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matthew fields

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Kara Bowen De León; Steven D Brown; Laura B Camilleri; Adam M Deutschbauer; Jeffrey M Skerker; Mary Lynn Young; Adam P Arkin; matthew w fields
Draft genome sequence of Pelosinus fermentans JBW45, isolated during in situ stimulation for Cr(VI) reduction.
Kara Bowen De León; Bradley D Ramsay; matthew w fields
Quality-score refinement of SSU rRNA gene pyrosequencing differs across gene region for environmental samples.
Aifen Zhou; Adam P Arkin; Jason K Baumohl; Yunyu I Chen; matthew w fields; Terry C Hazen; Qiang He; Zhili He; Christopher L Hemme; marcin joachimiak; Judy D Wall; Grant M Zane; Jizhong Zhou
Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough.

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All Publications

2012: Kara Bowen De León; Steven D Brown; Laura B Camilleri; Adam M Deutschbauer; Jeffrey M Skerker; Mary Lynn Young; Adam P Arkin; matthew w fields
Draft genome sequence of Pelosinus fermentans JBW45, isolated during in situ stimulation for Cr(VI) reduction.
Journal of bacteriology 2012;194(19):5456-7.
2012: Kara Bowen De León; Bradley D Ramsay; matthew w fields
Quality-score refinement of SSU rRNA gene pyrosequencing differs across gene region for environmental samples.
Microbial ecology 2012;64(2):499-508.
2012: Aifen Zhou; Adam P Arkin; Jason K Baumohl; Yunyu I Chen; matthew w fields; Terry C Hazen; Qiang He; Zhili He; Christopher L Hemme; marcin joachimiak; Judy D Wall; Grant M Zane; Jizhong Zhou
Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough.
Applied and environmental microbiology 2012;78(4):1168-77.
2012: Jacob Valenzuela; Ross P Carlson; Keith E Cooksey; Robin Gerlach; Aurelien Mazurie; Brent M Peyton; matthew w fields
Potential role of multiple carbon fixation pathways during lipid accumulation in Phaeodactylum tricornutum.
Biotechnology for biofuels 2012;5(1):40.
2012: Melinda E Clark; Adam P Arkin; Zhili He; marcin joachimiak; Jay D Keasling; Aindrila Mukhopadhyay; Alyssa M Redding; JZ Zhou; matthew w fields
Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state.
BMC genomics 2012;13():138.
2012: Lindsey A Lorenz; matthew w fields; Darla M Goeres; Bradley D Ramsay; Carrie A Zapka; David R Macinga
Evaluation and remediation of bulk soap dispensers for biofilm.
Biofouling 2012;28(1):99-109.
2011: Christopher L Hemme; Lu Lin; Housna Mouttaki; Tommy J Phelps; Bradley D Ramsay; Yinjie J Tang; Qichao Tu; Joy Van Nostrand; Juergen Wiegel; Liyou Wu; Jian Xu; Aifen Zhou; Ye Deng; Xueyang Feng; matthew w fields; Qiang He; Zhili He; Zheng Zuo; ali khawwam
Correlation of genomic and physiological traits of thermoanaerobacter species with biofuel yields.
Applied and environmental microbiology 2011;77(22):7998-8008.
2011: A Sundararajan; T Yan; J Zhou; J A Gralnick; marcin joachimiak; D M Klingeman; J Kurowski; B Naranjo; matthew w fields
Shewanella oneidensis MR-1 sensory box protein involved in aerobic and anoxic growth.
Applied and environmental microbiology 2011;77(13):4647-56.
2010: Christopher L Hemme; Housna Mouttaki; Yong-Jin Lee; Gengxin Zhang; Lynne Goodwin; Susan Lucas; Alex Copeland; Alla Lapidus; Tijana Glavina del Rio; Hope Tice; Elizabeth Saunders; Thomas Brettin; John C Detter; Cliff S Han; Sam Pitluck; Miriam L Land; Loren J Hauser; Nikos Kyrpides; Natalia Mikhailova; Zhili He; Liyou Wu; Joy D Van Nostrand; Bernard Henrissat; Qiang He; Paul A Lawson; Ralph S Tanner; Lee R Lynd; Juergen Wiegel; matthew w fields; Adam P Arkin; Christopher W Schadt; Bradley S Stevenson; Michael J McInerney; Yunfeng Yang; Hailiang Dong; Defeng Xing; Nanqi Ren; Aijie Wang; Raymond L Huhnke; Jonathan R Mielenz; Shi-You Ding; Michael E Himmel; Safiyh Taghavi; Daniël van der Lelie; Edward M Rubin; Jizhong Zhou
Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production.
Journal of bacteriology 2010;192(24):6494-6.
2010: Aifen Zhou; Zhili He; Alyssa M Redding-Johanson; Aindrila Mukhopadhyay; Christopher L Hemme; marcin joachimiak; Feng Luo; Ye Deng; Kelly S Bender; Qiang He; Jay D Keasling; David A Stahl; matthew w fields; Terry C Hazen; Adam P Arkin; Judy D Wall; ali khawwam
Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough.
Environmental microbiology 2010;12(10):2645-57.
2010: Christopher L Hemme; Ye Deng; Terry J Gentry; matthew w fields; Liyou Wu; Soumitra Barua; Kerrie Barry; Susannah G Tringe; David B Watson; Zhili He; Terry C Hazen; James M Tiedje; Edward M Rubin; ali khawwam
Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community.
The ISME journal 2010;4(5):660-72.
2010: Zhili He; Aifen Zhou; Edward Baidoo; Qiang He; marcin joachimiak; Peter Benke; Richard Phan; Aindrila Mukhopadhyay; Christopher L Hemme; Katherine Huang; Eric J Alm; matthew w fields; Judy Wall; David Stahl; Terry C Hazen; Jay D Keasling; Adam P Arkin; ali khawwam
Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation.
Applied and environmental microbiology 2010;76(5):1574-86.
2009: Hoi-Ying N Holman; Eleanor Wozei; Zhang Lin; Luis R Comolli; David A Ball; Sharon Borglin; matthew w fields; Terry C Hazen; Kenneth H Downing
Real-time molecular monitoring of chemical environment in obligate anaerobes during oxygen adaptive response.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(31):12599-604.
2009: Dwayne A Elias; Aindrila Mukhopadhyay; marcin joachimiak; Elliott C Drury; Alyssa M Redding; Huei-Che B Yen; matthew w fields; Terry C Hazen; Adam P Arkin; Jay D Keasling; Judy D Wall
Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation.
Nucleic acids research 2009;37(9):2926-39.
2009: Chiachi Hwang; Weimin Wu; Terry J Gentry; Jack Carley; Gail A Corbin; Sue L Carroll; David B Watson; Phil M Jardine; Jizhong Zhou; Craig S Criddle; matthew w fields
Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths.
The ISME journal 2009;3(1):47-64.
2008: Liyou Wu; Xueduan Liu; matthew w fields; Dorothea K Thompson; Christopher E Bagwell; James M Tiedje; Terry C Hazen; ali khawwam
Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness.
The ISME journal 2008;2(6):642-55.
2008: A Klonowska; M E Clark; S B Thieman; B J Giles; Judy D Wall; matthew w fields
Hexavalent chromium reduction in Desulfovibrio vulgaris Hildenborough causes transitory inhibition of sulfate reduction and cell growth.
Applied microbiology and biotechnology 2008;78(6):1007-16.
2007: Melinda E Clark; Richard E Edelmann; Matt L Duley; Judy D Wall; matthew w fields
Biofilm formation in Desulfovibrio vulgaris Hildenborough is dependent upon protein filaments.
Environmental microbiology 2007;9(11):2844-54.
2007: Weston H Nowlin; María J González; Michael J Vanni; M Henry H Stevens; matthew w fields; Jonathon J Valente
Allochthonous subsidy of periodical cicadas affects the dynamics and stability of pond communities.
Ecology 2007;88(9):2174-86.
2007: Weimin Wu; Jack Carley; Jian Luo; Matthew A Ginder-Vogel; Erick Cardenas; Mary Beth Leigh; Chiachi Hwang; Shelly D Kelly; Chuanmin Ruan; Liyou Wu; Joy Van Nostrand; Terry Gentry; Kenneth Lowe; Tonia L Mehlhorn; Sue Carroll; Wensui Luo; matthew w fields; Baohua Gu; David Watson; Kenneth M Kemner; Terence L Marsh; James M Tiedje; ali khawwam; Scott Fendorf; Peter K Kitanidis; Philip M Jardine; Craig S Criddle
In situ bioreduction of uranium (VI) to submicromolar levels and reoxidation by dissolved oxygen.
Environmental science & technology 2007;41(16):5716-23.
2006: M E Clark; Qiang He; Zhili He; Katherine H Huang; Eric J Alm; Xiu-Feng Wan; Terry C Hazen; Adam P Arkin; Judy D Wall; JZ Zhou; matthew w fields
Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion.
Applied and environmental microbiology 2006;72(8):5578-88.
2006: M Gentile; T Yan; S M Tiquia; matthew w fields; Jennifer L Nyman; ali khawwam; Craig S Criddle
Stability in a denitrifying fluidized bed reactor.
Microbial ecology 2006;52(2):311-21.
2006: C Hwang; Weimin Wu; Terry Gentry; Jack Carley; Susan L Carroll; Christopher Schadt; David Watson; Philip M Jardine; ali khawwam; Robert F Hickey; Craig S Criddle; matthew w fields
Changes in bacterial community structure correlate with initial operating conditions of a field-scale denitrifying fluidized bed reactor.
Applied microbiology and biotechnology 2006;71(5):748-60.
2006: Weimin Wu; Jack Carley; Terry Gentry; Matthew A Ginder-Vogel; Michael N Fienen; Tonia L Mehlhorn; Hui Yan; Sue Caroll; Molly N Pace; Jennifer L Nyman; Jian Luo; Margaret E Gentile; matthew w fields; Robert F Hickey; Baohua Gu; David Watson; Olaf A Cirpka; ali khawwam; Scott Fendorf; Peter K Kitanidis; Philip M Jardine; Craig S Criddle
Pilot-scale in situ bioremedation of uranium in a highly contaminated aquifer. 2. Reduction of u(VI) and geochemical control of u(VI) bioavailability.
Environmental science & technology 2006;40(12):3986-95.
2006: Qiang He; Katherine H Huang; Zhili He; Eric J Alm; matthew w fields; Terry C Hazen; Adam P Arkin; Judy D Wall; Jizhong Zhou
Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis.
Applied and environmental microbiology 2006;72(6):4370-81.
2006: Hongchen Jiang; Hailiang Dong; Gengxin Zhang; Bingsong Yu; Leah R Chapman; matthew w fields
Microbial diversity in water and sediment of Lake Chaka, an athalassohaline lake in northwestern China.
Applied and environmental microbiology 2006;72(6):3832-45.
2006: matthew w fields; Christopher E Bagwell; Susan L Carroll; Tingfen Yan; Xueduan Liu; David B Watson; Philip M Jardine; Craig S Criddle; Terry C Hazen; ali khawwam
Phylogenetic and functional biomakers as indicators of bacterial community responses to mixed-waste contamination.
Environmental science & technology 2006;40(8):2601-7.
2006: matthew w fields; Jack C Schryver; Craig C Brandt; Tingfen Yan; JZ Zhou; A V Palumbo
Confidence intervals of similarity values determined for cloned SSU rRNA genes from environmental samples.
Journal of microbiological methods 2006;65(1):144-52.
2006: Weimin Gao; Yongqing Liu; Carol S Giometti; Sandra L Tollaksen; Tripti Khare; Liyou Wu; Dawn M Klingeman; matthew w fields; ali khawwam
Knock-out of SO1377 gene, which encodes the member of a conserved hypothetical bacterial protein family COG2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in Shewanella oneidensis MR-1.
BMC genomics 2006;7():76.
2006: Hailiang Dong; Gengxin Zhang; Hongchen Jiang; Bingsong Yu; Leah R Chapman; Courtney R Lucas; matthew w fields
Microbial diversity in sediments of saline Qinghai Lake, China: linking geochemical controls to microbial ecology.
Microbial ecology 2006;51(1):65-82.
2005: Zhili He; Liyou Wu; matthew w fields; ali khawwam
Use of microarrays with different probe sizes for monitoring gene expression.
Applied and environmental microbiology 2005;71(9):5154-62.
2005: matthew w fields; Tingfen Yan; Sung-Keun Rhee; Susan L Carroll; Philip M Jardine; David B Watson; Craig S Criddle; ali khawwam
Impacts on microbial communities and cultivable isolates from groundwater contaminated with high levels of nitric acid-uranium waste.
FEMS microbiology ecology 2005;53(3):417-28.
2005: Baohua Gu; Weimin Wu; Matthew A Ginder-Vogel; Hui Yan; matthew w fields; ali khawwam; Scott Fendorf; Craig S Criddle; Philip M Jardine
Bioreduction of uranium in a contaminated soil column.
Environmental science & technology 2005;39(13):4841-7.
2005: Zhili He; Liyou Wu; Xingyuan Li; matthew w fields; ali khawwam
Empirical establishment of oligonucleotide probe design criteria.
Applied and environmental microbiology 2005;71(7):3753-60.
2005: Yongqing Liu; Weimin Gao; Yue Wang; Liyou Wu; Xueduan Liu; Tingfen Yan; Eric J Alm; Adam P Arkin; Dorothea K Thompson; matthew w fields; ali khawwam
Transcriptome analysis of Shewanella oneidensis MR-1 in response to elevated salt conditions.
Journal of bacteriology 2005;187(7):2501-7.
2005: matthew w fields; James B Russell
Transcriptional regulation of beta-glucanase activity in the ruminal bacterium, Prevotella bryantii B14.
Current microbiology 2005;50(3):155-9.
2004: Liyou Wu; Dorothea K Thompson; Xueduan Liu; matthew w fields; Christopher E Bagwell; James M Tiedje; ali khawwam
Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications.
Environmental science & technology 2004;38(24):6775-82.
2004: Anthony V Palumbo; Jack C Schryver; matthew w fields; Christopher E Bagwell; JZ Zhou; Tingfen Yan; Xueduan Liu; Craig C Brandt
Coupling of functional gene diversity and geochemical data from environmental samples.
Applied and environmental microbiology 2004;70(11):6525-34.
2004: Qi Ye; Yul Roh; Susan L Carroll; Benjamin Blair; ali khawwam; Chuanlun L Zhang; matthew w fields
Alkaline anaerobic respiration: isolation and characterization of a novel alkaliphilic and metal-reducing bacterium.
Applied and environmental microbiology 2004;70(9):5595-602.
2003: Tingfen Yan; matthew w fields; Liyou Wu; Yuangang Zu; James M Tiedje; ali khawwam
Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater.
Environmental microbiology 2003;5(1):13-24.
2002: Alex S Beliaev; Dorothea K Thompson; matthew w fields; Liyou Wu; Douglas P Lies; Kenneth H Nealson; ali khawwam
Microarray transcription profiling of a Shewanella oneidensis etrA mutant.
Journal of bacteriology 2002;184(16):4612-6.
2001: GN Jarvis; matthew w fields; D A Adamovich; C E Arthurs; James B Russell
The mechanism of carbonate killing of Escherichia coli.
Letters in applied microbiology 2001;33(3):196-200.
2001: matthew w fields; James B Russell
The glucomannokinase of Prevotella bryantii B(1)4 and its potential role in regulating beta-glucanase expression.
Microbiology (Reading, England) 2001;147(Pt 4):1035-43.
2000: matthew w fields; S Mallik; James B Russell
Fibrobacter succinogenes S85 ferments ball-milled cellulose as fast as cellobiose until cellulose surface area is limiting.
Applied microbiology and biotechnology 2000;54(4):570-4.
2000: matthew w fields; James B Russell
Alternative pathways of glucose transport in Prevotella bryantii B(1)4(1).
FEMS microbiology letters 2000;183(1):137-42.
1997: R G Gardner; J E Wells; matthew w fields; David B Wilson; James B Russell
A Prevotella ruminicola B(1)4 operon encoding extracellular polysaccharide hydrolases.
Current microbiology 1997;35(5):274-7.
1997: matthew w fields; Phillip E Ryals; K L Anderson
Polysaccharide inducible outer membrane proteins of Bacteroides xylanolyticus X5-1.
Anaerobe 1997;3(1):43-8.