TY - JOUR AU - Migula, W. PY - 1894 DA - 1894// TI - Über ein neues System der Bakterien JO - Arb Bakteriol Inst Karlsruhe. VL - 1 ID - Migula1894 ER - TY - STD TI - Trevisan V. I generi e le specie delle batteriacee. Zanaboni and Gabuzzi, Milan. 1889;1–35. ID - ref2 ER - TY - JOUR AU - Nelson, K. E. AU - Weinel, C. AU - Paulsen, I. T. AU - Dodson, R. J. AU - Hilbert, H. PY - 2002 DA - 2002// TI - Martins dos Santos VA et al. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440 JO - Environmental Microbiol VL - 4 UR - https://doi.org/10.1046/j.1462-2920.2002.00366.x DO - 10.1046/j.1462-2920.2002.00366.x ID - Nelson2002 ER - TY - STD TI - Nikel PI, Martínez-García E, Lorenzo V. Biotechnological domestication of Pseudomonas using synthetic biology. Nat Rev Microbiol. 2014;12(5):368–79. doi:10.1038/nrmicro3253. ID - ref4 ER - TY - STD TI - Ohji S, Yamazoe A, Hosoyama A, Tsuchikane K, Ezaki T, Fujita N. The complete genome sequence of Pseudomonas putida NBRC 14164T confirms high intraspecies variation. Genome Announc. 2014;2(1). doi:10.1128/genomeA.00029-14. ID - ref5 ER - TY - JOUR AU - Molina, L. AU - Ramos, C. AU - Duque, E. AU - Ronchel, M. C. AU - García, J. M. AU - Wyke, L. PY - 2000 DA - 2000// TI - Survival of Pseudomonas putida KT2440 in soil and in the rhizosphere of plants under greenhouse and environmental conditions JO - Soil Biol Biochem VL - 32 UR - https://doi.org/10.1016/S0038-0717(99)00156-X DO - 10.1016/S0038-0717(99)00156-X ID - Molina2000 ER - TY - JOUR AU - Santos, V. A. AU - Heim, S. AU - Moore, E. R. AU - Stratz, M. AU - Timmis, K. N. PY - 2004 DA - 2004// TI - Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440 JO - Environ Microbiol VL - 6 UR - https://doi.org/10.1111/j.1462-2920.2004.00734.x DO - 10.1111/j.1462-2920.2004.00734.x ID - Santos2004 ER - TY - JOUR AU - Chen, C. AU - Bauske, E. M. AU - Musson, G. AU - Rodriguez-Kabana, R. AU - Kloepper, J. W. PY - 1995 DA - 1995// TI - Biological control of Fusarium wilt on cotton by use of endophytic bacteria JO - Biol Control. VL - 5 UR - https://doi.org/10.1006/bcon.1995.1009 DO - 10.1006/bcon.1995.1009 ID - Chen1995 ER - TY - JOUR AU - Jiménez, J. I. AU - Miñambres, B. AU - García, J. L. AU - Díaz, E. PY - 2002 DA - 2002// TI - Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440 JO - Environ Microbiol VL - 4 UR - https://doi.org/10.1046/j.1462-2920.2002.00370.x DO - 10.1046/j.1462-2920.2002.00370.x ID - Jiménez2002 ER - TY - JOUR AU - Timmis, K. N. PY - 2002 DA - 2002// TI - Pseudomonas putida: a cosmopolitan opportunist par excellence JO - Environ Microbiol VL - 4 UR - https://doi.org/10.1046/j.1462-2920.2002.00365.x DO - 10.1046/j.1462-2920.2002.00365.x ID - Timmis2002 ER - TY - JOUR AU - Gomes, N. C. AU - Kosheleva, I. A. AU - Abraham, W. R. AU - Smalla, K. PY - 2005 DA - 2005// TI - Effects of the inoculant strain Pseudomonas putida KT2442 (pNF142) and of naphthalene contamination on the soil bacterial community JO - FEMS Microbiol Ecol VL - 54 UR - https://doi.org/10.1016/j.femsec.2005.02.005 DO - 10.1016/j.femsec.2005.02.005 ID - Gomes2005 ER - TY - JOUR AU - Ward, P. G. AU - Goff, M. AU - Donner, M. AU - Kaminsky, W. AU - O'Connor, K. E. PY - 2006 DA - 2006// TI - A two step chemo-biotechnological conversion of polystyrene to a biodegradable thermoplastic JO - Environ Sci Technol VL - 40 UR - https://doi.org/10.1021/es0517668 DO - 10.1021/es0517668 ID - Ward2006 ER - TY - JOUR AU - Denger, K. AU - Huhn, T. AU - Hollemeyer, K. AU - Schleheck, D. AU - Cook, A. M. PY - 2012 DA - 2012// TI - Sulfoquinovose degraded by pure cultures of bacteria with release of C3-organosulfonates: complete degradation in two-member communities JO - FEMS Microbiol Lett VL - 328 UR - https://doi.org/10.1111/j.1574-6968.2011.02477.x DO - 10.1111/j.1574-6968.2011.02477.x ID - Denger2012 ER - TY - JOUR AU - Benning, C. PY - 1998 DA - 1998// TI - Biosynthesis and function of the sulfolipid sulfoquinovosyl diacylglycerol JO - Annu Rev Plant Biol. VL - 49 UR - https://doi.org/10.1146/annurev.arplant.49.1.53 DO - 10.1146/annurev.arplant.49.1.53 ID - Benning1998 ER - TY - JOUR AU - Harwood, J. L. AU - Nicholls, R. G. PY - 1979 DA - 1979// TI - The plant sulpholipid-- a major component of the sulphur cycle JO - Biochem Soc Trans VL - 7 ID - Harwood1979 ER - TY - JOUR AU - Denger, K. AU - Weiss, M. AU - Felux, A. K. AU - Schneider, A. AU - Mayer, C. AU - Spiteller, D. PY - 2014 DA - 2014// TI - Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle JO - Nature VL - 507 UR - https://doi.org/10.1038/nature12947 DO - 10.1038/nature12947 ID - Denger2014 ER - TY - JOUR AU - Field, D. AU - Garrity, G. AU - Gray, T. AU - Morrison, N. AU - Selengut, J. AU - Sterk, P. PY - 2008 DA - 2008// TI - The minimum information about a genome sequence (MIGS) specification JO - Nat Biotechnol VL - 26 UR - https://doi.org/10.1038/nbt1360 DO - 10.1038/nbt1360 ID - Field2008 ER - TY - JOUR AU - Langmead, B. AU - Salzberg, S. L. PY - 2012 DA - 2012// TI - Fast gapped-read alignment with Bowtie 2 JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.1923 DO - 10.1038/nmeth.1923 ID - Langmead2012 ER - TY - JOUR AU - Zerbino, D. R. AU - Birney, E. PY - 2008 DA - 2008// TI - Velvet: algorithms for de novo short read assembly using de Bruijn graphs JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.074492.107 DO - 10.1101/gr.074492.107 ID - Zerbino2008 ER - TY - JOUR AU - Mavromatis, K. AU - Ivanova, N. N. AU - Chen, I. M. AU - Szeto, E. AU - Markowitz, V. M. AU - Kyrpides, N. C. PY - 2009 DA - 2009// TI - The DOE-JGI standard operating procedure for the annotations of microbial genomes JO - Stand Genomic Sci VL - 1 UR - https://doi.org/10.4056/sigs.632 DO - 10.4056/sigs.632 ID - Mavromatis2009 ER - TY - JOUR AU - Hyatt, D. AU - Chen, G. L. AU - Locascio, P. F. AU - Land, M. L. AU - Larimer, F. W. AU - Hauser, L. J. PY - 2010 DA - 2010// TI - Prodigal: prokaryotic gene recognition and translation initiation site identification JO - BMC Bioinformatics. VL - 11 UR - https://doi.org/10.1186/1471-2105-11-119 DO - 10.1186/1471-2105-11-119 ID - Hyatt2010 ER - TY - STD TI - Magrane M, Consortium U. UniProt Knowledgebase: a hub of integrated protein data. The Journal of Biological Databases and Curation. 2011;43:bar009. doi:10.1093/database/bar009. ID - ref22 ER - TY - JOUR AU - Haft, D. H. AU - Selengut, J. D. AU - White, O. PY - 2003 DA - 2003// TI - The TIGRFAMs database of protein families JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg128 DO - 10.1093/nar/gkg128 ID - Haft2003 ER - TY - JOUR AU - Finn, R. D. AU - Bateman, A. AU - Clements, J. AU - Coggill, P. AU - Eberhardt, R. Y. AU - Eddy, S. R. PY - 2014 DA - 2014// TI - Pfam: the protein families database JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1223 DO - 10.1093/nar/gkt1223 ID - Finn2014 ER - TY - JOUR AU - Kanehisa, M. AU - Goto, S. AU - Sato, Y. AU - Furumichi, M. AU - Tanabe, M. PY - 2012 DA - 2012// TI - KEGG for integration and interpretation of large-scale molecular data sets JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr988 DO - 10.1093/nar/gkr988 ID - Kanehisa2012 ER - TY - JOUR AU - Tatusov, R. L. AU - Galperin, M. Y. AU - Natale, D. A. AU - Koonin, E. V. PY - 2000 DA - 2000// TI - The COG database: a tool for genome-scale analysis of protein functions and evolution JO - Nucleic Acids Resesarch VL - 28 UR - https://doi.org/10.1093/nar/28.1.33 DO - 10.1093/nar/28.1.33 ID - Tatusov2000 ER - TY - JOUR AU - Hunter, S. AU - Apweiler, R. AU - Attwood, T. K. AU - Bairoch, A. AU - Bateman, A. AU - Binns, D. PY - 2009 DA - 2009// TI - InterPro: the integrative protein signature database JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn785 DO - 10.1093/nar/gkn785 ID - Hunter2009 ER - TY - JOUR AU - Lowe, T. M. AU - Eddy, S. R. PY - 1997 DA - 1997// TI - tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.5.0955 DO - 10.1093/nar/25.5.0955 ID - Lowe1997 ER - TY - JOUR AU - Pruesse, E. AU - Quast, C. AU - Knittel, K. AU - Fuchs, B. M. AU - Ludwig, W. AU - Peplies, J. PY - 2007 DA - 2007// TI - SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm864 DO - 10.1093/nar/gkm864 ID - Pruesse2007 ER - TY - JOUR AU - Daddaoua, A. AU - Krell, T. AU - Ramos, J. L. PY - 2009 DA - 2009// TI - Regulation of glucose metabolism in Pseudomonas: the phosphorylative branch and entner-doudoroff enzymes are regulated by a repressor containing a sugar isomerase domain JO - J Biol Chem VL - 284 UR - https://doi.org/10.1074/jbc.M109.014555 DO - 10.1074/jbc.M109.014555 ID - Daddaoua2009 ER - TY - JOUR AU - Tamura, K. AU - Stecher, G. AU - Peterson, D. AU - Filipski, A. AU - Kumar, S. PY - 2013 DA - 2013// TI - MEGA6: Molecular Evolutionary Genetics Analysis version 6.0 JO - Mol Biol Evol VL - 30 UR - https://doi.org/10.1093/molbev/mst197 DO - 10.1093/molbev/mst197 ID - Tamura2013 ER - TY - JOUR AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Botstein, D. AU - Butler, H. AU - Cherry, J. M. PY - 2000 DA - 2000// TI - Gene ontology: tool for the unification of biology. The Gene Ontology Consortium JO - Nat Genet. VL - 25 UR - https://doi.org/10.1038/75556 DO - 10.1038/75556 ID - Ashburner2000 ER - TY - STD TI - Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA. 1990;87(12):4576–9. doi:10.1073/pnas.87.12.4576. ID - ref33 ER - TY - STD TI - Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B. New York: Springer; 2005. p. 1. ID - ref34 ER - TY - STD TI - Validation of publication of new names and new combinations previously effectively published outside the IJSEM. List no. 106. Int J Syst Evol Micobiol. 2005;55:2235-8. ID - ref35 ER - TY - JOUR AU - Skerman, V. B. D. AU - McGowan, V. AU - Sneath, P. H. A. PY - 1980 DA - 1980// TI - Approved Lists of Bacterial Names JO - Int J Syst Bacteriol. VL - 30 UR - https://doi.org/10.1099/00207713-30-1-225 DO - 10.1099/00207713-30-1-225 ID - Skerman1980 ER - TY - JOUR AU - Orla-Jensen, S. PY - 1921 DA - 1921// TI - The main lines of the natural nacterial system JO - J Bacteriol VL - 6 ID - Orla-Jensen1921 ER - TY - STD TI - Garrity GM, Bell JA, Lilburn T. Order IX. Pseudomonadales. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B. New York: Springer; 2005. p. 323. ID - ref38 ER - TY - JOUR AU - Winslow, C. E. AU - Broadhurst, J. AU - Buchanan, R. E. AU - Krumwiede, C. AU - Rogers, L. A. AU - Smith, G. H. PY - 1917 DA - 1917// TI - The families and genera of the bacteria: preliminary report of the committee of the society of american bacteriologists on characterization and classification of bacterial types JO - J Bacteriol VL - 2 ID - Winslow1917 ER - TY - STD TI - Judicial Commission. Opinion 5: conservation of the generic name Pseudomonas Migula 1894 and designation of Pseudomonas aeruginosa (Schroeter) Migula 1900 as type species. Int Bull Bacteriol Nomencl Taxon. 1952;2:121–2. ID - ref40 ER -