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Margaret Romine

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Semen A Leyn; Xiaoqing Li; Pavel Novichkov; Andrei L Osterman; Samantha Reed; Margaret F Romine; Chen Yang; Qingxiang Zheng; James K Fredrickson; Dmitry A Rodionov
Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensis.
Bin Cao; Liang Shi; Roslyn N Brown; Yijia Xiong; Jim K Fredrickson; Margaret F Romine; Matthew J Marshall; Mary S Lipton; Haluk Beyenal
Extracellular polymeric substances from Shewanella sp. HRCR-1 biofilms: characterization by infrared spectroscopy and proteomics.
Dmitry A Rodionov; Irina A Rodionova; Margaret F Romine; Elena D Stavrovskaya; Adam P Arkin; Inna Dubchak; James K Fredrickson; Anna V Gerasimova; Alexey E Kazakov; Marat D Kazanov; Galina Yu Kovaleva; Olga N Laikova; Xiaoqing Li; Pavel Novichkov; Andrei Osterman; Ross Overbeek; Elizaveta A Permina; Dmitry A Ravcheev; Mikhail S Gelfand
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus.

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All Publications

2011: Semen A Leyn; Xiaoqing Li; Pavel Novichkov; Andrei L Osterman; Samantha Reed; Margaret F Romine; Chen Yang; Qingxiang Zheng; James K Fredrickson; Dmitry A Rodionov
Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensis.
The Journal of biological chemistry 2011;286(41):35782-94.
2011: Bin Cao; Liang Shi; Roslyn N Brown; Yijia Xiong; Jim K Fredrickson; Margaret F Romine; Matthew J Marshall; Mary S Lipton; Haluk Beyenal
Extracellular polymeric substances from Shewanella sp. HRCR-1 biofilms: characterization by infrared spectroscopy and proteomics.
Environmental microbiology 2011;13(4):1018-31.
2011: Dmitry A Rodionov; Irina A Rodionova; Margaret F Romine; Elena D Stavrovskaya; Adam P Arkin; Inna Dubchak; James K Fredrickson; Anna V Gerasimova; Alexey E Kazakov; Marat D Kazanov; Galina Yu Kovaleva; Olga N Laikova; Xiaoqing Li; Pavel Novichkov; Andrei Osterman; Ross Overbeek; Elizaveta A Permina; Dmitry A Ravcheev; Mikhail S Gelfand
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus.
BMC genomics 2011;12 Suppl 1():S3.
2011: Margaret F Romine
Genome-wide protein localization prediction strategies for gram negative bacteria.
BMC genomics 2011;12 Suppl 1():S1.
2011: Sheetal Shirodkar; Samantha Reed; Margaret F Romine; Daad A Saffarini
The octahaem SirA catalyses dissimilatory sulfite reduction in Shewanella oneidensis MR-1.
Environmental microbiology 2011;13(1):108-15.
2010: Roslyn N Brown; Margaret F Romine; Athena A Schepmoes; Richard D Smith; Mary S Lipton
Mapping the subcellular proteome of Shewanella oneidensis MR-1 using sarkosyl-based fractionation and LC-MS/MS protein identification.
Journal of proteome research 2010;9(9):4454-63.
2010: Grigoriy E Pinchuk; Eric A Hill; Oleg V Geydebrekht; Jessica De Ingeniis; Xiaolin Zhang; Andrei Osterman; James H Scott; Samantha B Reed; Margaret F Romine; Allan E Konopka; Alexander S Beliaev; Jim K Fredrickson; Jennifer L Reed
Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation.
PLoS computational biology 2010;6(6):e1000822.
2010: Haizhen Zhang; Roslyn N Brown; Wei-Jun Qian; Matthew Monroe; Samuel O Purvine; Ronald J Moore; Marina A Gritsenko; Liang Shi; Margaret F Romine; James K Fredrickson; Ljiljana Pasa-Tolić; Richard D Smith; Mary S Lipton
Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling.
Journal of proteome research 2010;9(5):2160-9.
2010: H W Harris; M Y El-Naggar; O Bretschger; M J Ward; Margaret F Romine; A Y Obraztsova; Kenneth H Nealson
Electrokinesis is a microbial behavior that requires extracellular electron transport.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(1):326-31.
2010: Dmitry A Rodionov; Chen Yang; Xiaoqing Li; Irina A Rodionova; Yanbing Wang; Anna Y Obraztsova; Olga Zagnitko; Ross Overbeek; Margaret F Romine; Samantha Reed; James K Fredrickson; Kenneth H Nealson; Andrei Osterman
Genomic encyclopedia of sugar utilization pathways in the Shewanella genus.
BMC genomics 2010;11():494.
2009: Grigory E Pinchuk; Dmitry A Rodionov; Chen Yang; Xiaoqing Li; Andrei Osterman; Etienne Dervyn; Oleg V Geydebrekht; Samantha B Reed; Margaret F Romine; Frank R Collart; James H Scott; James K Fredrickson; Alexander S Beliaev
Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(8):2874-9.
2008: James K Fredrickson; Margaret F Romine; Alexander S Beliaev; Jennifer M Auchtung; Michael E Driscoll; Timothy S Gardner; Kenneth H Nealson; Andrei L Osterman; Grigoriy Pinchuk; Jennifer L Reed; Dmitry A Rodionov; Jorge L M Rodrigues; Daad A Saffarini; Margrethe H Serres; Alfred M Spormann; Igor B Zhulin; James M Tiedje
Towards environmental systems biology of Shewanella.
Nature reviews. Microbiology 2008;6(8):592-603.
2008: Jeffrey S McLean; Paul D Majors; Catherine L Reardon; Christina L Bilskis; Samantha B Reed; Margaret F Romine; James K Fredrickson
Investigations of structure and metabolism within Shewanella oneidensis MR-1 biofilms.
Journal of microbiological methods 2008;74(1):47-56.
2008: Jeffrey S McLean; G E Pinchuk; O V Geydebrekht; C L Bilskis; B A Zakrajsek; E A Hill; Daad A Saffarini; Margaret F Romine; Y A Gorby; James K Fredrickson; Alexander S Beliaev
Oxygen-dependent autoaggregation in Shewanella oneidensis MR-1.
Environmental microbiology 2008;10(7):1861-76.
2008: Margaret F Romine; Timothy S Carlson; Angela D Norbeck; Lee Ann McCue; Mary S Lipton
Identification of mobile elements and pseudogenes in the Shewanella oneidensis MR-1 genome.
Applied and environmental microbiology 2008;74(10):3257-65.
2008: Grigoriy E Pinchuk; Christine Ammons; David E Culley; Shu-Mei W Li; Jeffrey S McLean; Margaret F Romine; Kenneth H Nealson; James K Fredrickson; Alexander S Beliaev
Utilization of DNA as a sole source of phosphorus, carbon, and energy by Shewanella spp.: ecological and physiological implications for dissimilatory metal reduction.
Applied and environmental microbiology 2008;74(4):1198-208.
2008: Matthew J Marshall; Andrew E Plymale; David W Kennedy; Liang Shi; Zheming Wang; Samantha B Reed; Alice Dohnalkova; Cody J Simonson; Chongxuan Liu; Daad A Saffarini; Margaret F Romine; John M Zachara; Alexander S Beliaev; James K Fredrickson
Hydrogenase- and outer membrane c-type cytochrome-facilitated reduction of technetium(VII) by Shewanella oneidensis MR-1.
Environmental microbiology 2008;10(1):125-36.
2007: Orianna Bretschger; Anna Obraztsova; Carter A Sturm; In Seop Chang; Yuri A Gorby; Samantha B Reed; David E Culley; Catherine L Reardon; Soumitra Barua; Margaret F Romine; Jizhong Zhou; Alexander S Beliaev; Rachida Bouhenni; Daad A Saffarini; Florian Mansfeld; Byung-Hong Kim; James K Fredrickson; Kenneth H Nealson
Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants.
Applied and environmental microbiology 2007;73(21):7003-12.
2007: Jun Li; Margaret F Romine; Mandy J Ward
Identification and analysis of a highly conserved chemotaxis gene cluster in Shewanella species.
FEMS microbiology letters 2007;273(2):180-6.
2006: Chen Yang; Dmitry A Rodionov; Xiaoqing Li; Olga N Laikova; Mikhail S Gelfand; Olga Zagnitko; Margaret F Romine; Anna Y Obraztsova; Kenneth H Nealson; Andrei Osterman
Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis.
The Journal of biological chemistry 2006;281(40):29872-85.
2006: Matthew J Marshall; Alexander S Beliaev; Alice Dohnalkova; David W Kennedy; Liang Shi; Zheming Wang; Maxim I Boyanov; Barry Lai; Kenneth M Kemner; Jeffrey S McLean; Samantha B Reed; David E Culley; Vanessa L Bailey; Cody J Simonson; Daad A Saffarini; Margaret F Romine; John M Zachara; James K Fredrickson
c-Type cytochrome-dependent formation of U(IV) nanoparticles by Shewanella oneidensis.
PLoS biology 2006;4(9):e268.
2006: Yuri A Gorby; Svetlana Yanina; Jeffrey S McLean; Kevin M Rosso; Dianne Moyles; Alice Dohnalkova; Terry J Beveridge; In Seop Chang; Byung Hong Kim; Kyung Shik Kim; David E Culley; Samantha B Reed; Margaret F Romine; Daad A Saffarini; Eric A Hill; Liang Shi; Dwayne A Elias; David W Kennedy; Grigoriy Pinchuk; Kazuya Watanabe; Shunichi Ishii; Bruce Logan; Kenneth H Nealson; James K Fredrickson
Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(30):11358-63.
2006: Mary S Lipton; Margaret F Romine; Matthew Monroe; Dwayne A Elias; Ljiljana Pasa-Tolic; Gordon A Anderson; David J Anderson; James K Fredrickson; Kim K Hixson; Christophe Masselon; Heather M Mottaz; Nikola Tolic; Richard D Smith
AMT tag approach to proteomic characterization of Deinococcus radiodurans and Shewanella oneidensis.
Methods of biochemical analysis 2006;49():113-34.
2005: Alexander S Beliaev; D M Klingeman; J A Klappenbach; L Wu; Margaret F Romine; James M Tiedje; Kenneth H Nealson; James K Fredrickson; J Zhou
Global transcriptome analysis of Shewanella oneidensis MR-1 exposed to different terminal electron acceptors.
Journal of bacteriology 2005;187(20):7138-45.
2005: Dwayne A Elias; Matthew Monroe; Matthew J Marshall; Margaret F Romine; Alexander S Belieav; James K Fredrickson; Gordon A Anderson; Richard D Smith; Mary S Lipton
Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics.
Proteomics 2005;5(12):3120-30.
2005: James K Fredrickson; Margaret F Romine
Genome-assisted analysis of dissimilatory metal-reducing bacteria.
Current opinion in biotechnology 2005;16(3):269-74.
2005: Feng Yang; Bogdan Bogdanov; Eric F Strittmatter; Andrey N Vilkov; Marina A Gritsenko; Liang Shi; Dwayne A Elias; Shuisong Ni; Margaret F Romine; Ljiljana Pasa-Tolić; Mary S Lipton; Richard D Smith
Characterization of purified c-type heme-containing peptides and identification of c-type heme-attachment sites in Shewanella oneidenis cytochromes using mass spectrometry.
Journal of proteome research 2005;4(3):846-54.
2004: James K Fredrickson; John M Zachara; David L Balkwill; David Kennedy; Shu-Mei W Li; Heather M Kostandarithes; Michael J Daly; Margaret F Romine; Fred J Brockman
Geomicrobiology of high-level nuclear waste-contaminated vadose sediments at the hanford site, washington state.
Applied and environmental microbiology 2004;70(7):4230-41.
2004: Margaret F Romine; Dwayne A Elias; Matthew Monroe; Kenneth J Auberry; Ruihua Fang; James K Fredrickson; Gordon A Anderson; Richard D Smith; Mary S Lipton
Validation of Shewanella oneidensis MR-1 small proteins by AMT tag-based proteome analysis.
Omics : a journal of integrative biology 2004;8(3):239-54.
2002: Mary S Lipton; Ljiljana Pasa-Tolic'; Gordon A Anderson; David J Anderson; Deanna L Auberry; John R Battista; Michael J Daly; James K Fredrickson; Kim K Hixson; Heather M Kostandarithes; Christophe Masselon; Lye Meng Markillie; Ronald J Moore; Margaret F Romine; Yufeng Shen; Eric Stritmatter; Nikola Tolic'; Harold R Udseth; Amudhan Venkateswaran; Kwong-Kwok Wong; Rui Zhao; Richard D Smith
Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(17):11049-54.
1999: Margaret F Romine; L C Stillwell; K K Wong; SJ Thurston; E C Sisk; Christoph Wilhelm Sensen; T Gaasterland; James K Fredrickson; JD Saffer
Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199.
Journal of bacteriology 1999;181(5):1585-602.
1997: F B Metting; Margaret F Romine
Microbial genomics: the floodgates open.
Trends in microbiology 1997;5(3):91-2.
1997: David L Balkwill; Gwendolyn R Drake; R H Reeves; James K Fredrickson; David C White; DB Ringelberg; Darrell P Chandler; Margaret F Romine; D W Kennedy; C M Spadoni
Taxonomic study of aromatic-degrading bacteria from deep-terrestrial-subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov.
International journal of systematic bacteriology 1997;47(1):191-201.
1996: Margaret F Romine; F J Brockman
Recruitment and expression of toluene/trichloroethylene biodegradation genes in bacteria native to deep-subsurface sediments.
Applied and environmental microbiology 1996;62(7):2647-50.
1996: E Kim; P J Aversano; Margaret F Romine; R P Schneider; Gerben J Zylstra
Homology between genes for aromatic hydrocarbon degradation in surface and deep-subsurface Sphingomonas strains.
Applied and environmental microbiology 1996;62(4):1467-70.
1995: L C Stillwell; S J Thurston; R P Schneider; Margaret F Romine; James K Fredrickson; JD Saffer
Physical mapping and characterization of a catabolic plasmid from the deep-subsurface bacterium Sphingomonas sp. strain F199.
Journal of bacteriology 1995;177(15):4537-9.
1995: James K Fredrickson; David L Balkwill; Gwendolyn R Drake; Margaret F Romine; D B Ringelberg; D C White
Aromatic-degrading Sphingomonas isolates from the deep subsurface.
Applied and environmental microbiology 1995;61(5):1917-22.