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FSFA Publications

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2016

Anderson L. N., Koech P. K., Plymale A. E., Landorf E. V., Konopka A., Collart F. R., Lipton M. S., Romine M. F. and Wright A. T. (2016) Live cell discovery of microbial vitamin transport and enzyme-cofactor interactions. ACS Chemical Biology, 11, 345-354; DOI: 10.1021/acschembio.5b00918.

Beam J., Bernstein H., Jay Z. J., Kozubal M., Jennings R., Tringe S. G. and Inskeep W. (2016) Assembly and succession of iron oxide microbial mat communities in acidic geothermal springs. Frontiers in Microbiology, 7, 25; DOI: 10.3389/fmicb.2016.00025.

Biteen J. S., Blainey P. C., Cardon Z. G., Chun M. Y., Church G. M., Dorrestein P. C., Fraser S. E., Gilbert J. A., Jansson J. K., Knight R., Miller J. F., Ozcan A., Prather K. A., Quake S. R., Ruby E. G., Silver P. A., Taha S., van den Engh G., Weiss P. S., Wong G. C. L., Wright A. T. and Young T. D. (2016) Tools for the microbiome: Nano and beyond. ACS Nano, 10, 6-37; DOI: 10.1021/acsnano.5b07826.

Colman D. P., Jay Z. J., Inskeep W. P., Jennings R. D., Maas K. P., Rusch D. B. and Takacs-Vesbach C. D. (2016) Novel, deep-branching heterotrophic bacterial populations recovered from thermal spring metagenomes. Frontiers in Microbiology, 7, 14; DOI: 10.3380/fmicb.2016.00304.

Faria J. P., Overbeek R., Taylor R., Conrad N., Vonstein V., Goelzer A., Fromion V., Rocha M., Rocha I. and Henry C. (2016) Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data. Frontiers in Microbiology, 7, 25; DOI: 10.3389/fmicb.2016.00275.

Henry C., Bernstein H., Weisenhorn P. B., Taylor R., Lee J.-Y., Zucker J. and Song H. (2016) Microbial community metabolic modeling: A community data-driven netwrok reconstruction. Journal of Cellular Physiology, 231, 2239-2345; DOI: 10.1002/jcp.25428. Accepted.

Klotz M. G., Bryant D., Fredrickson J., Inskeep W. P. and Kuhl M. (2016) Editorial: Systems biology and ecology of microbial mat communities. Frontiers in Microbiology, 7, 115; DOI: 10.3389/fmicb.2016.00115 .

Melendrez M. C., Becraft E. D., Wood J. M., Olsen M. T., Bryant D. A., Heidelberg J. F., Rusch D. B., Cohan F. M. and Ward D. M. (2016) Recombination does not hinder formation or detection of ecological species of synechococcus inhabiting a hot spring cyanobacterial mat. Frontiers in Microbiology, 6, 20; DOI: 10.3389/fmicb.2015.01540.

Moran J. J., Whitmore L. M., Isern N. G., Romine M. F., Riha K. M., Inskeep W. P. and Kreuzer H. W. (2016) Formaldehyde as a carbon and electron shuttle between autotroph and heterotroph populations in acidic hydrothermal vents of Norris Geyser Basin, Yellowstone National Park. Extremophiles, 20, 291-299; doi: 10.1007/s00792-016-0821-2.

Nakayasu E. S., Nicora C. D., Sims A. C., Burnum-Johnson K. E., Kim Y.-M., Kyle J. E., Matzke M. M., Shukla A. K., Chu R. K., Schepmoes A. A., Jacobs J. M., Baric R. S., Webb-Robertson B.-J., Smith R. D. and Metz T. O. (2016) MPLEx: A robust and universal protocol for single-sample integrative proteomic, metabolomic, and lipidomic analyses. mSystems, 1, e00043-00016; DOI: 10.1128/mSystems.00043-16

Nelson W. C., Maezato Y., Wu Y., Romine M. and Lindemann S. (2016) Identification and resolution of microdiversity through metagenomic sequencing of parallel consortia. Applied and Environmental Microbiology, 82, 255-267; DOI: 10.1128/AEM.02274-15.

Renslow R., Lindemann S., Cole J., Zhu Z. and Anderton C. (2016) Quantifying element incorporation in multispecies biofilms using nanoscale secondary ion mass spectrometry image analysis. Biointerphases, 11, 02A322; DOI: 10.1116/1.4941764.

Renslow R., Lindemann S. and Song H. (2016) A generalized spatial measure for resilience of microbial systems. Frontiers in Microbiology, 7, 443; doi: 10.3389/fmicb.2016.00443.

Zachara J., Moran J., Resch C. T., Lindemann S., Felmy A., Bowden M., Cory A. B. and Fredrickson J. (2016) Geo- and biogeochemical processes in a heliothermal hypersaline lake. Geochimica et Cosmochimica Acta, 181, 144-163; DOI: 10.1016/j.gca.2016.02.001.

2015

Beam J. P., Bernstein H. C., Jay Z. J., Kozubal M. A., Jennings R. d., Tringe S. G. and Inskeep W. P. (2015) Assembly and succession of iron oxide microbial mat communities in acidic geothermal springs. Frontiers in Microbiology, 7, 25; doi: 10.3389/fmicb.2016.00025.

Beam J. P., Jay Z. J. S., M.C., Rusch D. B., Romine M. F., Jennings R. d., Kozubal M. A., Tringe S. G., Wagner M. and Inskeep W. P. (2015) Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous 'streamer' community. ISME Journal, 10, 210-224; doi: 10.1038/ismej.2015.83.

Beck A., Hunt K., Bernstein H. C. and Carlson R. P. (2015) Interpreting and designing microbial communities for bioprocess applications, from components to interactions to emergent properties. In Biotechnology for Biofuel Production and Optimization, Elsevier, 407-432.

Becraft E. D., Wood J. M., Rusch D. B., Kuhl M., Jensen S., Bryant D. A., Roberts D. W., Cohan F. M. and Ward D. M. (2015) The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park. Frontiers in Microbiology, 6, 18; DOI: 10.3389/fmicb.2015.00590.

Bernstein H. C., Charania M. A., McClure R. S., Sadler N. C., Melnicki M. R., Hill E. A., Markillie L. M., Nicora C. D., Wright A. T., Romine M. F. and Beliaev A. S. (2015) Multi-omic dynamics associate oxygenic photosynthesis with nitrogenase-mediated H2 production in Cyanothece sp. ATCC 51142. Scientific Reports, 5, 16004; doi: 10.1038/srep16004.

Fredrickson J. K. (2015) Ecological communities by design. Science, 348, 1425-1427; doi: 10.1126/science.aab0946.

Ha P. T., Renslow R., Atci E., Reardon P. N., Lindemann S., Fredrickson J., Call D. R. and Beyenal H. (2015) Regulation of electron transfer processes affects phototrophic mat structure and activity. Frontiers in Microbiology, 6, 909; doi: 10.3389/fmicb.2015.00909.

Jay Z. J., Beam J. P., Dohnalkova A., Lohmayer R., Bodle B., Planer-Friedrich B., Romine M. and Inskeep W. P. (2015) Pyrobaculum yellowstonensis str. WP30 respires on elemental sulfur and/or arsenate in circumneutral sulfidic geothermal sediments of Yellowstone National Park. Applied & Environmental Microbiology, 81, 5907-5916; doi: 10.1128/AEM.01095-15.

Jay Z. J. and Inskeep W. P. (2015) The distribution, diversity and implications of 16S rRNA gene introns in the order Thermoproteales. BMC Biology, 35, 1-10; doi: 10.1186/s13062-015-0065-6.

Kim Y.-M., Nowack S., Olsen M., Becraft E. D., Wood J. M., Thiel V., Klapper I., Kühl M., Fredrickson J. K., Bryant D. A., Ward D. M. and Metz T. O. (2015) Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms. Frontiers in Microbiology, 6, 209; doi: 10.3389/fmicb.2015.00209.

Leyn S. A., Rodionov I. A., Li X. and Rodionov D. A. (2015) Novel transcriptional regulons for autotrophic cycle genes in Crenarchaeota. Journal of Bacteriology, 197, 2383-2391; doi: 10.1128/JB.00249-15.

Liu Y., Fredrickson J., Sadler N. C., Nandhikonda P., Smith R. D. and Wright A. T. (2015) Advancing understanding of microbial bioenergy conversion processes by activity-based protein profiling. Biotechnology for Biofuels, 8, 156; doi: 10.1186/s13068-015-0343-7.

McDermott J. E., Bruillard P., Overall C., Gosink L. and Lindemann S. (2015) Prediction of multi-drug resistance transporters using a novel sequence analysis method. F1000Research, 4, 60; doi: 10.12688/f1000research.6200.2.

Nowack S., Olsen M. T., Schaible G. A., Becraft E. D., Shen G. Z., Klapper I., Bryant D. A. and Ward D. M. (2015) The molecular dimension of microbial species: 2. Synechococcus strains representative of putative ecotypes inhabiting different depths in the Mushroom Spring microbial mat exhibit different adaptive and acclimative responses to light. Frontiers in Microbiology, 6, 13; DOI: 10.3389/fmicb.2015.00626.

Olsen M. T., Nowack S., Wood J. M., Becraft E. D., LaButti K., Lipzen A., Martin J., Schackwitz W. S., Rusch D. B., Cohan F. M., Bryant D. A. and Ward D. M. (2015) The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat. Frontiers in Microbiology, 6, 13; DOI: 10.3389/fmicb.2015.00604.

Sadler N. C. and Wright A. T. (2015) Activity-based protein profiling of microbes. Current Opinion in Chemical Biology, 24, 139-144; DOI: 10.1016/j.cbpa.2014.10.022.

Song H. and Liu C. (2015) Dynamic metabolic modeling of denitrifying bacterial growth: The cybernetic approach. Industrial & Engineering Chemistry Research, 54, 10221-10227; doi: 10.1021/acs.iecr.5b01615.

Song H., McClure R., Bernstein H., Overall C., Hill E. A. and Beliaev A. (2015) Integrated in silico analyses of regulatory and metabolic networks of Synechococcus sp. PCC 7002 reveal relationships between gene centrality and essentiality. Life, 5 1127-1140; doi: 10.3390/life5021127.

Song H., Renslow R., Fredrickson J. and Lindemann S. (2015) Integrating ecological and engineering concepts of resilience in microbial communities. Frontiers in Microbiology 6, 1298; doi: 10.3389/fmicb.2015.01298.

Tank M. and Bryant D. A. (2015) Nutrient requirements and growth physiology of the photoheterotrophic Acidobacterium, Chloracidobacterium thermophilum. Frontiers in Microbiology, 6, 14; DOI: 10.3389/fmicb.2015.00226.

2014

Ansong C., Sadler N. C., Hill E. A., Lewis M. P., Zink E. M., Smith R. D., Beliaev A. S., Konopka A. and Wright A. T. (2014) Characterization of protein redox dynamics induced during light-to-dark transitions and nutrient limitation in cyanobacteria. Frontiers in Microbiology, Online 03 July 2014. DOI: 10.3389/fmicb.2014.00325

Babauta J. T., Atci E., Ha P. T., Lindemann S. R., Ewing T., Call D. R., Fredrickson J. K. and Beyenal H. (2014) Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat. Frontiers in Microbiology 5, 11 doi: 10.3389/fmicb.2014.00011.

Beam J. P., Jay Z. J., Kozubal M. A. and Inskeep W. P. (2014) Niche specialization of novel Thaumarchaeota to oxic and hypoxic acidic geothermal springs of Yellowstone National Park. ISME Journal 8, 938-951 doi: 10.1038/ismej.2013.193

Beliaev A. S., Romine M. F., Serres M. H., Bernstein H. C., Linggi B. E., Markille L. M., Isern N. G., Chrisler W. B., Kucek L. A., Hill E. A., Pinchuk G. E., Bryant D. A., Wiley H. S., Fredrickson J. K. and Konopka A. (2014) Inference of interactions in cyanobacterial-heterotrophic co-cultures via transcriptome sequencing. ISME Journal 8, 2243-2255 doi:10.1038/ismej.2014.69

Bernstein H. C., Kesaano M., Moll K., Smith T., Gerlach R., Carlson R. P., Miller C. D., Peyton B. M., Cooksey K. E., Gardner R. D. and Sims R. C. (2014) Direct measurement and characterization of active photosynthesis zones inside wastewater remediating and biofuel producing microalgal biofilms. Bioresource Technology 156C, 206-215 doi: 10.1016/j.biortech.2014.01.001

Cole J. K., Hutchison J. R., Renslow R. S., Kim Y.-M., Chrisler W. B., Engelmann H. E., Dohnalkova A. C., Hu D., Metz T. O., Fredrickson J. K. and Lindemann S. R. (2014) Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions. Frontiers in Microbiology 5:109 doi: 10.3389/fmicb.2014.00109

Jay Z. J., Rusch D. B., Tringe S. G., Bailey C., Jennings R. M. and Inskeep W. P. (2014) Predominant Acidilobus-like populations from geothermal environments in Yellowstone National Park exhibit similar metabolic potential in different hypoxic microbial communities. Applied and Environmental Microbiology 80, 294-305 doi: 10.1128/AEM.02860-13

Jennings R. M., Whitmore L. M., Moran J. J., Kreuzer H. W. and Inskeep W. P. (2014) Carbon dioxide fixation by Metallosphaera yellowstonensis and acidothermophilic iron-oxidizing microbial communities from Yellowstone National Park. Applied and Environmental Microbiology 80, 2665-2671 doi: 10.1128/AEM.03416-13

Konopka A., Lindemann S. and Fredrickson J. (2014) Dynamics in microbial communities: unraveling mechanisms to identify principles. The ISME Journal, 9, 1488-1495; DOI: 10.1038/ismej.2014.251.

Kreuzer H. W., Hill E. A., Moran J. J., Bartholomew R. A., Yang H. and Hegg E. L. (2014) Contributions of the [ NiFe]-and [ FeFe]-hydrogenase to H2 production in Shewanella oneidensis MR-1 as revealed by isotope ratio analysis of evolved H2. FEMS Microbiology Letters 352, 18-24 doi: 10.1111/1574-6968.12361

Leyn S. A. and Rodionov D. A. (2014) Comparative genomics of DtxR-family regulons for metal homeostasis in Archaea. Journal of Bacteriology 197, 451-458 doi: 10.1128/JB.02386-14

Leyn S. A., Suvorova I., Kholina T. D., Sherstneva S. S., Novichkov P. S., Gelfand M. S. and Rodionov D. A. (2014) Comparative genomics of transcriptional regulation of methionine metabolism in Proteobacteria. PLOS ONE. doi: 10.1371/journal.pone.0113714.

Liu Y. M., Wang Z. M., Liu J., Levar C., Edwards M. J., Babauta J. T., Kennedy D. W., Shi Z., Beyenal H., Bond D. R., Clarke T. A., Butt J. N., Richardson D. J., Rosso K. M., Zachara J. M., Fredrickson J. K. and Shi L. (2014) A trans-outer membrane porin-cytochrome protein complex for extracellular electron transfer by Geobacter sulfurreducens PCA. Environmental Microbiology Reports, 6, 776-785; DOI: 10.1111/1758-2229.12204.

Moran J. J., Doll C. G., Bernstein H. C., Renslow R. S., Cory A. B., Hutchison J. R., Lindemann S. R. and Fredrickson J. K. (2014). "Spatially tracking labeled 13C-labelled substrate (bicarbonate) accumulation in microbial communities using laser ablation isotope ratio mass spectrometry." Environmental Microbiology Reports 6, 786-791 doi: 10.1111/1758-2229.12211

Ong W. K., Vu T. T., Lovendahl K. N., Llull J. M., Serres M. H., Romine M. F. and Reed J. L. (2014) Comparisons of Shewanella strains based on genome annotations, modeling, and experiments. BMC Systems Biology 8, 31 doi: 10.1186/1752-0509-8-31

Ravcheev D. A., Khoroshkin M. S., Laikova O. N., Tsoy O. V., Sernova N. V., Petrova S. A., Rakhmaninova A. B., Novichkov P. S., Gelfand M. S. and Rodionov D. A. (2014) Comparative genomics and evolution of regulons of the LacI-family transcription factors. Frontiers in Microbiology 5, 294 doi: 10.3389//fmicb.2014.00294

Rodionov I. A., Li X., Plymale A. E., Motamedchaboki K., Konopka A., Romine M., Fredrickson J. K., Osterman A. and Rodionov D. A. (2014) Genomic distribution of B-vitamin auxotrophy and uptake transporters in environmental bacteria from the Chloroflexi phylum. Environmental Microbiology Reports, 7, 204-210; DOI: 10.1111/1758-2229.12227

Sadler N. C., Melnicki M. R., Serres M. H., Merkley E. D., Chrisler W. B., Hill E. A., Romine M. F., Kim S., Zink E. M., Datta S., Smith R. D., Beliaev A. S., Konopka A. and Wright A. T. (2014) Live cell chemical profiling of temporal redox dynamics in a photoautotrophic cyanobacterium. ACS Chemical Biology 9, 291-300 doi: 10.1021/cb400769v

Shao W., Price M. N., Deutschbauer A. M., Romine M. and Arkin A. P. (2014) "Conservation of transcription start sites within genes across a bacterial genus." mBio 5, e01398-01414 doi: 10.1128/mBio.01398-14

Slysz G. W., Steinke L., Ward D. M., Klatt C. G., Clauss T. R., Purvine S. O., Payne S. H., Anderson G. A., Smith R. D. and Lipton M. S. (2014) Automated data extraction from in situ protein-stable isotope probing studies. Journal of Proteome Research 13, 1200-1210 doi: 10.1021/pr400633

Song H.-S., Cannon, W.R., Beliaev A.S., and Konopka, A. 2014. Mathematical modeling of microbial community dynamics: a methodological review. Processes, 2, 711-752 doi: 10.3390/pr2040711

Stolyar S., Liu Z., Thiel V., Tomsho L. P., Pinel N., Nelson W. C., Lindemann S. R., Romine M. F., Haruta S., Schuster S. C., Bryant D. A. and Fredrickson J. K. (2014) Genome sequence of the thermophilic cyanobacterium Thermosynechococcus sp. strain NK55a. Genome Announcements 2, e01060-01013. doi: 10.1128/genomeA.01060-13

Sun E. I. and Rodionov D. A. (2014) Computational analysis of riboswitch-based regulation. Biochimica et Biophysica Acta 1839(10):900-907. doi: 10.1016/j.bbagrm.2014.02.011

2013

Bernstein H. C., Beam J. P., Kozubal M. A., Carlson R. P. and Inskeep W. P. (2013) In situ analysis of oxygen consumption and diffusive transport in high-temperature acidic iron-oxide microbial mats. Environmental Microbiology 15, 2360-2370 doi: 10.1111/1462-2920.12109

Bryant DA. 2013. "Green bacteria: chlorophyll biosynthesis, light harvesting, reaction centers and electron transport." In: Encyclopedia of Biological Chemistry, 2nd Edition, pp. 501-108 (WJ Lennarz and MD Lane, Eds.), Elsevier, New York.

Cialabrini L., Ruggieri S., Kazanov M. D., Sorci L., Mazzola F., Orsomando G., Osterman A. L. and Raffaelli N. (2013) Genomics-guided analysis of nad recycling yields functional elucidation of COG1058 as a new family of pyrophosphatases. PLoS One, 8, 12; DOI: 10.1371/journal.pone.0065595.

Clingenpeel S., Kan J., Macur R. E., Woyke T., Lovalvo D., Varley J., Inskeep W. P., Nealson K. and McDermott T. R. (2013) Yellowstone lake nanoarchaeota. Frontiers in Microbiology 4, 274 doi: 10.3389/fmicb.2013.00274

Hess B. M., Xue J., Markillie L. M., Taylor R. C., Wiley H. S., Ahring B. K. and Linggi B. (2013) Coregulation of terpenoid pathway genes and prediction of isoprene production in using transcriptomics. PLOS ONE 8, e66104 doi: 10.1371/journal.pone.0066104

Klatt C. G., Liu Z., Ludwig M., Kuhl M., Jensen S. I., Bryant D. A. and Ward D. M. (2013) Temporal metatranscriptomic patterning in phototrophic Chloroflexi inhabiting a microbial mat in a geothermal spring. ISME Journal 7, 1775-1789 doi: 10.1038/ismej.2013.52

Kozubal M, MF Romine, R Jennings, Z Jay, SG Tringe, DB Rusch, J Beam, LA McCue, and WP Inskeep. 2013. Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park. ISME Journal. 7, 622-634 doi:10.1038/ismej.2012.132

Lindemann S. R., Moran J. J., Stegen J. C., Renslow R. S., Hutchison J. R., Cole J. K., Dohnalkova A. C., Tremblay J., Singh K., Malfatti S. A., Chen F., Tringe S. G., Beyenal H. and Fredrickson J. K. (2013) The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling. Frontiers in Microbiology 4, 323 doi: 10.3389/fmicb.2013.00323

Melnicki M. R., Pinchuk G. E., Hill E. A., Kucek L. A., Stolyar S. M., Fredrickson J. K., Konopka A. E. and Beliaev A. S. (2013) Feedback-controlled LED photobioreactor for photophysiological studies of cyanobacteria. Bioresource Technology 134, 127-133 doi: 10.1016/j.biortech.2013.01.079

Novichkov P. S., Kazakov A. E., Ravcheev D. A., Leyn S. A., Kovaleva G. Y., Sutormin R. A., Kazanov M. D., Riehl W., Arkin A. P., Dubchak I. and Rodionov D. A. (2013) RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics 14, 745 doi: 10.1186/1471-2164-14-745

Rodionova I. A., Li X., Thiel V., Stolyar S., Stanton K., Fredrickson J. K., Bryant D. A., Osterman A. L., Best A. A. and Rodionov D. A. (2013) Comparative genomics and functional analysis of rhamnose catabolic pathways and regulons in bacteria. Frontiers in Microbiology 4, 407 doi: 10.3389/fmicb.2013.00407

Song H. S., Ramkrishna D., Pinchuk G. E., Beliaev A. S., Konopka A. E. and Fredrickson J. K. (2013) Dynamic modeling of aerobic growth of Shewanella oneidensis. Predicting triauxic growth, flux distributions, and energy requirement for growth. Metabolic Engineering, 15, 25-33; DOI: 10.1016/j.ymben.2012.08.004.

Sun E. I., Leyn S. A., Kazanov M. D., Saier M. H., Jr., Novichkov P. S. and Rodionov D. A. (2013) Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. BMC Genomics 14, 597 doi: 10.1186/1471-2164-14-597

Taylor R. C., Webb Robertson B. J., Markillie L. M., Serres M. H., Linggi B. E., Aldrich J. T., Hill E. A., Romine M. F., Lipton M. S. and Wiley H. S. (2013) Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria. Integrative Biology 5, 1393-1406 doi: 10.1039/c3ib40120k

2012

Bryant DA, Z Liu, T Li, F Zhoa, AM Garcia Costas, CG Klatt, DM Ward, NU Frigaard, and J Overmann. 2012. Comparative and functional genomics of anoxygenic green bacteria from the taxa Chlorobi, Chloroflexi, and Acidobacteria. In: Advances in Photosynthesis and Respiration, Vol. 33, Functional Genomics and Evolution of Photosynthetic Systems. (RL Burnap and W Vermaas, Eds.), pp. 47-102, Springer, Dordrecht, The Netherlands.

Chauvigne-Hines L. M., Anderson L. N., Weaver H. M., Brown J. N., Koech P. K., Nicora C. D., Hofstad B. A., Smith R. D., Wilkins M. J., Callister S. J. and Wright A. T. (2012) Suite of activity-based probes for cellulose-degrading enzymes. Journal of the American Chemical Society, 134, 20521-20532; DOI: 10.1021/ja309790w.

Cao L, DA Bryant, AA Schepmoes, K Vogl, RD Smith, MS Lipton, and SJ Callister. 2012. "Comparison of Chloroflexus aurantiacus strain j-10-fl proteomes of cells grown chemoheterotrophically and photoheterotrophically. Photosynthetic Research 110(3):153-168.

De Ingeniis J, MD Kazanov, K Shatalin, MS Gelfand, AL Osterman, and L Sorci. 2012. "Glutamine versus ammonia utilization in the NAD synthetase family." PLoS One 7(6): e39115. doi:10.1371/journal.pone.0039115.

Fredrickson JK and MF Romine. 2012. FSFA Annual Report: Genomic Science Program Foundational Scientific Focus Area: Biological Systems Interactions. PNNL-21552, Pacific Northwest National Laboratory, Richland, WA.

Fu N, Y Xiong, and TC Squier. 2012. "Synthesis of a targeted biarsenical Cy3-Cy5 affinity probe for superresolution fluorescence imaging." Journal of the American Chemical Society 134(45):18530-18533. doi:10.1021/JA308503x.

Garcia Costas AM, Z Liu, LP Tomsho, SC Schuster, DM Ward, and DA Bryant 2012. "Complete genome of Candidatus Chloracidobacterium thermophilum, a chlorophyll-based photoheterotroph belonging to the Phylum Acidobacteria." Environmental Microbiology 14(1):177-190.

Jeanguenin L, A Lara-Núñez, DA Rodionov, AL Osterman, NY Komarova, D Rentsch, JF Gregory III, and AD Hanson. 2012. "Comparative genomics and functional analysis of the NiaP family uncover nicotinate transporters from bacteria, plants, and mammals." Functional & Integrative Genomics 12(1):25-34.

Kozubal MA, RE Macur, ZJ Jay, JP Beam, SA Malfatti, SG Tringe, BD Kocar, T Borch, and WP Inskeep. 2012. "Microbial iron cycling in acidic geothermal springs of Yellowstone National Park: integrating molecular surveys, geochemical processes, and isolation of novel Fe-active microorganisms." Frontiers in Microbiology 3:109. doi: 10.3389/fmicb.2012.00109

Kreuzer HW, L Quaroni, DW Podlesak, T Zlateva, N Bollinger, A McAllister, MJ Lott, and EL Hegg. 2012. "Detection of metabolic fluxes of O and H atoms into intracellular water in mammalian cells." PLoS ONE 7(7):Article No. e39685. doi:10.1371/journal.pone.0039685

Leyn SA, F Gao, C Yang, and DA. Rodionov. 2012. "N-acetylgalactosamine utilization pathway and regulon in Proteobacteria: Genomic reconstruction and experimental characterization in Shewanella." Journal of Biological Chemistry 287(33):28047-28056. doi: 10.1074/jbc.M112.382333.

Liu Z, CG Klatt, M Ludwig, DB Rusch, SI Jensen, M K¨hl, DM Ward, and DA Bryant. 2012. "Candidatus thermochlorobacter aerophilum: an aerobic chlorophotoheterotrophic member of the phylum Chlorobi defined by metagenomics and metatranscriptomics." The ISME Journal 6(10):1869-82. doi: 10.1038/ismej.2012.24.

Ludwig M and DA. Bryant. 2012. "Acclimation of the global transcriptome of the cyanobacterium Synechococcus sp. strain PCC 7002 to nutrient limitations and different nitrogen sources." Frontiers in Microbiology 3:145. doi: 10.3389/fmicb.2012.00145

Peterson E. S., McCue L. A., Schrimpe-Rutledge A. C., Jensen J. L., Walker H., Kobold M. A., Webb S. R., Payne S. H., Ansong C., Adkins J. N., Cannon W. R. and Webb-Robertson B. J. M. (2012) VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data. BMC Genomics, 13, 12; DOI: 10.1186/1471-2164-13-131.

Vu TT, Stolyar SM, Pinchuk GE, Hill EA, Kucek LA, Brown RN, Lipton MS, Osterman A, Fredrickson JK, Konopka AE, Beliaev AS, Reed JL. 2012. "Genome-scale modeling of light-driven reductant partitioning and carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142." PLoS Computational Biology 8(4):e1002460. doi:10.1371/journal.pcbi.1002460.

Ward DM, RW Castenholz, and SR Miller. 2012. "Cyanobacteria in geothermal habitats." In: Ecology of Cyanobacteria II (B.A. Whitton, Ed.), pp. 39-63. Springer Dordrecht Heidelberg New York London.

Ward DM, CG Klatt, J Wood, FM Cohan, and DA Bryant. 2012. "Functional genomics in an ecological and evolutionary context: maximizing the value of genomes in systems biology." In: Advances in Photosynthesis and Respiration, Vol. 33, Functional Genomics and Evolution of Photosynthetic Systems. (R.L. Burnap and W Vermaas, Eds.), pp. 1-16, Springer, Dordrecht, the Netherlands.

2011

Becraft ED, FM Cohan, M K¨hl, SI Jensen, and DM Ward. 2011. "Fine-scale distribution patterns of Synechococcus ecological diversity in the microbial mat of Mushroom Spring, Yellowstone National Park." Applied and Environmental Microbiology 7(21):7689-7697.

Bryant D. A., Z. Liu Z., Li T., Zhao F., Garcia Costas A. M., Klatt C. G., Ward D. M., Frigaard N. U. and Overmann J. (2011) Comparative and functional genomics of anoxygenic green bacteria from the taxa Chlorobi, Chloroflexi, and Acidobacteria. In: Burnap, R. L. and W. Vermaas Eds., Functional Genomics and Evolution of Photosynthetic Systems. Springer, Dordrecht, The Netherlands.

Cannon W. R., Rawlins M. M., Baxter D. J., Callister S. J., Lipton M. S. and Bryant D. A. (2011) Large improvements in MS/MS-based peptide identification rates using a hybrid analysis. Journal of Proteome Research 10, 2306-2317.

Cruz-Garcia C., Murray A. E., Rodrigues J. L., Gralnick J. A., McCue L. A., Romine M. F., Loffler F. E. and Tiedje J. M. (2011) Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1. BMC Microbiology 11, 64.

Galeazzi L, P Bocci, A Amici, L Brunetti, S Ruggieri, MF Romine, SB Reed, AL Osterman, DA Rodionov, L Sorci, and N Raffaelli. 2011. "Identification of nicotinamide mononucleotide deamidase of the bacterial pyridine nucleotide cycle reveals a novel broadly conserved amidohydrolase family." Journal of Biological Chemistry 286(46):40365-40375. doi:10.1074/jbc.M111.275818

Giuliani SE, AM Frank, DM Corgliano, C Seifert, L Hauser, and RF Collart. 2011. "Environment sensing and response mediated by ABC transporters." BMC Genomics 12(Suppl 1):S8. doi:10.1186/1471-2164-12-S1-S8

Klatt CG, JM Wood, DB Rusch, MM Bateson, N Hamamura, JF Heidelberg, AR Grossman, D Bhaya, FM Cohan, M K¨hl, DA Bryant, and DM Ward. 2011. "Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential." The ISME Journal 5:1262-1278. doi:10.1038/ismej.2011.73

Leyn SA, X Li, Q Zheng, PS Novichkov, SB Reed, MF Romine, JK Fredrickson, C Yang, AL Osterman, and DA Rodionov. 2011. "Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: A case study in Shewanella oneidensis." Journal of Biological Chemistry 286(41):35782-35794. doi: 10.1074/jbc.M111.267963

Liu Z, CG Klatt, JM Wood, DB Rusch, M Ludwig, N Wittekindt, LP Tomsho, SC Schuster, DM Ward, and DA Bryant. 2011. "Metatranscriptomic analyses of chlorophototrophs of a hot spring microbial mat." The ISME Journal 5:1279-1290. doi:10.1038/ismej.2011.37

Ludwig, M and DA Bryant 2011. "Transcriptional profiling of the model cyanobacterium Synechococcus sp. strain PCC 7002 by Next-Gen (SOLiD™) sequencing of cDNA." Frontiers in Microbiology 2(41):1-23. doi: 10.3389/fmicb.2011.00041

Melendrez MC, RK Lange, FM Cohan, and DM Ward. 2011. "Influence of molecular resolution on sequence-based discovery of ecological diversity among Synechococcus populations in an alkaline siliceous hot spring microbial mat." Applied Environmental Microbiology 77(4):1359-1367.

Pinchuk G. E., Geydebrekht O. V., Hill E. A., Reed J. L., Konopka A. E., Beliaev A. S. and Fredrickson J. K. (2011) Pyruvate and lactate metabolism by Shewanella oneidensis MR-1 under fermentation, oxygen limitation, and fumarate respiration conditions. Applied and Environmental Microbiology 77, 8234-8240.

Rodionov DA, PS Novichkov, ED Stavrovskaya, IA Rodionova, X Li, MD Kazanov, DA Ravcheev, AV Gerasimova, AE Kazakov, GY Kovaleva, EA Permina, ON Laikova, R Overbeek, MF Romine, JK Fredrickson, AP Arkin, I Dubchak, AL Osterman, and MS Gelfand. 2011. "Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus." BMC Genomics 12 (Suppl1): S3. doi: 10.1186/1471-2164-12-S1-S3.

Romine MF. 2011. "Genome-wide protein localization prediction strategies for gram negative bacteria." BMC Genomics 12(Suppl 1):S1. doi: 10.1186/1471-2164-12-S1-S1.

Ward D. M., Klatt C. G., Wood J., Cohan F. M. and Bryant D. A. (2011) Functional genomics in an ecological and evolutionary context: maximizing the value of genomes in systems biology. In: Burnap, R. L. and W. Vermaas Eds., Functional Genomics and Evolution of Photosynthetic Systems. Springer, Dordrecht, The Netherlands.

Ward DM, MC Melendrez, ED Becraft, CG Klatt, JM Wood, and FM Cohan. 2011. "Metagenomic approaches for the identification of microbial species." In: Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches (F.J. de Bruijn, Ed.), pp. 105-109. John Wiley & Sons, Inc., Hoboken, NJ.

Xiong Y, B Chen, L Shi, JK Fredrickson, DJ Bigelow, and TC Squier. 2011. "Targeted protein degradation of outer membrane decaheme cytochrome MtrC metal reductase in Shewanella oneidensis MR-1 measured using biarsenical probe CrAsH-EDT2." Biochemistry 50(45):9738-51. doi: 10.1021/bi200602f

Zhang S and DA Bryant. 2011. "The tricarboxylic acid cycle in cyanobacteria." Science 334(6062):1551-1553. doi:10.1126/science.1210858

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