-
1
-
-
84866887118
-
Large variations in bacterial ribosomal RNA genes
-
Lim K, Furuta Y, Kobayashi I. Large variations in bacterial ribosomal RNA genes. Mol Biol Evol. 2012; 29(10):2937-48.
-
(2012)
Mol Biol Evol
, vol.29
, Issue.10
, pp. 2937-2948
-
-
Lim, K.1
Furuta, Y.2
Kobayashi, I.3
-
2
-
-
84881138595
-
Insight into the phylogeny and coding potential of microbial dark matter
-
Rinke C, Schwientek P, Sczybra A, Ivanova NN, Anderson IJ, Cheng JF, et al.Insight into the phylogeny and coding potential of microbial dark matter. Nature. 2013; 499:431-7.
-
(2013)
Nature
, vol.499
, pp. 431-437
-
-
Rinke, C.1
Schwientek, P.2
Sczybra, A.3
Ivanova, N.N.4
Anderson, I.J.5
Cheng, J.F.6
-
3
-
-
0029789623
-
A quantitative map of nucleotide substitution rates in bacterial rRNA
-
Van de Peer Y, Chapelle S, De Wachter R. A quantitative map of nucleotide substitution rates in bacterial rRNA. Nucl Acids Res. 1996; 24:3381-91.
-
(1996)
Nucl Acids Res
, vol.24
, pp. 3381-3391
-
-
Van de Peer, Y.1
Chapelle, S.2
-
4
-
-
84878666389
-
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
-
Klindworth A, Pruesse E, Schweer T, Pelies J, Quast C, Horn M, et al.Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2012; 20:1-11.
-
(2012)
Nucleic Acids Res
, vol.20
, pp. 1-11
-
-
Klindworth, A.1
Pruesse, E.2
Schweer, T.3
Pelies, J.4
Quast, C.5
Horn, M.6
-
5
-
-
84892488033
-
The effect of primer choice and short read sequences on the outcom of 16S rRNA gene based diversity studies
-
Ghyselinck J, Pfeiffer S, Heylen K, Sessitsch A, De Vos P. The effect of primer choice and short read sequences on the outcom of 16S rRNA gene based diversity studies. PLoS One. 2013; 8(8):e71360.
-
(2013)
PLoS One
, vol.8
, Issue.8
-
-
Ghyselinck, J.1
Pfeiffer, S.2
Heylen, K.3
Sessitsch, A.4
De Vos, P.5
-
6
-
-
84865060813
-
PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets
-
Pinto AJ, Raskin L. PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One. 2012; 7(8):e43093.
-
(2012)
PLoS One
, vol.7
, Issue.8
-
-
Pinto, A.J.1
Raskin, L.2
-
7
-
-
84862631902
-
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences
-
Soergel DAW, Dey N, Knight R, Brenner SE. Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. ISME J. 2012; 6:1440-4.
-
(2012)
ISME J
, vol.6
, pp. 1440-1444
-
-
Soergel, D.A.W.1
Dey, N.2
Knight, R.3
Brenner, S.E.4
-
8
-
-
33747073504
-
Microbial diversity in the deep sea and the underexplored "rare biosphere"
-
Sogin ML, Morrison HG, Huber JA, MarkWelch D, Huse SM, Neal PR, et al.Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A. 2006; 103:12115-20.
-
(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
MarkWelch, D.4
Huse, S.M.5
Neal, P.R.6
-
9
-
-
84920629237
-
A renaissance for the pioneering 16S rRNA gene
-
Tringe SG, Hugenholtz P. A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol. 2008; 11:442-6.
-
(2008)
Curr Opin Microbiol
, vol.11
, pp. 442-446
-
-
Tringe, S.G.1
Hugenholtz, P.2
-
10
-
-
69549112742
-
Accurate determination of microbial diversity from 454 pyrosequencing data
-
Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, Head IM, et al.Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods. 2009; 6:639-41.
-
(2009)
Nat Methods
, vol.6
, pp. 639-641
-
-
Quince, C.1
Lanzen, A.2
Curtis, T.P.3
Davenport, R.J.4
Hall, N.5
Head, I.M.6
-
12
-
-
77956304094
-
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions
-
Reeder J, Knight R. Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods. 2010; 7:668-9.
-
(2010)
Nat Methods
, vol.7
, pp. 668-669
-
-
Reeder, J.1
Knight, R.2
-
13
-
-
35549007148
-
Short pyrosequencing reads suffice for accurate microbial community analysis
-
Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucl Acids Res. 2007; 35(18):e120.
-
(2007)
Nucl Acids Res
, vol.35
, Issue.18
-
-
Liu, Z.1
Lozupone, C.2
Hamady, M.3
Bushman, F.D.4
Knight, R.5
-
14
-
-
84862620989
-
Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys
-
Werner JJ, Zhou D, Caporaso JG, Knight R, Angenent LT. Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys. ISME J. 2012; 6(7):1273-6.
-
(2012)
ISME J
, vol.6
, Issue.7
, pp. 1273-1276
-
-
Werner, J.J.1
Zhou, D.2
Caporaso, J.G.3
Knight, R.4
Angenent, L.T.5
-
15
-
-
84893723345
-
Library preparation methods for next-generation sequencing: tone down the bias
-
van Dijk EL, Jaszczyszyn Y, Thermes C. Library preparation methods for next-generation sequencing: tone down the bias. Exp Cell Res. 2014; 322(1):12-20.
-
(2014)
Exp Cell Res
, vol.322
, Issue.1
, pp. 12-20
-
-
van Dijk, E.L.1
Jaszczyszyn, Y.2
Thermes, C.3
-
16
-
-
78650568308
-
SAMStat: monitoring biases in next generation sequencing data
-
Lassmann T, Hayashizaki Y, Daub CO. SAMStat: monitoring biases in next generation sequencing data. Bioinformatics. 2011; 27(1):130-1.
-
(2011)
Bioinformatics
, vol.27
, Issue.1
, pp. 130-131
-
-
Lassmann, T.1
Hayashizaki, Y.2
Daub, C.O.3
-
17
-
-
84906567656
-
Microbiology: Microbiome science needs a healthy dose of scepticism
-
Hanage WP. Microbiology: Microbiome science needs a healthy dose of scepticism. Nature. 2014; 512(7514):247-8.
-
(2014)
Nature
, vol.512
, Issue.7514
, pp. 247-248
-
-
Hanage, W.P.1
-
19
-
-
84954354477
-
Assessing the accuracy of quantitative molecular microbial profiling
-
O'Sullivan DM, Laver T, Temisak S, Redshaw N, Harris KA, Foy CA, et al.Assessing the accuracy of quantitative molecular microbial profiling. Int J Mol Sci. 2014; 15(11):21476-91.
-
(2014)
Int J Mol Sci
, vol.15
, Issue.11
, pp. 21476-21491
-
-
O'Sullivan, D.M.1
Laver, T.2
Temisak, S.3
Redshaw, N.4
Harris, K.A.5
Foy, C.A.6
-
20
-
-
84875389052
-
Considerations for the development and application of control materials to improve metagenomic microbial community profiling
-
Huggett JF, Laver T, Tamisak S, Nixon G, O'Sullivan DM, Elaswarapu R, et al.Considerations for the development and application of control materials to improve metagenomic microbial community profiling. Accred Qual Assur. 2013; 18(2):77-83.
-
(2013)
Accred Qual Assur
, vol.18
, Issue.2
, pp. 77-83
-
-
Huggett, J.F.1
Laver, T.2
Tamisak, S.3
Nixon, G.4
O'Sullivan, D.M.5
Elaswarapu, R.6
-
21
-
-
75549083380
-
Reducing the impact of pcr-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity dna polymerase
-
Lahr DJ, Katz LA. Reducing the impact of pcr-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity dna polymerase. Biotechniques. 2009; 47(4):857-66.
-
(2009)
Biotechniques
, vol.47
, Issue.4
, pp. 857-866
-
-
Lahr, D.J.1
Katz, L.A.2
-
22
-
-
34547834963
-
The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing
-
Binladen J, Gilbert MTP, Bollback JP, Panitz F, Bendixen C, Nielsen R, et al.The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS ONE. 2007; 2(2):e197.
-
(2007)
PLoS ONE
, vol.2
, Issue.2
-
-
Binladen, J.1
Gilbert, M.T.P.2
Bollback, J.P.3
Panitz, F.4
Bendixen, C.5
Nielsen, R.6
-
23
-
-
33846096244
-
Gene capture and random amplification for quantitative recovery of homologous genes
-
Crosby LD, Criddle CS. Gene capture and random amplification for quantitative recovery of homologous genes. Mol Cell Probes. 2007; 21(2):140-7.
-
(2007)
Mol Cell Probes
, vol.21
, Issue.2
, pp. 140-147
-
-
Crosby, L.D.1
Criddle, C.S.2
-
24
-
-
34548588390
-
Targeted high-throughput sequencing of tagged nucleic acid samples
-
Meyer M, Stenzel U, Myles S, Prufer K, Hofreiter M. Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Res. 2007; 35(15):e97.
-
(2007)
Nucleic Acids Res
, vol.35
, Issue.15
, pp. e97
-
-
Meyer, M.1
Stenzel, U.2
Myles, S.3
Prufer, K.4
Hofreiter, M.5
-
25
-
-
39449089394
-
Parallel tagged sequencing on the 454 platform
-
Meyer M, Stenzel U, Hofreiter M. Parallel tagged sequencing on the 454 platform. Nat Protoc. 2008; 3(2):267-78.
-
(2008)
Nat Protoc
, vol.3
, Issue.2
, pp. 267-278
-
-
Meyer, M.1
Stenzel, U.2
Hofreiter, M.3
-
26
-
-
72549096279
-
Depauperate genetic variability detected in the American and European bison using genomic techniques
-
Pertoldi C, Tokarska M, Wojcik JM, Demontis D, Loeschcke V, Gregersen VR, et al.Depauperate genetic variability detected in the American and European bison using genomic techniques. Biol Direct. 2009; 4:48.
-
(2009)
Biol Direct
, vol.4
, pp. 48
-
-
Pertoldi, C.1
Tokarska, M.2
Wojcik, J.M.3
Demontis, D.4
Loeschcke, V.5
Gregersen, V.R.6
-
27
-
-
84855194204
-
Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics
-
Bybee SM, Bracken-Grissom H, Haynes BD, Hermansen RA, Byers RL, Clement MJ, et al.Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics. Genome Biol Evol. 2011; 3:1312-23.
-
(2011)
Genome Biol Evol
, vol.3
, pp. 1312-1323
-
-
Bybee, S.M.1
Bracken-Grissom, H.2
Haynes, B.D.3
Hermansen, R.A.4
Byers, R.L.5
Clement, M.J.6
-
28
-
-
84878647680
-
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities
-
Shakya M, Quince C, Campbell JH, Yang ZK, Schadt CW, Podar M. Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environ Microbiol. 2013; 15(6):1882-99.
-
(2013)
Environ Microbiol
, vol.15
, Issue.6
, pp. 1882-1899
-
-
Shakya, M.1
Quince, C.2
Campbell, J.H.3
Yang, Z.K.4
Schadt, C.W.5
Podar, M.6
-
29
-
-
84863981120
-
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
-
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al.Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012; 6(8):1621-4.
-
(2012)
ISME J
, vol.6
, Issue.8
, pp. 1621-1624
-
-
Caporaso, J.G.1
Lauber, C.L.2
Walters, W.A.3
Berg-Lyons, D.4
Huntley, J.5
Fierer, N.6
-
30
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215:403-10.
-
(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
-
31
-
-
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; 25:1754-60.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
32
-
-
68549104404
-
The sequence alignment/map (SAM) format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al.The sequence alignment/map (SAM) format and SAMtools. Bioinformatics. 2009; 25:2078-9.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
-
33
-
-
84863229597
-
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
-
Koboldt D, Zhang Q, Larson D, Shen D, McLellan M, Lin L, et al.VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012; 22(3):568-76.
-
(2012)
Genome Res
, vol.22
, Issue.3
, pp. 568-576
-
-
Koboldt, D.1
Zhang, Q.2
Larson, D.3
Shen, D.4
McLellan, M.5
Lin, L.6
-
35
-
-
84934769334
-
Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform
-
Schirmer M, Ijaz UZ, D'Amore R, Hall N, Quince C. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Res. 2015; 43(6):e37.
-
(2015)
Nucleic Acids Res
, vol.43
, Issue.6
-
-
Schirmer, M.1
Ijaz, U.Z.2
D'Amore, R.3
Hall, N.4
Quince, C.5
-
36
-
-
77957244650
-
Search and clustering orders of magnitude faster than blast
-
Edgar RC. Search and clustering orders of magnitude faster than blast. Bioinformatics. 2010; 26:2460-1.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
37
-
-
34548293679
-
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microb. 2007; 73(16):5261-7.
-
(2007)
Appl Environ Microb
, vol.73
, Issue.16
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
38
-
-
84855295457
-
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
-
Kircher M, Sawyer S, Meyer M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 2012; 40:e3.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Kircher, M.1
Sawyer, S.2
Meyer, M.3
-
39
-
-
84899531657
-
Analysis, optimization and verification of illumina-generated 16s rrna gene amplicon surveys
-
Nelson MC, Morrison HG, Benjamino J, Grim SL, Graf J. Analysis, optimization and verification of illumina-generated 16s rrna gene amplicon surveys. PLoS ONE. 2014; 9(4):e94249.
-
(2014)
PLoS ONE
, vol.9
, Issue.4
-
-
Nelson, M.C.1
Morrison, H.G.2
Benjamino, J.3
Grim, S.L.4
Graf, J.5
-
40
-
-
84884907694
-
Practical innovations for high-throughput amplicon sequencing
-
Lundberg DS, Yourstone S, Mieczkowski P, Jones CD, Dangl JL. Practical innovations for high-throughput amplicon sequencing. Nat Methods. 2013; 10:999-1002.
-
(2013)
Nat Methods
, vol.10
, pp. 999-1002
-
-
Lundberg, D.S.1
Yourstone, S.2
Mieczkowski, P.3
Jones, C.D.4
Dangl, J.L.5
|