TY - JOUR AU - Chelius, M. K. AU - Triplett, E. W. PY - 2000 DA - 2000// TI - Dyadobacter fermentans gen. nov., sp. nov., a novel Gram-negative bacterium isolated from surface-sterilized Zea mays stems JO - Int J Syst Evol Microbiol VL - 50 UR - https://doi.org/10.1099/00207713-50-2-751 DO - 10.1099/00207713-50-2-751 ID - Chelius2000 ER - TY - JOUR AU - Lee, C. AU - Grasso, C. AU - Sharlow, M. F. PY - 2002 DA - 2002// TI - Multiple sequence alignment using partial order graphs JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.3.452 DO - 10.1093/bioinformatics/18.3.452 ID - Lee2002 ER - TY - JOUR AU - Castresana, J. PY - 2000 DA - 2000// TI - Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026334 DO - 10.1093/oxfordjournals.molbev.a026334 ID - Castresana2000 ER - TY - BOOK AU - Swofford, D. L. PY - 2002 DA - 2002// TI - PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 b10 PB - Sinauer Associates CY - Sunderland, MA ID - Swofford2002 ER - TY - JOUR AU - Liolios, K. AU - Mavromatis, K. AU - Tavernarakis, N. AU - Kyrpides, N. C. PY - 2008 DA - 2008// TI - The Genomes OnLine Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkm884 DO - 10.1093/nar/gkm884 ID - Liolios2008 ER - TY - STD TI - Garrity GM, Lilburn TG, Cole JR, Harrison SH, Euzéby J, Tindall BJ. Taxonomic Outline of the Bacteria and Archaea. Release 7.7 March 6, 2007. Michigan State University Board of Trustees. DOI: 10.1601/TOBA7.7. http://www.taxonomicoutline.org UR - http://www.taxonomicoutline.org ID - ref6 ER - TY - JOUR AU - Field, D. AU - Garrity, G. AU - Gray, T. AU - Morrison, N. AU - Selengut, J. AU - Sterk, P. AU - Tatusova, T. AU - Thomson, N. AU - Allen, M. J. AU - Angiuoli, S. V. PY - 2008 DA - 2008// TI - Towards a richer description of our complete collection of genomes and metagenomes: 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 - STD TI - Skerman VBD, McGrowan V, Sneath PHA, eds. Approved list of bacterial names. Int J Syst Bacteriol 1980; 30: 225–420. ID - ref8 ER - TY - JOUR AU - Willumsen, P. A. AU - Johansen, J. E. AU - Karlson, U. AU - Hansen, B. M. PY - 2005 DA - 2005// TI - Isolation and taxonomic affiliation of N-heterocyclic aromatic hydrocarbon-transforming bacteria JO - Appl Microbiol Biotechnol VL - 67 UR - https://doi.org/10.1007/s00253-004-1799-8 DO - 10.1007/s00253-004-1799-8 ID - Willumsen2005 ER - TY - STD TI - Anonymous. Biological Agents: Technical rules for biological agents www.baua.de. UR - http://www.baua.de ID - ref10 ER - TY - JOUR AU - Botstein, D. AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Butler, H. AU - Cherry, J. M. AU - Davis, A. P. AU - Dolinski, K. AU - Dwight, S. S. AU - Eppig, J. T. 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 - Botstein2000 ER - TY - JOUR AU - Nour, S. M. AU - Lawrence, J. R. AU - Zhu, H. AU - Swerhone, G. D. AU - Welsh, M. AU - Welacky, T. W. AU - Topp, E. PY - 2003 DA - 2003// TI - Bacteria associated with cysts of the soybean cyst nematode (Heterodera glycines) JO - Appl Environ Microbiol VL - 69 UR - https://doi.org/10.1128/AEM.69.1.607-615.2003 DO - 10.1128/AEM.69.1.607-615.2003 ID - Nour2003 ER - TY - JOUR AU - Chaturvedi, P. AU - Reddy, G. S. N. AU - Shivaji, S. PY - 2005 DA - 2005// TI - Dyadobacter hamtensis sp. nov., from Hamta glacier, located in the Himalayas, India JO - Int J Syst Evol Microbiol VL - 55 UR - https://doi.org/10.1099/ijs.0.63806-0 DO - 10.1099/ijs.0.63806-0 ID - Chaturvedi2005 ER - TY - JOUR AU - Dong, Z. AU - Guo, X. AU - Zhang, X. AU - Qiu, F. AU - Sun, L. AU - Gong, H. AU - Zhang, F. PY - 2007 DA - 2007// TI - Dyadobacter beijingensis sp. nov., isolated from the rhizosphere of turf grasses in China JO - Int J Syst Evol Microbiol VL - 57 UR - https://doi.org/10.1099/ijs.0.64754-0 DO - 10.1099/ijs.0.64754-0 ID - Dong2007 ER - TY - JOUR AU - Reddy, G. S. N. AU - Garcia-Pichel, F. PY - 2005 DA - 2005// TI - Dyadobacter crusticola sp. nov., from biological soil crusts in the Colorado Plateau, USA, and an emended description of the genus Dyadobacter Chelius and Triplett 2000 JO - Int J Syst Evol Microbiol VL - 55 UR - https://doi.org/10.1099/ijs.0.63498-0 DO - 10.1099/ijs.0.63498-0 ID - Reddy2005 ER - TY - JOUR AU - Liu, Q. M. AU - Im, W. T. AU - Lee, M. AU - Yang, D. C. AU - Lee, S. T. PY - 2006 DA - 2006// TI - Dyadobacter ginsengisoli sp. nov., isolated from soil of a ginseng field JO - Int J Syst Evol Microbiol VL - 56 UR - https://doi.org/10.1099/ijs.0.64322-0 DO - 10.1099/ijs.0.64322-0 ID - Liu2006 ER - TY - JOUR AU - Baik, K. S. AU - Kim, M. S. AU - Kim, E. M. AU - Kim, H. R. AU - Seong, C. N. PY - 2007 DA - 2007// TI - Dyadobacter koreensis sp. nov., isolated from fresh water JO - Int J Syst Evol Microbiol VL - 57 UR - https://doi.org/10.1099/ijs.0.64902-0 DO - 10.1099/ijs.0.64902-0 ID - Baik2007 ER - TY - JOUR AU - Tang, Y. AU - Dai, J. AU - Zhang, L. AU - Mo, Z. AU - Wang, Y. AU - Li, Y. AU - Ji, S. AU - Fang, C. AU - Zheng, C. PY - 2009 DA - 2009// TI - Dyadobacter alkalitolerans sp. nov., isolated from desert sand JO - Int J Syst Evol Microbiol VL - 59 UR - https://doi.org/10.1099/ijs.0.001404-0 DO - 10.1099/ijs.0.001404-0 ID - Tang2009 ER - TY - JOUR AU - Hosoya, R. AU - Hamana, K. PY - 2004 DA - 2004// TI - Distribution of two triamines, spermidine and homospermidine, and an aromatic amine, 2-phenylethylamine, within the phylum Bacteroidetes JO - J Gen Appl Microbiol VL - 50 UR - https://doi.org/10.2323/jgam.50.255 DO - 10.2323/jgam.50.255 ID - Hosoya2004 ER - TY - STD TI - List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php UR - http://www.dsmz.de/ ID - ref20 ER - TY - STD TI - Wu M, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova N, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopedia of Bacteria and Archaea. Nature 2009; (In press). ID - ref21 ER - TY - JOUR AU - Ewing, B. AU - Hillier, L. AU - Wendl, M. C. AU - Green, P. PY - 1998 DA - 1998// TI - Base-calling of automated sequencer traces using phred. I. Accuracy assessment JO - Genome Res VL - 8 UR - https://doi.org/10.1101/gr.8.3.175 DO - 10.1101/gr.8.3.175 ID - Ewing1998 ER - TY - JOUR AU - Ewing, B. AU - Green, P. PY - 1998 DA - 1998// TI - Base-calling of automated sequencer traces using phred. II. Error probabilities JO - Genome Res VL - 8 UR - https://doi.org/10.1101/gr.8.3.186 DO - 10.1101/gr.8.3.186 ID - Ewing1998 ER - TY - JOUR AU - Gordon, D. AU - Abajian, C. AU - Green, P. PY - 1998 DA - 1998// TI - Consed: a graphical tool for sequence finishing JO - Genome Res VL - 8 UR - https://doi.org/10.1101/gr.8.3.195 DO - 10.1101/gr.8.3.195 ID - Gordon1998 ER - TY - STD TI - Han CS, Chain P. Finishing repeat regions automatically with Dupfinisher. In: Proceeding of the 2006 international conference on bioinformatics & computational biology. Hamid R Arabnia & Homayoun Valafar (eds), CSREA Press. June 26–29, 2006:141–146 ID - ref25 ER - TY - STD TI - Anonymous. Prodigal Prokaryotic Dynamic Programming Genefinding Algorithm. Oak Ridge National Laboratory and University of Tennessee 2009 http://compbio.ornl.gov/prodigal. UR - http://compbio.ornl.gov/ ID - ref26 ER - TY - STD TI - Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes. (Submitted). ID - ref27 ER - TY - JOUR AU - Markowitz, V. M. AU - Mavromatis, K. AU - Ivanova, N. N. AU - Chen, I. M. A. AU - Chu, K. AU - Kyrpides, N. C. PY - 2009 DA - 2009// TI - Expert Review of Functional Annotations for Microbial Genomes JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp393 DO - 10.1093/bioinformatics/btp393 ID - Markowitz2009 ER -