-
1
-
-
84875609855
-
Filtering duplicate reads from 454 pyrosequencing data
-
Balzer,S. et al. (2013) Filtering duplicate reads from 454 pyrosequencing data. Bioinformatics, 29, 830-836.
-
(2013)
Bioinformatics
, vol.29
, pp. 830-836
-
-
Balzer, S.1
-
2
-
-
0031722856
-
Analysis of the quality and utility of random shotgun sequencing at low redundancies
-
Bouck,J. et al. (1998) Analysis of the quality and utility of random shotgun sequencing at low redundancies. Genome Res., 8, 1074-1084.
-
(1998)
Genome Res.
, vol.8
, pp. 1074-1084
-
-
Bouck, J.1
-
3
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso,J.G. et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat. Methods, 7, 335-336.
-
(2010)
Nat. Methods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
-
4
-
-
84856582558
-
Bacterial species may exist, metagenomics reveal
-
Caro-Quintero,A. and Konstantinidis,K.T. (2012) Bacterial species may exist, metagenomics reveal. Environ. Microbiol., 14, 347-355.
-
(2012)
Environ. Microbiol.
, vol.14
, pp. 347-355
-
-
Caro-Quintero, A.1
Konstantinidis, K.T.2
-
5
-
-
0001463548
-
Nonparametric estimation of the number of classes in a population
-
Chao,A. (1984) Nonparametric estimation of the number of classes in a population. Scand. J. Stat., 11, 265-270.
-
(1984)
Scand. J. Stat.
, vol.11
, pp. 265-270
-
-
Chao, A.1
-
6
-
-
77957151956
-
SolexaQA: At-A-Glance quality assessment of Illumina secondgeneration sequencing data
-
Cox,M.P. et al. (2010) SolexaQA: at-a-glance quality assessment of Illumina secondgeneration sequencing data. BMC Bioinformatics, 11, 485.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 485
-
-
Cox, M.P.1
-
7
-
-
84875700725
-
Predicting the molecular complexity of sequencing libraries
-
Daley,T. and Smith,A.D. (2013) Predicting the molecular complexity of sequencing libraries. Nat. Methods, 10, 325-327.
-
(2013)
Nat. Methods
, vol.10
, pp. 325-327
-
-
Daley, T.1
Smith, A.D.2
-
8
-
-
84860160394
-
In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids
-
Denef,V.J. and Banfield,J.F. (2012) In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids. Science, 336, 462-466.
-
(2012)
Science
, vol.336
, pp. 462-466
-
-
Denef, V.J.1
Banfield, J.F.2
-
9
-
-
0019610360
-
An adaptive nonlinear least-squares algorithm
-
Dennis,J.E. et al. (1981) An adaptive nonlinear least-squares algorithm. ACM Trans. Math. Softw., 7, 348-368.
-
(1981)
ACM Trans. Math. Softw.
, vol.7
, pp. 348-368
-
-
Dennis, J.E.1
-
10
-
-
52649157765
-
Substantial biases in ultra-short read data sets from highthroughput DNA sequencing
-
Dohm,J.C. et al. (2008) Substantial biases in ultra-short read data sets from highthroughput DNA sequencing. Nucleic Acids Res., 36, e105.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Dohm, J.C.1
-
11
-
-
0000760438
-
The efficiency of good's nonparametric coverage estimator
-
Esty,W.W. (1986) The efficiency of good's nonparametric coverage estimator. Ann. Stat., 14, 1257-1260.
-
(1986)
Ann. Stat.
, vol.14
, pp. 1257-1260
-
-
Esty, W.W.1
-
12
-
-
84871826193
-
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
-
Fierer,N. et al. (2012) Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc. Natl Acad. Sci. USA, 109, 21390-21395.
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. 21390-21395
-
-
Fierer, N.1
-
13
-
-
0000803388
-
The population frequencies of species and the estimation of population parameters
-
Good,I.J. (1953) The population frequencies of species and the estimation of population parameters. Biometrika, 40, 237-264.
-
(1953)
Biometrika
, vol.40
, pp. 237-264
-
-
Good, I.J.1
-
14
-
-
33846555715
-
DNA-DNA hybridization values and their relationship to whole-genome sequence similarities
-
Goris,J. et al. (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol., 57, 81-91.
-
(2007)
Int. J. Syst. Evol. Microbiol.
, vol.57
, pp. 81-91
-
-
Goris, J.1
-
15
-
-
77949524553
-
Estimating DNA coverage and abundance in metagenomes using a gamma approximation
-
Hooper,S.D. et al. (2010) Estimating DNA coverage and abundance in metagenomes using a gamma approximation. Bioinformatics, 26, 295-301.
-
(2010)
Bioinformatics
, vol.26
, pp. 295-301
-
-
Hooper, S.D.1
-
16
-
-
0035487318
-
Counting the uncountable: Statistical approaches to estimating microbial diversity
-
Hughes,J.B. et al. (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol., 67, 4399-4406.
-
(2001)
Appl. Environ. Microbiol.
, vol.67
, pp. 4399-4406
-
-
Hughes, J.B.1
-
17
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
HumanMicrobiome Project Consortium
-
HumanMicrobiome Project Consortium. (2012) Structure, function and diversity of the healthy human microbiome. Nature, 486, 207-214.
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
-
18
-
-
35748954014
-
Prokaryotic taxonomy and phylogeny in the genomic era: Advancements and challenges ahead
-
Konstantinidis,K.T. and Tiedje,J.M. (2007) Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr. Opin. Microbiol., 10, 504-509.
-
(2007)
Curr. Opin. Microbiol.
, vol.10
, pp. 504-509
-
-
Konstantinidis, K.T.1
Tiedje, J.M.2
-
19
-
-
62549131646
-
PEMer: A computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
-
Korbel,J.O. et al. (2009) PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol., 10, R23.
-
(2009)
Genome Biol.
, vol.10
-
-
Korbel, J.O.1
-
20
-
-
73349110099
-
Wrinkles in the rare biosphere: Pyrosequencing errors can lead to artificial inflation of diversity estimates
-
Kunin,V. et al. (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ. Microbiol., 12, 118-123.
-
(2010)
Environ. Microbiol.
, vol.12
, pp. 118-123
-
-
Kunin, V.1
-
21
-
-
0023988195
-
Genomic mapping by fingerprinting random clones: A mathematical analysis
-
Lander,E.S. and Waterman,M.S. (1988) Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics, 2, 231-239.
-
(1988)
Genomics
, vol.2
, pp. 231-239
-
-
Lander, E.S.1
Waterman, M.S.2
-
22
-
-
84871780204
-
Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms
-
Liu,J. et al. (2013) Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms. Nucleic Acids Res., 41, e3.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Liu, J.1
-
23
-
-
83555174830
-
Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw
-
Mackelprang,R. et al. (2011) Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature, 480, 368-371.
-
(2011)
Nature
, vol.480
, pp. 368-371
-
-
Mackelprang, R.1
-
24
-
-
80052753042
-
Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem
-
Oh,S. et al. (2011) Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem. Appl. Environ. Microbiol., 77, 6000-6011.
-
(2011)
Appl. Environ. Microbiol.
, vol.77
, pp. 6000-6011
-
-
Oh, S.1
-
25
-
-
79952750340
-
Vaginal microbiome of reproductive-age women
-
Ravel,J. et al. (2011) Vaginal microbiome of reproductive-age women. Proc. Natl Acad. Sci. USA, 108 (Suppl. 1), 4680-4687.
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, Issue.SUPPL. 1
, pp. 4680-4687
-
-
Ravel, J.1
-
26
-
-
10944226351
-
Metagenomics: Genomic analysis of microbial communities
-
Riesenfeld,C.S. et al. (2004) Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet., 38, 525-552.
-
(2004)
Annu. Rev. Genet.
, vol.38
, pp. 525-552
-
-
Riesenfeld, C.S.1
-
27
-
-
39049092823
-
A statistical toolbox for metagenomics: Assessing functional diversity in microbial communities
-
Schloss,P.D. and Handelsman,J. (2008) A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. BMC Bioinformatics, 9, 34.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 34
-
-
Schloss, P.D.1
Handelsman, J.2
-
28
-
-
72949107142
-
Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss,P.D. 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
-
29
-
-
77955631533
-
Occupancy modeling, maximum contig size probabilities and designing metagenomics experiments
-
Stanhope,S.A. (2010) Occupancy modeling, maximum contig size probabilities and designing metagenomics experiments. PLoS One, 5, e11652.
-
(2010)
PLoS One
, vol.5
-
-
Stanhope, S.A.1
-
30
-
-
84860855706
-
COVER: A priori estimation of coverage for metagenomic sequencing
-
Tamames,J. et al. (2012) COVER: a priori estimation of coverage for metagenomic sequencing. Environ. Microbiol. Rep., 4, 335-341.
-
(2012)
Environ. Microbiol. Rep.
, vol.4
, pp. 335-341
-
-
Tamames, J.1
-
31
-
-
84874536596
-
The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses
-
Vetrovský.T. and Baldrian,P. (2013) The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS One, 8, e57923.
-
(2013)
PLoS One
, vol.8
-
-
Vetrovský, T.1
Baldrian, P.2
-
32
-
-
33749242769
-
A general coverage theory for shotgun DNA sequencing
-
Wendl,M.C. (2006) A general coverage theory for shotgun DNA sequencing. J. Comput. Biol., 13, 1177-1196.
-
(2006)
J. Comput. Biol.
, vol.13
, pp. 1177-1196
-
-
Wendl, M.C.1
-
33
-
-
84885381231
-
Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem
-
Wendl,M.C. et al. (2012) Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem. J. Math. Biol., 67, 1141-1161.
-
(2012)
J. Math. Biol.
, vol.67
, pp. 1141-1161
-
-
Wendl, M.C.1
-
34
-
-
72949101201
-
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
-
Wu,D. 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
|