-
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
-
-
40449099160
-
Trans-fer of Bacteroides splanchnicus to Odoribacter gen. nov. as Odoribacter splanchnicus comb. nov., and description of Odoribacter denticanis sp. nov., isolated from the crevicular spaces of canine periodontitis patients
-
PubMed doi:10.1099/ijs.0.63458-0
-
Hardham JM, King KW, Dreier K, Wong J, Striet-zel C, Eversole RR, Sfintescu C, Evans RT. Trans-fer of Bacteroides splanchnicus to Odoribacter gen. nov. as Odoribacter splanchnicus comb. nov., and description of Odoribacter denticanis sp. nov., isolated from the crevicular spaces of canine periodontitis patients. Int J Syst Evol Mi-crobiol 2008; 58:103-109. PubMed doi:10.1099/ijs.0.63458-0
-
(2008)
Int J Syst Evol Mi-crobiol
, vol.58
, pp. 103-109
-
-
Hardham, J.M.1
King, K.W.2
Dreier, K.3
Wong, J.4
Striet-Zel, C.5
Eversole, R.R.6
Sfintescu, C.7
Evans, R.T.8
-
5
-
-
0000240137
-
The genus Bacteroides and re-lated species
-
In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer K.-H (ed.), 2nd ed. Springer, New York
-
Shah HN. 1992. The genus Bacteroides and re-lated species, p.3593-3607. In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer K.-H (ed.), The prokaryotes, 2nd ed. Springer, New York.
-
(1992)
The Prokaryotes
, pp. 3593-3607
-
-
Shah, H.N.1
-
6
-
-
0022656650
-
Ribosomal ribonucleic acid homology among species of the genus Bacte-roides
-
doi:10.1099/00207713-36-1-71
-
Johnson JL, Harich B. Ribosomal ribonucleic acid homology among species of the genus Bacte-roides. Int J Syst Bacteriol 1986; 36:71-79. doi:10.1099/00207713-36-1-71
-
(1986)
Int J Syst Bacteriol
, vol.36
, pp. 71-79
-
-
Johnson, J.L.1
Harich, B.2
-
7
-
-
0028118435
-
Phylo-geny of Bacteroides, Prevotella, and Porphyromo-nas spp. and related bacteria
-
PubMed
-
Paster BJ, Dewhirst FE, Olsen I, Fraser GJ. Phylo-geny of Bacteroides, Prevotella, and Porphyromo-nas spp. and related bacteria. J Bacteriol 1994; 176:725-732. PubMed
-
(1994)
J Bacteriol
, vol.176
, pp. 725-732
-
-
Paster, B.J.1
Dewhirst, F.E.2
Olsen, I.3
Fraser, G.J.4
-
8
-
-
0017393785
-
Pelviperitonitis and bacteremia due to Bacteroides splanchnicus. Report of a case
-
PubMed
-
Labbe M, Mertens A, Schoutens E. Pelviperitonitis and bacteremia due to Bacteroides splanchnicus. Report of a case. Zentralbl Bakteriol Orig A 1977; 238:251-254. PubMed
-
(1977)
Zentralbl Bakteriol Orig A
, vol.238
, pp. 251-254
-
-
Labbe, M.1
Mertens, A.2
Schoutens, E.3
-
9
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible 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 compatible 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
-
11
-
-
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
-
12
-
-
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
-
13
-
-
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
-
14
-
-
36849014457
-
An empirical test of the midpoint rooting method
-
doi:10.1111/j.1095-8312.2007.00864.x
-
Hess PN, De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond 2007; 92:669-674. doi: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
-
15
-
-
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
-
16
-
-
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
-
17
-
-
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
-
18
-
-
56149117939
-
Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rear-rangements in P. gingivalis
-
PubMed doi:10.1093/dnares/dsn013
-
Naito M, Hirakawa H, Yamashita A, Ohara N, Shoji M, Yukitake H, Nakayama K, Toh H, Yo-shimura F, Kuhara S, et al. Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rear-rangements in P. gingivalis. DNA Res 2008; 15:215-225. PubMed doi:10.1093/dnares/dsn013
-
(2008)
DNA Res
, vol.15
, pp. 215-225
-
-
Naito, M.1
Hirakawa, H.2
Yamashita, A.3
Ohara, N.4
Shoji, M.5
Yukitake, H.6
Nakayama, K.7
Toh, H.8
Yo-Shimura, F.9
Kuhara, S.10
-
19
-
-
80053379167
-
Complete genome sequence of Pa-ludibacter propionicigenes type strain (WB4T)
-
PubMed doi:10.1038/nbt1360
-
Gronow S, Munk C, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, et al. Complete genome sequence of Pa-ludibacter propionicigenes type strain (WB4T). Stand Genomic Sci 2011; 4:36-44. PubMed doi:10.1038/nbt1360
-
(2011)
Stand Genomic Sci
, vol.4
, pp. 36-44
-
-
Gronow, S.1
Munk, C.2
Lapidus, A.3
Nolan, M.4
Lucas, S.5
Hammon, N.6
Deshpande, S.7
Cheng, J.F.8
Tapia, R.9
Han, C.10
-
20
-
-
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
-
21
-
-
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
-
22
-
-
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
-
23
-
-
70350704116
-
-
Taxonomic Outline 2008
-
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
-
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
-
24
-
-
80053359202
-
Complete genome sequence of Leadbetterella byssophila type strain (4M15T)
-
PubMed doi:10.4056/sigs.1413518
-
Abt B, Tashima H, Lucas S, Lapidus A, Glavina Del Rio T, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, et al. Complete genome sequence of Leadbetterella byssophila type strain (4M15T). Stand Genomic Sci 2011; 4:2-12. PubMed doi:10.4056/sigs.1413518
-
(2011)
Stand Genomic Sci
, vol.4
, pp. 2-12
-
-
Abt, B.1
Tashima, H.2
Lucas, S.3
Lapidus, A.4
del Rio, G.T.5
Nolan, M.6
Tice, H.7
Cheng, J.F.8
Pitluck, S.9
Liolios, K.10
-
25
-
-
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. Taxonomic outline of the Archaea and Bacteria, In. Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Syste-matic Bacteriology, 2nd ed, vol. 1. Springer, New York, 2001, p. 155-166.
-
(2001)
Bergey's Manual of Syste-matic Bacteriology
, vol.1
, pp. 155-166
-
-
Garrity, G.M.1
Holt, J.G.2
-
26
-
-
84860535320
-
-
Classification of bacteria and archaea in risk groups
-
Classification of bacteria and archaea in risk groups. http://www.baua.deTRBA466.
-
-
-
-
27
-
-
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
-
28
-
-
0000529588
-
Anaerob-ic Gram-negative straight, curved and helical rods
-
In: Krieg NR, Holt JG (eds), 1st ed, Williams & Wilkins, Baltimore, USA
-
Holdeman LV, Kelley RW, Moore WEC. Anaerob-ic Gram-negative straight, curved and helical rods. In: Krieg NR, Holt JG (eds), Bergey's Manual of Systematic Bacteriology, 1st ed, vol. 1 Williams & Wilkins, Baltimore, USA,1984, p. 602-662.
-
(1984)
Bergey's Manual of Systematic Bacteriology
, vol.1
, pp. 602-662
-
-
Holdeman, L.V.1
Kelley, R.W.2
Moore, W.E.C.3
-
29
-
-
0003535096
-
-
4th ed, Southern Printing Co., Blacksburg, Virginia, USA
-
Holdeman LV, Cato EP, Moore WEC. 1974. Anaerobe laboratory manual, 4th ed, Southern Printing Co., Blacksburg, Virginia, USA.
-
(1974)
Anaerobe Laboratory Manual
-
-
Holdeman, L.V.1
Cato, E.P.2
Moore, W.E.C.3
-
30
-
-
0021012378
-
Genus Bacteroides. A chemotaxonomical perspective
-
PubMed
-
Shah HN, Collins MD. Genus Bacteroides. A chemotaxonomical perspective. J Appl Bacteriol 1983; 55:403-416. PubMed
-
(1983)
J Appl Bacteriol
, vol.55
, pp. 403-416
-
-
Shah, H.N.1
Collins, M.D.2
-
31
-
-
0030795384
-
Formation of a dipeptidyl arylamidase by Bacteroides splanchni-cus NCTC 10825 with specificities towards gly-cylprolyl-x and valylalanine-x substrates
-
PubMed doi:10.1099/00222615-46-7-547
-
MacFarlane S, Macfarlane GT. Formation of a dipeptidyl arylamidase by Bacteroides splanchni-cus NCTC 10825 with specificities towards gly-cylprolyl-x and valylalanine-x substrates. J Med Microbiol 1997; 46:547-555. PubMed doi:10.1099/00222615-46-7-547
-
(1997)
J Med Microbiol
, vol.46
, pp. 547-555
-
-
Macfarlane, S.1
Macfarlane, G.T.2
-
32
-
-
0018246063
-
Distribution of sphingolipids in Bacteroides species
-
doi:10.2323/jgam.24.341
-
Miyagawa T, Azuma R, Suto T. Distribution of sphingolipids in Bacteroides species. J Gen Appl Microbiol 1978; 24:341-348. doi:10.2323/jgam.24.341
-
(1978)
J Gen Appl Microbiol
, vol.24
, pp. 341-348
-
-
Miyagawa, T.1
Azuma, R.2
Suto, T.3
-
33
-
-
77952889628
-
En route to a genome-based classification of Archaea and Bacteria?
-
PubMed doi:10.1016/j.syapm.2010.03.003
-
Klenk HP, Goeker 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
Goeker, M.2
-
34
-
-
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
-
36
-
-
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
-
37
-
-
84860526788
-
-
DOE Joint Genome Institute
-
DOE Joint Genome Institute. http://www.jgi.doe.gov
-
-
-
-
39
-
-
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
-
40
-
-
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
-
41
-
-
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
-
42
-
-
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
-
43
-
-
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
-
44
-
-
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
|