCID:PMC4114195
  22. Rajeev, L.; E.G. Luning and A. Mukhopadhyay (2014) DNA-affinity-purified chip (DAP-chip) method to determine gene targets for bacterial two component regulatory systems. Journal of Visualized Experiments. [doi]:10.3791/51715 {PMID}:25079303 PMCID:PMC4233932
  23. Ray, J.; K.L. Keller, M. Catena, T.R. Juba, M. Zemla, L. Rajeev, B. Knierim, G.M. Zane, J.J. Robertson, M. Auer, J.D. Wall and A. Mukhopadhyay (2014) Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough mobility. Frontiers in Microbiology. [doi]:10.3389/fmicb.2014.00077 {PMID}:24639670 PMCID:PMC3944678
  24. Shao, W.; M.N. Price, A.M. Deutschbauer, M.F. Romine and A.P. Arkin (2014) Conservation of Transcription Start Sites within Genes across a Bacterial Genus. mBio. [doi]:10.1128/mBio.01398-14 {PMID}:24987095 PMCID:PMC4161247
  25. Shatsky, M.; P. Arbelaez, B.G. Han, D. Typke, S.E. Brenner, J. Malik and R.M. Glaeser (2014) Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs. Journal of Structural Biology. [doi]:10.1016/j.jsb.2014.03.017 {PMID}:24694675
  26. Tu, Q.; H. Yu, Z. He, Y. Deng, L. Wu, J.D. Van Nostrand, A. Zhou, J. Voordeckers, Y.-J. Lee, Y. Qin, C.L. Hemme, Z. Shi, K. Xue, T. Yuan, A. Wang and J. Zhou (2014) GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis. Molecular Ecology Resources. [doi]:10.1111/1755-0998.12239 {PMID}:24520909
  27. Turkarslan, S.; E.J. Wurtmann, W.J. Wu, N. Jiang, J.C. Bare, K. Foley, D.J. Reiss, P. Novichkov and N.S. Baliga (2014) Network portal: a database for storage, analysis and visualization of biological networks. Nucleic Acids Research. [doi]:10.1093/nar/gkt1190 {PMID}:24271392 PMCID:PMC3964938
  28. Wurtmann, E.J.; A.V. Ratushny, M. Pan, K.D. Beer, J.D. Aitchison and N.S. Baliga (2014) An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation. Molecular Microbiology. [doi]:10.1111/mmi.12564 {PMID}:24612392 PMCID:PMC4060883
  29. Zaramela, L.S.; R.Z.N. Vencio, F. ten-Caten, N.S. Baliga and T. Koide (2014) Transcription Start Site Associated RNAs (TSSaRNAs) Are Ubiquitous in All Domains of Life. Public Library of Science ONE. [doi]:10.1371/journal.pone.0107680 {PMID}:25238539 PMCID:PMC4169567
  30. Zhou, J.; Y. Deng, P. Zhang, K. Xue, Y. Liang, J.D. Van Nostrand, Y. Yang, Z. He, L. Wu, D.A. Stahl, T.C. Hazen, J.M. Tiedje and A.P. Arkin (2014) Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proceedings of the National Academy of Sciences.[doi]:10.1073/pnas.1324044111 {PMID}:24550501 PMCID:PMC3948316 Highly Cited

Books/Books/Chapters

1. 1. Van Nostrand, J.D.; and J. Zhou (2014) Applications of functional gene microarrays for profiling microbial communities. Applications of Advanced Omics Technologies: From Genes to Metabolites. Editors: V, Garcia-Cañas, A. Cifuentes and C. Simo. [doi]:10.1016/B978-0-444-62650-9.00001-4

Synergistic Collaboration/Tool Development

1. 1. Ashworth, J.; C.L. Plaisier, F.Y. Lo, D.J. Reiss and N.S. Baliga (2014) Inference of expanded Lrp-like feast/famine transcription factor targets in a non-model organism using protein structure-based prediction. Public Library of Science ONE. [doi]:10.1371/journal.pone.0107863 {PMID}:25255272 PMCID:PMC4177876
  2. Gowda, H.; J. Ivanisevic, C.H. Johnson, M.E. Kurczy, H.P. Benton, D. Rinehart, T. Nguyen, J. Ray, J. Kuehl, B. Arevalo, P.D. Westenskow, J. Wang, A.P. Arkin, A.M. Deutschbauer, G.J. Patti and G. Siuzdak (2014) Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses. Analytical Chemistry. [doi]:10.1021/ac500734c {PMID}:24934772 PMCID:PMC4215863
  3. Rinehart, D.; C.H. Johnson, T. Nguyen, J. Ivanisevic, H.P. Benton, J. Lloyd, A.P. Arkin, A.M. Deutschbauer, G.J. Patti and G. Siuzdak (2014) Metabolomic data streaming for biology-dependent data acquisition. Nature Biotechnology. [doi]:10.1038/nbt.2927 {PMID}:24911492 PMCID:PMC4112958
    
    2013
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. Dubinsky, E.A.; Conrad, M.E.; Chakraborty, R.; Bill, M.; Borglin, S.E.; Hollibaugh, J.T.; Mason, O.U.; M Piceno, Y.; Reid, F.C.; Stringfellow, W.T.; Tom, L.M.; Hazen, T.C.; Andersen, G.L. (2013) Succession of hydrocarbon-degrading bacteria in the aftermath of the deepwater horizon oil spill in the gulf of Mexico. Environ. Sci. Technol. [doi]: 10.1021/es401676y {PMID}: 23937111
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
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Books/Book Chapters

1. 1. 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
  2. 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
  3. 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
  4. 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
  5. 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

Synergistic Collaboration/Tool Development

1. 1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
    
    2012
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. Chakraborty, R; T. C. Hazen, D. C. Joyner, K. Küsel, M. E. Singer, J. Sitte and T. Torok (2011). Use of immunomagnetic separation for the detection of Desulfovibrio vulgaris from environmental samples. Journal of Microbiological Methods 86(2):204-209. Epub 2011/05/25. [doi]:1016/j.mimet.2011.05.005. {PMID}:21605602
  17. 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
  18. David, L. A. and E. J. Alm (2011). Rapid evolutionary innovation during an Archaean genetic expansion. Nature 469(7328):93-96. Epub 2010/12/21. [doi]:1038/nature09649. {PMID}:21170026
  19. 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
  20. 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
  21. 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 Highly Cited!
  22. Deutschbauer, A; M. N. Price, K. M. Wetmore, W. Shao, J. K. Baumohl, Z. Xu, M. Nguyen, R. Tamse, R. W. Davis and A. P. Arkin (2011). Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. PLoS Genetics 7(11):e1002385. Epub 2011/11/30. [doi]:1371/journal.pgen.1002385. {PMID}:22125499
  23. 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 Highly Cited!
  24. 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
  25. 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
  26. Hauser, L. J; M. L. Land, S. D. Brown, F. Larimer, K. L. Keller, B. J. Rapp-Giles, M. N. Price, M. Lin, D. C. Bruce, J. C. Detter, R. Tapia, C. S. Han, L. A. Goodwin, J.-F. Cheng, S. Pitluck, A. Copeland, S. Lucas, M. Nolan, A. L. Lapidus, A. V. Palumbo and J. D. Wall (2011). The Complete Genome Sequence and Updated Annotation of Desulfovibrio alaskensis Journal of Bacteriology 193(16):4268-4269. Epub 2011/06/21. [doi]:1128/JB.05400-11. {PMID}:21685289
  27. Hazen, T.C.; and S. Wuertz (2012) Environmental biotechnology. Current Opinion in Biotechnology. [doi]:10.1016/j.copbio.2012.04.004 {PMID}:22560159
  28. 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
  29. 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
  30. Jajamovich, G. H; X. Wang, A. P. Arkin and M. S. Samoilov (2011). Bayesian multiple-instance motif discovery with BAMBI: inference of recombinase and transcription factor binding sites. Nucleic Acids Research 39(21):e146.4. Epub 2011/09/29. [doi]:1093/nar/gkr745. {PMID}:21948794
  31. Lancaster, W. A; J. L. Praissman, F. L. Poole, 2nd, A. Cvetkovic, A. L. Menon, J. W. Scott, F. E. Jenney, Jr; M. P. Thorgersen, E. Kalisiak, J. V. Apon, S. A. Trauger, G. Siuzdak, J. A. Tainer and M. W. Adams (2011). A computational framework for proteome-wide pursuit and prediction of metalloproteins using ICP-MS and MS/MS data. BMC Bioinformatics 12:64. Epub 2011/03/02. [doi]:1186/1471-2105-12-64. {PMID}:21356119
  32. **Liu, P; R. J. Meagher, Y. K. Light, S. Yilmaz, R. Chakraborty, A. P. Arkin, T. C. Hazen and A. K. Singh (2011). Microfluidic fluorescence in situ hybridization and flow cytometry (muFlowFISH). Lab on a Chip 11(16):2673-2679. [doi]:1039/c1lc20151d. {PMID}:21755095
  33. Mason, O.U.; Hazen, T.C.; Borglin, S.; Chain, P.S.G.; Dubinsky, E.A.; Fortney, J.L.; Han, J.; Holman, H.N; Hultman, J.; Lamendella, R.; Mackelprang, R.; Malfatti, S.T., Lauren M.; Tringe, S.G.; Woyke, T.; Zhou, J.; Rubin, E.M.; Jansson, J.K. (2012) Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. The ISME Journal. [doi]:10.1038/ismej.2012.59 {PMID}:22717885 PMCID:PMC3498917 OSTI:1153577
  34. 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
  35. 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
  36. Price, M. N; A. M. Deutschbauer, J. V. Kuehl, H. Liu, H. E. Witkowska and A. P. Arkin (2011). Evidence-Based Annotation of Transcripts and Proteins in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough. Journal of Bacteriology 193(20):5716-5727. Epub 2011/08/16. [doi]:1128/JB.05563-11. {PMID}:21840973
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
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Books/Books Chapters

1. 1. 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
  2. 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
  3. 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

Synergistic Collaboration/Tool Development

1. 1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. **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 Top-5 cited article in ISME J since inception
  7. 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
  8. 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
  9. Patti GJ, Yanes O, Siuzdak G. (2012) Innovation: Metabolomics: The Apogee of the Omic Trilogy. Nature Reviews Molecular Cell Biology. 13(4):263-9. Epub 2012/03/23. doi: 10.1038/nrm3314. PMID: 22436749.
  10. Patti, G.J.; Tautenhahn, R.; Siuzdak, G. (2012) Meta-analysis of untargeted metabolomic data from multiple profiling experiments. Nature Protocols. [doi]: 10.1038/nprot.2011.454 {PMID}: 22343432 PMCID: PMC3683249
  11. Tautenhahn, R.; Cho, K.; Uritboonthai, W.; Zhu, Z.; Patti, G.J.; Siuzdak, G. (2012) An accelerated workflow for untargeted metabolomics using the METLIN database. Nature Biotechnology. [doi]: 10.1038/nbt.2348 PMCID: PMC3666346
  12. Tautenhahn R., Patti G.J., Rinehart D., Siuzdak G. (2012) XCMS Online: A web-based platform to process untargeted metabolomic data. http://xcmsonline.scripps.edu) Analytical Chemistry. 84 (11), 5035-5039
  13. 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
  14. Zhou, J.; Xue, K.; Xie, J.; Deng, Y.; Wu, L.; Cheng, X.; Fei, S.; Deng, S.; He, Z.; Van Nostrand, J.D.; Luo, Y. (2012) Microbial mediation of carbon-cycle feedbacks to climate warming. Nature Climate Change. [doi]: 10.1038/nclimate1331

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