-
1
-
-
80053350587
-
NamesforLife. BrowserTool takes ex-pertise out of the database and puts it right in the browser
-
Garrity G. NamesforLife. BrowserTool takes ex-pertise out of the database and puts it right in the browser. Microbiol Today 2010; 7:1.
-
(2010)
Microbiol Today
, vol.7
, pp. 1
-
-
Garrity, G.1
-
2
-
-
27844547968
-
Bacteroides coprosuis sp. nov., iso-lated from swine-manure storage pits
-
PubMed doi:10.1099/ijs.0.63869-0
-
Whitehead TR, Cotta MA, Collins MD, Falsen E, Lawson PA. Bacteroides coprosuis sp. nov., iso-lated from swine-manure storage pits. Int J Syst Evol Microbiol 2005; 55:2515-2518. PubMed doi:10.1099/ijs.0.63869-0
-
(2005)
Int J Syst Evol Microbiol
, vol.55
, pp. 2515-2518
-
-
Whitehead, T.R.1
Cotta, M.A.2
Collins, M.D.3
Falsen, E.4
Lawson, P.A.5
-
3
-
-
67649406203
-
Importance of glycans to the host-bacteroides mutualism in the mammalian intes-tine
-
PubMed doi:10.1016/j.chom.2009.05.010
-
Comstock LE. Importance of glycans to the host-bacteroides mutualism in the mammalian intes-tine. Cell Host Microbe 2009; 5:522-526. PubMed doi:10.1016/j.chom.2009.05.010
-
(2009)
Cell Host Microbe
, vol.5
, pp. 522-526
-
-
Comstock, L.E.1
-
4
-
-
15544369658
-
Host-bacterial mutualism in the human intestine
-
PubMed doi:10.1126/science.1104816
-
Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science 2005; 307:1915-1920. PubMed doi:10.1126/science.1104816
-
(2005)
Science
, vol.307
, pp. 1915-1920
-
-
Bäckhed, F.1
Ley, R.E.2
Sonnenburg, J.L.3
Peterson, D.A.4
Gordon, J.I.5
-
6
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compat-ible with ARB
-
PubMed doi: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 compat-ible with ARB. Appl Environ Microbiol 2006; 72:5069-5072. PubMed doi: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
-
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
-
-
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. Bioinformat-ics 2002; 18:452-464. PubMed doi:10.1093/bioinformatics/18.3.452
-
(2002)
Bioinformat-ics
, vol.18
, pp. 452-464
-
-
Lee, C.1
Grasso, C.2
Sharlow, M.F.3
-
10
-
-
50249100595
-
A rapid bootstrap algorithm for the RAxML Web servers
-
PubMed doi:10.1080/10635150802429642
-
Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 2008; 57:758-771. PubMed doi:10.1080/10635150802429642
-
(2008)
Syst Biol
, vol.57
, pp. 758-771
-
-
Stamatakis, A.1
Hoover, P.2
Rougemont, J.3
-
11
-
-
67650340717
-
How many bootstrap replicates are necessary?
-
doi:10.1007/978-3-642-02008-7_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:10.1007/978-3-642-02008-7_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
-
12
-
-
75549086416
-
The Genomes On Line Database (GOLD) in 2009: Status of genomic and metagenomic projects and their associated metadata
-
PubMed doi:10.1093/nar/gkp848
-
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 doi: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
-
13
-
-
20044387585
-
Extensive DNA inversions in the B. fragilis genome control varia-ble gene expression
-
PubMed doi:10.1126/science.1107008
-
Cerdeño-Tárraga AM, Patrick S, Crossman LC, Blakely G, Abratt V, Lennard N, Poxton I, Duer-den B, Harris B, Quail MA, et al. Extensive DNA inversions in the B. fragilis genome control varia-ble gene expression. Science 2005; 307:1463-1465. PubMed doi:10.1126/science.1107008
-
(2005)
Science
, vol.307
, pp. 1463-1465
-
-
Cerdeño-Tárraga, A.M.1
Patrick, S.2
Crossman, L.C.3
Blakely, G.4
Abratt, V.5
Lennard, N.6
Poxton, I.7
Duer-Den, B.8
Harris, B.9
Quail, M.A.10
-
14
-
-
80053354421
-
Complete genome sequence of Bac-teroides helcogenes type strain (P36-108T)
-
PubMed doi:10.4056/sigs.1513795
-
Pati A, Gronow S, Zeytun A, Lapidus A, Nolan M, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, et al. Complete genome sequence of Bac-teroides helcogenes type strain (P36-108T). Stand Genomic Sci 2011; 4:45-53. PubMed doi:10.4056/sigs.1513795
-
(2011)
Stand Genomic Sci
, vol.4
, pp. 45-53
-
-
Pati, A.1
Gronow, S.2
Zeytun, A.3
Lapidus, A.4
Nolan, M.5
Hammon, N.6
Deshpande, S.7
Cheng, J.F.8
Tapia, R.9
Han, C.10
-
15
-
-
0037470975
-
A genom-ic view of the human-Bacteroides thetaiotaomi-cron symbiosis
-
PubMed doi:10.1126/science.1080029
-
Xu J, Bjursell MK, Himrod J, Deng S, Carmichael LK, Chiang HC, Hooper LV, Gordon JI. A genom-ic view of the human-Bacteroides thetaiotaomi-cron symbiosis. Science 2003; 299:2074-2076. PubMed doi:10.1126/science.1080029
-
(2003)
Science
, vol.299
, pp. 2074-2076
-
-
Xu, J.1
Bjursell, M.K.2
Himrod, J.3
Deng, S.4
Carmichael, L.K.5
Chiang, H.C.6
Hooper, L.V.7
Gordon, J.I.8
-
16
-
-
34447516925
-
Evolution of symbiotic bacteria in the distal human intestine
-
PubMed doi:10.1371/journal.pbio.0050156
-
Xu J, Mahowald MA, Ley RE, Lozupone CA, Ha-mady M, Martens EC, Henrissat B, Coutinho PM, Minx P, Latreille P, et al. Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol 2007; 5:e156. PubMed doi:10.1371/journal.pbio.0050156
-
(2007)
PLoS Biol
, vol.5
-
-
Xu, J.1
Mahowald, M.A.2
Ley, R.E.3
Lozupone, C.A.4
Ha-Mady, M.5
Martens, E.C.6
Henrissat, B.7
Coutinho, P.M.8
Minx, P.9
Latreille, P.10
-
17
-
-
80053540920
-
Complete genome sequence of Bacteroides salanitronis type strain (BL78T)
-
Gronow S, Held B, Lucas S, Lapidus A, Glavina Del Rio T, Nolan M, Tice H, Deshpande S, Cheng JF, Pitluck S, et al. Complete genome sequence of Bacteroides salanitronis type strain (BL78T). Stand Genomic Sci 2011; 4:191-199.
-
(2011)
Stand Genomic Sci
, vol.4
, pp. 191-199
-
-
Gronow, S.1
Held, B.2
Lucas, S.3
Lapidus, A.4
del Rio, G.T.5
Nolan, M.6
Tice, H.7
Deshpande, S.8
Cheng, J.F.9
Pitluck, S.10
-
18
-
-
43449108562
-
The minimum information about a genome sequence (MIGS) specification
-
PubMed doi:10.1038/nbt1360
-
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 doi: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
-
-
0025300402
-
Towards a natural system of organisms: Proposal for the do-mains Archaea, Bacteria, and Eucarya
-
PubMed doi: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. PubMed doi: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
-
20
-
-
0000685441
-
The Road Map to the Ma-nual
-
In: Garrity GM, Boone DR, Castenholz RW (eds), Second Edition, Springer, New York
-
Garrity GM, Holt JG. The Road Map to the Ma-nual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriolo-gy, Second Edition, Volume 1, Springer, New York, 2001, p. 119-169.
-
(2001)
Bergey's Manual of Systematic Bacteriolo-gy
, vol.1
, pp. 119-169
-
-
Garrity, G.M.1
Holt, J.G.2
-
21
-
-
70350704116
-
-
Taxonomic Outline
-
Ludwig W, Euzeby J, Whitman WG. Draft tax-onomic outline of the Bacteroidetes, Planctomy-cetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes. http://www.bergeys.org/outlines/Bergeys_Vol_4_Outline.pdf. Taxonomic Outline 2008.
-
(2008)
Draft Tax-onomic Outline of the Bacteroidetes, Planctomy-cetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes
-
-
Ludwig, W.1
Euzeby, J.2
Whitman, W.G.3
-
22
-
-
0000685441
-
Taxonomic outline of the Archaea and Bacteria
-
In: Garrity GM, Boone DR, Castenholz RW (eds), 2nd ed, Springer, New York
-
Garrity GM, Holt JG. 2001. Taxonomic outline of the Archaea and Bacteria, p. 155-166. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, 2nd ed, vol. 1. Springer, New York.
-
(2001)
Bergey's Manual of Systematic Bacteriology
, vol.1
, pp. 155-166
-
-
Garrity, G.M.1
Holt, J.G.2
-
25
-
-
0004198066
-
Genus Bacteroides Castellani and Chalmers, 1918
-
Third Edition, Williams, Wood and Co., New York
-
Castellani A, Chalmers AJ. Genus Bacteroides Castellani and Chalmers, 1918. Manual of Tropi-cal Medicine, Third Edition, Williams, Wood and Co., New York, 1919, p. 959-960.
-
(1919)
Manual of Tropi-cal Medicine
, pp. 959-960
-
-
Castellani, A.1
Chalmers, A.J.2
-
26
-
-
0343204930
-
Bacteroides Castellani and Chalmers 1919, 959
-
In: Buchanan RE, Gibbons NE (eds), Eighth Edition, The Wil-liams and Wilkins Co., Baltimore
-
Holdeman LV, Moore WEC., Genus I. Bacteroides Castellani and Chalmers 1919, 959. In: Buchanan RE, Gibbons NE (eds), Bergey's Manual of Deter-minative Bacteriology, Eighth Edition, The Wil-liams and Wilkins Co., Baltimore, 1974, p. 385-404.
-
(1974)
Bergey's Manual of Deter-minative Bacteriology
, pp. 385-404
-
-
Holdeman, L.V.1
Moore, W.E.C.2
Genus, I.3
-
27
-
-
0020379599
-
Bacteroides zoogleoformans, Weinberg, Nati-velle, and Prévot 1937) corrig. comb. nov.: Emended description
-
doi:10.1099/00207713-32-3-271
-
Cato EP, Kelley RW, Moore WEC, Holdeman LV. Bacteroides zoogleoformans, Weinberg, Nati-velle, and Prévot 1937) corrig. comb. nov.: emended description. Int J Syst Bacteriol 1982; 32:271-274. doi:10.1099/00207713-32-3-271
-
(1982)
Int J Syst Bacteriol
, vol.32
, pp. 271-274
-
-
Cato, E.P.1
Kelley, R.W.2
Moore, W.E.C.3
Holdeman, L.V.4
-
28
-
-
0024529810
-
Proposal to restrict the genus Bacteroides (Castellani and Chalmers) to Bacteroides fragilis and closely related species
-
doi:10.1099/00207713-39-1-85
-
Shah HN, Collins MD. Proposal to restrict the genus Bacteroides (Castellani and Chalmers) to Bacteroides fragilis and closely related species. Int J Syst Bacteriol 1989; 39:85-87. doi:10.1099/00207713-39-1-85
-
(1989)
Int J Syst Bacteriol
, vol.39
, pp. 85-87
-
-
Shah, H.N.1
Collins, M.D.2
-
29
-
-
80053374956
-
Classification of bacteria and archaea in risk groups
-
BAuA
-
BAuA. Classification of bacteria and archaea in risk groups. TRBA 2005; 466:84.
-
(2005)
TRBA
, vol.466
, pp. 84
-
-
-
30
-
-
0034069495
-
Gene Ontology: Tool for the unification of biology
-
PubMed doi:10.1038/75556
-
Ashburner M, Ball CA, Blake JA, Botstein D, But-ler 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
But-Ler, 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 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
-
32
-
-
72949101201
-
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
-
PubMed doi: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. PubMed doi: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
-
34
-
-
79953824958
-
The DNA Bank Network: The start from a German initiative
-
doi:10.1089/bio.2010.0029
-
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. Biopreservation and Biobanking 2011; 9:51-55. doi:10.1089/bio.2010.0029
-
(2011)
Biopreservation and Biobanking
, 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
-
35
-
-
84860509577
-
-
The DOE Joint Genome Institute
-
The DOE Joint Genome Institute. http://www.jgi.doe.gov
-
-
-
-
37
-
-
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
-
38
-
-
79551643756
-
Complete genome sequence of Kytococcus sedentarius type strain (541T)
-
PubMed doi:10.4056/sigs.761
-
Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, et al. Complete genome sequence of Kytococcus sedentarius type strain (541T). Stand Genomic Sci 2009; 1:12-20. PubMed 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
del Rio, G.T.7
Nolan, M.8
Chen, F.9
Lucas, S.10
-
39
-
-
80053373249
-
-
AGBT, Marco Island, FL
-
Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for us-ing ultra short reads in microbial genome assem-bly and finishing. AGBT, Marco Island, FL, 2008.
-
(2008)
POLISHER: An Effective Tool For Us-ing Ultra Short Reads In Microbial Genome Assem-bly and Finishing
-
-
Lapidus, A.1
Labutti, K.2
Foster, B.3
Lowry, S.4
Trong, S.5
Goltsman, E.6
-
40
-
-
77952299957
-
Prodigal: Prokaryotic gene recognition and translation initiation site identifi-cation
-
PubMed doi:10.1186/1471-2105-11-119
-
Hyatt D, Chen GL, LoCascio PF, Land ML, Lari-mer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identifi-cation. BMC Bioinformatics 2010; 11:119. PubMed doi: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
Lari-Mer, F.W.5
Hauser, L.J.6
-
41
-
-
77953023066
-
Gene-PRIMP: A gene prediction improvement pipeline for prokaryotic genomes
-
PubMed doi:10.1038/nmeth.1457
-
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 doi: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
-
42
-
-
69949116874
-
IMG ER: A system for microbial ge-nome annotation expert review and curation
-
PubMed doi:10.1093/bioinformatics/btp393
-
Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial ge-nome annotation expert review and curation. Bio-informatics 2009; 25:2271-2278. PubMed doi: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
-
43
-
-
77952891913
-
Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome se-quence comparison
-
PubMed doi:10.4056/sigs.531120
-
Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome se-quence comparison. Stand Genomic Sci 2010; 2:117-134. PubMed doi:10.4056/sigs.531120
-
(2010)
Stand Genomic Sci
, vol.2
, pp. 117-134
-
-
Auch, A.F.1
von Jan, M.2
Klenk, H.P.3
Göker, M.4
-
44
-
-
77952891045
-
Standard opera-tional procedure for calculation genome-to-genome distances based on high-scoring se-quence pairs
-
PubMed doi:10.4056/sigs.541628
-
Auch AF, Klenk HP, Göker M. Standard opera-tional procedure for calculation genome-to-genome distances based on high-scoring se-quence pairs. Stand Genomic Sci 2010; 2:142-148. PubMed doi:10.4056/sigs.541628
-
(2010)
Stand Genomic Sci
, vol.2
, pp. 142-148
-
-
Auch, A.F.1
Klenk, H.P.2
Göker, M.3
|