-
1
-
-
84874612821
-
The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters
-
Aagaard, K., Petrosino, J., Keitel, W., Watson, M., Katancik, J., Garcia, N., et al. The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. FASEB J 27 (2013), 1012–1022.
-
(2013)
FASEB J
, vol.27
, pp. 1012-1022
-
-
Aagaard, K.1
Petrosino, J.2
Keitel, W.3
Watson, M.4
Katancik, J.5
Garcia, N.6
-
2
-
-
84864037467
-
Metabolic reconstruction for metagenomic data and its application to the human microbiome
-
Abubucker, S., Segata, N., Goll, J., Schubert, A.M., Izard, J., Cantarel, B.L., et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol, 8, 2012, e1002358.
-
(2012)
PLoS Comput Biol
, vol.8
, pp. e1002358
-
-
Abubucker, S.1
Segata, N.2
Goll, J.3
Schubert, A.M.4
Izard, J.5
Cantarel, B.L.6
-
3
-
-
84941331779
-
Back to basics: the influence of DNA extraction and primer choice on phylogenetic analysis of activated sludge communities
-
e0132783–15
-
Albertsen, M., Karst, S.M., Ziegler, A.S., Kirkegaard, R.H., Nielsen, P.H., Back to basics: the influence of DNA extraction and primer choice on phylogenetic analysis of activated sludge communities. PloS One, 10, 2015 e0132783–15.
-
(2015)
PloS One
, vol.10
-
-
Albertsen, M.1
Karst, S.M.2
Ziegler, A.S.3
Kirkegaard, R.H.4
Nielsen, P.H.5
-
4
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7 (2010), 335–336.
-
(2010)
Nat Methods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
Kuczynski, J.2
Stombaugh, J.3
Bittinger, K.4
Bushman, F.D.5
Costello, E.K.6
-
5
-
-
79952005915
-
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
-
Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Lozupone, C.A., Turnbaugh, P.J., et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences of the United States of America. 108 (2011), 4516–4522.
-
(2011)
Proceedings of the National Academy of Sciences of the United States of America.
, vol.108
, pp. 4516-4522
-
-
Caporaso, J.G.1
Lauber, C.L.2
Walters, W.A.3
Berg-Lyons, D.4
Lozupone, C.A.5
Turnbaugh, P.J.6
-
6
-
-
34147182303
-
A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria
-
Chakravorty, S., Helb, D., Burday, M., Connell, N., Alland, D., A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Bicrobiol Methods 69 (2007), 330–339.
-
(2007)
J Bicrobiol Methods
, vol.69
, pp. 330-339
-
-
Chakravorty, S.1
Helb, D.2
Burday, M.3
Connell, N.4
Alland, D.5
-
7
-
-
84867391206
-
Species-level analysis of DNA sequence data from the NIH Human Microbiome Project
-
Conlan, S., Kong, H.H., Segre, J.A., Species-level analysis of DNA sequence data from the NIH Human Microbiome Project. PloS One 7 (2012), e47075–e47077.
-
(2012)
PloS One
, vol.7
, pp. e47075-e47077
-
-
Conlan, S.1
Kong, H.H.2
Segre, J.A.3
-
8
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis, T.Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72 (2006), 5069–5072.
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 5069-5072
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
Keller, K.6
-
9
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar, R.C., Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26 (2010), 2460–2461.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
10
-
-
84879414990
-
Topographic diversity of fungal and bacterial communities in human skin
-
Findley, K., Oh, J., Yang, J., Conlan, S., Deming, C., Meyer, J.A., et al. Topographic diversity of fungal and bacterial communities in human skin. Nature. 498 (2013), 367–370.
-
(2013)
Nature.
, vol.498
, pp. 367-370
-
-
Findley, K.1
Oh, J.2
Yang, J.3
Conlan, S.4
Deming, C.5
Meyer, J.A.6
-
11
-
-
84884413581
-
Propionibacterium acnes strain populations in the human skin microbiome associated with acne
-
Fitz-Gibbon, S., Tomida, S., Chiu, B.-H., Nguyen, L., Du, C., Liu, M., et al. Propionibacterium acnes strain populations in the human skin microbiome associated with acne. J Invest Dermatol 133 (2013), 2152–2160.
-
(2013)
J Invest Dermatol
, vol.133
, pp. 2152-2160
-
-
Fitz-Gibbon, S.1
Tomida, S.2
Chiu, B.-H.3
Nguyen, L.4
Du, C.5
Liu, M.6
-
12
-
-
84874444175
-
The neuropathic diabetic foot ulcer microbiome is associated with clinical factors
-
Gardner, S.E., Hillis, S.L., Heilmann, K., Segre, J.A., Grice, E.A., The neuropathic diabetic foot ulcer microbiome is associated with clinical factors. Diabetes 62 (2013), 923–930.
-
(2013)
Diabetes
, vol.62
, pp. 923-930
-
-
Gardner, S.E.1
Hillis, S.L.2
Heilmann, K.3
Segre, J.A.4
Grice, E.A.5
-
13
-
-
84906829581
-
The Earth Microbiome project: successes and aspirations
-
Gilbert, J.A., Jansson, J.K., Knight, R., The Earth Microbiome project: successes and aspirations. BMC Biol, 12, 2014, 69.
-
(2014)
BMC Biol
, vol.12
, pp. 69
-
-
Gilbert, J.A.1
Jansson, J.K.2
Knight, R.3
-
14
-
-
84978047241
-
-
Pgirmess: data analysis in ecology. R package version 1.6.4
-
Giraudoux P. Pgirmess: data analysis in ecology. R package version 1.6.4, http://CRAN.R-project.org/package=pgirmess; 2015.
-
(2015)
-
-
Giraudoux, P.1
-
15
-
-
66349083859
-
Topographical and temporal diversity of the human skin microbiome
-
Grice, E.A., Kong, H.H., Conlan, S., Deming, C.B., Davis, J., Young, A.C., et al. Topographical and temporal diversity of the human skin microbiome. Science 324 (2009), 1190–1192.
-
(2009)
Science
, vol.324
, pp. 1190-1192
-
-
Grice, E.A.1
Kong, H.H.2
Conlan, S.3
Deming, C.B.4
Davis, J.5
Young, A.C.6
-
16
-
-
84885796893
-
Taxonomic precision of different hypervariable regions of 16S rRNA gene and annotation methods for functional bacterial groups in biological wastewater treatment
-
Guo, F., Ju, F., Cai, L., Zhang, T., Taxonomic precision of different hypervariable regions of 16S rRNA gene and annotation methods for functional bacterial groups in biological wastewater treatment. PloS One, 8, 2013, e76185.
-
(2013)
PloS One
, vol.8
, pp. e76185
-
-
Guo, F.1
Ju, F.2
Cai, L.3
Zhang, T.4
-
17
-
-
79952006773
-
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
-
Haas, B.J., Gevers, D., Earl, A.M., Feldgarden, M., Ward, D.V., Giannoukos, G., et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21 (2011), 494–504.
-
(2011)
Genome Res
, vol.21
, pp. 494-504
-
-
Haas, B.J.1
Gevers, D.2
Earl, A.M.3
Feldgarden, M.4
Ward, D.V.5
Giannoukos, G.6
-
18
-
-
84889010432
-
Microbial ecology of the skin in the era of metagenomics and molecular microbiology
-
a015362–2
-
Hannigan, G.D., Grice, E.A., Microbial ecology of the skin in the era of metagenomics and molecular microbiology. Cold Spring Harbor Perspect Med, 3, 2013 a015362–2.
-
(2013)
Cold Spring Harbor Perspect Med
, vol.3
-
-
Hannigan, G.D.1
Grice, E.A.2
-
19
-
-
84946600312
-
The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome
-
e01578–15
-
Hannigan, G.D., Meisel, J.S., Tyldsley, A.S., Zheng, Q., Hodkinson, B.P., SanMiguel, A.J., et al. The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. MBio, 6, 2015 e01578–15.
-
(2015)
MBio
, vol.6
-
-
Hannigan, G.D.1
Meisel, J.S.2
Tyldsley, A.S.3
Zheng, Q.4
Hodkinson, B.P.5
SanMiguel, A.J.6
-
20
-
-
84862286169
-
A framework for human microbiome research
-
Human Microbiome Project Consortium. A framework for human microbiome research. Nature 486 (2012), 215–221.
-
(2012)
Nature
, vol.486
, pp. 215-221
-
-
-
21
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486 (2012), 207–214.
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
-
22
-
-
84862192626
-
Evaluation of 16S rDNA-based community profiling for human microbiome research
-
Jumpstart Consortium Human Microbiome Project Data Generation Working Group. Evaluation of 16S rDNA-based community profiling for human microbiome research. PloS One, 7, 2012, e39315.
-
(2012)
PloS One
, vol.7
, pp. e39315
-
-
-
23
-
-
84884127512
-
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
-
Langille, M.G.I., Zaneveld, J., Caporaso, J.G., McDonald, D., Knights, D., Reyes, J.A., et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 31 (2013), 814–821.
-
(2013)
Nat Biotechnol.
, vol.31
, pp. 814-821
-
-
Langille, M.G.I.1
Zaneveld, J.2
Caporaso, J.G.3
McDonald, D.4
Knights, D.5
Reyes, J.A.6
-
24
-
-
77958610660
-
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
-
Matsen, F.A., Kodner, R.B., Armbrust, E.V., pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformat, 11, 2010, 538.
-
(2010)
BMC Bioinformat
, vol.11
, pp. 538
-
-
Matsen, F.A.1
Kodner, R.B.2
Armbrust, E.V.3
-
25
-
-
84874613039
-
The microbiome extends to subepidermal compartments of normal skin
-
Nakatsuji, T., Chiang, H.-I., Jiang, S.B., Nagarajan, H., Zengler, K., Gallo, R.L., The microbiome extends to subepidermal compartments of normal skin. Nat Commun, 4, 2013, 1431.
-
(2013)
Nat Commun
, vol.4
, pp. 1431
-
-
Nakatsuji, T.1
Chiang, H.-I.2
Jiang, S.B.3
Nagarajan, H.4
Zengler, K.5
Gallo, R.L.6
-
26
-
-
84899531657
-
Analysis, optimization and verification of illumina-generated 16S rRNA gene amplicon surveys
-
e94249–14
-
Nelson, M.C., Morrison, H.G., Benjamino, J., Grim, S.L., Graf, J., Analysis, optimization and verification of illumina-generated 16S rRNA gene amplicon surveys. PloS One, 9, 2014 e94249–14.
-
(2014)
PloS One
, vol.9
-
-
Nelson, M.C.1
Morrison, H.G.2
Benjamino, J.3
Grim, S.L.4
Graf, J.5
-
27
-
-
84908074440
-
Biogeography and individuality shape function in the human skin metagenome
-
Oh, J., Byrd, A.L., Deming, C., Conlan, S., NISC, Comparative Sequencing Program, Kong, H.H., et al. Biogeography and individuality shape function in the human skin metagenome. Nature. 514 (2014), 59–64.
-
(2014)
Nature.
, vol.514
, pp. 59-64
-
-
Oh, J.1
Byrd, A.L.2
Deming, C.3
Conlan, S.4
NISC, C.S.P.5
Kong, H.H.6
-
28
-
-
84940051817
-
Vegan: community ecology package
-
Oksanen, J., Guillaume Blanchet, F., Kindt, R., Legendre, P., Minchin, P., O'Hara, R.B., et al. Vegan: community ecology package. R package version 2.3-3, 2015 http://CRAN.R-project.org/package=vegan.
-
(2015)
R package version 2.3-3
-
-
Oksanen, J.1
Guillaume Blanchet, F.2
Kindt, R.3
Legendre, P.4
Minchin, P.5
O'Hara, R.B.6
-
29
-
-
84907095419
-
R: a language and environment for statistical computing
-
Austria Vienna
-
R Core Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing, 2015, Austria, Vienna.
-
(2015)
R Foundation for Statistical Computing
-
-
-
30
-
-
84920644670
-
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
-
Salter, S.J., Cox, M.J., Turek, E.M., Calus, S.T., Cookson, W.O., Moffatt, M.F., et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol, 12, 2014, 87.
-
(2014)
BMC Biol
, vol.12
, pp. 87
-
-
Salter, S.J.1
Cox, M.J.2
Turek, E.M.3
Calus, S.T.4
Cookson, W.O.5
Moffatt, M.F.6
-
31
-
-
79952390994
-
Fast identification and removal of sequence contamination from genomic and metagenomic datasets
-
Schmieder, R., Edwards, R., Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PloS One, 6, 2011, e17288.
-
(2011)
PloS One
, vol.6
, pp. e17288
-
-
Schmieder, R.1
Edwards, R.2
-
32
-
-
84881548286
-
Computational meta'omics for microbial community studies
-
666
-
Segata, N., Boernigen, D., Tickle, T.L., Morgan, X.C., Garrett, W.S., Huttenhower, C., Computational meta'omics for microbial community studies. Mol Syst Biol, 9, 2013 666.
-
(2013)
Mol Syst Biol
, vol.9
-
-
Segata, N.1
Boernigen, D.2
Tickle, T.L.3
Morgan, X.C.4
Garrett, W.S.5
Huttenhower, C.6
-
33
-
-
84864440400
-
Metagenomic microbial community profiling using unique clade-specific marker genes
-
Segata, N., Waldron, L., Ballarini, A., Narasimhan, V., Jousson, O., Huttenhower, C., Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods 9 (2012), 811–814.
-
(2012)
Nat Methods
, vol.9
, pp. 811-814
-
-
Segata, N.1
Waldron, L.2
Ballarini, A.3
Narasimhan, V.4
Jousson, O.5
Huttenhower, C.6
-
34
-
-
34548293679
-
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang, Q., Garrity, G.M., Tiedje, J.M., Cole, J.R., Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73 (2007), 5261–5267.
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
35
-
-
77955067191
-
Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags
-
Wu, G.D., Lewis, J.D., Hoffmann, C., Chen, Y.-Y., Knight, R., Bittinger, K., et al. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol 10 (2010), 206–214.
-
(2010)
BMC Microbiol
, vol.10
, pp. 206-214
-
-
Wu, G.D.1
Lewis, J.D.2
Hoffmann, C.3
Chen, Y.-Y.4
Knight, R.5
Bittinger, K.6
-
36
-
-
84961291157
-
Which is more important for classifying microbial communities: who's there or what they can do?
-
Xu, Z., Malmer, D., Langille, M.G.I., Way, S.F., Knight, R., Which is more important for classifying microbial communities: who's there or what they can do?. ISME J 8 (2014), 2357–2359.
-
(2014)
ISME J
, vol.8
, pp. 2357-2359
-
-
Xu, Z.1
Malmer, D.2
Langille, M.G.I.3
Way, S.F.4
Knight, R.5
|