-
2
-
-
20544444045
-
Diversity of the human intestinal microbial flora
-
Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, et al. (2005) Diversity of the human intestinal microbial flora. Science 308: 1635-1638.
-
(2005)
Science
, vol.308
, pp. 1635-1638
-
-
Eckburg, P.B.1
Bik, E.M.2
Bernstein, C.N.3
Purdom, E.4
Dethlefsen, L.5
-
3
-
-
33747073504
-
Microbial diversity in the deep sea and the underexplored ''rare biosphere''
-
Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, et al. (2006) Microbial diversity in the deep sea and the underexplored ''rare biosphere''. Proc Natl Acad Sci U S A 103: 12115-12120.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 12115-12120
-
-
Sogin, M.L.1
Morrison, H.G.2
Huber, J.A.3
Welch, D.M.4
Huse, S.M.5
-
4
-
-
58749112734
-
A core gut microbiome in obese and lean twins
-
Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, et al. (2009) A core gut microbiome in obese and lean twins. Nature 457: 480-484.
-
(2009)
Nature
, vol.457
, pp. 480-484
-
-
Turnbaugh, P.J.1
Hamady, M.2
Yatsunenko, T.3
Cantarel, B.L.4
Duncan, A.5
-
5
-
-
15444362001
-
Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness
-
Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-1506.
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 1501-1506
-
-
Schloss, P.D.1
Handelsman, J.2
-
6
-
-
56649124715
-
The influence of sex, handedness, and washing on the diversity of hand surface bacteria
-
Fierer N, Hamady M, Lauber CL, Knight R (2008) The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A 105: 17994-17999.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 17994-17999
-
-
Fierer, N.1
Hamady, M.2
Lauber, C.L.3
Knight, R.4
-
7
-
-
0042121237
-
Multiple sequence alignment with the Clustal series of programs
-
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, et al. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31: 3497-3500.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3497-3500
-
-
Chenna, R.1
Sugawara, H.2
Koike, T.3
Lopez, R.4
Gibson, T.J.5
-
8
-
-
68049142320
-
Multiple alignment of DNA sequences with MAFFT
-
Katoh K, Asimenos G, Toh H (2009) Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol 537: 39-64.
-
(2009)
Methods Mol Biol
, vol.537
, pp. 39-64
-
-
Katoh, K.1
Asimenos, G.2
Toh, H.3
-
9
-
-
13244255415
-
MUSCLE: A multiple sequence alignment method with reduced time and space complexity
-
Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
10
-
-
35148888609
-
Microbial population structures in the deep marine biosphere
-
Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, et al. (2007) Microbial population structures in the deep marine biosphere. Science 318: 97-100.
-
(2007)
Science
, vol.318
, pp. 97-100
-
-
Huber, J.A.1
Mark, W.D.B.2
Morrison, H.G.3
Huse, S.M.4
Neal, P.R.5
-
11
-
-
66549102207
-
Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation
-
Antonopoulos DA, Huse SM, Morrison HG, Schmidt TM, Sogin ML, et al. (2009) Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation. Infect Immun 77: 2367-2375.
-
(2009)
Infect Immun
, vol.77
, pp. 2367-2375
-
-
Antonopoulos, D.A.1
Huse, S.M.2
Morrison, H.G.3
Schmidt, T.M.4
Sogin, M.L.5
-
12
-
-
67249096511
-
ESPRIT: Estimating species richness using large collections of 16S rRNA pyrosequences
-
Sun Y, Cai Y, Liu L, Yu F, Farrell ML, et al. (2009) ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res 37: e76.
-
(2009)
Nucleic Acids Res
, vol.e76
, pp. 37
-
-
Sun, Y.1
Cai, Y.2
Liu, L.3
Yu, F.4
Farrell, M.L.5
-
13
-
-
17844386108
-
A benchmark of multiple sequence alignment programs upon structural RNAs
-
Gardner PP, Wilm A, Washietl S (2005) A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res 33: 2433-2439.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2433-2439
-
-
Gardner, P.P.1
Wilm, A.2
Washietl, S.3
-
15
-
-
58149200948
-
The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis
-
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-145.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Cole, J.R.1
Wang, Q.2
Cardenas, E.3
Fish, J.4
Chai, B.5
-
16
-
-
2542523843
-
ARB: A software environment for sequence data
-
Ludwig W, Strunk O, Westram R, Richter L, Meier H, et al. (2004) ARB: A software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1363-1371
-
-
Ludwig, W.1
Strunk, O.2
Westram, R.3
Richter, L.4
Meier, H.5
-
17
-
-
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 BM, Ludwig W, et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 7188-7196
-
-
Pruesse, E.1
Quast, C.2
Knittel, K.3
Fuchs, B.M.4
Ludwig, W.5
-
18
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-5072.
-
(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
-
19
-
-
33747827586
-
NAST: A multiple sequence alignment server for comparative analysis of 16S rRNA genes
-
DeSantis TZ Jr, Hugenholtz P, Keller K, Brodie EL, Larsen N, et al. (2006) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394-399.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Desantis Jr., T.Z.1
Hugenholtz, P.2
Keller, K.3
Brodie, E.L.4
Larsen, N.5
-
20
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
-
21
-
-
0001857117
-
16S/23S rRNA sequencing
-
In: Stackebrandt E, Goodfellow M, eds, New York: Wiley
-
Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M, eds. Nucleic Acid Techniques in Bacterial Systematics. New York: Wiley. Pp 115-175.
-
(1991)
Nucleic Acid Techniques In Bacterial Systematics
, pp. 115-175
-
-
Lane, D.J.1
-
22
-
-
63349105158
-
A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses
-
Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, et al. (2009) A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J 3: 442-453.
-
(2009)
ISME J
, vol.3
, pp. 442-453
-
-
Jones, R.T.1
Robeson, M.S.2
Lauber, C.L.3
Hamady, M.4
Knight, R.5
-
23
-
-
67651247607
-
Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale
-
Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75: 5111-5120.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 5111-5120
-
-
Lauber, C.L.1
Hamady, M.2
Knight, R.3
Fierer, N.4
-
24
-
-
67651245379
-
Characterization of airborne microbial communities at a high elevation site and their potential to act as atmospheric ice nuclei
-
Bowers RM, Lauber CL, Wiedinmyer C, Hamady M, Hallar AG, et al. (2009) Characterization of airborne microbial communities at a high elevation site and their potential to act as atmospheric ice nuclei. Appl Environ Microbiol 75: 5121-5130.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 5121-5130
-
-
Bowers, R.M.1
Lauber, C.L.2
Wiedinmyer, C.3
Hamady, M.4
Hallar, A.G.5
-
25
-
-
67650473912
-
Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation
-
Crawford PA, Crowley JR, Sambandam N, Muegge BD, Costello EK, et al. (2009) Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation. Proc Natl Acad Sci U S A 106: 11276-11281.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 11276-11281
-
-
Crawford, P.A.1
Crowley, J.R.2
Sambandam, N.3
Muegge, B.D.4
Costello, E.K.5
-
26
-
-
65549089957
-
Pyrosequencing of the chaperonin-60 universal target as a tool for determining microbial community composition
-
Schellenberg J, Links MG, Hill JE, Dumonceaux TJ, Peters GA, et al. (2009) Pyrosequencing of the chaperonin-60 universal target as a tool for determining microbial community composition. Appl Environ Microbiol 75: 2889-2898.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 2889-2898
-
-
Schellenberg, J.1
Links, M.G.2
Hill, J.E.3
Dumonceaux, T.J.4
Peters, G.A.5
-
27
-
-
56849106496
-
The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S Rrna sequencing
-
Dethlefsen L, Huse S, Sogin ML, Relman DA (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S Rrna sequencing. PLoS Biol 6: e280.
-
(2008)
PLoS Biol
, vol.e280
, pp. 6
-
-
Dethlefsen, L.1
Huse, S.2
Sogin, M.L.3
Relman, D.A.4
-
28
-
-
34547800097
-
Pyrosequencing enumerates and contrasts soil microbial diversity
-
Roesch LFW, Fulthorpe RR, Riva A, Casella G, Hadwin AKM, et al. (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1: 283-290.
-
(2007)
ISME J
, vol.1
, pp. 283-290
-
-
Roesch, L.F.W.1
Fulthorpe, R.R.2
Riva, A.3
Casella, G.4
Hadwin, A.K.M.5
-
29
-
-
0001704377
-
Online construction of suffix trees
-
Ukkonen E (1995) Online construction of suffix trees. Algorithmica 14: 249-260.
-
(1995)
Algorithmica
, vol.14
, pp. 249-260
-
-
Ukkonen, E.1
-
30
-
-
84976728067
-
The string-to-string correction problem with block moves
-
Tichy WF (1984) The string-to-string correction problem with block moves. ACM Trans Comput Syst 2: 309-321.
-
(1984)
ACM Trans Comput Syst
, vol.2
, pp. 309-321
-
-
Tichy, W.F.1
-
31
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-453.
-
(1970)
J Mol Biol
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
32
-
-
0023984847
-
Optimal alignments in linear space
-
Myers EW, Miller W (1988) Optimal alignments in linear space. Comput Appl Biosci 4: 11-17.
-
(1988)
Comput Appl Biosci
, vol.4
, pp. 11-17
-
-
Myers, E.W.1
Miller, W.2
-
33
-
-
0020484488
-
An improved algorithm for matching biological sequences
-
Gotoh O (1982) An improved algorithm for matching biological sequences. J Mol Biol 162: 705-708.
-
(1982)
J Mol Biol
, vol.162
, pp. 705-708
-
-
Gotoh, O.1
-
35
-
-
72949107142
-
Introducing mothur: Open source, platform-independent, community-supported software for describing and comparing microbial communities
-
doi:10.1128/AEM.01541-09.
-
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: Open source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol;doi:10.1128/AEM.01541-09.
-
(2009)
Appl Environ Microbiol
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
Hall, J.R.4
Hartmann, M.5
|