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2014 Publications

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

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

  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

  31. Books/Book Chapters

  32. 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

  33. Legacy and Synergistic External Research

  34. 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
  35. 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
  36. 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