-
1
-
-
0032192790
-
Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products
-
Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol. 1998;5:R245-9.
-
(1998)
Chem Biol
, vol.5
, pp. R245-R249
-
-
Handelsman, J.1
Rondon, M.R.2
Brady, S.F.3
Clardy, J.4
Goodman, R.M.5
-
2
-
-
18844481269
-
Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms
-
Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, et al. Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol. 2000;66:2541-7.
-
(2000)
Appl Environ Microbiol
, vol.66
, pp. 2541-2547
-
-
Rondon, M.R.1
August, P.R.2
Bettermann, A.D.3
Brady, S.F.4
Grossman, T.H.5
Liles, M.R.6
-
3
-
-
23944495106
-
Metagenomics for studying unculturable microorganisms: cutting the Gordian knot
-
Schloss PD, Handelsman J. Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol. 2005;6:229.
-
(2005)
Genome Biol
, vol.6
, pp. 229
-
-
Schloss, P.D.1
Handelsman, J.2
-
4
-
-
84867074831
-
A metagenome-wide association study of gut microbiota in type 2 diabetes
-
Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012;490:55-60.
-
(2012)
Nature
, vol.490
, pp. 55-60
-
-
Qin, J.1
Li, Y.2
Cai, Z.3
Li, S.4
Zhu, J.5
Zhang, F.6
-
5
-
-
84862141704
-
Human gut microbiome viewed across age and geography
-
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486:222-7.
-
(2012)
Nature
, vol.486
, pp. 222-227
-
-
Yatsunenko, T.1
Rey, F.E.2
Manary, M.J.3
Trehan, I.4
Dominguez-Bello, M.G.5
Contreras, M.6
-
6
-
-
84878709716
-
Gut metagenome in European women with normal, impaired and diabetic glucose control
-
Karlsson FH, Tremaroli V, Nookaew I, Bergström G, Behre CJ, Fagerberg B, et al. Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature. 2013;498:99-103.
-
(2013)
Nature
, vol.498
, pp. 99-103
-
-
Karlsson, F.H.1
Tremaroli, V.2
Nookaew, I.3
Bergström, G.4
Behre, C.J.5
Fagerberg, B.6
-
7
-
-
79953232393
-
Accessing the soil metagenome for studies of microbial diversity
-
Delmont TO, Robe P, Cecillon S, Clark IM, Constancias F, Simonet P, et al. Accessing the soil metagenome for studies of microbial diversity. Appl Environ Microbiol. 2011;77:1315-24.
-
(2011)
Appl Environ Microbiol
, vol.77
, pp. 1315-1324
-
-
Delmont, T.O.1
Robe, P.2
Cecillon, S.3
Clark, I.M.4
Constancias, F.5
Simonet, P.6
-
8
-
-
84925883482
-
Studying the microbiology of the indoor environment
-
Kelley ST, Gilbert JA. Studying the microbiology of the indoor environment. Genome Biol. 2013;14:202.
-
(2013)
Genome Biol
, vol.14
, pp. 202
-
-
Kelley, S.T.1
Gilbert, J.A.2
-
9
-
-
84903386153
-
Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses
-
Ferreira AJS, Siam R, Setubal JC, Moustafa A, Sayed A, Chambergo FS, et al. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses. PLoS One. 2014;9.
-
(2014)
PLoS One
, pp. 9
-
-
Ferreira, A.J.S.1
Siam, R.2
Setubal, J.C.3
Moustafa, A.4
Sayed, A.5
Chambergo, F.S.6
-
11
-
-
75749135218
-
Metagenomics: Facts and artifacts, and computational challenges
-
Wooley JC, Ye Y. Metagenomics: Facts and artifacts, and computational challenges. J Comput Sci Technol. 2009;25:71-81.
-
(2009)
J Comput Sci Technol
, vol.25
, pp. 71-81
-
-
Wooley, J.C.1
Ye, Y.2
-
12
-
-
84862024684
-
Unlocking the potential of metagenomics through replicated experimental design
-
Knight R, Jansson J, Field D, Fierer N, Desai N, Fuhrman JA, et al. Unlocking the potential of metagenomics through replicated experimental design. Nat Biotechnol. 2012;30:513-20.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 513-520
-
-
Knight, R.1
Jansson, J.2
Field, D.3
Fierer, N.4
Desai, N.5
Fuhrman, J.A.6
-
13
-
-
84937046992
-
The effects of variable sample biomass on comparative metagenomics
-
Chafee M, Maignien L, Simmons SL. The effects of variable sample biomass on comparative metagenomics. Environ Microbiol. 2015;17:2239-53.
-
(2015)
Environ Microbiol
, vol.17
, pp. 2239-2253
-
-
Chafee, M.1
Maignien, L.2
Simmons, S.L.3
-
14
-
-
85011974719
-
The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies
-
Brooks JP, Edwards DJ, Harwich MD, Rivera MC, Fettweis JM, Serrano MG, et al. The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies. BMC Microbiol. 2015;15:1-14.
-
(2015)
BMC Microbiol
, vol.15
, pp. 1-14
-
-
Brooks, J.P.1
Edwards, D.J.2
Harwich, M.D.3
Rivera, M.C.4
Fettweis, J.M.5
Serrano, M.G.6
-
16
-
-
38549139537
-
IMG/M: A data management and analysis system for metagenomes
-
Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, et al. IMG/M: A data management and analysis system for metagenomes. Nucleic Acids Res. 2008;36 Suppl 1:D534-8.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. D534-D538
-
-
Markowitz, V.M.1
Ivanova, N.N.2
Szeto, E.3
Palaniappan, K.4
Chu, K.5
Dalevi, D.6
-
17
-
-
84862024797
-
IMG/M: the integrated metagenome data management and comparative analysis system
-
Markowitz VM, Chen I-M A, Chu K, Szeto E, Palaniappan K, Grechkin Y, et al. IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res. 2012;40(Database issue):D123-9.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
, pp. D123-D129
-
-
Markowitz, V.M.1
Chen I-M, A.2
Chu, K.3
Szeto, E.4
Palaniappan, K.5
Grechkin, Y.6
-
18
-
-
70349993601
-
ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes
-
Kristiansson E, Hugenholtz P, Dalevi D. ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes. Bioinformatics. 2009;25:2737-8.
-
(2009)
Bioinformatics
, vol.25
, pp. 2737-2738
-
-
Kristiansson, E.1
Hugenholtz, P.2
Dalevi, D.3
-
19
-
-
66249145772
-
Statistical methods for detecting differentially abundant features in clinical metagenomic samples
-
White JR, Nagarajan N, Pop M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol. 2009;5:e1000352.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
White, J.R.1
Nagarajan, N.2
Pop, M.3
-
21
-
-
77951945504
-
Identifying biologically relevant differences between metagenomic communities
-
Parks DH, Beiko RG. Identifying biologically relevant differences between metagenomic communities. Bioinformatics. 2010;26:715-21.
-
(2010)
Bioinformatics
, vol.26
, pp. 715-721
-
-
Parks, D.H.1
Beiko, R.G.2
-
22
-
-
79959383523
-
Metagenomic biomarker discovery and explanation
-
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, et al. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12:R60.
-
(2011)
Genome Biol
, vol.12
-
-
Segata, N.1
Izard, J.2
Waldron, L.3
Gevers, D.4
Miropolsky, L.5
Garrett, W.S.6
-
24
-
-
84888865593
-
Differential abundance analysis for microbial marker-gene surveys
-
Paulson JN, Stine OC, Bravo HC, Pop M. Differential abundance analysis for microbial marker-gene surveys. Nat Methods. 2013;10:1200-2.
-
(2013)
Nat Methods
, vol.10
, pp. 1200-1202
-
-
Paulson, J.N.1
Stine, O.C.2
Bravo, H.C.3
Pop, M.4
-
25
-
-
4544341015
-
Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
-
Smyth GK. Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments. Stat Appl Genet Mol Biol. 2004;3:1-25.
-
(2004)
Stat Appl Genet Mol Biol
, vol.3
, pp. 1-25
-
-
Smyth, G.K.1
-
26
-
-
75249087100
-
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139-40.
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
27
-
-
84882921441
-
Investigating the effect of two methane-mitigating diets on the rumen microbiome using massively parallel sequencing
-
Ross EM, Moate PJ, Marett L, Cocks BG, Hayes BJ. Investigating the effect of two methane-mitigating diets on the rumen microbiome using massively parallel sequencing. J Dairy Sci. 2013;96:6030-46.
-
(2013)
J Dairy Sci
, vol.96
, pp. 6030-6046
-
-
Ross, E.M.1
Moate, P.J.2
Marett, L.3
Cocks, B.G.4
Hayes, B.J.5
-
28
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2
-
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biol. 2014;15:550.
-
(2014)
Genome Biol
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
29
-
-
84928911036
-
Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics Analyses
-
Dugat-Bony E, Straub C, Teissandier A, Onésime D, Loux V, Monnet C, et al. Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics Analyses. PLoS ONE. 2015;10:e0124360.
-
(2015)
PLoS ONE
, vol.10
-
-
Dugat-Bony, E.1
Straub, C.2
Teissandier, A.3
Onésime, D.4
Loux, V.5
Monnet, C.6
-
30
-
-
84896735766
-
Voom: precision weights unlock linear model analysis tools for RNA-seq read counts
-
Law CW, Chen Y, Shi W, Smyth GK. Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 2014;15:R29.
-
(2014)
Genome Biol
, vol.15
-
-
Law, C.W.1
Chen, Y.2
Shi, W.3
Smyth, G.K.4
-
31
-
-
84908108405
-
The Sphagnum microbiome supports bog ecosystem functioning under extreme conditions
-
Bragina A, Oberauner-Wappis L, Zachow C, Halwachs B, Thallinger GG, Müller H, et al. The Sphagnum microbiome supports bog ecosystem functioning under extreme conditions. Mol Ecol. 2014;4498-4510.
-
(2014)
Mol Ecol
, pp. 4498-4510
-
-
Bragina, A.1
Oberauner-Wappis, L.2
Zachow, C.3
Halwachs, B.4
Thallinger, G.G.5
Müller, H.6
-
32
-
-
84869014474
-
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae
-
Nookaew I, Papini M, Pornputtapong N, Scalcinati G, Fagerberg L, Uhlén M, et al. A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res. 2012;40:10084-97.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 10084-10097
-
-
Nookaew, I.1
Papini, M.2
Pornputtapong, N.3
Scalcinati, G.4
Fagerberg, L.5
Uhlén, M.6
-
33
-
-
84874677498
-
A comparison of methods for differential expression analysis of RNA-seq data
-
Soneson C, Delorenzi M. A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinformatics. 2013;14:91.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 91
-
-
Soneson, C.1
Delorenzi, M.2
-
35
-
-
0001243836
-
The Transformation of Poisson. Binomial and Negative-Binomial Data
-
Anscombe FJ. The Transformation of Poisson. Binomial and Negative-Binomial Data. Biometrika. 1948;35:246.
-
(1948)
Biometrika
, vol.35
, pp. 246
-
-
Anscombe, F.J.1
-
38
-
-
84901363655
-
Waste not, want not: why rarefying microbiome data is inadmissible
-
McMurdie PJ, Holmes S. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol. 2014;10:e1003531.
-
(2014)
PLoS Comput Biol
, vol.10
-
-
McMurdie, P.J.1
Holmes, S.2
-
40
-
-
84936076693
-
Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses
-
Liu R, Holik AZ, Su S, Jansz N, Chen K, Leong HS, et al. Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses. Nucleic Acids Res. 2015;43:e97.
-
(2015)
Nucleic Acids Res
, vol.43
-
-
Liu, R.1
Holik, A.Z.2
Su, S.3
Jansz, N.4
Chen, K.5
Leong, H.S.6
-
41
-
-
84961945798
-
Controlling the false discovery rate: a practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995;57:289-300.
-
(1995)
J R Stat Soc Ser B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
42
-
-
0042424602
-
Statistical significance for genomewide studies
-
Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci U S A. 2003;100:9440-5.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 9440-9445
-
-
Storey, J.D.1
Tibshirani, R.2
-
43
-
-
84905454882
-
Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue
-
Karlsson FH, Nookaew I, Nielsen J. Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue. PLoS Comput Biol. 2014;10:e1003706.
-
(2014)
PLoS Comput Biol
, vol.10
-
-
Karlsson, F.H.1
Nookaew, I.2
Nielsen, J.3
-
44
-
-
84908597294
-
Binning metagenomic contigs by coverage and composition
-
Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, et al. Binning metagenomic contigs by coverage and composition. Nat Methods. 2014;11:1144-6.
-
(2014)
Nat Methods
, vol.11
, pp. 1144-1146
-
-
Alneberg, J.1
Bjarnason, B.S.2
Bruijn, I.3
Schirmer, M.4
Quick, J.5
Ijaz, U.Z.6
-
45
-
-
79952159600
-
The effect of correlation in false discovery rate estimation
-
Schwartzman A, Lin X. The effect of correlation in false discovery rate estimation. Biometrika. 2011;98:199-214.
-
(2011)
Biometrika
, vol.98
, pp. 199-214
-
-
Schwartzman, A.1
Lin, X.2
-
46
-
-
77954834592
-
Average genome size: a potential source of bias in comparative metagenomics
-
Beszteri B, Temperton B, Frickenhaus S, Giovannoni SJ. Average genome size: a potential source of bias in comparative metagenomics. ISME J. 2010;4:1075-7.
-
(2010)
ISME J
, vol.4
, pp. 1075-1077
-
-
Beszteri, B.1
Temperton, B.2
Frickenhaus, S.3
Giovannoni, S.J.4
-
47
-
-
84941635324
-
A robust approach for identifying differentially abundant features in metagenomic samples
-
Sohn MB, Du R, An L. A robust approach for identifying differentially abundant features in metagenomic samples. Bioinformatics. 2015;31:2269-75.
-
(2015)
Bioinformatics
, vol.31
, pp. 2269-2275
-
-
Sohn, M.B.1
Du, R.2
An, L.3
-
48
-
-
79953276286
-
Quantitative Metagenomic Analyses Based on Average Genome Size Normalization
-
Frank JA, Sorensen SJ. Quantitative Metagenomic Analyses Based on Average Genome Size Normalization. Appl Environ Microbiol. 2011;77:2513-21.
-
(2011)
Appl Environ Microbiol
, vol.77
, pp. 2513-2521
-
-
Frank, J.A.1
Sorensen, S.J.2
-
49
-
-
36448981743
-
Moderated statistical tests for assessing differences in tag abundance
-
Robinson MD, Smyth GK. Moderated statistical tests for assessing differences in tag abundance. Bioinformatics. 2007;23:2881-7.
-
(2007)
Bioinformatics
, vol.23
, pp. 2881-2887
-
-
Robinson, M.D.1
Smyth, G.K.2
-
50
-
-
84858041341
-
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
-
McCarthy DJ, Chen Y, Smyth GK. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 2012;40:4288-97.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 4288-4297
-
-
McCarthy, D.J.1
Chen, Y.2
Smyth, G.K.3
-
51
-
-
84963641621
-
R: A Language and Environment for Statistical Computing
-
Vienna, Austria
-
R Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria; 2014. http://www.R-project.org/
-
(2014)
-
-
-
53
-
-
77953176036
-
A scaling normalization method for differential expression analysis of RNA-seq data
-
Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11:R25.
-
(2010)
Genome Biol
, vol.11
-
-
Robinson, M.D.1
Oshlack, A.2
-
54
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11:R106.
-
(2010)
Genome Biol
, vol.11
-
-
Anders, S.1
Huber, W.2
-
55
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59-65.
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
Li, R.2
Raes, J.3
Arumugam, M.4
Burgdorf, K.S.5
Manichanh, C.6
-
56
-
-
0037249633
-
The TIGRFAMs database of protein families
-
Haft DH. The TIGRFAMs database of protein families. Nucleic Acids Res. 2003;31:371-3.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 371-373
-
-
Haft, D.H.1
-
57
-
-
80055082271
-
Accelerated Profile HMM Searches
-
Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011;7:e1002195.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Eddy, S.R.1
-
58
-
-
84979530154
-
Tentacle: distributed quantification of genes in metagenomes
-
Boulund F, Sjögren A, Kristiansson E. Tentacle: distributed quantification of genes in metagenomes. Gigascience. 2015;4:40.
-
(2015)
Gigascience
, vol.4
, pp. 40
-
-
Boulund, F.1
Sjögren, A.2
Kristiansson, E.3
-
59
-
-
0036226603
-
BLAT---The BLAST-Like Alignment Tool
-
Kent WJ. BLAT---The BLAST-Like Alignment Tool. Genome Res. 2002;12:656-64.
-
(2002)
Genome Res
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
60
-
-
53549118607
-
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
-
Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, et al. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008;9:386.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 386
-
-
Meyer, F.1
Paarmann, D.2
D'Souza, M.3
Olson, R.4
Glass, E.M.5
Kubal, M.6
-
61
-
-
33646023117
-
An introduction to ROC analysis
-
Fawcett T. An introduction to ROC analysis. Pattern Recognit Lett. 2006;27:861-74.
-
(2006)
Pattern Recognit Lett
, vol.27
, pp. 861-874
-
-
Fawcett, T.1
|