-
2
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The gene ontology consortium
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: Tool for the unification of biology. the gene ontology consortium. Nat Genet 25: 25-29.
-
(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
-
3
-
-
25644458211
-
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
-
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, et al. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33: 5691-02.
-
(2005)
Nucleic. Acids Res.
, vol.33
, pp. 5691-5602
-
-
Overbeek, R.1
Begley, T.2
Butler, R.M.3
Choudhuri, J.V.4
Chuang, H.Y.5
-
4
-
-
0033982936
-
Kegg: Kyoto encyclopedia of genes and genomes
-
Kanehisa M, Goto S (2000) Kegg: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30.
-
(2000)
Nucleic. Acids Res.
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
5
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
6
-
-
13444304389
-
Genbank
-
Benson D, Karsch-Mizrachi I, Lipman D, Ostell J, Wheeler D (2005) Genbank. Nucleic Acids Res 1: D34-38.
-
(2005)
Nucleic. Acids Res.
, vol.1
-
-
Benson, D.1
Karsch-Mizrachi, I.2
Lipman, D.3
Ostell, J.4
Wheeler, D.5
-
8
-
-
52449114817
-
Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities
-
Gilbert JA, Field D, Huang Y, Edwards R, Li W, et al. (2008) Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One 3: e3042.
-
(2008)
PLoS One
, vol.3
-
-
Gilbert, J.A.1
Field, D.2
Huang, Y.3
Edwards, R.4
Li, W.5
-
9
-
-
52949096084
-
Next-generation DNA sequencing methods
-
Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9: 387-402.
-
(2008)
Annu. Rev. Genomics Hum. Genet.
, vol.9
, pp. 387-402
-
-
Mardis, E.R.1
-
10
-
-
53649106195
-
Next-generation DNA sequencing
-
Shendure J, JiH(2008) Next-generation DNA sequencing. Nat Biotechnol 26: 1135-45.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1135-1145
-
-
Shendure, J.1
Ji, H.2
-
11
-
-
33845957530
-
Accurate phylogenetic classification of variable-length DNA fragments
-
McHardy AC, Martin HG, Tsirigos A, Hugenholtz P, Rigoutsos I (2007) Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods 4: 63-72.
-
(2007)
Nat. Methods
, vol.4
, pp. 63-72
-
-
McHardy, A.C.1
Martin, H.G.2
Tsirigos, A.3
Hugenholtz, P.4
Rigoutsos, I.5
-
12
-
-
84886609730
-
NBC: The naive Bayes classification tool webserver for taxonomic classification of metagenomic reads
-
Rosen GL, Reichenberger E, Rosenfeld A (2010) NBC: The naive Bayes classification tool webserver for taxonomic classification of metagenomic reads. Bioinformatics : AdVanced access.
-
(2010)
Bioinformatics : AdVanced Access
-
-
Rosen, G.L.1
Reichenberger, E.2
Rosenfeld, A.3
-
14
-
-
11144354360
-
Environmental genome shotgun sequencing of the sargasso sea
-
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
-
(2004)
Science
, vol.304
, pp. 66-74
-
-
Venter, J.C.1
Remington, K.2
Heidelberg, J.F.3
Halpern, A.L.4
Rusch, D.5
-
15
-
-
55649110049
-
A simple, fast, and accurate method of phylogenomic inference
-
Wu M, Eisen JA (2008) A simple, fast, and accurate method of phylogenomic inference. Genome Biol 9: R151.
-
(2008)
Genome Biol.
, vol.9
-
-
Wu, M.1
Eisen, J.A.2
-
16
-
-
33847291893
-
Quantitative phylogenetic assessment of microbial communities in diverse environments
-
von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, et al. (2007) Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315: 1126-30.
-
(2007)
Science
, vol.315
, pp. 1126-1130
-
-
Von Mering, C.1
Hugenholtz, P.2
Raes, J.3
Tringe, S.G.4
Doerks, T.5
-
17
-
-
1542377296
-
Community structure and metabolism through reconstruction of microbial genomes from the environment
-
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43.
-
(2004)
Nature
, vol.428
, pp. 37-43
-
-
Tyson, G.W.1
Chapman, J.2
Hugenholtz, P.3
Allen, E.E.4
Ram, R.J.5
-
18
-
-
0001337675
-
A new similarity index based on probability
-
Goodall DW (1966) A new similarity index based on probability. Biometrics 22: 882-907.
-
(1966)
Biometrics
, vol.22
, pp. 882-907
-
-
Goodall, D.W.1
-
19
-
-
33748713890
-
Unifrac -An online tool for comparing microbial community diversity in a phylogenetic context
-
Lozupone C, Hamady M, Knight R (2006) Unifrac -an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7: 371.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 371
-
-
Lozupone, C.1
Hamady, M.2
Knight, R.3
-
20
-
-
30744470609
-
Application of phylogenetic networks in evolutionary studies
-
Huson D, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23: 254-267.
-
(2006)
Molecular Biology and Evolution
, vol.23
, pp. 254-267
-
-
Huson, D.1
Bryant, D.2
-
21
-
-
1542347067
-
Neighbor-net: An agglomerative method for the construction of phylogenetic networks
-
Bryant D, Moulton V (2004) Neighbor-net: An agglomerative method for the construction of phylogenetic networks. Molecular Biology and Evolution 21: 255-265.
-
(2004)
Molecular Biology and Evolution
, vol.21
, pp. 255-265
-
-
Bryant, D.1
Moulton, V.2
-
22
-
-
77956995596
-
Comparison of multiple metagenomes using phylogenetic networks based on ecological indices
-
Mitra S, Gilbert JA, Field D, Huson DH (2010) Comparison of multiple metagenomes using phylogenetic networks based on ecological indices. ISME J 4: 1236-1242.
-
(2010)
ISME J.
, vol.4
, pp. 1236-1242
-
-
Mitra, S.1
Gilbert, J.A.2
Field, D.3
Huson, D.H.4
-
23
-
-
77951497989
-
Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction
-
Morris RM, Nunn BL, Frazar C, Goodlett DR, Ting YS, et al. (2010) Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction. ISME J 4: 673-685.
-
(2010)
ISME J.
, vol.4
, pp. 673-685
-
-
Morris, R.M.1
Nunn, B.L.2
Frazar, C.3
Goodlett, D.R.4
Ting, Y.S.5
-
24
-
-
33947238287
-
The Sorcerer II global ocean sampling expedition: Northwest Atlantic through eastern tropical Pacific
-
Rusch DB, Halpern AL, Sutton G, Heidelberg KB,Williamson S, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5: e77.
-
(2007)
PLoS Biol.
, vol.5
-
-
Rusch, D.B.1
Halpern, A.L.2
Sutton, G.3
Heidelberg, K.B.4
Williamson, S.5
-
26
-
-
37549027613
-
SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
-
Pruesse E, Quast C, Knittel K, Fuchs B, Ludwig W, et al. (2007) SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nuc Acids Res 35: 7188-7196.
-
(2007)
Nuc. Acids Res.
, vol.35
, pp. 7188-7196
-
-
Pruesse, E.1
Quast, C.2
Knittel, K.3
Fuchs, B.4
Ludwig, W.5
-
27
-
-
72949101201
-
A phylogeny-driven genomic encyclopaedia of bacteria and archaea
-
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, et al. (2009) A phylogeny-driven genomic encyclopaedia of bacteria and archaea. Nature 462: 1056-1060.
-
(2009)
Nature
, vol.462
, pp. 1056-1060
-
-
Wu, D.1
Hugenholtz, P.2
Mavromatis, K.3
Pukall, R.4
Dalin, E.5
-
28
-
-
35348968286
-
The human microbiome project
-
Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, et al. (2007) The Human Microbiome Project. Nature 449: 804-810.
-
(2007)
Nature
, vol.449
, pp. 804-810
-
-
Turnbaugh, P.J.1
Ley, R.E.2
Hamady, M.3
Fraser-Liggett, C.M.4
Knight, R.5
-
29
-
-
41849127118
-
Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome
-
Turnbaugh PJ, Backhed F, Fulton L, Gordon JI (2008) Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3: 213-223.
-
(2008)
Cell Host. Microbe
, vol.3
, pp. 213-223
-
-
Turnbaugh, P.J.1
Backhed, F.2
Fulton, L.3
Gordon, J.I.4
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