-
1
-
-
0031854856
-
Desulfurobacterium thermolithotrophum gen. nov., sp. nov., a novel autotrophic, sulphurreducing bacterium isolated from a deep-sea hydrothermal vent
-
PubMed
-
L'Haridon S, Cilia V, Messner P, Raguénès G, Gambacorta A, Sleytr UB, Prieur D, Jeanthon C. Desulfurobacterium thermolithotrophum gen. nov., sp. nov., a novel autotrophic, sulphurreducing bacterium isolated from a deep-sea hydrothermal vent. Int J Syst Bacteriol 1998; 48:701-711. PubMed http://dx.doi.org/10.1099/00207713-48-3-701
-
(1998)
Int J Syst Bacteriol
, vol.48
, pp. 701-711
-
-
L'haridon, S.1
Cilia, V.2
Messner, P.3
Raguénès, G.4
Gambacorta, A.5
Sleytr, U.B.6
Prieur, D.7
Jeanthon, C.8
-
2
-
-
22544439061
-
-
List of Changes in Taxonomic Opinion N° 2, PubMed
-
List of Changes in Taxonomic Opinion N° 2. Int J Syst Evol Microbiol 2005; 55:1403-1404. PubMed
-
(2005)
Int J Syst Evol Microbiol
, vol.55
, pp. 1403-1404
-
-
-
3
-
-
0025183708
-
Basic local alignment search tool
-
PubMed
-
Altschul SF, Gish W, Miller W, Myers EW, Lip-man DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-410. PubMed
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lip-Man, D.J.5
-
5
-
-
33746061683
-
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
-
PubMed
-
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. PubMed http://dx.doi.org/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
-
7
-
-
0036203448
-
Multiple sequence alignment using partial order graphs
-
PubMed
-
Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformat-ics 2002; 18:452-464. PubMed http://dx.doi.org/10.1093/bioinformatics/18.3.452
-
(2002)
Bioinformat-ics
, vol.18
, pp. 452-464
-
-
Lee, C.1
Grasso, C.2
Sharlow, M.F.3
-
8
-
-
0034043778
-
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
-
PubMed
-
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed
-
(2000)
Mol Biol Evol
, vol.17
, pp. 540-552
-
-
Castresana, J.1
-
9
-
-
50249100595
-
A rapid bootstrap algorithm for the RAxML web-servers
-
PubMed
-
Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web-servers. Syst Biol 2008; 57:758-771. PubMed http://dx.doi.org/10.1080/10635150802429642
-
(2008)
Syst Biol
, vol.57
, pp. 758-771
-
-
Stamatakis, A.1
Hoover, P.2
Rougemont, J.3
-
10
-
-
36849014457
-
An empirical test of the midpoint rooting method
-
Hess PN, De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond 2007; 92:669-674. http://dx.doi.org/10.1111/j.1095-8312.2007.00864.x
-
(2007)
Biol J Linn Soc Lond
, vol.92
, pp. 669-674
-
-
Hess, P.N.1
de Moraes Russo, C.A.2
-
11
-
-
77950820827
-
How many bootstrap replicatesa necessary?
-
Pattengale ND, Alipour M, Bininda-Emonds OR, Moret BM, Stamatakis A. How many bootstrap replicatesa necessary? J Comput Biol 2010; 17:337-354.
-
(2010)
J Comput Biol
, vol.17
, pp. 337-354
-
-
Pattengale, N.D.1
Alipour, M.2
Bininda-Emonds, O.R.3
Moret, B.M.4
Stamatakis, A.5
-
13
-
-
75549086416
-
The Genomes On Line Database (GOLD) in 2009: Status of genomic and metagenomic projects and their associated metadata
-
PubMed
-
Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346-D354. PubMed http://dx.doi.org/10.1093/nar/gkp848
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Liolios, K.1
Chen, I.M.2
Mavromatis, K.3
Tavernarakis, N.4
Hugenholtz, P.5
Markowitz, V.M.6
Kyrpides, N.C.7
-
14
-
-
63049100194
-
Complete and draft genome sequences of six members of the Aquifi-cales
-
PubMed
-
Reysenbach AL, Hamamura N, Podar M, Griffiths E, Ferreira S, Hochstein R, Heidelberg J, Johnson J, Mead D, Pohorille A, et al. Complete and draft genome sequences of six members of the Aquifi-cales. J Bacteriol 2009; 191:1992-1993. PubMed http://dx.doi.org/10.1128/JB.01645-08
-
(2009)
J Bacteriol
, vol.191
, pp. 1992-1993
-
-
Reysenbach, A.L.1
Hamamura, N.2
Podar, M.3
Griffiths, E.4
Ferreira, S.5
Hochstein, R.6
Heidelberg, J.7
Johnson, J.8
Mead, D.9
Pohorille, A.10
-
15
-
-
80053488702
-
T)
-
PubMed
-
T). Stand Genomic Sci 2011; 4:131-143. PubMed http://dx.doi.org/10.4056/sigs.1463589
-
(2011)
Stand Genomic Sci
, vol.4
, pp. 131-143
-
-
Zeytun, A.1
Sikorski, J.2
Nolan, M.3
Lapidus, A.4
Lucas, S.5
Han, J.6
Tice, H.7
Cheng, J.F.8
Tapia, R.9
Goodwin, L.10
-
16
-
-
77952021090
-
Complete genome sequence of the thermophilic, obligately chemolithoautotrophic hydrogen-oxidizing bacterium Hydrogenobacter thermophilus TK-6
-
PubMed
-
Arai H, Kanbe H, Ishii M, Igarashi Y. Complete genome sequence of the thermophilic, obligately chemolithoautotrophic hydrogen-oxidizing bacterium Hydrogenobacter thermophilus TK-6. J Bac-teriol 2010; 192:2651-2652. PubMed http://dx.doi.org/10.1128/JB.00158-10
-
(2010)
J Bac-teriol
, vol.192
, pp. 2651-2652
-
-
Arai, H.1
Kanbe, H.2
Ishii, M.3
Igarashi, Y.4
-
17
-
-
79957549093
-
T)
-
PubMed
-
T). Stand Ge-nomic Sci 2010; 2:194-202. PubMed http://dx.doi.org/10.4056/sigs.761490
-
(2010)
Stand Ge-nomic Sci
, vol.2
, pp. 194-202
-
-
Wirth, R.1
Sikorski, J.2
Brambilla, E.3
Misra, M.4
Lapidus, A.5
Copeland, A.6
Nolan, M.7
Lucas, S.8
Chen, F.9
Tice, H.10
-
18
-
-
43449108562
-
The minimum information about a genome sequence (MIGS) specification
-
PubMed
-
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, An-giuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. PubMed http://dx.doi.org/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
An-Giuoli, S.V.10
-
19
-
-
77955908592
-
NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser
-
Garrity G. NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser. Microbiol Today 2010; 37:9.
-
(2010)
Microbiol Today
, vol.37
, pp. 9
-
-
Garrity, G.1
-
20
-
-
0025300402
-
Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya
-
PubMed
-
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed http://dx.doi.org/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
-
21
-
-
0000685441
-
The Road Map to the Manual
-
In: Garrity GM, Boone DR, Castenholz RW, 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, p. 119-169.
-
(2001)
Bergey's Manual of Systematic Bacteriology
, vol.1
, pp. 119-169
-
-
Garrity, G.M.1
Holt, J.G.2
-
22
-
-
0000864719
-
Aquificae
-
In: Garrity GM, Boone DR, Castenholz RW, Second Edition, Springer, New York
-
Reysenbach AL. Phylum BI. Aquificae. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 359-367.
-
(2001)
Bergey's Manual of Systematic Bacteriology
, vol.1
, pp. 359-367
-
-
Reysenbach, A.L.1
Phylum, B.I.2
-
23
-
-
0036560850
-
Validation List no. 85. Validation of publication of new names and new combinations previously effectively published outside the IJ-SEM
-
List Editor, PubMed
-
List Editor. Validation List no. 85. Validation of publication of new names and new combinations previously effectively published outside the IJ-SEM. Int J Syst Evol Microbiol 2002; 52:685-690. PubMed http://dx.doi.org/10.1099/ijs.0.02358-0
-
(2002)
Int J Syst Evol Microbiol
, vol.52
, pp. 685-690
-
-
-
24
-
-
0000864719
-
Aquificae class. nov
-
In: Garrity GM, Boone DR, Castenholz RW, Second Edition, Springer, New York
-
Reysenbach AL. Class I. Aquificae class. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 359.
-
(2001)
Bergey's Manual of Systematic Bacteriology
, vol.1
, pp. 359
-
-
Reysenbach, A.L.1
Class, I.2
-
25
-
-
33845721741
-
Desulfurobacterium atlanticum sp. nov., Desulfuro-bacterium pacificum sp. nov. and Thermovibrio guaymasensis sp. nov., three thermophilic members of the Desulfurobacteriaceae fam. nov., a deep branching lineage within the Bacteria
-
PubMed
-
Lharidon S, Reysenbach AL, Tindall BJ, Schönheit P, Banta A, Johnsen U, Schumann P, Gambacorta A, Stackebrandt E, Jeanthon C. Desulfurobacterium atlanticum sp. nov., Desulfuro-bacterium pacificum sp. nov. and Thermovibrio guaymasensis sp. nov., three thermophilic members of the Desulfurobacteriaceae fam. nov., a deep branching lineage within the Bacteria. Int J Syst Evol Microbiol 2006; 56:2843-2852. PubMed http://dx.doi.org/10.1099/ijs.0.63994-0
-
(2006)
Int J Syst Evol Microbiol
, vol.56
, pp. 2843-2852
-
-
Lharidon, S.1
Reysenbach, A.L.2
Tindall, B.J.3
Schönheit, P.4
Banta, A.5
Johnsen, U.6
Schumann, P.7
Gambacorta, A.8
Stackebrandt, E.9
Jeanthon, C.10
-
26
-
-
0000864719
-
Aquificales ord. nov
-
In: Garrity GM, Boone DR, Castenholz RW, Second Edition, Springer, New York
-
Reysenbach AL. Order I. Aquificales ord. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 359.
-
(2001)
Bergey's Manual of Systematic Bacteriology
, vol.1
, pp. 359
-
-
Reysenbach, A.L.1
Order, I.2
-
27
-
-
0842272953
-
Desulfurobacte-rium crinifex sp. nov., a novel thermophilic, pinkish-streamer forming, chemolithoauto-trophic bacterium isolated from a Juan de Fuca Ridge hy-drothermal vent and amendment of the genus De-sulfurobacterium
-
PubMed
-
Alain K, Rolland S, Crassous P, Lesongeur F, Zbinden M, le Gall C, Godfroy A, Page A, Juniper SK, Cambon-Bonavita MA, et al. Desulfurobacte-rium crinifex sp. nov., a novel thermophilic, pinkish-streamer forming, chemolithoauto-trophic bacterium isolated from a Juan de Fuca Ridge hy-drothermal vent and amendment of the genus De-sulfurobacterium. Extremophiles 2003; 7:361-370. PubMed http://dx.doi.org/10.1007/s00792-003-0329-4
-
(2003)
Extremophiles
, vol.7
, pp. 361-370
-
-
Alain, K.1
Rolland, S.2
Crassous, P.3
Lesongeur, F.4
Zbinden, M.5
le Gall, C.6
Godfroy, A.7
Page, A.8
Juniper, S.K.9
Cambon-Bonavita, M.A.10
-
29
-
-
0030788862
-
Distribution of microorganisms in deep-sea hydrothermal vent chimneys investigated by whole-cell hybridization and enrichments of thermophilic subpopula-tions
-
PubMed
-
Harmsen HJM, Prieur D, Jeanthon C. Distribution of microorganisms in deep-sea hydrothermal vent chimneys investigated by whole-cell hybridization and enrichments of thermophilic subpopula-tions. Appl Environ Microbiol 1997; 63:2876-2883. PubMed
-
(1997)
Appl Environ Microbiol
, vol.63
, pp. 2876-2883
-
-
Harmsen, H.J.M.1
Prieur, D.2
Jeanthon, C.3
-
30
-
-
0034069495
-
Gene Ontology: Tool for the unification of biology
-
PubMed
-
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 http://dx.doi.org/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
-
31
-
-
77952889628
-
En route to a genome-based classification of Archaea and Bacteria?
-
PubMed
-
Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175-182. PubMed http://dx.doi.org/10.1016/j.syapm.2010.03.003
-
(2010)
Syst Appl Microbiol
, vol.33
, pp. 175-182
-
-
Klenk, H.P.1
Göker, M.2
-
32
-
-
72949101201
-
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
-
PubMed
-
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. PubMed http://dx.doi.org/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
-
33
-
-
69949116874
-
IMG ER: A system for microbial genome annotation expert review and curation
-
PubMed
-
Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bio-informatics 2009; 25:2271-2278. PubMed http://dx.doi.org/10.1093/bioinformatics/btp393
-
(2009)
Bio-informatics
, 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
-
34
-
-
84863420517
-
-
List of growth media used at DSMZ
-
List of growth media used at DSMZ: http//www.dsmz.de/catalogues/catalogue-microorganisms/culture-technology/list-of-media-for-microorganisms.html.
-
-
-
-
35
-
-
79953824958
-
The DNA Bank Network: The start from a German initiative
-
Gemeinholzer B, Dröge G, Zetzsche H, Haszpru-nar G, Klenk HP, Güntsch A, Berendsohn WG, Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreserv Biobank 2011; 9:51-55. http://dx.doi.org/10.1089/bio.2010.0029
-
(2011)
Biopreserv Biobank
, vol.9
, pp. 51-55
-
-
Gemeinholzer, B.1
Dröge, G.2
Zetzsche, H.3
Haszpru-Nar, G.4
Klenk, H.P.5
Güntsch, A.6
Berendsohn, W.G.7
Wägele, J.W.8
-
36
-
-
84863420518
-
-
JGI website
-
JGI website. http://www.jgi.doe.gov/
-
-
-
-
37
-
-
84863410450
-
-
The Phred/Phrap/Consed software package
-
The Phred/Phrap/Consed software package. http://www.phrap.com
-
-
-
-
38
-
-
43149115851
-
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
-
PubMed
-
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821-829. PubMed http://dx.doi.org/10.1101/gr.074492.107
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
40
-
-
80053373249
-
-
AGBT, 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)
POLISHER: An Effective Tool For Using Ultra Short Reads In Microbial Genome Assembly and Finishing
-
-
Lapidus, A.1
Labutti, K.2
Foster, B.3
Lowry, S.4
Trong, S.5
Goltsman, E.6
-
41
-
-
77952299957
-
Prodigal: Prokaryotic gene recognition and translation initiation site identification
-
PubMed
-
Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMed http://dx.doi.org/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
-
42
-
-
77953023066
-
Gene-PRIMP: A gene prediction improvement pipeline for prokaryotic genomes
-
PubMed
-
Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. Gene-PRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455-457. PubMed http://dx.doi.org/10.1038/nmeth.1457
-
(2010)
Nat Methods
, vol.7
, pp. 455-457
-
-
Pati, A.1
Ivanova, N.N.2
Mikhailova, N.3
Ovchinnikova, G.4
Hooper, S.D.5
Lykidis, A.6
Kyrpides, N.C.7
|