-
2
-
-
11144354360
-
Environmental genome shotgun sequencing of the Sargasso Sea
-
Venter JC, Remington K, Heidelberg JF, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004;304(5667):66-74.
-
(2004)
Science
, vol.304
, Issue.5667
, pp. 66-74
-
-
Venter, J.C.1
Remington, K.2
Heidelberg, J.F.3
-
3
-
-
41649109613
-
Functional metagenomics profiling of nine biomes
-
Dinsdale EA, Edwards RA, Hall D, et al. Functional metagenomics profiling of nine biomes. Nature 2008;452(7187): 629-32.
-
(2008)
Nature
, vol.452
, Issue.7187
, pp. 629-632
-
-
Dinsdale, E.A.1
Edwards, R.A.2
Hall, D.3
-
4
-
-
70350731109
-
Windshield splatter analysis with the Galaxy metagenomic pipeline
-
Pond SK, Wadhawan S, Chiaromonte F, et al. Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Res 2009;19(11):2144-53.
-
(2009)
Genome Res
, vol.19
, Issue.11
, pp. 2144-2153
-
-
Pond, S.K.1
Wadhawan, S.2
Chiaromonte, F.3
-
5
-
-
33747073504
-
Microbial diversity in the deep sea and the underexplored "rare biosphere"
-
Sogin ML, Morrison HG, Huber JA, et al. Microbial diversity in the deep sea and the underexplored "rare biosphere". ProcNatl Acad SciUSA 2006;103(32):12115-20.
-
(2006)
ProcNatl Acad SciUSA
, vol.103
, Issue.32
, pp. 12115-12120
-
-
Sogin, M.L.1
Morrison, H.G.2
Huber, J.A.3
-
6
-
-
58749112734
-
A core gut microbiome in obese and lean twins
-
Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature 2009; 457(7228):480-4.
-
(2009)
Nature
, vol.457
, Issue.7228
, pp. 480-484
-
-
Turnbaugh, P.J.1
Hamady, M.2
Yatsunenko, T.3
-
7
-
-
35348968286
-
The Human Microbiome Project
-
Turnbaugh PJ, Ley RE, Hamady M, et al. The Human Microbiome Project. Nature 2007;449(7164):804-10.
-
(2007)
Nature
, vol.449
, Issue.7164
, pp. 804-810
-
-
Turnbaugh, P.J.1
Ley, R.E.2
Hamady, M.3
-
8
-
-
77950250064
-
Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5
-
Vijay-Kumar M, Aitken JD, Carvalho FA, et al. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 2010;328(5975):228-31.
-
(2010)
Science
, vol.328
, Issue.5975
, pp. 228-231
-
-
Vijay-Kumar, M.1
Aitken, J.D.2
Carvalho, F.A.3
-
9
-
-
71349088748
-
Achievements and new knowledge unraveled by metagenomic approaches
-
Simon C, Daniel R. Achievements and new knowledge unraveled by metagenomic approaches. Appl Microbiol Biotechnol 2009;85(2):265-76.
-
(2009)
Appl Microbiol Biotechnol
, vol.85
, Issue.2
, pp. 265-276
-
-
Simon, C.1
Daniel, R.2
-
10
-
-
19144366814
-
Metagenomics and industrial applications
-
Lorenz P, Eck J. Metagenomics and industrial applications. Nat RevMicrobiol 2005;3(6):510-6.
-
(2005)
Nat RevMicrobiol
, vol.3
, Issue.6
, pp. 510-516
-
-
Lorenz, P.1
Eck, J.2
-
11
-
-
34249794257
-
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
-
Mavromatis K, Ivanova N, Barry K, et al. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. NatMethods 2007;4(6):495-500.
-
(2007)
NatMethods
, vol.4
, Issue.6
, pp. 495-500
-
-
Mavromatis, K.1
Ivanova, N.2
Barry, K.3
-
12
-
-
54949137701
-
MetaSim: A sequencing simulator for genomics and metagenomics
-
Richter DC, Ott F, Auch AF, et al. MetaSim: A sequencing simulator for genomics and metagenomics. PLoS ONE 2009;3(10):e3373.
-
(2009)
PLoS ONE
, vol.3
, Issue.10
-
-
Richter, D.C.1
Ott, F.2
Auch, A.F.3
-
13
-
-
0033957466
-
Database resources of the National Center for Biotechnology Information
-
Wheeler DJ, Chappey C, Lash AE, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000;28(1):10-4.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 10-14
-
-
Wheeler, D.J.1
Chappey, C.2
Lash, A.E.3
-
14
-
-
53649100100
-
The development and impact of 454 sequencing
-
Rothberg JM, Leamon JH. The development and impact of 454 sequencing. Nature Biotechnol 2008;26(10):1117-24.
-
(2008)
Nature Biotechnol
, vol.26
, Issue.10
, pp. 1117-1124
-
-
Rothberg, J.M.1
Leamon, J.H.2
-
15
-
-
69549112742
-
Accurate determination of microbial diversity from 454 pyrosequencing data
-
Quince C, Lanzén A, Curtis TP, et al. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 2009;6(9):639-41.
-
(2009)
Nat Methods
, vol.6
, Issue.9
, pp. 639-641
-
-
Quince, C.1
Lanzén, A.2
Curtis, T.P.3
-
17
-
-
58149200948
-
The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis
-
Cole JR, Wang Q, Cardenas E, et al. The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009;37(D):141-5.
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.D
, pp. 141-145
-
-
Cole, J.R.1
Wang, Q.2
Cardenas, E.3
-
18
-
-
40849089606
-
-
TOBA release 7.7. Michigan State University Board of Trustees. (29 March, date last accessed)
-
Garrity GM, Lilburn TG, Cole JR, et al. TheTaxonomic Outline of Bacteria and Archaea. TOBA release 7.7. Michigan State University Board of Trustees. http://www.taxonomicoutline.org/,2007 (29 March 2011, date last accessed).
-
(2007)
TheTaxonomic Outline of Bacteria and Archaea
-
-
Garrity, G.M.1
Lilburn, T.G.2
Cole, J.R.3
-
20
-
-
0000594195
-
Evolution and measurement of species diversity
-
Whittaker RH. Evolution and measurement of species diversity. Taxon 1972;21(2-3):213-51.
-
(1972)
Taxon
, vol.21
, Issue.2-3
, pp. 213-251
-
-
Whittaker, R.H.1
-
22
-
-
0010497387
-
-
2nd edn. Menlo Park, CA: Benjamin Cummings
-
Krebs CJ. EcologicalMethodology. 2nd edn. Menlo Park, CA: Benjamin Cummings, 1998.
-
(1998)
EcologicalMethodology
-
-
Krebs, C.J.1
-
23
-
-
0032434042
-
A taxonomic distinctness index and its statistical properties
-
Clarke KR, Warwick RM. A taxonomic distinctness index and its statistical properties. JAppl Ecol 1998;35(4):523-31.
-
(1998)
J Appl Ecol
, vol.35
, Issue.4
, pp. 523-531
-
-
Clarke, K.R.1
Warwick, R.M.2
-
24
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. JMol Biol 1990;215(3):403-10.
-
(1990)
J Mol Biol
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
-
25
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009; 25(14):1754-60.
-
(2009)
Bioinformatics
, vol.25
, Issue.14
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
26
-
-
77949587649
-
Fast and accurate long-read alignment with Burrows-Wheeler transform
-
Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010;26(5): 589-95.
-
(2010)
Bioinformatics
, vol.26
, Issue.5
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
27
-
-
0036226603
-
BLAT: the BLAST-like alignment tool
-
Kent WJ. BLAT: the BLAST-like alignment tool. Genome Res 2002;12(4):656-64.
-
(2002)
Genome Res
, vol.12
, Issue.4
, pp. 656-664
-
-
Kent, W.J.1
-
28
-
-
78751615621
-
-
(29 March, date last accessed)
-
Ribeca P. GEM: GEnomic Multi-tool. http://gemlibrary.sourceforge.net/, 2009 (29 March, 2011 date last accessed).
-
(2009)
GEM: GEnomic Multi-tool
-
-
Ribeca, P.1
-
29
-
-
33847702910
-
MEGAN analysis of metagenomic data
-
Huson DH, Auch AF, Qi J, et al. MEGAN analysis of metagenomic data. Genome Res 2007;17(3):377-86.
-
(2007)
Genome Res
, vol.17
, Issue.3
, pp. 377-386
-
-
Huson, D.H.1
Auch, A.F.2
Qi, J.3
-
32
-
-
37549027613
-
SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
-
Pruesse E, Quast C, Knittel K, et al. SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007;35(21):7188-96.
-
(2007)
Nucleic Acids Res
, vol.35
, Issue.21
, pp. 7188-7196
-
-
Pruesse, E.1
Quast, C.2
Knittel, K.3
-
33
-
-
72949107142
-
Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss PD, Westcott SL, Ryabin T, et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl EnvironMicrobiol 2009;75(23): 7537-41.
-
(2009)
Appl EnvironMicrobiol
, vol.75
, Issue.23
, pp. 7537-7541
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
-
34
-
-
0037342499
-
Alignment-free sequence comparison: A review
-
Vinga S, Almeida J. Alignment-free sequence comparison: A review. Bioinformatics 2003;19(4):513-23.
-
(2003)
Bioinformatics
, vol.19
, Issue.4
, pp. 513-523
-
-
Vinga, S.1
Almeida, J.2
-
35
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970;48(3):443-53.
-
(1970)
J Mol Biol
, vol.48
, Issue.3
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
36
-
-
44849128805
-
Species divergence and the measurement of microbial diversity
-
Lozupone CA, Knight R. Species divergence and the measurement of microbial diversity. FEMS Microbiol Rev 2008; 32(4):557-8.
-
(2008)
FEMS Microbiol Rev
, vol.32
, Issue.4
, pp. 557-558
-
-
Lozupone, C.A.1
Knight, R.2
-
37
-
-
0036324293
-
Phylogenetic approaches for describing and comparing the diversity of microbial communities
-
Martin AP. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl EnvironMicrobiol 2002;68(8):3673-82.
-
(2002)
Appl EnvironMicrobiol
, vol.68
, Issue.8
, pp. 3673-3682
-
-
Martin, A.P.1
-
38
-
-
53849104257
-
The rational exploration of microbial diversity
-
Quince C, Curtis TP, Sloan WT. The rational exploration of microbial diversity. The ISME J 2008;2(10):997-1006.
-
(2008)
The ISME J
, vol.2
, Issue.10
, pp. 997-1006
-
-
Quince, C.1
Curtis, T.P.2
Sloan, W.T.3
-
39
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. NatMethods 2010;7:335-6.
-
(2010)
NatMethods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
Kuczynski, J.2
Stombaugh, J.3
-
40
-
-
33745634395
-
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006;22(13):1658-9.
-
(2006)
Bioinformatics
, vol.22
, Issue.13
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
41
-
-
0029942146
-
Polyphasic taxonomy, a consensus approach to bacterial systematics
-
Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swings J. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 1996;60(2):407-38.
-
(1996)
Microbiol Rev
, vol.60
, Issue.2
, pp. 407-438
-
-
Vandamme, P.1
Pot, B.2
Gillis, M.3
de Vos, P.4
Kersters, K.5
Swings, J.6
-
42
-
-
34548293679
-
Naïve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang Q, Garrity GM, Tiedje JM, et al. Naïve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl EnvironMicrobiol 2007;73(16): 5261-7.
-
(2007)
Appl EnvironMicrobiol
, vol.73
, Issue.16
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
|