-
1
-
-
0034068152
-
Syntrophothermus lipocalidus gen. nov., sp. nov., a novel thermophilic, syntrophic, fatty-acid-oxidizing anaerobe which utilizes isobutyrate
-
PubMed
-
Sekiguchi Y, Kamagata Y, Nakamura K, Ohashi A, Harada H. Syntrophothermus lipocalidus gen. nov., sp. nov., a novel thermophilic, syntrophic, fatty-acid-oxidizing anaerobe which utilizes isobutyrate. Int J Syst vol Microbiol 2000; 50:771-779. PubMed
-
(2000)
Int J Syst Vol Microbiol
, vol.50
, pp. 771-779
-
-
Sekiguchi, Y.1
Kamagata, Y.2
Nakamura, K.3
Ohashi, A.4
Harada, H.5
-
2
-
-
41349122137
-
-
The Prokaryotes, doi:10.1007/0-387-30744-3_37
-
Sobieraj M, Boone DR. Syntrophomonadaceae. The Prokaryotes 2006; 4:1041-1049. doi:10.1007/0-387-30744-3_37
-
(2006)
Syntrophomonadaceae
, vol.4
, pp. 1041-1049
-
-
Sobieraj, M.1
Boone, D.R.2
-
3
-
-
0034043778
-
Selection of conserved blocks from multiple alignments for their use in phylogenetic 273 Syntrophothermus lipocalidus type strain (TGB-C1T) analysis
-
PubMed
-
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic 273 Syntrophothermus lipocalidus type strain (TGB-C1T) analysis. Mol Biol Evol 2000; 17:540-552. PubMed
-
(2000)
Mol Biol Evol
, vol.17
, pp. 540-552
-
-
Castresana, J.1
-
4
-
-
0036203448
-
Multiple sequence alignment using partial order graphs
-
PubMed doi:10.1093/bioinformatics/18.3.452
-
Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452-464. PubMed doi:10.1093/bioinformatics/18.3.452
-
(2002)
BioinformatIcs
, vol.18
, pp. 452-464
-
-
Lee, C.1
Grasso, C.2
Sharlow, M.F.3
-
5
-
-
50249100595
-
A rapid bootstrap algorithm for the RAxML web servers
-
PubMeddoi:10.1080/10635150802429642
-
Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 2008; 57:758-771. PubMeddoi:10.1080/10635150802429642
-
(2008)
Syst Biol
, vol.57
, pp. 758-771
-
-
Stamatakis, A.1
Hoover, P.2
Rougemont, J.3
-
6
-
-
52149085893
-
The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains
-
PubMeddoi:10.1016/j.syapm.2008.07.001
-
Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rosselló Móra R. The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. yst Appl Microbiol 2008; 31:241-250. PubMeddoi:10.1016/j.syapm.2008.07.001
-
(2008)
Yst Appl Microbiol
, vol.31
, pp. 241-250
-
-
Yarza, P.1
Richter, M.2
Peplies, J.3
Euzeby, J.4
Amann, R.5
Schleifer, K.H.6
Ludwig, W.7
Glöckner, F.O.8
Rosselló Móra, R.9
-
7
-
-
67650340717
-
How many bootstrap replicates are necessary?
-
doi:10.1007/978-3-64202008-7_13
-
Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary? Lect Notes Comput Sci 2009; 5541:184-200. doi:10.1007/978-3-64202008-7_13
-
(2009)
Lect Notes Comput Sci
, vol.5541
, pp. 184-200
-
-
Pattengale, N.D.1
Alipour, M.2
Bininda-Emonds, O.R.P.3
Moret, B.M.E.4
Stamatakis, A.5
-
8
-
-
38549144166
-
The Genomes On Line Database (GOLD) in 2007: Status of genomic and metagenomic projects and their associated metadata
-
PubMeddoi:10.1093/nar/gkm884
-
Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2008; 36:D475-D479. PubMeddoi:10.1093/nar/gkm884
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Liolios, K.1
Mavromatis, K.2
Tavernarakis, N.3
Kyrpides, N.C.4
-
9
-
-
77955241649
-
The genome of Syntrophomonas wolfei: New insights into syntrophic metabolism and biohydrogen production
-
Sieber JR, Sims DR, Han C, Kim E, Lykidis A, Lapidus AL, McDonnald E, Rohlin L, Culley DE, Gunsalus R, et al. The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production. Environ Microbiol 2010; 12:2289-2301.
-
(2010)
Environ MicroBiol
, vol.12
, pp. 2289-2301
-
-
Sieber, J.R.1
Sims, D.R.2
Han, C.3
Kim, E.4
Lykidis, A.5
Lapidus, A.L.6
McDonnald, E.7
Rohlin, L.8
Culley, D.E.9
Gunsalus, R.10
-
10
-
-
0029846623
-
Thermosyntropha lipolytica gen. nov., sp. nov., a lipolytic, anaerobic, alkalitolerant, thermophilic bacterium utilizing shortand long-chain fatty acids in syntrophic coculture with a methanogenic archaeum
-
PubMed doi:10.1099/00207713-46-4-1131
-
Svetlitshnyi V, Rainey F, Wiegel J. Thermosyntropha lipolytica gen. nov., sp. nov., a lipolytic, anaerobic, alkalitolerant, thermophilic bacterium utilizing shortand long-chain fatty acids in syntrophic coculture with a methanogenic archaeum. Int J Syst Bacteriol 1996; 46:1131-1137. PubMed doi:10.1099/00207713-46-4-1131
-
(1996)
Int J Syst Bacteriol
, vol.46
, pp. 1131-1137
-
-
Svetlitshnyi, V.1
Rainey, F.2
Wiegel, J.3
-
11
-
-
72649088719
-
Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm
-
PubMed doi:10.1038/ismej.2009.79
-
Brazelton WJ, Baross JA. Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm. ISME J 2009; 3:1420-1424. PubMed doi:10.1038/ismej.2009.79
-
(2009)
ISME J
, vol.3
, pp. 1420-1424
-
-
Brazelton, W.J.1
Baross, J.A.2
-
12
-
-
38449088143
-
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
-
PubMed doi:10.1093/dnares/dsm018
-
Kurokawa K, Itoh T. Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP, et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 2007; 14:169-181. PubMed doi:10.1093/dnares/dsm018
-
(2007)
DNA Res
, vol.14
, pp. 169-181
-
-
Kurokawa, K.1
Itoh, T.2
Kuwahara, T.3
Oshima, K.4
Toh, H.5
Toyoda, A.6
Takami, H.7
Morita, H.8
Sharma, V.K.9
Srivastava, T.P.10
-
13
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
PubMeddoi:10.1128/AEM.03006-05
-
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL ̧Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006; 72:5069-5072. PubMeddoi:10.1128/AEM.03006-05
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 5069-5072
-
-
Desantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
Keller, K.6
Huber, T.7
Dalevi, D.8
Hu, P.9
Andersen, G.L.10
-
14
-
-
43449108562
-
The minimum information about a genome sequence (MIGS) specification
-
PubMeddoi:10.1038/nbt1360
-
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli V, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547 PubMeddoi:10.1038/nbt1360
-
(2008)
Nat Biotechnol
, vol.26
, pp. 541-547
-
-
Field, D.1
Garrity, G.2
Gray, T.3
Morrison, N.4
Selengut, J.5
Sterk, P.6
Tatusova, T.7
Thomson, N.8
Allen, M.J.9
Angiuoli, V.10
-
15
-
-
0025300402
-
Towards a natural system of organisms: Proposal for the do mains Archaea, Bacteria, and Eucarya
-
PubMeddoi:10.1073/pnas.87.12.4576
-
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the do mains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMeddoi:10.1073/pnas.87.12.4576
-
(1990)
Proc Natl Acad Sci USA
, vol.87
, pp. 4576-4579
-
-
Woese, C.R.1
Kandler, O.2
Wheelis, M.L.3
-
16
-
-
0000685441
-
-
In: Garrity GM, Boone DR, Castenholz RW, Bergey's Manual of Systematic Bacteriology, Second Edition, Springer, New York
-
Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1. Springer, New York 2001:119-169.
-
(2001)
The Road Map to The MaNual
, vol.1
, pp. 119-169
-
-
Garrity, G.M.1
-
17
-
-
0017843547
-
Proposals concerning the higher taxa of Bacteria
-
doi:10.1099/00207713-28-1-1
-
Gibbons NE, Murray RGE. Proposals concerning the higher taxa of Bacteria. Int J Syst Bacteriol 1978; 28:1-6. doi:10.1099/00207713-28-1-1
-
(1978)
Int J Syst Bacteriol
, vol.28
, pp. 1-6
-
-
Gibbons, N.E.1
Murray, R.G.E.2
-
18
-
-
80053365349
-
List of new names and new combinations previously effectively
-
Validation list 132, but not validly, published, doi:10.1099/ijs.0.022855-0
-
Validation list 132. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2010; 60:469-472. doi:10.1099/ijs.0.022855-0
-
(2010)
Int J Syst Evol Microbiol
, vol.60
, pp. 469-472
-
-
-
19
-
-
80053366426
-
Class II Clostridia class nov
-
In P. De Vos, G. Garrity, D. Jones, N. R. Krieg, W. Ludwig, F. A. Rainey, K. H. Schleifer, and W. B. Whitman (ed.), Bergey's Manual of Systematic Bacteriology, Second Edition ed, Springer, New York
-
Rainey FA. 2009. Class II. Clostridia class nov., p. 736. In P. De Vos, G. Garrity, D. Jones, N. R. Krieg, W. Ludwig, F. A. Rainey, K. H. Schleifer, and W. B. Whitman (ed.), Bergey's Manual of Systematic Bacteriology, Second Edition ed, vol. 3. Springer, New York.
-
(2009)
Bergey's Manual of Systematic Bacteriology
, vol.3
, pp. 736
-
-
Rainey, F.A.1
-
20
-
-
84860457375
-
-
P. Hauduroy, G. Ehringer, G. Guillot, J. Magrou, A. R. Prévot, Rosset and A. Urbain: Dictionnaire des Bactéries Pathogènes, 2nd ed., Masson, Paris
-
Prévot AR. in: P. Hauduroy, G. Ehringer, G. Guillot, J. Magrou, A. R. Prévot, Rosset and A. Urbain: Dictionnaire des Bactéries Pathogènes, 2nd ed., Masson, Paris, 1953, pp. 1-692.
-
(1953)
, pp. 1-692
-
-
Prévot, A.R.1
-
22
-
-
0027460195
-
Assignment of fatty acid-β-oxidizing syntrophic bacteria to Syntrophomonadaceae fam. nov. on the basis of 16S rRNA sequence analyses
-
PubMeddoi:10.1099/00207713-43-2-278
-
Zhao H, Yang D, Woese CR, Bryant MP. Assignment of fatty acid-β-oxidizing syntrophic bacteria to Syntrophomonadaceae fam. nov. on the basis of 16S rRNA sequence analyses. Int J Syst Bacteriol 1993; 43:278-286. PubMeddoi:10.1099/00207713-43-2-278
-
(1993)
Int J Syst Bacteriol
, vol.43
, pp. 278-286
-
-
Zhao, H.1
Yang, D.2
Woese, C.R.3
Bryant, M.P.4
-
23
-
-
67649828064
-
Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes'
-
PubMeddoi:10.1099/ijs.0.006718-0
-
Jumas-Bilak E, Roudiere L, Marchandin H. Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes'. Int J Syst Evol Microbiol 2009; 59:1028-1035. PubMeddoi:10.1099/ijs.0.006718-0
-
(2009)
Int J Syst Evol MiCrobiol
, vol.59
, pp. 1028-1035
-
-
Jumas-Bilak, E.1
Roudiere, L.2
Marchandin, H.3
-
24
-
-
84860473323
-
-
Classification of bacteria and archaea in risk groups, TRBA 466
-
Classification of bacteria and archaea in risk groups. http://www.baua.de TRBA 466.
-
-
-
-
25
-
-
0034069495
-
Gene Ontology: Tool for the unification of biology
-
PubMed doi:10.1038/75556
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25-29. PubMed doi:10.1038/75556
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
-
26
-
-
80053360071
-
T)
-
doi:10.4056/sigs.902116
-
T). Stand Genomic Sci 2010; 2:280-289.doi:10.4056/sigs.902116
-
(2010)
Stand Genomic Sci
, vol.2
, pp. 280-289
-
-
Chertkov, O.1
Sikorski, J.2
Brambilla, E.3
Lapidus, A.4
Copeland, A.5
Rio, T.G.D.6
Nolan, M.7
Lucas, S.8
Tice, H.9
Cheng, J.F.10
-
27
-
-
0019420777
-
Syntrophomonas wolfei gen. nov. sp. nov., an anaerobic, syntrophic, fatty acid-oxidizing bacterium
-
PubMed
-
McInerney MJ, Bryant MP, Hespell RB, Costerton JW. Syntrophomonas wolfei gen. nov. sp. nov., an anaerobic, syntrophic, fatty acid-oxidizing bacterium. Appl Environ Microbiol 1981; 41:1029-1039. PubMed
-
(1981)
Appl Environ Microbiol
, vol.41
, pp. 1029-1039
-
-
McInerney, M.J.1
Bryant, M.P.2
Hespell, R.B.3
Costerton, J.W.4
-
28
-
-
77952889628
-
En route to a genome-based classification of Archaea and Bacteria?
-
PubMed doi:10.1016/j.syapm.2010.03.003
-
Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175-182. PubMed doi:10.1016/j.syapm.2010.03.003
-
(2010)
Syst Appl Microbiol
, vol.33
, pp. 175-182
-
-
Klenk, H.P.1
Göker, M.2
-
29
-
-
72949101201
-
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
-
PubMeddoi:10.1038/nature08656
-
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009; 462:1056-1060. PubMeddoi:10.1038/nature08656
-
(2009)
Nature
, vol.462
, pp. 1056-1060
-
-
Wu, D.1
Hugenholtz, P.2
Mavromatis, K.3
Pukall, R.4
Dalin, E.5
Ivanova, N.N.6
Kunin, V.7
Goodwin, L.8
Wu, M.9
Tindall, B.J.10
-
30
-
-
84860457054
-
-
List of growth media used at DSMZ
-
List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php.
-
-
-
-
31
-
-
84860457379
-
-
DOE Joint Genome Institute
-
DOE Joint Genome Institute http://www.jgi.doe.gov
-
-
-
-
32
-
-
43149115851
-
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
-
PubMed doi:10.1101/gr.074492.107
-
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821-829. PubMed doi:10.1101/gr.074492.107
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
33
-
-
84860457383
-
-
Phrap and Phred for Windows, MacOS, Linux, and Unix
-
Phrap and Phred for Windows, MacOS, Linux, and Unix. http://www.phrap.com
-
-
-
-
34
-
-
79551643756
-
T)
-
doi:10.4056/sigs.761
-
T). Stand Genomic Sci 2009; 1:12-20. doi:10.4056/sigs.761
-
(2009)
Stand Genomic Sci
, vol.1
, pp. 12-20
-
-
Sims, D.1
Brettin, T.2
Detter, J.C.3
Han, C.4
Lapidus, A.5
Copeland, A.6
Glavina del Rio, T.7
Nolan, M.8
Chen, F.9
Lucas, S.10
-
35
-
-
80053362233
-
POLISHER: An effective tool for using ultra short reads in microbial genome assembly and finishing
-
Marco Island, FL
-
Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for using ultra short reads in microbial genome assembly and finishing. AGBT, Marco Island, FL, 2008.
-
(2008)
AGBT
-
-
Lapidus, A.1
Labutti, K.2
Foster, B.3
Lowry, S.4
Trong, S.5
Goltsman, E.6
-
36
-
-
77952299957
-
Podigal: Prokaryotic gene recognition and translation initiation site identification
-
PubMeddoi:10.1186/1471-2105-11-119
-
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Podigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMeddoi:10.1186/1471-2105-11-119
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 119
-
-
Hyatt, D.1
Chen, G.L.2
Locascio, P.F.3
Land, M.L.4
Larimer, F.W.5
Hauser, L.J.6
-
37
-
-
77953023066
-
GenePRIMP: A gene prediction improvement pipeline for microbial genomes
-
PubMed doi:10.1038/nmeth.1457
-
Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A gene prediction improvement pipeline for microbial genomes. Nat Methods 2010; 7:455-457. PubMed doi:10.1038/nmeth.1457
-
(2010)
Nat Methods
, vol.7
, pp. 455-457
-
-
Pati, A.1
Ivanova, N.2
Mikhailova, N.3
Ovchinikova, G.4
Hooper, S.D.5
Lykidis, A.6
Kyrpides, N.C.7
-
38
-
-
69949116874
-
IMG ER: A system for microbial genome annotation expert review and curation
-
PubMeddoi:10.1093/bioinformatics/btp393
-
Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271-2278. PubMeddoi:10.1093/bioinformatics/btp393
-
(2009)
BioInformatics
, vol.25
, pp. 2271-2278
-
-
Markowitz, V.M.1
Ivanova, N.N.2
Chen, I.M.A.3
Chu, K.4
Kyrpides, N.C.5
|