TY - JOUR AU - Ali, Z. AU - Cousin, S. AU - Frühling, A. AU - Brambilla, E. AU - Schumann, P. AU - Yang, Y. PY - 2009 DA - 2009// TI - Flavobacterium rivuli sp. nov., Flavobacterium subsaxonicum sp. nov., Flavobacterium swingsii sp. nov. and Flavobacterium reichenbachii sp. nov., isolated from a hard water rivulet JO - Int J Syst Evol Microbiol VL - 59 UR - https://doi.org/10.1099/ijs.0.008771-0 DO - 10.1099/ijs.0.008771-0 ID - Ali2009 ER - TY - JOUR PY - 2012 DA - 2012// TI - Validation List N° 143 JO - Int J Syst Evol Microbiol VL - 62 UR - https://doi.org/10.1099/ijs.0.039487-0 DO - 10.1099/ijs.0.039487-0 ID - ref2 ER - TY - JOUR PY - 2012 DA - 2012// TI - Validation List N° 145 JO - Int J Syst Evol Microbiol VL - 62 UR - https://doi.org/10.1099/ijs.0.043240-0 DO - 10.1099/ijs.0.043240-0 ID - ref3 ER - TY - STD TI - Anon. List of growth media used at the DSMZ. http://www.dsmz.de/. UR - http://www.dsmz.de/ ID - ref4 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 - The Gene Ontology Consortium. Nat Genet VL - 25 ID - Ashburner2000 ER - TY - JOUR AU - Auch, A. F. AU - Klenk, H. -. P. AU - Göker, M. PY - 2010 DA - 2010// TI - Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs JO - Stand Genomic Sci VL - 2 UR - https://doi.org/10.4056/sigs.541628 DO - 10.4056/sigs.541628 ID - Auch2010 ER - TY - JOUR AU - Auch, A. F. AU - Jan, M. AU - Klenk, H. -. P. AU - Göker, M. PY - 2010 DA - 2010// TI - Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison JO - Stand Genomic Sci VL - 2 UR - https://doi.org/10.4056/sigs.531120 DO - 10.4056/sigs.531120 ID - Auch2010 ER - TY - STD TI - BAuA 2010 – 2012 update, Classification of bacteria and archaea in risk groups. http://www.baua.de. TRBA 466. 19. UR - http://www.baua.de ID - ref8 ER - TY - JOUR AU - Bennett, S. PY - 2004 DA - 2004// TI - Solexa Ltd JO - Pharmacogenomics VL - 5 UR - https://doi.org/10.1517/14622416.5.4.433 DO - 10.1517/14622416.5.4.433 ID - Bennett2004 ER - TY - BOOK AU - Bergey, D. H. AU - Harrison, F. C. AU - Breed, R. S. AU - Hammer, B. W. AU - Huntoon, F. M. PY - 1923 DA - 1923// TI - Bergey’s Manual of Determinative Bacteriology 1st edn PB - Williams and Wilkins Co. CY - Baltimore ID - Bergey1923 ER - TY - CHAP AU - Bernardet, J. -. F. ED - Krieg, N. R. ED - Staley, J. T. ED - Brown, D. R. ED - Hedlund, B. P. ED - Paster, B. J. ED - Ward, N. L. ED - Ludwig, W. W. W. B. PY - 2010 DA - 2010// TI - Class II. Flavobacteriia class. nov BT - Bergey's Manual of Systematic Bacteriology PB - Springer CY - New York ID - Bernardet2010 ER - TY - CHAP AU - Bernardet, J. F. AU - Bowman, J. P. AU - Genus, I. PY - 2011 DA - 2011// TI - Flavobacterium Bergey, Harrison, Breed, Hammer and Huntoon 1923, 97AL emend. Bernardet, Segers, Vancanneyt, Berthe, Kersters and Vandamme 1996, 139 BT - Bergey's Manual of Systematic Bacteriology PB - Springer CY - New York ID - Bernardet2011 ER - TY - STD TI - Bernardet JF, Family I. Flavobacteriaceae Reichenbach 1992b, 327VP (Effective publication: Reichenbach 1989b, 2013.) emend. Bernardet, Segers, Vancanneyt, Berthe, Kersters and Vandamme 1996, 145 emend. Bernardet, Nakagawa and Holmes 2002, 1057. In: Bergey's Manual of Systematic Bacteriology, vol. 4. 2nd ed. New York: The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. Springer; 2011. p. 106–314. ID - ref13 ER - TY - CHAP AU - Bernardet, J. F. AU - Order, I. ED - Krieg, N. R. ED - Staley, J. T. ED - Brown, D. R. ED - Hedlund, B. P. ED - Paster, B. J. ED - Ward, N. L. ED - Ludwig, W. ED - Whitman, W. B. PY - 2011 DA - 2011// TI - Flavobacteriales ord. nov BT - Bergey's Manual of Systematic Bacteriology PB - Springer CY - New York ID - Bernardet2011 ER - TY - JOUR AU - Bernardet, J. F. AU - Segers, P. AU - Vancanneyt, M. AU - Berthe, F. AU - Kersters, K. AU - Vandamme, P. PY - 1996 DA - 1996// TI - Cutting a gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis Strohl and Tait 1978) JO - Int J Syst Bacteriol VL - 46 UR - https://doi.org/10.1099/00207713-46-1-128 DO - 10.1099/00207713-46-1-128 ID - Bernardet1996 ER - TY - JOUR AU - Bjursell, M. K. AU - Martens, E. C. AU - Gordon, J. I. PY - 2006 DA - 2006// TI - Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period JO - J Biol Chem VL - 281 UR - https://doi.org/10.1074/jbc.M606509200 DO - 10.1074/jbc.M606509200 ID - Bjursell2006 ER - TY - JOUR AU - Brambilla, E. AU - Päuker, O. AU - Cousin, S. AU - Steiner, U. AU - Reimer, A. AU - Stackebrandt, E. PY - 2007 DA - 2007// TI - High phylogenetic diversity of Flavobacterium spp. isolated from a hardwater creek, Harz Mountains, Germany JO - Org Divers Evol VL - 7 UR - https://doi.org/10.1016/j.ode.2006.03.003 DO - 10.1016/j.ode.2006.03.003 ID - Brambilla2007 ER - TY - JOUR AU - Cantarel, B. L. AU - Coutinho, P. M. AU - Rancurel, C. AU - Bernard, T. AU - Lombard, V. AU - Henrissat, B. PY - 2009 DA - 2009// TI - The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn663 DO - 10.1093/nar/gkn663 ID - Cantarel2009 ER - TY - JOUR AU - Caspi, R. AU - Altman, T. AU - Billington, R. AU - Dreher, K. AU - Foerster, H. AU - Fulcher, C. A. PY - 2014 DA - 2014// TI - The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1103 DO - 10.1093/nar/gkt1103 ID - Caspi2014 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 - STD TI - DOE Joint Genome Institute. A DOE office of science user facility of Lawrence Berkeley national laboratory. DOE Jt Genome Inst. http://jgi.doe.gov. UR - http://jgi.doe.gov ID - ref21 ER - TY - JOUR AU - Dong, K. AU - Xu, B. AU - Zhu, F. AU - Wang, G. PY - 2013 DA - 2013// TI - Flavobacterium hauense sp. nov., isolated from soil and emended descriptions of Flavobacterium subsaxonicum, Flavobacterium beibuense and Flavobacterium rivuli JO - Int J Syst Evol Microbiol VL - 63 UR - https://doi.org/10.1099/ijs.0.048652-0 DO - 10.1099/ijs.0.048652-0 ID - Dong2013 ER - TY - JOUR AU - Euzéby, J. P. PY - 1997 DA - 1997// TI - List of bacterial names with standing in nomenclature: A folder available on the Internet JO - Int J Syst Bacteriol VL - 47 UR - https://doi.org/10.1099/00207713-47-2-590 DO - 10.1099/00207713-47-2-590 ID - Euzéby1997 ER - TY - JOUR AU - Fernández-Gómez, B. AU - Richter, M. AU - Schüler, M. AU - Pinhassi, J. AU - Acinas, S. G. AU - González, J. M. PY - 2013 DA - 2013// TI - Ecology of marine Bacteroidetes: a comparative genomics approach JO - ISME J VL - 7 UR - https://doi.org/10.1038/ismej.2012.169 DO - 10.1038/ismej.2012.169 ID - Fernández-Gómez2013 ER - TY - JOUR AU - Field, D. AU - Amaral-Zettler, L. AU - Cochrane, G. AU - Cole, J. R. AU - Dawyndt, P. AU - Garrity, G. M. PY - 2011 DA - 2011// TI - The Genomic Standards Consortium JO - PLoS Biol VL - 9 UR - https://doi.org/10.1371/journal.pbio.1001088 DO - 10.1371/journal.pbio.1001088 ID - Field2011 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 - Field, D. AU - Sterk, P. AU - Kottmann, R. AU - Smet, J. W. AU - Amaral-Zettler, L. AU - Cochrane, G. PY - 2014 DA - 2014// TI - Genomic Standards Consortium Projects JO - Stand Genomic Sci VL - 9 UR - https://doi.org/10.4056/sigs.5559608 DO - 10.4056/sigs.5559608 ID - Field2014 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 - Frankland, G. C. AU - Frankland, P. F. PY - 1889 DA - 1889// TI - Über einige typische Mikroorganismen im Wasser und im Boden JO - Zeitschrift fur Hyg und Infekt Medizinische Mikrobiol Immunol und Virol VL - 6 ID - Frankland1889 ER - TY - JOUR AU - Fu, Y. AU - Tang, X. AU - Lai, Q. AU - Zhang, C. AU - Zhong, H. AU - Li, W. PY - 2011 DA - 2011// TI - Flavobacterium beibuense sp. nov., isolated from marine sediment JO - Int J Syst Evol Microbiol VL - 61 UR - https://doi.org/10.1099/ijs.0.018846-0 DO - 10.1099/ijs.0.018846-0 ID - Fu2011 ER - TY - JOUR AU - Garrity, G. PY - 2010 DA - 2010// TI - NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser JO - Microbiol Today VL - 37 ID - Garrity2010 ER - TY - JOUR AU - Gemeinholzer, B. AU - Dröge, G. AU - Zetzsche, H. AU - Haszprunar, G. AU - Klenk, H. -. P. AU - Güntsch, A. PY - 2011 DA - 2011// TI - Bank Network: The start from a German initiative JO - Biopreserv Biobank VL - 9 UR - https://doi.org/10.1089/bio.2010.0029 DO - 10.1089/bio.2010.0029 ID - Gemeinholzer2011 ER - TY - JOUR AU - Gnerre, S. AU - Maccallum, I. AU - Przybylski, D. AU - Ribeiro, F. J. AU - Burton, J. N. AU - Walker, B. J. PY - 2011 DA - 2011// TI - High-quality draft assemblies of mammalian genomes from massively parallel sequence data JO - Proc Natl Acad Sci U S A VL - 108 UR - https://doi.org/10.1073/pnas.1017351108 DO - 10.1073/pnas.1017351108 ID - Gnerre2011 ER - TY - JOUR AU - Göker, M. AU - Cleland, D. AU - Saunders, E. AU - Lapidus, A. AU - Nolan, M. AU - Lucas, S. PY - 2011 DA - 2011// TI - Complete genome sequence of Isosphaera pallida type strain (IS1BT) JO - Stand Genomic Sci VL - 4 UR - https://doi.org/10.4056/sigs.1533840 DO - 10.4056/sigs.1533840 ID - Göker2011 ER - TY - JOUR AU - Göker, M. AU - Klenk, H. -. P. PY - 2013 DA - 2013// TI - Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects JO - Stand Genomic Sci VL - 8 UR - https://doi.org/10.4056/sigs.3446951 DO - 10.4056/sigs.3446951 ID - Göker2013 ER - TY - JOUR AU - Holmes, B. AU - Owen, R. J. PY - 1979 DA - 1979// TI - Proposal that Flavobacterium breve be substituted as the type species of the genus in place of Flavobacterium aquatile and emended description of the genus Flavobacterium: status of the named species of Flavobacterium, Request for an Opinion JO - Int J Syst Bacteriol VL - 29 UR - https://doi.org/10.1099/00207713-29-4-416 DO - 10.1099/00207713-29-4-416 ID - Holmes1979 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 - JOUR AU - Kabisch, A. AU - Otto, A. AU - König, S. AU - Becher, D. AU - Albrecht, D. AU - Schüler, M. PY - 2014 DA - 2014// TI - Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes ‘Gramella forsetii’ KT0803 JO - ISME J VL - 8 UR - https://doi.org/10.1038/ismej.2014.4 DO - 10.1038/ismej.2014.4 ID - Kabisch2014 ER - TY - JOUR AU - Kirchman, D. L. PY - 2002 DA - 2002// TI - The ecology of Cytophaga-Flavobacteria in aquatic environments JO - FEMS Microbiol Ecol VL - 39 ID - Kirchman2002 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 - CHAP AU - Krieg, N. R. AU - Ludwig, W. AU - Euzéby, J. AU - Whitman, W. B. AU - Phylum, X. I. V. ED - Krieg, N. R. ED - Staley, J. T. ED - Brown, D. R. PY - 2010 DA - 2010// TI - Bacteroidetes phyl. nov BT - The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes PB - Springer CY - New York ID - Krieg2010 ER - TY - JOUR AU - Kyrpides, N. C. AU - Hugenholtz, P. AU - Eisen, J. A. AU - Woyke, T. AU - Göker, M. AU - Parker, C. T. PY - 2014 DA - 2014// TI - Genomic Encyclopedia of Bacteria and Archaea: sequencing a myriad of type strains JO - PLoS Biol VL - 12 UR - https://doi.org/10.1371/journal.pbio.1001920 DO - 10.1371/journal.pbio.1001920 ID - Kyrpides2014 ER - TY - STD TI - Kyrpides NC, Woyke T, Eisen JA. Genomic Encyclopedia of Type Strains, Phase I : The one thousand microbial genomes (KMG-I) project. Stand Genomic Sci 2014:628–634. ID - ref43 ER - TY - BOOK AU - Lapage, S. AU - Sneath, P. AU - Lessel, E. AU - Skerman, V. AU - Seeliger, H. AU - Clark, W. PY - 1992 DA - 1992// TI - International code of nomenclature of bacteria (1990 Revision) PB - American Society for Microbiology CY - Washington, D.C. ID - Lapage1992 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 - STD TI - Li H. wgsim. 2011: https://github.com/lh3/wgsim. UR - https://github.com/lh3/wgsim ID - ref46 ER - TY - JOUR AU - Lombard, V. AU - Golaconda Ramulu, H. AU - Drula, E. AU - Coutinho, P. M. AU - Henrissat, B. PY - 2014 DA - 2014// TI - The carbohydrate-active enzymes database (CAZy) in 2013 JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1178 DO - 10.1093/nar/gkt1178 ID - Lombard2014 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. I. M. G. E. R. PY - 2009 DA - 2009// TI - 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 - Mavromatis, K. AU - Land, M. L. AU - Brettin, T. S. AU - Quest, D. J. AU - Copeland, A. AU - Clum, A. PY - 2012 DA - 2012// TI - The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0048837 DO - 10.1371/journal.pone.0048837 ID - Mavromatis2012 ER - TY - JOUR AU - McBride, M. J. AU - Xie, G. AU - Martens, E. C. AU - Lapidus, A. AU - Henrissat, B. AU - Rhodes, R. G. PY - 2009 DA - 2009// TI - Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis JO - Appl Env Microbiol VL - 75 UR - https://doi.org/10.1128/AEM.01495-09 DO - 10.1128/AEM.01495-09 ID - McBride2009 ER - TY - JOUR AU - McBride, M. J. AU - Zhu, Y. PY - 2013 DA - 2013// TI - Gliding motility and Por secretion system genes are widespread among members of the phylum Bacteroidetes JO - J Bacteriol VL - 195 UR - https://doi.org/10.1128/JB.01962-12 DO - 10.1128/JB.01962-12 ID - McBride2013 ER - TY - JOUR AU - Medema, M. H. AU - Takano, E. AU - Breitling, R. PY - 2013 DA - 2013// TI - Detecting sequence homology at the gene cluster level with MultiGeneBlast JO - Mol Biol Evol VL - 30 UR - https://doi.org/10.1093/molbev/mst025 DO - 10.1093/molbev/mst025 ID - Medema2013 ER - TY - JOUR AU - Meier-Kolthoff, J. P. AU - Auch, A. F. AU - Klenk, H. -. P. AU - Göker, M. PY - 2013 DA - 2013// TI - Genome sequence-based species delimitation with confidence intervals and improved distance functions JO - BMC Bioinformatics VL - 14 UR - https://doi.org/10.1186/1471-2105-14-60 DO - 10.1186/1471-2105-14-60 ID - Meier-Kolthoff2013 ER - TY - JOUR AU - Meier-Kolthoff, J. P. AU - Auch, A. F. AU - Klenk, H. -. P. AU - Göker, M. PY - 2014 DA - 2014// TI - Highly parallelized inference of large genome-based phylogenies JO - Concurr Comput Pract Exp VL - 26 UR - https://doi.org/10.1002/cpe.3112 DO - 10.1002/cpe.3112 ID - Meier-Kolthoff2014 ER - TY - JOUR AU - Meier-Kolthoff, J. P. AU - Göker, M. AU - Spröer, C. AU - Klenk, H. P. PY - 2013 DA - 2013// TI - When should a DDH experiment be mandatory in microbial taxonomy? JO - Arch Microbiol VL - 195 UR - https://doi.org/10.1007/s00203-013-0888-4 DO - 10.1007/s00203-013-0888-4 ID - Meier-Kolthoff2013 ER - TY - JOUR AU - Meier-Kolthoff, J. P. AU - Klenk, H. -. P. AU - Göker, M. PY - 2014 DA - 2014// TI - Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age JO - Int J Syst Evol Microbiol VL - 64 UR - https://doi.org/10.1099/ijs.0.056994-0 DO - 10.1099/ijs.0.056994-0 ID - Meier-Kolthoff2014 ER - TY - JOUR AU - Montero-Calasanz, M. D. C. AU - Göker, M. AU - Rohde, M. AU - Spröer, C. AU - Schumann, P. AU - Busse, H. J. PY - 2014 DA - 2014// TI - Chryseobacterium oleae sp. nov., an efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea L.) cuttings and emended descriptions of the genus Chryseobacterium, C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense JO - Syst Appl Microbiol VL - 37 UR - https://doi.org/10.1016/j.syapm.2014.04.004 DO - 10.1016/j.syapm.2014.04.004 ID - Montero-Calasanz2014 ER - TY - JOUR AU - Montero-Calasanz, M. D. C. AU - Göker, M. AU - Rohde, M. AU - Spröer, C. AU - Schumann, P. AU - Busse, H. J. PY - 2013 DA - 2013// TI - Chryseobacterium hispalense sp. nov., a plantgrowth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium JO - Int J Syst Evol Microbiol VL - 63 UR - https://doi.org/10.1099/ijs.0.052456-0 DO - 10.1099/ijs.0.052456-0 ID - Montero-Calasanz2013 ER - TY - JOUR AU - Pagani, I. AU - Liolios, K. AU - Jansson, J. AU - Chen, I. M. A. AU - Smirnova, T. AU - Nosrat, B. PY - 2012 DA - 2012// TI - The Genomes OnLine Database (GOLD) v. 4: Status of genomic and metagenomic projects and their associated metadata JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr1100 DO - 10.1093/nar/gkr1100 ID - Pagani2012 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 - Piao, H. AU - Froula, J. AU - Du, C. AU - Kim, T. W. AU - Hawley, E. R. AU - Bauer, S. PY - 2014 DA - 2014// TI - Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation JO - Biotechnol Bioeng VL - 111 UR - https://doi.org/10.1002/bit.25250 DO - 10.1002/bit.25250 ID - Piao2014 ER - TY - JOUR AU - Pinhassi, J. AU - Sala, M. M. AU - Havskum, H. AU - Peters, F. AU - Guadayol, O. AU - Malits, A. PY - 2004 DA - 2004// TI - Changes in bacterioplankton composition under different phytoplankton regimens JO - Appl Env Microbiol VL - 70 UR - https://doi.org/10.1128/AEM.70.11.6753-6766.2004 DO - 10.1128/AEM.70.11.6753-6766.2004 ID - Pinhassi2004 ER - TY - BOOK PY - 2014 DA - 2014// TI - R: a language and environment for statistical computing ID - ref63 ER - TY - JOUR AU - Rawlings, N. D. AU - Waller, M. AU - Barrett, A. J. AU - Bateman, A. PY - 2014 DA - 2014// TI - MEROPS: the database of proteolytic enzymes, their substrates and inhibitors JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt953 DO - 10.1093/nar/gkt953 ID - Rawlings2014 ER - TY - CHAP AU - Reichenbach, H. ED - Staley, J. T. ED - Bryant, M. P. ED - Pfennig, N. ED - Holt, J. G. PY - 1989 DA - 1989// TI - Order 1. Cytophagales Leadbetter 1974, 99AL BT - Bergey’s Manual of Systematic Bacteriology, vol. 3 PB - Springer New York CY - New York ID - Reichenbach1989 ER - TY - JOUR AU - Ryu, S. H. AU - Park, M. AU - Jeon, Y. AU - Lee, J. R. AU - Park, W. AU - Jeon, C. O. PY - 2007 DA - 2007// TI - Flavobacterium filum sp. nov., isolated from a wastewater treatment plant in Korea JO - Int J Syst Evol Microbiol VL - 57 UR - https://doi.org/10.1099/ijs.0.65138-0 DO - 10.1099/ijs.0.65138-0 ID - Ryu2007 ER - TY - JOUR AU - Sonnenburg, E. D. AU - Zheng, H. AU - Joglekar, P. AU - Higginbottom, S. K. AU - Firbank, S. J. AU - Bolam, D. N. PY - 2010 DA - 2010// TI - Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations JO - Cell VL - 141 UR - https://doi.org/10.1016/j.cell.2010.05.005 DO - 10.1016/j.cell.2010.05.005 ID - Sonnenburg2010 ER - TY - CHAP AU - Stutzer, M. ED - Stutzer, M. ED - Kwaschnina, A. PY - 1929 DA - 1929// TI - Aussaaten aus den Fäzes des Menschen gelbe Kolonien bildende Bakterien (Gattung Flavobacterium u.a.) BT - Zentralblatt fur Bakteriologie, Parasitenkunde, Infektionskrankheiten und Hygiene. Abteilung I.vol 113 ID - Stutzer1929 ER - TY - JOUR AU - Täubel, M. AU - Rintala, H. AU - Pitkäranta, M. AU - Paulin, L. AU - Laitinen, S. AU - Pekkanen, J. PY - 2009 DA - 2009// TI - The occupant as a source of house dust bacteria JO - J Allergy Clin Immunol VL - 124 UR - https://doi.org/10.1016/j.jaci.2009.07.045 DO - 10.1016/j.jaci.2009.07.045 ID - Täubel2009 ER - TY - JOUR AU - Teeling, H. AU - Fuchs, B. M. AU - Becher, D. AU - Klockow, C. AU - Gardebrecht, A. AU - Bennke, C. M. PY - 2012 DA - 2012// TI - Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom JO - Science VL - 336 UR - https://doi.org/10.1126/science.1218344 DO - 10.1126/science.1218344 ID - Teeling2012 ER - TY - JOUR AU - Vancanneyt, M. AU - Segers, P. AU - Torck, U. AU - Hoste, B. AU - Bernardet, J. -. F. AU - Vandamme, P. PY - 1996 DA - 1996// TI - Reclassification of Flavobacterium odoratum (Stutzer 1929) strains to a new genus, Myroides, as Myroides odoratus comb. nov. and Myroides odoratimimus sp. nov JO - Int J Syst Bacteriol VL - 46 UR - https://doi.org/10.1099/00207713-46-4-926 DO - 10.1099/00207713-46-4-926 ID - Vancanneyt1996 ER - TY - BOOK AU - Wickham, H. PY - 2009 DA - 2009// TI - ggplot2: Elegant graphics for data analysis PB - Springer CY - New York UR - https://doi.org/10.1007/978-0-387-98141-3 DO - 10.1007/978-0-387-98141-3 ID - Wickham2009 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 - JOUR AU - Wu, D. AU - Hugenholtz, P. AU - Mavromatis, K. AU - Pukall, R. AU - Dalin, E. AU - Ivanova, N. N. 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 - JOUR AU - Ye, Y. AU - Choi, J. -. H. AU - Tang, H. PY - 2011 DA - 2011// TI - RAPSearch: a fast protein similarity search tool for short reads JO - BMC Bioinformatics VL - 12 UR - https://doi.org/10.1186/1471-2105-12-159 DO - 10.1186/1471-2105-12-159 ID - Ye2011 ER - TY - JOUR AU - Yin, Y. AU - Mao, X. AU - Yang, J. AU - Chen, X. AU - Mao, F. AU - Xu, Y. PY - 2012 DA - 2012// TI - dbCAN: A web resource for automated carbohydrate-active enzyme annotation JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gks479 DO - 10.1093/nar/gks479 ID - Yin2012 ER - TY - JOUR AU - Zerbino, D. R. AU - Velvet, B. E. PY - 2008 DA - 2008// TI - 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 - Zhao, Y. AU - Tang, H. AU - Ye, Y. PY - 2012 DA - 2012// TI - RAPSearch2: A fast and memory-efficient protein similarity search tool for next-generation sequencing data JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/btr595 DO - 10.1093/bioinformatics/btr595 ID - Zhao2012 ER -