TY - JOUR AU - Mohn, W. W. AU - Westerberg, K. AU - Cullen, W. R. AU - Reimer, K. J. PY - 1997 DA - 1997// TI - Aerobic biodegradation of biphenyl and polychlorinated biphenyls by Arctic soil microorganisms JO - Appl Environ Microbiol VL - 63 ID - Mohn1997 ER - TY - BOOK PY - 2002 DA - 2002// TI - Tenth report on carcinogens PB - National Academy Press CY - Washington ID - ref2 ER - TY - CHAP AU - McElroy, A. E. AU - Farrington, J. W. AU - Teal, J. M. ED - Varanasi, U. PY - 1989 DA - 1989// TI - Bioavailability of polycyclic aromatic hydrocarbons in the aquatic environment BT - Metabolism of polycyclic aromatic hydrocarbons in the aquatic environment PB - CRC Press Inc CY - Boca Raton ID - McElroy1989 ER - TY - JOUR AU - Kweon, O. AU - Kim, S. J. AU - Holland, R. D. AU - Chen, H. AU - Kim, D. W. AU - Gao, Y. PY - 2001 DA - 2001// TI - Polycyclic aromatic hydrocarbon metabolic network in Mycobacterium vanbaalenii PYR-1 JO - J Bacteriol VL - 193 UR - https://doi.org/10.1128/JB.00215-11 DO - 10.1128/JB.00215-11 ID - Kweon2001 ER - TY - JOUR AU - Rodríguez-Blanco, A. AU - Vetion, G. AU - Escande, M. -. L. AU - Delille, D. AU - Ghiglione, J. -. F. PY - 2010 DA - 2010// TI - Gallaecimonas pentaromativorans gen. nov., sp. nov., a bacterium carrying 16S rRNA gene heterogeneity and able to degrade high-molecular-mass polycyclic aromatic hydrocarbons JO - Int J Syst Evol Microbiol VL - 60 UR - https://doi.org/10.1099/ijs.0.013532-0 DO - 10.1099/ijs.0.013532-0 ID - Rodríguez-Blanco2010 ER - TY - JOUR AU - Kim, S. -. J. AU - Kwon, K. K. AU - Hyun, J. -. H. AU - Svetashev, V. I. PY - 2004 DA - 2004// TI - Bioremediation of PAHs in marine sediment JO - J Ocean Sci Tech VL - 1 ID - Kim2004 ER - TY - JOUR AU - Sohn, J. H. AU - Kwon, K. K. AU - Kang, J. -. H. AU - Jung, H. -. B. AU - Kim, S. -. J. PY - 2004 DA - 2004// TI - Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment JO - Int J Syst Evol Microbiol VL - 54 UR - https://doi.org/10.1099/ijs.0.02945-0 DO - 10.1099/ijs.0.02945-0 ID - Sohn2004 ER - TY - JOUR AU - Luo, Y. R. AU - Kang, S. G. AU - Kim, S. -. J. AU - Kim, M. -. R. AU - Li, N. AU - Lee, J. -. H. PY - 2011 DA - 2011// TI - Genome sequence of Benzo(a)pyrene-degrading bacterium Novosphingobium pentaromativorans US6-1 JO - J Bacteriol VL - 194 UR - https://doi.org/10.1128/JB.06476-11 DO - 10.1128/JB.06476-11 ID - Luo2011 ER - TY - JOUR AU - Yun, S. H. AU - Choi, C. -. W. AU - Lee, S. -. Y. AU - Lee, Y. G. AU - Kwon, J. AU - Leem, S. H. PY - 2014 DA - 2014// TI - Proteomic characterization of plasmid pLA1 for biodegradation of polycyclic aromatic hydrocarbons in the marine bacterium, Novosphingobium pentaromativorans US6-1 JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0090812 DO - 10.1371/journal.pone.0090812 ID - Yun2014 ER - TY - JOUR AU - D’Argenio, V. AU - Notomista, E. AU - Petrillo, M. AU - Cantiello, P. AU - Cafaro, P. AU - Izzo, V. PY - 2013 DA - 2013// TI - Complete sequencing of Novosphingobium sp. PP1Y reveals a biotechnologically meaningful metabolic pattern JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-384 DO - 10.1186/1471-2164-15-384 ID - D’Argenio2013 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 - 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 initiati on 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 - 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 - Chen, I. M. AU - Markowitz, V. M. AU - Chu, K. AU - Anderson, I. AU - Mavromatis, K. AU - Kyrpides, N. C. PY - 2013 DA - 2013// TI - Improving microbial genome annotations in an integrated database context JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0054859 DO - 10.1371/journal.pone.0054859 ID - Chen2013 ER - TY - JOUR AU - Pati, A. AU - Ivanova, N. N. AU - Mikhailova, N. AU - Ovchinnikova, G. AU - Hooper, S. D. AU - Lykidis, A. PY - 2010 DA - 2010// TI - GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes JO - Nat Methods VL - 7 UR - https://doi.org/10.1038/nmeth.1457 DO - 10.1038/nmeth.1457 ID - Pati2010 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 - Eddy, S. R. PY - 1998 DA - 1998// TI - Profile hidden Markov models JO - Bioinformatics VL - 14 UR - https://doi.org/10.1093/bioinformatics/14.9.755 DO - 10.1093/bioinformatics/14.9.755 ID - Eddy1998 ER - TY - JOUR AU - Kim, O. -. S. AU - Cho, Y. -. J. AU - Lee, K. AU - Yoon, S. -. H. AU - Kim, M. AU - Na, H. PY - 2012 DA - 2012// TI - Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species JO - Int J Syst Evol Microbiol VL - 62 UR - https://doi.org/10.1099/ijs.0.038075-0 DO - 10.1099/ijs.0.038075-0 ID - Kim2012 ER - TY - JOUR AU - Overbeek, R. AU - Begley, T. AU - Butler, R. M. AU - Choudhuri, J. V. AU - Chuang, H. Y. AU - Cohoon, M. PY - 2005 DA - 2005// TI - The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki866 DO - 10.1093/nar/gki866 ID - Overbeek2005 ER - TY - JOUR AU - Pruitt, K. D. AU - Tatusova, T. AU - Klimke, W. AU - Maglott, D. R. PY - 2009 DA - 2009// TI - NCBI Reference Sequences: current status, policy and new initiatives JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn721 DO - 10.1093/nar/gkn721 ID - Pruitt2009 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 Res 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 - Yu, C. AU - Zavaljevski, N. AU - Desai, V. AU - Reifman, J. PY - 2009 DA - 2009// TI - Genome-wide enzyme annotation with precision control: catalytic families (CatFam) databases JO - Proteins VL - 74 UR - https://doi.org/10.1002/prot.22167 DO - 10.1002/prot.22167 ID - Yu2009 ER - TY - JOUR AU - Markowitz, V. M. AU - Mavromatis, K. AU - Ivanova, N. N. AU - Chen, I. M. AU - Chu, K. AU - Kyrpides, N. C. PY - 2009 DA - 2009// TI - IMG ER: a system for microbial genome annotation expert review and curation JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp393 DO - 10.1093/bioinformatics/btp393 ID - Markowitz2009 ER - TY - JOUR AU - Kim, M. AU - Oh, H. -. S. AU - Park, S. -. C. AU - Chun, J. PY - 2014 DA - 2014// TI - Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes JO - Int J Syst Evol Microbiol VL - 64 UR - https://doi.org/10.1099/ijs.0.059774-0 DO - 10.1099/ijs.0.059774-0 ID - Kim2014 ER - TY - JOUR AU - Gan, H. M. AU - Hudson, A. O. AU - Rahman, A. Y. A. AU - Chan, K. G. AU - Savka, M. A. PY - 2014 DA - 2014// TI - Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation JO - BMC Genomics VL - 14 UR - https://doi.org/10.1186/1471-2164-14-431 DO - 10.1186/1471-2164-14-431 ID - Gan2014 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 - Felsenstein, J. PY - 1981 DA - 1981// TI - Evolutionary trees from DNA sequences: a maximum likelihood approach JO - J Mol Evol VL - 17 UR - https://doi.org/10.1007/BF01734359 DO - 10.1007/BF01734359 ID - Felsenstein1981 ER - TY - JOUR AU - Kluge, A. G. AU - Farris, J. S. PY - 1969 DA - 1969// TI - Quantitative phyletics and the evolution of anurans JO - Syst Zool VL - 18 UR - https://doi.org/10.2307/2412407 DO - 10.2307/2412407 ID - Kluge1969 ER - TY - JOUR AU - Felsenstein, J. PY - 1985 DA - 1985// TI - Confidence limits on phylogenies: an approach using bootstrap JO - Evolution VL - 39 UR - https://doi.org/10.2307/2408678 DO - 10.2307/2408678 ID - Felsenstein1985 ER - TY - JOUR AU - Jukes, T. AU - Cantor, C. R. PY - 1969 DA - 1969// TI - Evolution of protein molecules JO - Mamm Protein Metab VL - 3 UR - https://doi.org/10.1016/B978-1-4832-3211-9.50009-7 DO - 10.1016/B978-1-4832-3211-9.50009-7 ID - Jukes1969 ER - TY - JOUR AU - Tamura, K. AU - Peterson, D. AU - Peterson, N. AU - Stecher, G. AU - Nei, M. AU - Kumar, S. PY - 2011 DA - 2011// TI - MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods JO - Mol Biol Evol VL - 28 UR - https://doi.org/10.1093/molbev/msr121 DO - 10.1093/molbev/msr121 ID - Tamura2011 ER - TY - JOUR AU - Richter, M. AU - Rosselló-Móra, R. PY - 2009 DA - 2009// TI - Shifting the genomic gold standard for the prokaryotic species definition JO - Proc Natl Acad Sci U S A VL - 106 UR - https://doi.org/10.1073/pnas.0906412106 DO - 10.1073/pnas.0906412106 ID - Richter2009 ER - TY - JOUR AU - Woese, C. R. AU - Kandler, O. AU - Wheelis, M. L. PY - 1990 DA - 1990// TI - Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya JO - Proc Natl Acad Sci U S A VL - 87 UR - https://doi.org/10.1073/pnas.87.12.4576 DO - 10.1073/pnas.87.12.4576 ID - Woese1990 ER - TY - CHAP AU - Garrity, G. M. AU - Bell, J. A. AU - Lilbum, T. ED - Garrity, G. M. ED - Brenner, D. J. ED - Krieg, N. R. ED - Staley, J. T. PY - 2005 DA - 2005// TI - Phylum XIV. Proteobacteria phyl. nov BT - Bergey’s manual of systematic bacteriology PB - Springer CY - New York UR - https://doi.org/10.1007/0-387-29298-5_1 DO - 10.1007/0-387-29298-5_1 ID - Garrity2005 ER - TY - CHAP AU - Garrity, G. M. AU - Bell, J. A. AU - Lilburn, T. ED - Garrity, G. M. ED - Brenner, D. J. ED - Krieg, N. R. ED - Staley, J. T. PY - 2005 DA - 2005// TI - Class I. Alphaproteobacteria class. nov BT - Bergey’s manual of systematic bacteriology PB - Springer CY - New York UR - https://doi.org/10.1007/0-387-29298-5_1 DO - 10.1007/0-387-29298-5_1 ID - Garrity2005 ER - TY - STD TI - Validation List No. 107: List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol. 2006; 56:1-6. ID - ref36 ER - TY - CHAP AU - Yabuuchi, E. AU - Kosako, Y. ED - Garrity, G. M. ED - Brenner, D. J. ED - Krieg, N. R. ED - Staley, J. T. PY - 2005 DA - 2005// TI - Order IV. Sphingomonadales ord. nov BT - Bergey’s manual of systematic bacteriology PB - Springer CY - New York ID - Yabuuchi2005 ER - TY - JOUR AU - Kosako, Y. AU - Yabuuchi, E. AU - Naka, T. AU - Fujiwara, N. AU - Kobayashi, K. PY - 2000 DA - 2000// TI - Proposal of Sphingomonadaceae fam. nov., consisting of Sphingomonas Yabuuchi et al. 1990, Erythrobacter Shiba and Shimidu 1982, Erythromicrobium Yurkov et al. 1994, Porphyrobacter Fuerst et al. 1993, Zymomonas Kluyver and van Niel 1936, and Sandaracinobacter Yurkov et al. 1997, with the type genus Sphingomonas Yabuuchi et al. 1990 JO - Microbiol Immunol VL - 44 UR - https://doi.org/10.1111/j.1348-0421.2000.tb02535.x DO - 10.1111/j.1348-0421.2000.tb02535.x ID - Kosako2000 ER - TY - STD TI - Validation List no. 77: Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol. 2000; 50:1953. ID - ref39 ER - TY - JOUR AU - Takeuchi, M. AU - Hamana, K. AU - Hiraishi, A. PY - 2001 DA - 2001// TI - Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses JO - Int J Syst Evol Microbiol VL - 51 UR - https://doi.org/10.1099/00207713-51-4-1405 DO - 10.1099/00207713-51-4-1405 ID - Takeuchi2001 ER - TY - JOUR AU - Gomila, M. AU - Gascó, J. AU - Busquets, A. AU - Gil, J. AU - Bernabeu, R. AU - Buades, J. M. PY - 2005 DA - 2005// TI - Identification of culturable bacteria present in haemodialysis water and fluid JO - FEMS Microbiol Ecol VL - 52 UR - https://doi.org/10.1016/j.femsec.2004.10.015 DO - 10.1016/j.femsec.2004.10.015 ID - Gomila2005 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 JO - Gene Ontol Consortium Nat Genet VL - 25 ID - Ashburner2000 ER -