TY - JOUR AU - Diaz, E. PY - 2004 DA - 2004// TI - Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility JO - Int Microbiol VL - 7 ID - Diaz2004 ER - TY - JOUR AU - Chakraborty, R. AU - Coates, J. D. PY - 2004 DA - 2004// TI - Anaerobic degradation of monoaromatic hydrocarbons JO - Appl Microbiol Biotechnol VL - 64 UR - https://doi.org/10.1007/s00253-003-1526-x DO - 10.1007/s00253-003-1526-x ID - Chakraborty2004 ER - TY - JOUR AU - Harwood, C. S. AU - Gibson, J. PY - 1997 DA - 1997// TI - Shedding light on anaerobic benzene ring degradation: a process unique to prokaryotes? JO - J Bacteriol VL - 179 ID - Harwood1997 ER - TY - JOUR AU - Heider, J. AU - Fuchs, G. PY - 1997 DA - 1997// TI - Anaerobic metabolism of aromatic compounds JO - Eur J Biochem VL - 243 UR - https://doi.org/10.1111/j.1432-1033.1997.00577.x DO - 10.1111/j.1432-1033.1997.00577.x ID - Heider1997 ER - TY - JOUR AU - Boll, M. PY - 2005 DA - 2005// TI - Dearomatizing benzene ring reductases JO - J Mol Microbiol Biotechnol VL - 10 UR - https://doi.org/10.1159/000091560 DO - 10.1159/000091560 ID - Boll2005 ER - TY - JOUR AU - Gibson, J. AU - Harwood, C. S. PY - 2002 DA - 2002// TI - Metabolic diversity in aromatic compound utilization by anaeroic microbes JO - Annu Rev Microbiol VL - 56 UR - https://doi.org/10.1146/annurev.micro.56.012302.160749 DO - 10.1146/annurev.micro.56.012302.160749 ID - Gibson2002 ER - TY - JOUR AU - Harwood, C. S. AU - Burchhardt, G. AU - Herrmann, H. AU - Fuchs, G. PY - 1999 DA - 1999// TI - Anaerobic metabolism of aromatic compounds via the benzoyl-CoA pathway JO - FEMS Microbiol Rev VL - 22 UR - https://doi.org/10.1111/j.1574-6976.1998.tb00380.x DO - 10.1111/j.1574-6976.1998.tb00380.x ID - Harwood1999 ER - TY - JOUR AU - Dorner, E. AU - Boll, M. PY - 2002 DA - 2002// TI - Properties of 2-oxoglutarate:ferredoxin oxidoreductase from Thauera aromatica and its role in enzymatic reduction of the aromatic ring JO - J Bacteriol VL - 184 UR - https://doi.org/10.1128/JB.184.14.3975-3983.2002 DO - 10.1128/JB.184.14.3975-3983.2002 ID - Dorner2002 ER - TY - JOUR AU - Boll, M. AU - Fuchs, G. PY - 1995 DA - 1995// TI - Benzoyl-coenzyme A reductase (dearomatizing), a key enzyme of anaerobic aromatic metabolism. ATP dependence of the reaction, purification and some properties of the enzyme from Thauera aromatica strain K172 JO - Eur J Biochem VL - 234 UR - https://doi.org/10.1111/j.1432-1033.1995.921_a.x DO - 10.1111/j.1432-1033.1995.921_a.x ID - Boll1995 ER - TY - JOUR AU - Boll, M. AU - Fuchs, G. PY - 1998 DA - 1998// TI - Identification and characterization of the natural electron donor ferredoxin and of FAD as a possible prosthetic group of benzoyl-CoA reductase (dearomatizing), a key enzyme of anaerobic aromatic metabolism JO - Eur J Biochem VL - 251 UR - https://doi.org/10.1046/j.1432-1327.1998.2510946.x DO - 10.1046/j.1432-1327.1998.2510946.x ID - Boll1998 ER - TY - JOUR AU - Albrechtsen, H. J. AU - Christensen, T. H. PY - 1994 DA - 1994// TI - Evidence for microbial iron reduction in a landfill leachate-polluted aquifer (Vejen, Denmark) JO - Appl Environ Microbiol VL - 60 ID - Albrechtsen1994 ER - TY - JOUR AU - Lovley, D. R. AU - Baedecker, M. J. AU - Lonergan, D. J. AU - Philips, E. J. AU - Siegel, D. I. PY - 1989 DA - 1989// TI - Oxidation of aromatic contaminants coupled to microbial iron reduction JO - Nature VL - 339 UR - https://doi.org/10.1038/339297a0 DO - 10.1038/339297a0 ID - Lovley1989 ER - TY - JOUR AU - Ludvigsen, L. AU - Albrechtsen, H. AU - Ringelberg, D. B. AU - Ekelund, F. AU - Christensen, T. H. PY - 1999 DA - 1999// TI - Distribution and composition of microbial populations in a landfill leachate contaminated aquifer (Grindsted, Denmark) JO - Microb Ecol VL - 37 UR - https://doi.org/10.1007/s002489900143 DO - 10.1007/s002489900143 ID - Ludvigsen1999 ER - TY - JOUR AU - Roling, W. F. AU - van Breukelen, B. M. AU - Braster, M. AU - Lin, B. AU - van Verseveld, H. W. PY - 2001 DA - 2001// TI - Relationships between microbial community structure and hydrochemistry in a landfill leachate-polluted aquifer JO - Appl Environ Microbiol VL - 67 UR - https://doi.org/10.1128/AEM.67.10.4619-4629.2001 DO - 10.1128/AEM.67.10.4619-4629.2001 ID - Roling2001 ER - TY - JOUR AU - Elshahed, M. S. AU - Bhupathiraju, V. K. AU - Wofford, N. Q. AU - Nanny, M. A. AU - McInerney, M. J. PY - 2001 DA - 2001// TI - Metabolism of benzoate, cyclohex-1-ene carboxylate, and cyclohexane carboxylate by "Syntrophus aciditrophicus" strain SB in syntrophic association with H(2)-using microorganisms JO - Appl Environ Microbiol VL - 67 UR - https://doi.org/10.1128/AEM.67.4.1728-1738.2001 DO - 10.1128/AEM.67.4.1728-1738.2001 ID - Elshahed2001 ER - TY - JOUR AU - Peters, F. AU - Rother, M. AU - Boll, M. PY - 2004 DA - 2004// TI - Selenocysteine-containing proteins in anaerobic benzoate metabolism of Desulfococcus multivorans JO - J Bacteriol VL - 186 UR - https://doi.org/10.1128/JB.186.7.2156-2163.2004 DO - 10.1128/JB.186.7.2156-2163.2004 ID - Peters2004 ER - TY - JOUR AU - Schocke, L. AU - Schink, B. PY - 1999 DA - 1999// TI - Energetics and biochemistry of fermetative benzoate degradation by Syntrophus gentianae JO - Arch Microbiol VL - 171 UR - https://doi.org/10.1007/s002030050718 DO - 10.1007/s002030050718 ID - Schocke1999 ER - TY - JOUR AU - Snoeyenbos-West, O. L. AU - Nevin, K. P. AU - Anderson, R. T. AU - Lovley, D. R. PY - 2000 DA - 2000// TI - Enrichment of Geobacter species in response to stimulation of Fe(III) reduction in sandy aquifer sediments JO - Microb Ecol VL - 39 UR - https://doi.org/10.1007/s002480000018 DO - 10.1007/s002480000018 ID - Snoeyenbos-West2000 ER - TY - JOUR AU - Rooney-Varga, J. N. AU - Anderson, R. T. AU - Fraga, J. L. AU - Ringelberg, D. AU - Lovley, D. R. PY - 1999 DA - 1999// TI - Microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer JO - Appl Environ Microbiol VL - 65 ID - Rooney-Varga1999 ER - TY - JOUR AU - Lovley, D. R. AU - Lonergan, D. J. PY - 1990 DA - 1990// TI - Anaerobic oxidation of toluene, phenol, and p-cresol by the dissimilatory iron-reducing organism, GS-15 JO - Appl Environ Microbiol VL - 56 ID - Lovley1990 ER - TY - JOUR AU - Lovley, D. R. AU - Giovannoni, S. J. AU - White, D. C. AU - Champine, J. E. AU - Phillips, E. J. AU - Gorby, Y. A. AU - Goodwin, S. PY - 1993 DA - 1993// TI - Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals JO - Arch Microbiol VL - 159 UR - https://doi.org/10.1007/BF00290916 DO - 10.1007/BF00290916 ID - Lovley1993 ER - TY - JOUR AU - Hosoda, A. AU - Kasai, Y. AU - Hamamura, N. AU - Takahata, Y. AU - Watanabe, K. PY - 2005 DA - 2005// TI - Development of a PCR method for the detection and quantification of benzoyl-CoA reductase genes and its application to monitored natural attenuation JO - Biodegradation VL - 16 UR - https://doi.org/10.1007/s10532-005-0826-5 DO - 10.1007/s10532-005-0826-5 ID - Hosoda2005 ER - TY - JOUR AU - Wischgoll, S. AU - Heintz, D. AU - Peters, F. AU - Erxleben, A. AU - Sarnighausen, E. AU - Reski, R. AU - Van Dorsselaer, A. AU - Boll, M. PY - 2005 DA - 2005// TI - Gene clusters involved in anaerobic benzoate degradation of Geobacter metallireducens JO - Molecular Microbiology VL - 58 UR - https://doi.org/10.1111/j.1365-2958.2005.04909.x DO - 10.1111/j.1365-2958.2005.04909.x ID - Wischgoll2005 ER - TY - CHAP AU - Copeland, A. AU - Lucas, S. AU - Lapidus, A. AU - Barry, K. AU - Detter, J. C. AU - Glavina, T. AU - Hammon, N. AU - Israni, S. AU - Pitluck, S. AU - Di Bartolo, G. AU - Chain, P. AU - Schmutz, J. AU - Larimer, F. AU - Land, M. AU - Kyrpides, N. AU - Ivanova, N. AU - Richardson, P. PY - 2005 DA - 2005// TI - Complete sequence of Geobacter metallireducens GS-15 BT - unpublished ID - Copeland2005 ER - TY - JOUR AU - Schuhle, K. AU - Fuchs, G. PY - 2004 DA - 2004// TI - Phenylphosphate carboxylase: a new C-C lyase involved in anaerobic phenol metabolism in Thauera aromatica JO - J Bacteriol VL - 186 UR - https://doi.org/10.1128/JB.186.14.4556-4567.2004 DO - 10.1128/JB.186.14.4556-4567.2004 ID - Schuhle2004 ER - TY - JOUR AU - Schmeling, S. AU - Narmandakh, A. AU - Schmitt, O. AU - Gad'on, N. AU - Schuhle, K. AU - Fuchs, G. PY - 2004 DA - 2004// TI - Phenylphosphate synthase: a new phosphotransferase catalyzing the first step in anaerobic phenol metabolism in Thauera aromatica JO - J Bacteriol VL - 186 UR - https://doi.org/10.1128/JB.186.23.8044-8057.2004 DO - 10.1128/JB.186.23.8044-8057.2004 ID - Schmeling2004 ER - TY - JOUR AU - Breinig, S. AU - Schiltz, E. AU - Fuchs, G. PY - 2000 DA - 2000// TI - Genes involved in anaerobic metabolism of phenol in the bacterium Thauera aromatica JO - J Bacteriol VL - 182 UR - https://doi.org/10.1128/JB.182.20.5849-5863.2000 DO - 10.1128/JB.182.20.5849-5863.2000 ID - Breinig2000 ER - TY - JOUR AU - Cronin, C. N. AU - Kim, J. AU - Fuller, J. H. AU - Zhang, X. AU - McIntire, W. S. PY - 1999 DA - 1999// TI - Organization and sequences of p-hydroxybenzaldehyde dehydrogenase and other plasmid-encoded genes for early enzymes of the p-cresol degradative pathway in Pseudomonas putida NCIMB 9866 and 9869 JO - DNA Seq VL - 10 ID - Cronin1999 ER - TY - JOUR AU - Rabus, R. AU - Kube, M. AU - Heider, J. AU - Beck, A. AU - Heitmann, K. AU - Widdel, F. AU - Reinhardt, R. PY - 2005 DA - 2005// TI - The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1 JO - Arch Microbiol VL - 183 UR - https://doi.org/10.1007/s00203-004-0742-9 DO - 10.1007/s00203-004-0742-9 ID - Rabus2005 ER - TY - JOUR AU - Breese, K. AU - Fuchs, G. PY - 1998 DA - 1998// TI - 4-Hydroxybenzoyl-CoA reductase (dehydroxylating) from the denitrifying bacterium Thauera aromatica--prosthetic groups, electron donor, and genes of a member of the molybdenum-flavin-iron-sulfur proteins JO - Eur J Biochem VL - 251 UR - https://doi.org/10.1046/j.1432-1327.1998.2510916.x DO - 10.1046/j.1432-1327.1998.2510916.x ID - Breese1998 ER - TY - JOUR AU - Greated, A. AU - Lambertsen, L. AU - Williams, P. A. AU - Thomas, C. M. PY - 2002 DA - 2002// TI - Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida JO - Environ Microbiol VL - 4 UR - https://doi.org/10.1046/j.1462-2920.2002.00305.x DO - 10.1046/j.1462-2920.2002.00305.x ID - Greated2002 ER - TY - JOUR AU - Kim, J. AU - Hetzel, M. AU - Boiangiu, C. D. AU - Buckel, W. PY - 2004 DA - 2004// TI - Dehydration of (R)-2-hydroxyacyl-CoA to enoyl-CoA in the fermentation of alpha-amino acids by anaerobic bacteria JO - FEMS Microbiol Rev VL - 28 UR - https://doi.org/10.1016/j.femsre.2004.03.001 DO - 10.1016/j.femsre.2004.03.001 ID - Kim2004 ER - TY - JOUR AU - Hans, M. AU - Sievers, J. AU - Muller, U. AU - Bill, E. AU - Vorholt, J. A. AU - Linder, D. AU - Buckel, W. PY - 1999 DA - 1999// TI - 2-hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum JO - Eur J Biochem VL - 265 UR - https://doi.org/10.1046/j.1432-1327.1999.00748.x DO - 10.1046/j.1432-1327.1999.00748.x ID - Hans1999 ER - TY - JOUR AU - Locher, K. P. AU - Hans, M. AU - Yeh, A. P. AU - Schmid, B. AU - Buckel, W. AU - Rees, D. C. PY - 2001 DA - 2001// TI - Crystal structure of the Acidaminococcus fermentans 2-hydroxyglutaryl-CoA dehydratase component A JO - J Mol Biol VL - 307 UR - https://doi.org/10.1006/jmbi.2000.4496 DO - 10.1006/jmbi.2000.4496 ID - Locher2001 ER - TY - JOUR AU - Breese, K. AU - Boll, M. AU - Alt-Morbe, J. AU - Schagger, H. AU - Fuchs, G. PY - 1998 DA - 1998// TI - Genes coding for the benzoyl-CoA pathway of anaerobic aromatic metabolism in the bacterium Thauera aromatica JO - Eur J Biochem VL - 256 UR - https://doi.org/10.1046/j.1432-1327.1998.2560148.x DO - 10.1046/j.1432-1327.1998.2560148.x ID - Breese1998 ER - TY - JOUR AU - Hu, Y. AU - Faham, S. AU - Roy, R. AU - Adams, M. W. AU - Rees, D. C. PY - 1999 DA - 1999// TI - Formaldehyde ferredoxin oxidoreductase from Pyrococcus furiosus: the 1.85 A resolution crystal structure and its mechanistic implications JO - J Mol Biol VL - 286 UR - https://doi.org/10.1006/jmbi.1998.2488 DO - 10.1006/jmbi.1998.2488 ID - Hu1999 ER - TY - JOUR AU - Chan, M. K. AU - Mukund, S. AU - Kletzin, A. AU - Adams, M. W. AU - Rees, D. C. PY - 1995 DA - 1995// TI - Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase JO - Science VL - 267 UR - https://doi.org/10.1126/science.7878465 DO - 10.1126/science.7878465 ID - Chan1995 ER - TY - JOUR AU - Elshahed, M. S. AU - McInerney, M. J. PY - 2001 DA - 2001// TI - Benzoate fermentation by the anaerobic bacterium Syntrophus aciditrophicus in the absence of hydrogen-using microorganisms JO - Appl Environ Microbiol VL - 67 UR - https://doi.org/10.1128/AEM.67.12.5520-5525.2001 DO - 10.1128/AEM.67.12.5520-5525.2001 ID - Elshahed2001 ER - TY - JOUR AU - Lopez Barragan, M. J. AU - Carmona, M. AU - Zamarro, M. T. AU - Thiele, B. AU - Boll, M. AU - Fuchs, G. AU - Garcia, J. L. AU - Diaz, E. PY - 2004 DA - 2004// TI - The bzd gene cluster, coding for anaerobic benzoate catabolism, in Azoarcus sp. strain CIB JO - J Bacteriol VL - 186 UR - https://doi.org/10.1128/JB.186.17.5762-5774.2004 DO - 10.1128/JB.186.17.5762-5774.2004 ID - Lopez Barragan2004 ER - TY - JOUR AU - Lopez Barragan, M. J. AU - Diaz, E. AU - Garcia, J. L. AU - Carmona, M. PY - 2004 DA - 2004// TI - Genetic clues on the evolution of anaerobic catabolism of aromatic compounds JO - Microbiology VL - 150 UR - https://doi.org/10.1099/mic.0.27186-0 DO - 10.1099/mic.0.27186-0 ID - Lopez Barragan2004 ER - TY - JOUR AU - Rabus, R. PY - 2005 DA - 2005// TI - Functional genomics of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1 JO - Appl Microbiol Biotechnol VL - 68 UR - https://doi.org/10.1007/s00253-005-0030-x DO - 10.1007/s00253-005-0030-x ID - Rabus2005 ER - TY - JOUR AU - Tan, H. M. PY - 1999 DA - 1999// TI - Bacterial catabolic transposons JO - Appl Microbiol Biotechnol VL - 51 UR - https://doi.org/10.1007/s002530051356 DO - 10.1007/s002530051356 ID - Tan1999 ER - TY - JOUR AU - Ochman, H. AU - Lawrence, J. G. AU - Groisman, E. A. PY - 2000 DA - 2000// TI - Lateral gene transfer and the nature of bacterial innovation JO - Nature VL - 405 UR - https://doi.org/10.1038/35012500 DO - 10.1038/35012500 ID - Ochman2000 ER - TY - JOUR AU - Karlin, S. AU - Campbell, A. M. AU - Mrazek, J. PY - 1998 DA - 1998// TI - Comparative DNA analysis across diverse genomes JO - Annu Rev Genet VL - 32 UR - https://doi.org/10.1146/annurev.genet.32.1.185 DO - 10.1146/annurev.genet.32.1.185 ID - Karlin1998 ER - TY - JOUR AU - Siguier, P. AU - Perochon, J. AU - Lestrade, L. AU - Mahillon, J. AU - Chandler, M. PY - 2006 DA - 2006// TI - ISfinder: the reference centre for bacterial insertion sequences JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj014 DO - 10.1093/nar/gkj014 ID - Siguier2006 ER - TY - JOUR AU - Mahillon, J. AU - Chandler, M. PY - 1998 DA - 1998// TI - Insertion sequences JO - Microbiol Mol Biol Rev VL - 62 ID - Mahillon1998 ER - TY - JOUR AU - Dobrindt, U. AU - Hochhut, B. AU - Hentschel, U. AU - Hacker, J. PY - 2004 DA - 2004// TI - Genomic islands in pathogenic and environmental microorganisms JO - Nat Rev Microbiol VL - 2 UR - https://doi.org/10.1038/nrmicro884 DO - 10.1038/nrmicro884 ID - Dobrindt2004 ER - TY - JOUR AU - Hacker, J. AU - Blum-Oehler, G. AU - Muhldorfer, I. AU - Tschape, H. PY - 1997 DA - 1997// TI - Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution JO - Mol Microbiol VL - 23 UR - https://doi.org/10.1046/j.1365-2958.1997.3101672.x DO - 10.1046/j.1365-2958.1997.3101672.x ID - Hacker1997 ER - TY - JOUR AU - Lawrence, J. G. AU - Ochman, H. PY - 1997 DA - 1997// TI - Amelioration of bacterial genomes: rates of change and exchange JO - J Mol Evol VL - 44 UR - https://doi.org/10.1007/PL00006158 DO - 10.1007/PL00006158 ID - Lawrence1997 ER - TY - JOUR AU - Champine, J. E. AU - Goodwin, S. PY - 1991 DA - 1991// TI - Acetate catabolism in the dissimilatory iron-reducing isolate GS-15 JO - J Bacteriol VL - 173 ID - Champine1991 ER - TY - JOUR AU - Galushko, A. S. AU - Schink, B. PY - 2000 DA - 2000// TI - Oxidation of acetate through reactions of the citric acid cycle by Geobacter sulfurreducens in pure culture and in syntrophic coculture JO - Arch Microbiol VL - 174 UR - https://doi.org/10.1007/s002030000208 DO - 10.1007/s002030000208 ID - Galushko2000 ER - TY - JOUR AU - Cortay, J. C. AU - Negre, D. AU - Galinier, A. AU - Duclos, B. AU - Perriere, G. AU - Cozzone, A. J. PY - 1991 DA - 1991// TI - Regulation of the acetate operon in Escherichia coli: purification and functional characterization of the IclR repressor JO - Embo J VL - 10 ID - Cortay1991 ER - TY - JOUR AU - Petrie, L. AU - North, N. N. AU - Dollhopf, S. L. AU - Balkwill, D. L. AU - Kostka, J. E. PY - 2003 DA - 2003// TI - Enumeration and characterization of iron(III)-reducing microbial communities from acidic subsurface sediments contaminated with uranium(VI) JO - Appl Environ Microbiol VL - 69 UR - https://doi.org/10.1128/AEM.69.12.7467-7479.2003 DO - 10.1128/AEM.69.12.7467-7479.2003 ID - Petrie2003 ER - TY - JOUR AU - North, N. N. AU - Dollhopf, S. L. AU - Petrie, L. AU - Istok, J. D. AU - Balkwill, D. L. AU - Kostka, J. E. PY - 2004 DA - 2004// TI - Change in bacterial community structure during in situ biostimulation of subsurface sediment cocontaminated with uranium and nitrate JO - Appl Environ Microbiol VL - 70 UR - https://doi.org/10.1128/AEM.70.8.4911-4920.2004 DO - 10.1128/AEM.70.8.4911-4920.2004 ID - North2004 ER - TY - JOUR AU - van der Meer, J. R. AU - Sentchilo, V. PY - 2003 DA - 2003// TI - Genomic islands and the evolution of catabolic pathways in bacteria JO - Curr Opin Biotechnol VL - 14 UR - https://doi.org/10.1016/S0958-1669(03)00058-2 DO - 10.1016/S0958-1669(03)00058-2 ID - van der Meer2003 ER - TY - JOUR AU - Muller, T. A. AU - Werlen, C. AU - Spain, J. AU - Van Der Meer, J. R. PY - 2003 DA - 2003// TI - Evolution of a chlorobenzene degradative pathway among bacteria in a contaminated groundwater mediated by a genomic island in Ralstonia JO - Environ Microbiol VL - 5 UR - https://doi.org/10.1046/j.1462-2920.2003.00400.x DO - 10.1046/j.1462-2920.2003.00400.x ID - Muller2003 ER - TY - JOUR AU - Lovley, D. R. PY - 2003 DA - 2003// TI - Cleaning up with genomics: applying molecular biology to bioremediation JO - Nat Rev Microbiol VL - 1 UR - https://doi.org/10.1038/nrmicro731 DO - 10.1038/nrmicro731 ID - Lovley2003 ER - TY - JOUR AU - Holmes, D. E. AU - Nevin, K. P. AU - O'Neil, R. A. AU - Ward, J. E. AU - Adams, L. A. AU - Woodard, T. L. AU - Vrionis, H. A. AU - Lovley, D. R. PY - 2005 DA - 2005// TI - Potential for quantifying expression of the Geobacteraceae citrate synthase gene to assess the activity of Geobacteraceae in the subsurface and on current-harvesting electrodes JO - Appl Environ Microbiol VL - 71 UR - https://doi.org/10.1128/AEM.71.11.6870-6877.2005 DO - 10.1128/AEM.71.11.6870-6877.2005 ID - Holmes2005 ER - TY - JOUR AU - Holmes, D. E. AU - Nevin, K. P. AU - Lovley, D. R. PY - 2004 DA - 2004// TI - In situ expression of nifD in Geobacteraceae in subsurface sediments JO - Appl Environ Microbiol VL - 70 UR - https://doi.org/10.1128/AEM.70.12.7251-7259.2004 DO - 10.1128/AEM.70.12.7251-7259.2004 ID - Holmes2004 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schaffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - JOUR AU - Benson, D. A. AU - Karsch-Mizrachi, I. AU - Lipman, D. J. AU - Ostell, J. AU - Wheeler, D. L. PY - 2005 DA - 2005// TI - GenBank JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki063 DO - 10.1093/nar/gki063 ID - Benson2005 ER - TY - JOUR AU - Bairoch, A. AU - Apweiler, R. AU - Wu, C. H. AU - Barker, W. C. AU - Boeckmann, B. AU - Ferro, S. AU - Gasteiger, E. AU - Huang, H. AU - Lopez, R. AU - Magrane, M. AU - Martin, M. J. AU - Natale, D. A. AU - O'Donovan, C. AU - Redaschi, N. AU - Yeh, L. S. PY - 2005 DA - 2005// TI - The Universal Protein Resource (UniProt) JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki070 DO - 10.1093/nar/gki070 ID - Bairoch2005 ER - TY - JOUR AU - Mulder, N. J. AU - Apweiler, R. AU - Attwood, T. K. AU - Bairoch, A. AU - Bateman, A. AU - Binns, D. AU - Bradley, P. AU - Bork, P. AU - Bucher, P. AU - Cerutti, L. AU - Copley, R. AU - Courcelle, E. AU - Das, U. AU - Durbin, R. AU - Fleischmann, W. AU - Gough, J. AU - Haft, D. AU - Harte, N. AU - Hulo, N. AU - Kahn, D. AU - Kanapin, A. AU - Krestyaninova, M. AU - Lonsdale, D. AU - Lopez, R. AU - Letunic, I. AU - Madera, M. AU - Maslen, J. AU - McDowall, J. AU - Mitchell, A. AU - Nikolskaya, A. N. AU - Orchard, S. AU - Pagni, M. AU - Ponting, C. P. AU - Quevillon, E. AU - Selengut, J. AU - Sigrist, C. J. AU - Silventoinen, V. AU - Studholme, D. J. AU - Vaughan, R. AU - Wu, C. H. PY - 2005 DA - 2005// TI - InterPro, progress and status in 2005 JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki106 DO - 10.1093/nar/gki106 ID - Mulder2005 ER - TY - JOUR AU - Gardy, J. L. AU - Laird, M. R. AU - Chen, F. AU - Rey, S. AU - Walsh, C. J. AU - Ester, M. AU - Brinkman, F. S. PY - 2005 DA - 2005// TI - PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti057 DO - 10.1093/bioinformatics/bti057 ID - Gardy2005 ER - TY - JOUR AU - Thompson, J. D. AU - Gibson, T. J. AU - Plewniak, F. AU - Jeanmougin, F. AU - Higgins, D. G. PY - 1997 DA - 1997// TI - The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.24.4876 DO - 10.1093/nar/25.24.4876 ID - Thompson1997 ER - TY - JOUR AU - Saitou, N. AU - Nei, M. PY - 1987 DA - 1987// TI - The neighbor-joining method: a new method for reconstructing phylogenetic trees JO - Mol Biol Evol VL - 4 ID - Saitou1987 ER - TY - JOUR AU - Kumar, S. AU - Tamura, K. AU - Nei, M. PY - 2004 DA - 2004// TI - MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment JO - Brief Bioinform VL - 5 UR - https://doi.org/10.1093/bib/5.2.150 DO - 10.1093/bib/5.2.150 ID - Kumar2004 ER - TY - JOUR AU - Tatusov, R. L. AU - Koonin, E. V. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - A genomic perspective on protein families JO - Science VL - 278 UR - https://doi.org/10.1126/science.278.5338.631 DO - 10.1126/science.278.5338.631 ID - Tatusov1997 ER - TY - JOUR AU - Rubin, G. M. AU - Yandell, M. D. AU - Wortman, J. R. AU - Gabor Miklos, G. L. AU - Nelson, C. R. AU - Hariharan, I. K. AU - Fortini, M. E. AU - Li, P. W. AU - Apweiler, R. AU - Fleischmann, W. AU - Cherry, J. M. AU - Henikoff, S. AU - Skupski, M. P. AU - Misra, S. AU - Ashburner, M. AU - Birney, E. AU - Boguski, M. S. AU - Brody, T. AU - Brokstein, P. AU - Celniker, S. E. AU - Chervitz, S. A. AU - Coates, D. AU - Cravchik, A. AU - Gabrielian, A. AU - Galle, R. F. AU - Gelbart, W. M. AU - George, R. A. AU - Goldstein, L. S. AU - Gong, F. AU - Guan, P. AU - Harris, N. L. AU - Hay, B. A. AU - Hoskins, R. A. AU - Li, J. AU - Li, Z. AU - Hynes, R. O. AU - Jones, S. J. AU - Kuehl, P. M. AU - Lemaitre, B. AU - Littleton, J. T. AU - Morrison, D. K. AU - Mungall, C. AU - O'Farrell, P. H. AU - Pickeral, O. K. AU - Shue, C. AU - Vosshall, L. B. AU - Zhang, J. AU - Zhao, Q. AU - Zheng, X. H. AU - Lewis, S. PY - 2000 DA - 2000// TI - Comparative genomics of the eukaryotes JO - Science VL - 287 UR - https://doi.org/10.1126/science.287.5461.2204 DO - 10.1126/science.287.5461.2204 ID - Rubin2000 ER - TY - JOUR AU - Rice, P. AU - Longden, I. AU - Bleasby, A. PY - 2000 DA - 2000// TI - EMBOSS: the European Molecular Biology Open Software Suite JO - Trends Genet VL - 16 UR - https://doi.org/10.1016/S0168-9525(00)02024-2 DO - 10.1016/S0168-9525(00)02024-2 ID - Rice2000 ER - TY - JOUR AU - van Passel, M. W. AU - Luyf, A. C. AU - van Kampen, A. H. AU - Bart, A. AU - van der Ende, A. PY - 2005 DA - 2005// TI - Deltarho-web, an online tool to assess composition similarity of individual nucleic acid sequences JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti460 DO - 10.1093/bioinformatics/bti460 ID - van Passel2005 ER - TY - JOUR AU - Esteve-Nunez, A. AU - Rothermich, M. AU - Sharma, M. AU - Lovley, D. PY - 2005 DA - 2005// TI - Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture JO - Environ Microbiol VL - 7 UR - https://doi.org/10.1111/j.1462-2920.2005.00731.x DO - 10.1111/j.1462-2920.2005.00731.x ID - Esteve-Nunez2005 ER - TY - JOUR AU - He, Q. AU - Huang, K. H. AU - He, Z. AU - Alm, E. J. AU - Fields, M. W. AU - Hazen, T. C. AU - Arkin, A. P. AU - Wall, J. D. AU - Zhou, J. PY - 2006 DA - 2006// TI - Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis JO - Appl Environ Microbiol VL - 72 UR - https://doi.org/10.1128/AEM.02609-05 DO - 10.1128/AEM.02609-05 ID - He2006 ER - TY - JOUR AU - Thompson, D. K. AU - Beliaev, A. S. AU - Giometti, C. S. AU - Tollaksen, S. L. AU - Khare, T. AU - Lies, D. P. AU - Nealson, K. H. AU - Lim, H. AU - Yates, J. AU - Brandt, C. C. AU - Tiedje, J. M. AU - Zhou, J. PY - 2002 DA - 2002// TI - Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress JO - Appl Environ Microbiol VL - 68 UR - https://doi.org/10.1128/AEM.68.2.881-892.2002 DO - 10.1128/AEM.68.2.881-892.2002 ID - Thompson2002 ER - TY - JOUR AU - He, Z. AU - Wu, L. AU - Li, X. AU - Fields, M. W. AU - Zhou, J. PY - 2005 DA - 2005// TI - Empirical establishment of oligonucleotide probe design criteria JO - Appl Environ Microbiol VL - 71 UR - https://doi.org/10.1128/AEM.71.7.3753-3760.2005 DO - 10.1128/AEM.71.7.3753-3760.2005 ID - He2005 ER - TY - JOUR AU - Gao, H. AU - Wang, Y. AU - Liu, X. AU - Yan, T. AU - Wu, L. AU - Alm, E. AU - Arkin, A. AU - Thompson, D. K. AU - Zhou, J. PY - 2004 DA - 2004// TI - Global transcriptome analysis of the heat shock response of Shewanella oneidensis JO - J Bacteriol VL - 186 UR - https://doi.org/10.1128/JB.186.22.7796-7803.2004 DO - 10.1128/JB.186.22.7796-7803.2004 ID - Gao2004 ER -