-
1
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
Human Microbiome Project Consortium. (2012) Structure, function and diversity of the healthy human microbiome. Nature, 486, 207-214.
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
-
2
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K.S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T. et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 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
Nielsen, T.7
Pons, N.8
Levenez, F.9
Yamada, T.10
-
3
-
-
58749112734
-
A core gut microbiome in obese and lean twins
-
Turnbaugh, P.J., Hamady, M., Yatsunenko, T., Cantarel, B.L., Duncan, A., Ley, R.E., Sogin, M.L., Jones, W.J., Roe, B.A., Affourtit, J.P. et al. (2009) A core gut microbiome in obese and lean twins. Nature, 457, 480-484.
-
(2009)
Nature
, vol.457
, pp. 480-484
-
-
Turnbaugh, P.J.1
Hamady, M.2
Yatsunenko, T.3
Cantarel, B.L.4
Duncan, A.5
Ley, R.E.6
Sogin, M.L.7
Jones, W.J.8
Roe, B.A.9
Affourtit, J.P.10
-
4
-
-
84911468185
-
Members of the human gut microbiota involved in recovery from vibrio cholerae infection
-
Hsiao, A., Ahmed, A.M., Subramanian, S., Griffin, N.W., Drewry, L.L., Petri, W.A. Jr, Haque, R., Ahmed, T. and Gordon, J.I. (2014) Members of the human gut microbiota involved in recovery from Vibrio cholerae infection. Nature, 515, 423-426.
-
(2014)
Nature
, vol.515
, pp. 423-426
-
-
Hsiao, A.1
Ahmed, A.M.2
Subramanian, S.3
Griffin, N.W.4
Drewry, L.L.5
Petri, W.A.6
Haque, R.7
Ahmed, T.8
Gordon, J.I.9
-
5
-
-
77952168929
-
Evolutionary dynamics of clostridium difficile over short and long time scales
-
He, M., Sebaihia, M., Lawley, T.D., Stabler, R.A., Dawson, L.F., Martin, M.J., Holt, K.E., Seth-Smith, H.M., Quail, M.A., Rance, R. et al. (2010) Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc. Natl. Acad. Sci. U.S.A., 107, 7527-7532.
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, pp. 7527-7532
-
-
He, M.1
Sebaihia, M.2
Lawley, T.D.3
Stabler, R.A.4
Dawson, L.F.5
Martin, M.J.6
Holt, K.E.7
Seth-Smith, H.M.8
Quail, M.A.9
Rance, R.10
-
6
-
-
84868201561
-
Intracontinental spread of human invasive salmonella typhimurium pathovariants in sub-saharan Africa
-
Okoro, C.K., Kingsley, R.A., Connor, T.R., Harris, S.R., Parry, C.M., Al-Mashhadani, M.N., Kariuki, S., Msefula, C.L., Gordon, M.A., de Pinna, E. et al. (2012) Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat. Genet., 44, 1215-1221.
-
(2012)
Nat. Genet.
, vol.44
, pp. 1215-1221
-
-
Okoro, C.K.1
Kingsley, R.A.2
Connor, T.R.3
Harris, S.R.4
Parry, C.M.5
Al-Mashhadani, M.N.6
Kariuki, S.7
Msefula, C.L.8
Gordon, M.A.9
De Pinna, E.10
-
7
-
-
84865683817
-
Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe
-
Holt, K.E., Baker, S., Weill, F.X., Holmes, E.C., Kitchen, A., Yu, J., Sangal, V., Brown, D.J., Coia, J.E., Kim, D.W. et al. (2012) Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat. Genet., 44, 1056-1059.
-
(2012)
Nat. Genet.
, vol.44
, pp. 1056-1059
-
-
Holt, K.E.1
Baker, S.2
Weill, F.X.3
Holmes, E.C.4
Kitchen, A.5
Yu, J.6
Sangal, V.7
Brown, D.J.8
Coia, J.E.9
Kim, D.W.10
-
8
-
-
80053133499
-
Evidence for several waves of global transmission in the seventh cholera pandemic
-
Mutreja, A., Kim, D.W., Thomson, N.R., Connor, T.R., Lee, J.H., Kariuki, S., Croucher, N.J., Choi, S.Y., Harris, S.R., Lebens, M. et al. (2011) Evidence for several waves of global transmission in the seventh cholera pandemic. Nature, 477, 462-465.
-
(2011)
Nature
, vol.477
, pp. 462-465
-
-
Mutreja, A.1
Kim, D.W.2
Thomson, N.R.3
Connor, T.R.4
Lee, J.H.5
Kariuki, S.6
Croucher, N.J.7
Choi, S.Y.8
Harris, S.R.9
Lebens, M.10
-
9
-
-
0032965099
-
The link between phylogeny and virulence in Escherichia coli extraintestinal infection
-
Picard, B., Garcia, J.S., Gouriou, S., Duriez, P., Brahimi, N., Bingen, E., Elion, J. and Denamur, E. (1999) The link between phylogeny and virulence in Escherichia coli extraintestinal infection. Infect. Immun., 67, 546-553.
-
(1999)
Infect. Immun.
, vol.67
, pp. 546-553
-
-
Picard, B.1
Garcia, J.S.2
Gouriou, S.3
Duriez, P.4
Brahimi, N.5
Bingen, E.6
Elion, J.7
Denamur, E.8
-
10
-
-
84871990888
-
Emergence and global spread of epidemic healthcare-associated clostridium difficile
-
He, M., Miyajima, F., Roberts, P., Ellison, L., Pickard, D.J., Martin, M.J., Connor, T.R., Harris, S.R., Fairley, D., Bamford, K.B. et al. (2013) Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nat. Genet., 45, 109-113.
-
(2013)
Nat. Genet.
, vol.45
, pp. 109-113
-
-
He, M.1
Miyajima, F.2
Roberts, P.3
Ellison, L.4
Pickard, D.J.5
Martin, M.J.6
Connor, T.R.7
Harris, S.R.8
Fairley, D.9
Bamford, K.B.10
-
11
-
-
84891820094
-
IMG 4 version of the integrated microbial genomes comparative analysis system
-
Markowitz, V.M., Chen, I.M., Palaniappan, K., Chu, K., Szeto, E., Pillay, M., Ratner, A., Huang, J., Woyke, T., Huntemann, M. et al. (2014) IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res., 42, D560-D567.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D560-D567
-
-
Markowitz, V.M.1
Chen, I.M.2
Palaniappan, K.3
Chu, K.4
Szeto, E.5
Pillay, M.6
Ratner, A.7
Huang, J.8
Woyke, T.9
Huntemann, M.10
-
12
-
-
84891822499
-
EBI metagenomics - A new resource for the analysis and archiving of metagenomic data
-
Hunter, S., Corbett, M., Denise, H., Fraser, M., Gonzalez-Beltran, A., Hunter, C., Jones, P., Leinonen, R., McAnulla, C., Maguire, E. et al. (2014) EBI metagenomics-a new resource for the analysis and archiving of metagenomic data. Nucleic Acids Res., 42, D600-D606.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D600-D606
-
-
Hunter, S.1
Corbett, M.2
Denise, H.3
Fraser, M.4
Gonzalez-Beltran, A.5
Hunter, C.6
Jones, P.7
Leinonen, R.8
McAnulla, C.9
Maguire, E.10
-
13
-
-
84891763315
-
MetaRef: A pan-genomic database for comparative and community microbial genomics
-
Huang, K., Brady, A., Mahurkar, A., White, O., Gevers, D., Huttenhower, C. and Segata, N. (2014) MetaRef: a pan-genomic database for comparative and community microbial genomics. Nucleic Acids Res., 42, D617-D624.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D617-D624
-
-
Huang, K.1
Brady, A.2
Mahurkar, A.3
White, O.4
Gevers, D.5
Huttenhower, C.6
Segata, N.7
-
14
-
-
75549091981
-
MetaBioME: A database to explore commercially useful enzymes in metagenomic datasets
-
Sharma, V.K., Kumar, N., Prakash, T. and Taylor, T.D. (2010) MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets. Nucleic Acids Res., 38, D468-D472.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. D468-D472
-
-
Sharma, V.K.1
Kumar, N.2
Prakash, T.3
Taylor, T.D.4
-
15
-
-
84862286169
-
A framework for human microbiome research
-
Human Microbiome Project Consortium. (2012) A framework for human microbiome research. Nature, 486, 215-221.
-
(2012)
Nature
, vol.486
, pp. 215-221
-
-
-
16
-
-
84964253062
-
Systematic discovery of probiotics
-
Forster, S.C. and Lawley, T.D. (2015) Systematic discovery of probiotics. Nat. Biotechnol., 33, 47-49.
-
(2015)
Nat. Biotechnol.
, vol.33
, pp. 47-49
-
-
Forster, S.C.1
Lawley, T.D.2
-
17
-
-
84887625620
-
Bacteriotherapy for the treatment of intestinal dysbiosis caused by clostridium difficile infection
-
Adamu, B.O. and Lawley, T.D. (2013) Bacteriotherapy for the treatment of intestinal dysbiosis caused by Clostridium difficile infection. Curr. Opin. Microbiol., 16, 596-601.
-
(2013)
Curr. Opin. Microbiol.
, vol.16
, pp. 596-601
-
-
Adamu, B.O.1
Lawley, T.D.2
-
18
-
-
84946073050
-
Content discovery and retrieval services at the European nucleotide archive
-
Silvester, N., Alako, B., Amid, C., Cerdeno-Tarraga, A., Cleland, I., Gibson, R., Goodgame, N., Ten Hoopen, P., Kay, S., Leinonen, R. et al. (2015) Content discovery and retrieval services at the European Nucleotide Archive. Nucleic Acids Res., 43, D23-29.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D23-D29
-
-
Silvester, N.1
Alako, B.2
Amid, C.3
Cerdeno-Tarraga, A.4
Cleland, I.5
Gibson, R.6
Goodgame, N.7
Ten Hoopen, P.8
Kay, S.9
Leinonen, R.10
-
19
-
-
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, E.M., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A. et al. (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics, 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
Paczian, T.7
Rodriguez, A.8
Stevens, R.9
Wilke, A.10
-
20
-
-
84905049901
-
Trimmomatic: A flexible trimmer for illumina sequence data
-
Bolger, A.M., Lohse, M. and Usadel, B. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114-2120.
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
21
-
-
78651326786
-
FragGeneScan: Predicting genes in short and error-prone reads
-
Rho, M., Tang, H. and Ye, Y. (2010) FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res., 38, e191.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. e191
-
-
Rho, M.1
Tang, H.2
Ye, Y.3
-
22
-
-
84899518211
-
InterProScan 5: Genome-scale protein function classification
-
Jones, P., Binns, D., Chang, H.Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G. et al. (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics, 30, 1236-1240.
-
(2014)
Bioinformatics
, vol.30
, pp. 1236-1240
-
-
Jones, P.1
Binns, D.2
Chang, H.Y.3
Fraser, M.4
Li, W.5
McAnulla, C.6
McWilliam, H.7
Maslen, J.8
Mitchell, A.9
Nuka, G.10
-
23
-
-
0036226603
-
BLAT - The BLAST-like alignment tool
-
Kent, W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
-
(2002)
Genome Res.
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
24
-
-
84899090573
-
Kraken: Ultrafast metagenomic sequence classification using exact alignments
-
Wood, D.E. and Salzberg, S.L. (2014) Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol., 15, R46.
-
(2014)
Genome Biol.
, vol.15
, pp. R46
-
-
Wood, D.E.1
Salzberg, S.L.2
-
25
-
-
35348857386
-
Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases
-
Frank, D.N., St Amand, A.L., Feldman, R.A., Boedeker, E.C., Harpaz, N. and Pace, N.R. (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. U.S.A., 104, 13780-13785.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 13780-13785
-
-
Frank, D.N.1
St Amand, A.L.2
Feldman, R.A.3
Boedeker, E.C.4
Harpaz, N.5
Pace, N.R.6
-
26
-
-
84866549438
-
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
-
Morgan, X.C., Tickle, T.L., Sokol, H., Gevers, D., Devaney, K.L., Ward, D.V., Reyes, J.A., Shah, S.A., LeLeiko, N., Snapper, S.B. et al. (2012) Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol., 13, R79.
-
(2012)
Genome Biol.
, vol.13
, pp. R79
-
-
Morgan, X.C.1
Tickle, T.L.2
Sokol, H.3
Gevers, D.4
Devaney, K.L.5
Ward, D.V.6
Reyes, J.A.7
Shah, S.A.8
LeLeiko, N.9
Snapper, S.B.10
-
27
-
-
84904048875
-
A decrease of the butyrate-producing species roseburia hominis and faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis
-
Machiels, K., Joossens, M., Sabino, J., De Preter, V., Arijs, I., Eeckhaut, V., Ballet, V., Claes, K., Van Immerseel, F., Verbeke, K. et al. (2014) A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis. Gut, 63, 1275-1283.
-
(2014)
Gut
, vol.63
, pp. 1275-1283
-
-
Machiels, K.1
Joossens, M.2
Sabino, J.3
De Preter, V.4
Arijs, I.5
Eeckhaut, V.6
Ballet, V.7
Claes, K.8
Van Immerseel, F.9
Verbeke, K.10
|