-
1
-
-
69549112742
-
Accurate determination of microbial diversity from 454 pyrosequencing data
-
10.1038/nmeth.1361
-
Quince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, et al. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Meth 6: 639-641 doi:10.1038/nmeth.1361.
-
(2009)
Nat Meth
, vol.6
, pp. 639-641
-
-
Quince, C.1
Lanzén, A.2
Curtis, T.P.3
Davenport, R.J.4
Hall, N.5
-
2
-
-
34948842866
-
Accuracy and quality of massively parallel DNA pyrosequencing
-
Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM, (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8: R143.
-
(2007)
Genome Biol
, vol.8
-
-
Huse, S.M.1
Huber, J.A.2
Morrison, H.G.3
Sogin, M.L.4
Welch, D.M.5
-
3
-
-
73349110099
-
Wrinkles in the rare biosphere: Pyrosequencing errors can lead to artificial inflation of diversity estimates
-
10.1111/j.1462-2920.2009.02051.x
-
Kunin V, Engelbrektson A, Ochman H, Hugenholtz P, (2010) Wrinkles in the rare biosphere: Pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12: 118-123 doi:10.1111/j.1462-2920.2009.02051.x.
-
(2010)
Environ Microbiol
, vol.12
, pp. 118-123
-
-
Kunin, V.1
Engelbrektson, A.2
Ochman, H.3
Hugenholtz, P.4
-
4
-
-
67249096511
-
ESPRIT: Estimating species richness using large collections of 16S rRNA pyrosequences
-
10.1093/nar/gkp285
-
Sun Y, Cai Y, Liu L, Yu F, Farrell ML, et al. (2009) ESPRIT: Estimating species richness using large collections of 16S rRNA pyrosequences. Nuc Acid Res 37: e76-e76 doi:10.1093/nar/gkp285.
-
(2009)
Nuc Acid Res
, vol.37
-
-
Sun, Y.1
Cai, Y.2
Liu, L.3
Yu, F.4
Farrell, M.L.5
-
5
-
-
74949134895
-
Defining the healthy "core microbiome" of oral microbial communities
-
10.1186/1471-2180-9-259
-
Zaura E, Keijser BJ, Huse SM, Crielaard W, (2009) Defining the healthy "core microbiome" of oral microbial communities. BMC Microbiol 9: 259 doi:10.1186/1471-2180-9-259.
-
(2009)
BMC Microbiol
, vol.9
, pp. 259
-
-
Zaura, E.1
Keijser, B.J.2
Huse, S.M.3
Crielaard, W.4
-
6
-
-
79251565226
-
Removing noise from pyrosequenced amplicons
-
10.1186/1471-2105-12-38
-
Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ, (2011) Removing noise from pyrosequenced amplicons. BMC Bioinform 12: 38 doi:10.1186/1471-2105-12-38.
-
(2011)
BMC Bioinform
, vol.12
, pp. 38
-
-
Quince, C.1
Lanzen, A.2
Davenport, R.J.3
Turnbaugh, P.J.4
-
7
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
10.1038/nmeth.f.303
-
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Meth 7: 335-336 doi:10.1038/nmeth.f.303.
-
(2010)
Nat Meth
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
Kuczynski, J.2
Stombaugh, J.3
Bittinger, K.4
Bushman, F.D.5
-
8
-
-
72949107142
-
Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
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 75: 7537-7541.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
Hall, J.R.4
Hartmann, M.5
-
9
-
-
0035955396
-
Diversity and productivity in a long-term grassland experiment
-
Tilman D, Reich PB, Knops J, Wedin D, Mielke T, et al. (2001) Diversity and productivity in a long-term grassland experiment. Science 294: 843-845.
-
(2001)
Science
, vol.294
, pp. 843-845
-
-
Tilman, D.1
Reich, P.B.2
Knops, J.3
Wedin, D.4
Mielke, T.5
-
10
-
-
77749303986
-
Rapid and specific method for evaluating Streptomyces competitive dynamics in complex soil communities
-
10.1128/AEM.02320-09
-
Schlatter DC, Samac DA, Tesfaye M, Kinkel LL, (2010) Rapid and specific method for evaluating Streptomyces competitive dynamics in complex soil communities. Appl Environ Microbiol 76: 2009-2012 doi:10.1128/AEM.02320-09.
-
(2010)
Appl Environ Microbiol
, vol.76
, pp. 2009-2012
-
-
Schlatter, D.C.1
Samac, D.A.2
Tesfaye, M.3
Kinkel, L.L.4
-
11
-
-
0035722040
-
PCR primers targeting the 16S rRNA gene for the specific detection of streptomycetes
-
Rintala H, Nevalainen A, Ronka E, Suutari M, (2001) PCR primers targeting the 16S rRNA gene for the specific detection of streptomycetes. Mol Cell Probes 15: 337-347.
-
(2001)
Mol Cell Probes
, vol.15
, pp. 337-347
-
-
Rintala, H.1
Nevalainen, A.2
Ronka, E.3
Suutari, M.4
-
12
-
-
0030483312
-
Molecular evidence for the presence of novel actinomycete lineages in a temperate forest soil
-
McVeigh HP, Munro J, Embley TM, (1996) Molecular evidence for the presence of novel actinomycete lineages in a temperate forest soil. J Indust Microbiol 17: 197-204.
-
(1996)
J Indust Microbiol
, vol.17
, pp. 197-204
-
-
McVeigh, H.P.1
Munro, J.2
Embley, T.M.3
-
13
-
-
36148937913
-
A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing
-
Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, et al. (2007) A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nuc Acid Res 35: e130.
-
(2007)
Nuc Acid Res
, vol.35
-
-
Parameswaran, P.1
Jalili, R.2
Tao, L.3
Shokralla, S.4
Gharizadeh, B.5
-
14
-
-
50149095793
-
The Genome Sequencer FLX™ System - Longer reads, more applications, straight forward bioinformatics and more complete data sets
-
10.1016/j.jbiotec.2008.03.021
-
Droege M, Hill B, (2008) The Genome Sequencer FLX™ System- Longer reads, more applications, straight forward bioinformatics and more complete data sets. J Biotech 136: 3-10 doi:10.1016/j.jbiotec.2008.03.021.
-
(2008)
J Biotech
, vol.136
, pp. 3-10
-
-
Droege, M.1
Hill, B.2
-
15
-
-
37549027613
-
SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
-
10.1093/nar/gkm864
-
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. Nuc Acid Res 35: 7188-7196 doi:10.1093/nar/gkm864.
-
(2007)
Nuc Acid Res
, vol.35
, pp. 7188-7196
-
-
Pruesse, E.1
Quast, C.2
Knittel, K.3
Fuchs, B.M.4
Ludwig, W.5
-
16
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
10.1093/bioinformatics/btr381
-
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R, (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200 doi:10.1093/bioinformatics/btr381.
-
(2011)
Bioinformatics
, vol.27
, pp. 2194-2200
-
-
Edgar, R.C.1
Haas, B.J.2
Clemente, J.C.3
Quince, C.4
Knight, R.5
-
17
-
-
33750983947
-
Clearcut: A fast implementation of relaxed neighbor joining
-
10.1093/bioinformatics/btl478
-
Sheneman L, Evans J, Foster JA, (2006) Clearcut: A fast implementation of relaxed neighbor joining. Bioinformatics 22: 2823-2824 doi:10.1093/bioinformatics/btl478.
-
(2006)
Bioinformatics
, vol.22
, pp. 2823-2824
-
-
Sheneman, L.1
Evans, J.2
Foster, J.A.3
-
18
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
10.1093/bioinformatics/btm404
-
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948 doi:10.1093/bioinformatics/btm404.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
-
19
-
-
38749091304
-
Pyrobayes: An improved base caller for SNP discovery in pyrosequences
-
10.1038/nmeth.1172
-
Quinlan AR, Stewart DA, Strömberg MP, Marth GT, (2008) Pyrobayes: An improved base caller for SNP discovery in pyrosequences. Nat Meth 5: 179-181 doi:10.1038/nmeth.1172.
-
(2008)
Nat Meth
, vol.5
, pp. 179-181
-
-
Quinlan, A.R.1
Stewart, D.A.2
Strömberg, M.P.3
Marth, G.T.4
-
20
-
-
0030748867
-
Inhibition and facilitation of nucleic acid amplification
-
Wilson I, (1997) Inhibition and facilitation of nucleic acid amplification. Appl Environ Microbiol 63: 3741-3751.
-
(1997)
Appl Environ Microbiol
, vol.63
, pp. 3741-3751
-
-
Wilson, I.1
-
21
-
-
78149365938
-
Insidious effects of sequencing errors on perceived diversity in molecular surveys
-
10.1111/j.1469-8137.2010.03473.x
-
Dickie IA, (2010) Insidious effects of sequencing errors on perceived diversity in molecular surveys. New Phytol 188: 916-918 doi:10.1111/j.1469-8137.2010.03473.x.
-
(2010)
New Phytol
, vol.188
, pp. 916-918
-
-
Dickie, I.A.1
-
22
-
-
29144464937
-
UniFrac: A new phylogenetic method for comparing microbial communities
-
Lozupone C, Knight R, (2005) UniFrac: A new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 8228-8235
-
-
Lozupone, C.1
Knight, R.2
-
23
-
-
77956304094
-
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions
-
10.1038/nmeth0910-668b
-
Reeder J, Knight R, (2010) Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Meth 7: 668-669 doi:10.1038/nmeth0910-668b.
-
(2010)
Nat Meth
, vol.7
, pp. 668-669
-
-
Reeder, J.1
Knight, R.2
-
24
-
-
83355173006
-
Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies
-
10.1371/journal.pone.0027310
-
Schloss PD, Gevers D, Westcott SL, (2011) Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 6: e27310 doi:10.1371/journal.pone.0027310.
-
(2011)
PLoS ONE
, vol.6
-
-
Schloss, P.D.1
Gevers, D.2
Westcott, S.L.3
|