TY - JOUR AU - Yoon, J. AU - Yasumoto-Hirose, M. AU - Katsuta, A. AU - Sekiguchi, H. AU - Matsuda, S. AU - Kasai, H. AU - Yokota, A. PY - 2007 DA - 2007// TI - Coraliomargarita akajimensis gen. nov., sp. nov., a novel member of the phylum ‘Verrucomicrobia’ isolated from seawater in Japan JO - Int J Syst Evol Microbiol VL - 57 UR - https://doi.org/10.1099/ijs.0.64755-0 DO - 10.1099/ijs.0.64755-0 ID - Yoon2007 ER - TY - JOUR AU - Hugenholtz, P. AU - Goebel, B. M. AU - Pace, N. R. PY - 1998 DA - 1998// TI - Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity JO - J Bacteriol VL - 180 ID - Hugenholtz1998 ER - TY - CHAP AU - Garrity, G. AU - Bell, J. A. AU - Lilburn, T. G. PY - 2003 DA - 2003// TI - Taxonomic outline of the prokaryotes BT - Bergey’s Manual of Systematic Bacteriology PB - Springer CY - New York ID - Garrity2003 ER - TY - JOUR AU - Janssen, P. H. AU - Schuhmann, A. AU - Morschel, E. AU - Rainey, F. A. PY - 1997 DA - 1997// TI - Novel anaerobic ultramicrobacteria belonging to the Verrucomicrobiales lineage of bacterial descent isolated by dilution culture from anoxic rice paddy soil JO - Appl Environ Microbiol VL - 63 ID - Janssen1997 ER - TY - JOUR AU - Chin, K. J. AU - Hahn, D. AU - Hengstmann, U. AU - Liesack, W. AU - Janssen, P. H. PY - 1999 DA - 1999// TI - Characterization and identification of numerically abundant culturable bacteria from the anoxic bulk soil of rice paddy microcosms JO - Appl Environ Microbiol VL - 65 ID - Chin1999 ER - TY - JOUR AU - Chin, K. J. AU - Liesack, W. AU - Janssen, P. H. PY - 2001 DA - 2001// TI - Opitutus terrae gen. nov., sp. nov., to accommodate novel strains of the division ‘Verrucomicrobia’ isolated from rice paddy soil JO - Int J Syst Evol Microbiol VL - 51 UR - https://doi.org/10.1099/00207713-51-6-1965 DO - 10.1099/00207713-51-6-1965 ID - Chin2001 ER - TY - JOUR AU - Sakai, T. AU - Ishizuka, K. AU - Shimanaka, K. AU - Ikai, K. AU - Kato, I. PY - 2003 DA - 2003// TI - Structures of oligosaccharides derived from Cladosiphon okamuranus fucoidan by digestion with marine bacterial enzymes JO - Mar Biotechnol VL - 5 UR - https://doi.org/10.1007/s10126-002-0107-9 DO - 10.1007/s10126-002-0107-9 ID - Sakai2003 ER - TY - JOUR AU - Shieh, W. Y. AU - Jean, W. D. PY - 1998 DA - 1998// TI - Alterococcus agarolyticus, gen. nov., sp. nov., a halophilic thermophilic bacterium capable of agar degradation JO - Can J Microbiol VL - 44 UR - https://doi.org/10.1139/cjm-44-7-637 DO - 10.1139/cjm-44-7-637 ID - Shieh1998 ER - TY - JOUR AU - Choo, Y. J. AU - Lee, K. AU - Song, J. AU - Cho, J. C. PY - 2007 DA - 2007// TI - Puniceicoccus vermicola gen. nov., sp. nov., a novel marine bacterium, and description of Puniceicoccaceae fam. nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov. and Opitutae classis nov. in the phylum ‘Verrucomicrobia’ JO - Int J Syst Evol Microbiol VL - 57 UR - https://doi.org/10.1099/ijs.0.64616-0 DO - 10.1099/ijs.0.64616-0 ID - Choo2007 ER - TY - JOUR AU - Yoon, J. AU - Matsuo, Y. AU - Matsuda, S. AU - Adachi, K. AU - Kasai, H. AU - Yokota, A. PY - 2007 DA - 2007// TI - Cerasicoccus arenae gen. nov., sp. nov., a carotenoid-producing marine representative of the family Puniceicoccaceae within the phylum ‘Verrucomicrobia’, isolated from marine sand JO - Int J Syst Evol Microbiol VL - 57 UR - https://doi.org/10.1099/ijs.0.65102-0 DO - 10.1099/ijs.0.65102-0 ID - Yoon2007 ER - TY - JOUR AU - Yoon, J. AU - Yasumoto-Hirose, S. AU - Matsuda, S. AU - Nozawa, M. AU - Matsuda, S. AU - Kasai, H. AU - Yokota, A. PY - 2007 DA - 2007// TI - Pelagicoccus mobilis gen. nov., sp. nov., Pelagicoccus albus sp. nov. and Pelagicoccus litoralis sp. nov., three novel members of subdivision 4 within the phylum ‘Verrucomicrobia’, isolated from seawater by in situ cultivation JO - Int J Syst Evol Microbiol VL - 57 UR - https://doi.org/10.1099/ijs.0.64970-0 DO - 10.1099/ijs.0.64970-0 ID - Yoon2007 ER - TY - JOUR AU - Yoon, J. AU - Oku, N. AU - Matsuda, S. AU - Kasai, H. AU - Yokota, A. PY - 2007 DA - 2007// TI - Pelagicoccus croceus sp. nov., a novel marine member of the family Puniceicoccaceae within the phylum ‘Verrucomicrobia’ isolated from sea-grass JO - Int J Syst Evol Microbiol VL - 57 UR - https://doi.org/10.1099/ijs.0.65286-0 DO - 10.1099/ijs.0.65286-0 ID - Yoon2007 ER - TY - JOUR AU - Chun, J. AU - Lee, J. H. AU - Jung, Y. AU - Kim, M. AU - Kim, S. AU - Kim, B. K. AU - Lim, Y. W. PY - 2007 DA - 2007// TI - EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences JO - Int J Syst Evol Microbiol VL - 57 UR - https://doi.org/10.1099/ijs.0.64915-0 DO - 10.1099/ijs.0.64915-0 ID - Chun2007 ER - TY - JOUR AU - Sakai, T. AU - Ishizuka, K. AU - Kato, I. PY - 2003 DA - 2003// TI - Isolation and characterization of fucoidan-degrading marine bacterium JO - Mar Biotechnol VL - 5 UR - https://doi.org/10.1007/s10126-002-0118-6 DO - 10.1007/s10126-002-0118-6 ID - Sakai2003 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 - JOUR AU - Stamatakis, A. AU - Hoover, P. AU - Rougemont, J. PY - 2008 DA - 2008// TI - A Rapid bootstrap algorithm for the RAxML web servers JO - Syst Biol VL - 57 UR - https://doi.org/10.1080/10635150802429642 DO - 10.1080/10635150802429642 ID - Stamatakis2008 ER - TY - JOUR AU - Euzeby, J. P. PY - 1997 DA - 1997// TI - List of Bacterial Names with Standing in Nomenclature: a folder on the Internet JO - Syst Appl Bacteriol VL - 47 ID - Euzeby1997 ER - TY - JOUR AU - Pattengale, N. D. AU - Alipour, M. AU - Bininda-Emonds, O. R. P. AU - Moret, B. M. E. AU - Stamatakis, A. PY - 2009 DA - 2009// TI - How many bootstrap replicates are necessary? JO - Lect Notes Comput Sci VL - 5541 UR - https://doi.org/10.1007/978-3-642-02008-7_13 DO - 10.1007/978-3-642-02008-7_13 ID - Pattengale2009 ER - TY - JOUR AU - Liolios, K. AU - Chen, I. M. AU - Mavromatis, K. AU - Tavernarakis, N. AU - Hugenholtz, P. AU - Markowitz, V. M. AU - Kyrpides, N. C. PY - 2010 DA - 2010// TI - The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkp848 DO - 10.1093/nar/gkp848 ID - Liolios2010 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 - 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 - 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 and Bacteria JO - Proc Natl Acad Sci USA VL - 87 UR - https://doi.org/10.1073/pnas.87.12.4576 DO - 10.1073/pnas.87.12.4576 ID - Woese1990 ER - TY - JOUR AU - Hedlund, B. P. AU - Gosink, J. J. AU - Staley, J. T. PY - 1997 DA - 1997// TI - Verrucomicrobia div. nov., a new division of the bacteria containing three new species of Prosthecobacter JO - Antonie Van Leeuwenhoek VL - 72 UR - https://doi.org/10.1023/A:1000348616863 DO - 10.1023/A:1000348616863 ID - Hedlund1997 ER - TY - CHAP AU - Garrity, G. M. AU - Holt, J. G. ED - Garrity, G. M. ED - Boone, D. R. ED - Castenholz, R. W. PY - 2001 DA - 2001// TI - The Road Map to the Manual BT - Bergey’s Manual of Systematic Bacteriology PB - Springer CY - New York UR - https://doi.org/10.1007/978-0-387-21609-6_15 DO - 10.1007/978-0-387-21609-6_15 ID - Garrity2001 ER - TY - STD TI - Classification of bacteria and archaea in risk groups. www.baua.de TRBA 466, supplement 2010; in press. UR - http://www.baua.de ID - ref25 ER - TY - JOUR AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Botstein, D. 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 JO - Nat Genet VL - 25 UR - https://doi.org/10.1038/75556 DO - 10.1038/75556 ID - Ashburner2000 ER - TY - JOUR AU - Klenk, H. P. AU - Göker, M. PY - 2010 DA - 2010// TI - En route to a genome-based classification of Archaea and Bacteria? JO - Syst Appl Microbiol VL - 33 UR - https://doi.org/10.1016/j.syapm.2010.03.003 DO - 10.1016/j.syapm.2010.03.003 ID - Klenk2010 ER - TY - JOUR AU - Wu, D. AU - Hugenholtz, P. AU - Mavromatis, K. AU - Pukall, R. AU - Dalin, E. AU - Ivanova, N. N. AU - Kunin, V. AU - Goodwin, L. AU - Wu, M. AU - Tindall, B. J. PY - 2009 DA - 2009// TI - A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea JO - Nature VL - 462 UR - https://doi.org/10.1038/nature08656 DO - 10.1038/nature08656 ID - Wu2009 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 - ref29 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 - Sims, D. AU - Brettin, T. AU - Detter, J. AU - Han, C. AU - Lapidus, A. AU - Copeland, A. AU - Glavina Del Rio, T. AU - Nolan, M. AU - Chen, F. AU - Lucas, S. PY - 2009 DA - 2009// TI - Complete genome sequence of Kytococcus sedentarius type strain (541T) JO - Stand Genomic Sci VL - 1 UR - https://doi.org/10.4056/sigs.761 DO - 10.4056/sigs.761 ID - Sims2009 ER - TY - BOOK AU - Lapidus, A. AU - LaButti, K. AU - Foster, B. AU - Lowry, S. AU - Trong, S. AU - Goltsman, E. PY - 2008 DA - 2008// TI - POLISHER: An effective tool for using ultra short reads in microbial genome assembly and finishing PB - AGBT CY - Marco Island, FL ID - Lapidus2008 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 Dynamic Programming Genefinding Algorithm 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 - Pati, A. AU - Ivanova, N. AU - Mikhailova, N. AU - Ovchinikova, G. AU - Hooper, S. D. AU - Lykidis, A. AU - Kyrpides, N. C. PY - 2010 DA - 2010// TI - GenePRIMP: A Gene Prediction Improvement Pipeline for microbial 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 - Markowitz, V. M. AU - Ivanova, N. N. AU - Chen, I. M. A. 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 -