-
1
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
Human Microbiome Project. C. Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214 (2012).
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
Human Microbiome Project C1
-
2
-
-
84905730165
-
An integrated catalog of reference genes in the human gut microbiome
-
Li, J. et al. An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol 32, 834-841 (2014).
-
(2014)
Nat Biotechnol
, vol.32
, pp. 834-841
-
-
Li, J.1
-
3
-
-
79952401369
-
Metatranscriptomic approach to analyze the functional human gut microbiota
-
Gosalbes, M. J. et al. Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS One 6, e17447 (2011).
-
(2011)
PLoS One
, vol.6
-
-
Gosalbes, M.J.1
-
4
-
-
84858864044
-
The activity level of a microbial community function can be predicted from its metatranscriptome
-
Helbling, D. E., Ackermann, M., Fenner, K., Kohler, H. P. & Johnson, D. R. The activity level of a microbial community function can be predicted from its metatranscriptome. ISME J 6, 902-904 (2012).
-
(2012)
ISME J
, vol.6
, pp. 902-904
-
-
Helbling, D.E.1
Ackermann, M.2
Fenner, K.3
Kohler, H.P.4
Johnson, D.R.5
-
5
-
-
84878366831
-
A quantitative reference transcriptome for Nematostella vectensis early embryonic development: A pipeline for de novo assembly in emerging model systems
-
Tulin, S., Aguiar, D., Istrail, S. & Smith, J. A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems. Evodevo 4, 16 (2013).
-
(2013)
Evodevo
, vol.4
, pp. 16
-
-
Tulin, S.1
Aguiar, D.2
Istrail, S.3
Smith, J.4
-
6
-
-
84880911975
-
A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets
-
Leimena, M. M. et al. A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets. BMC Genomics 14, 530 (2013).
-
(2013)
BMC Genomics
, vol.14
, pp. 530
-
-
Leimena, M.M.1
-
7
-
-
84876087439
-
Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood-and dung-feeding higher termites
-
He, S. et al. Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood-and dung-feeding higher termites. PLoS One 8, e61126 (2013).
-
(2013)
PLoS One
, vol.8
-
-
He, S.1
-
8
-
-
84857066577
-
Metatranscriptomic analysis of microbes in an Oceanfront deep-subsurface hot spring reveals novel small RNAs and type-specific tRNA degradation
-
Murakami, S., Fujishima, K., Tomita, M. & Kanai, A. Metatranscriptomic analysis of microbes in an Oceanfront deep-subsurface hot spring reveals novel small RNAs and type-specific tRNA degradation. Appl Environ Microbiol 78, 1015-1022 (2012).
-
(2012)
Appl Environ Microbiol
, vol.78
, pp. 1015-1022
-
-
Murakami, S.1
Fujishima, K.2
Tomita, M.3
Kanai, A.4
-
9
-
-
84893741669
-
Anal gas evacuation and colonic microbiota in patients with flatulence: Effect of diet
-
Manichanh, C. et al. Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet. Gut 63, 401-408 (2014).
-
(2014)
Gut
, vol.63
, pp. 401-408
-
-
Manichanh, C.1
-
10
-
-
67650711615
-
SOAP2: An improved ultrafast tool for short read alignment
-
Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966-1967 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1966-1967
-
-
Li, R.1
-
11
-
-
84857122937
-
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
-
McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610-618 (2012).
-
(2012)
ISME J
, vol.6
, pp. 610-618
-
-
McDonald, D.1
-
12
-
-
84922220803
-
A RESTful API for accessing microbial community data for MG-RAST
-
Wilke, A. et al. A RESTful API for accessing microbial community data for MG-RAST. PLoS Comput Biol 11, e1004008 (2015).
-
(2015)
PLoS Comput Biol
, vol.11
-
-
Wilke, A.1
-
13
-
-
84899090573
-
Kraken: Ultrafast metagenomic sequence classification using exact alignments
-
Wood, D. E. & Salzberg, S. L. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 15, R46 (2014).
-
(2014)
Genome Biol
, vol.15
, pp. R46
-
-
Wood, D.E.1
Salzberg, S.L.2
-
14
-
-
58149179980
-
RrnDB: Documenting the number of rRNA and tRNA genes in bacteria and archaea
-
Lee, Z. M., Bussema, C., 3rd & Schmidt, T. M. rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res 37, D489-493 (2009).
-
(2009)
Nucleic Acids Res
, vol.37
, pp. D489-493
-
-
Lee, Z.M.1
Bussema, C.2
Schmidt, T.M.3
-
15
-
-
84888783300
-
Impact of RNA-seq attributes on false positive rates in differential expression analysis of de novo assembled transcriptomes
-
Gonzalez, E. & Joly, S. Impact of RNA-seq attributes on false positive rates in differential expression analysis of de novo assembled transcriptomes. BMC Res Notes 6, 503 (2013).
-
(2013)
BMC Res Notes
, vol.6
, pp. 503
-
-
Gonzalez, E.1
Joly, S.2
-
16
-
-
84925021592
-
Fast and sensitive protein alignment using DIAMOND
-
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat Methods 12, 59-60 (2015).
-
(2015)
Nat Methods
, vol.12
, pp. 59-60
-
-
Buchfink, B.1
Xie, C.2
Huson, D.H.3
-
17
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
18
-
-
84902986307
-
A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tractassociated bacteria
-
Meehan, C. J. & Beiko, R. G. A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tractassociated bacteria. Genome Biol Evol 6, 703-713 (2014).
-
(2014)
Genome Biol Evol
, vol.6
, pp. 703-713
-
-
Meehan, C.J.1
Beiko, R.G.2
-
19
-
-
0029833218
-
Ruminococcus hydrogenotrophicus sp. nov., a new H2/CO2-utilizing acetogenic bacterium isolated from human feces
-
Bernalier, A., Willems, A., Leclerc, M., Rochet, V. & Collins, M. D. Ruminococcus hydrogenotrophicus sp. nov., a new H2/CO2-utilizing acetogenic bacterium isolated from human feces. Arch Microbiol 166, 176-183 (1996).
-
(1996)
Arch Microbiol
, vol.166
, pp. 176-183
-
-
Bernalier, A.1
Willems, A.2
Leclerc, M.3
Rochet, V.4
Collins, M.D.5
-
20
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65 (2010).
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
-
21
-
-
84940775779
-
Polyester: Simulating RNA-seq datasets with differential transcript expression
-
Frazee, A. C., Jaffe, A. E., Langmead, B. & Leek, J. T. Polyester: simulating RNA-seq datasets with differential transcript expression. Bioinformatics 31, 2778-2784 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 2778-2784
-
-
Frazee, A.C.1
Jaffe, A.E.2
Langmead, B.3
Leek, J.T.4
-
22
-
-
84918559643
-
IM-TORNADO: A tool for comparison of 16S reads from paired-end libraries
-
Jeraldo, P. et al. IM-TORNADO: a tool for comparison of 16S reads from paired-end libraries. PLoS One 9, e114804 (2014).
-
(2014)
PLoS One
, vol.9
-
-
Jeraldo, P.1
-
23
-
-
84857145150
-
ART: A next-generation sequencing read simulator
-
Huang, W., Li, L., Myers, J. R. & Marth, G. T. ART: a next-generation sequencing read simulator. Bioinformatics 28, 593-594 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 593-594
-
-
Huang, W.1
Li, L.2
Myers, J.R.3
Marth, G.T.4
-
24
-
-
84864344549
-
Storage conditions of intestinal microbiota matter in metagenomic analysis
-
Cardona, S. et al. Storage conditions of intestinal microbiota matter in metagenomic analysis. BMC Microbiol 12, 158 (2012).
-
(2012)
BMC Microbiol
, vol.12
, pp. 158
-
-
Cardona, S.1
-
25
-
-
84883492771
-
Kraken: A set of tools for quality control and analysis of high-throughput sequence data
-
Davis, M. P., van Dongen, S., Abreu-Goodger, C., Bartonicek, N. & Enright, A. J. Kraken: a set of tools for quality control and analysis of high-throughput sequence data. Methods 63, 41-49 (2013).
-
(2013)
Methods
, vol.63
, pp. 41-49
-
-
Davis, M.P.1
Van Dongen, S.2
Abreu-Goodger, C.3
Bartonicek, N.4
Enright, A.J.5
-
26
-
-
84870814915
-
SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
-
Kopylova, E., Noe, L. & Touzet, H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28, 3211-3217 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 3211-3217
-
-
Kopylova, E.1
Noe, L.2
Touzet, H.3
-
27
-
-
37549027613
-
SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
-
Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35, 7188-7196 (2007).
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 7188-7196
-
-
Pruesse, E.1
-
28
-
-
84874266637
-
Rfam 11.0: 10 years of RNA families
-
Burge, S. W. et al. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res 41, D226-232 (2013).
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D226-232
-
-
Burge, S.W.1
-
29
-
-
58149189877
-
GtRNAdb: A database of transfer RNA genes detected in genomic sequence
-
Chan, P. P. & Lowe, T. M. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 37, D93-97 (2009).
-
(2009)
Nucleic Acids Res
, vol.37
, pp. D93-97
-
-
Chan, P.P.1
Lowe, T.M.2
-
30
-
-
78651326786
-
FragGeneScan: Predicting genes in short and error-prone reads
-
Rho, M., Tang, H. & Ye, Y. FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res 38, e191 (2010).
-
(2010)
Nucleic Acids Res
, vol.38
, pp. e191
-
-
Rho, M.1
Tang, H.2
Ye, Y.3
-
31
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550 (2014).
-
(2014)
Genome Biol
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
32
-
-
79959954965
-
IPath2.0: Interactive pathway explorer
-
Yamada, T., Letunic, I., Okuda, S., Kanehisa, M. & Bork, P. iPath2.0: interactive pathway explorer. Nucleic Acids Res 39, W412-415 (2011).
-
(2011)
Nucleic Acids Res
, vol.39
, pp. W412-415
-
-
Yamada, T.1
Letunic, I.2
Okuda, S.3
Kanehisa, M.4
Bork, P.5
-
33
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7, 335-336 (2010).
-
(2010)
Nat Methods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
-
34
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72, 5069-5072 (2006).
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 5069-5072
-
-
DeSantis, T.Z.1
-
35
-
-
79952006773
-
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
-
Haas, B. J. et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21, 494-504 (2011).
-
(2011)
Genome Res
, vol.21
, pp. 494-504
-
-
Haas, B.J.1
-
36
-
-
67649327176
-
FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix
-
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26, 1641-1650 (2009).
-
(2009)
Mol Biol Evol
, vol.26
, pp. 1641-1650
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
|