-
1
-
-
70350343544
-
Induction of intestinal Th17 cells by segmented filamentous bacteria
-
PMID: 19836068
-
Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U, et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell. 2009; 139: 485-98. doi: 10.1016/j.cell.2009.09.033 PMID: 19836068
-
(2009)
Cell
, vol.139
, pp. 485-498
-
-
Ivanov, I.I.1
Atarashi, K.2
Manel, N.3
Brodie, E.L.4
Shima, T.5
Karaoz, U.6
-
2
-
-
55949124035
-
Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients
-
PMID: 18936492
-
Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermúdez-Humarán LG, Gratadoux J-J, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A. 2008; 105: 16731-6. doi: 10.1073/pnas. 0804812105 PMID: 18936492
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 16731-16736
-
-
Sokol, H.1
Pigneur, B.2
Watterlot, L.3
Lakhdari, O.4
Bermúdez-Humarán, L.G.5
Gratadoux, J.-J.6
-
3
-
-
84920613211
-
The gut commensal bacteroides thetaiotaomicron exacerbates enteric infection through modification of the metabolic landscape
-
PMID: 25498343
-
Curtis MM, Hu Z, Klimko C, Narayanan S, Deberardinis R, Sperandio V. The gut commensal Bacteroides thetaiotaomicron exacerbates enteric infection through modification of the metabolic landscape. Cell Host Microbe. 2014; 16: 759-769. doi: 10.1016/j.chom.2014.11.005 PMID: 25498343
-
(2014)
Cell Host Microbe.
, vol.16
, pp. 759-769
-
-
Curtis, M.M.1
Hu, Z.2
Klimko, C.3
Narayanan, S.4
Deberardinis, R.5
Sperandio, V.6
-
4
-
-
84895932141
-
Expansion of urease- and uricase-containing, indole- and p-cresol-forming and contraction of short-chain fatty acid-producing intestinal microbiota in ESRD
-
PMID: 24643131
-
Wong J, Piceno YM, DeSantis TZ, Pahl M, Andersen GL, Vaziri ND. Expansion of urease- and uricase-containing, indole- and p-cresol-forming and contraction of short-chain fatty acid-producing intestinal microbiota in ESRD. Am J Nephrol. 2014; 39: 230-237. doi: 10.1159/000360010 PMID: 24643131
-
(2014)
Am J Nephrol.
, vol.39
, pp. 230-237
-
-
Wong, J.1
Piceno, Y.M.2
DeSantis, T.Z.3
Pahl, M.4
Andersen, G.L.5
Vaziri, N.D.6
-
5
-
-
84884127512
-
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
-
Nature Publishing Group. PMID: 23975157
-
Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes J a, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. Nature Publishing Group; 2013; 31: 814-21. doi: 10.1038/nbt.2676 PMID: 23975157
-
(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
-
6
-
-
84983143193
-
Multilocus sequence analysis (MLSA) in prokaryotic taxonomy
-
PMID: 25959541
-
Glaeser SP, Kämpfer P. Multilocus sequence analysis (MLSA) in prokaryotic taxonomy. Syst Appl Microbiol. 2015; 38: 237-245. doi: 10.1016/j.syapm.2015.03.007 PMID: 25959541
-
(2015)
Syst Appl Microbiol.
, vol.38
, pp. 237-245
-
-
Glaeser, S.P.1
Kämpfer, P.2
-
7
-
-
84884127512
-
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
-
PMID: 23975157
-
Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013; 31: 814-21. doi: 10.1038/nbt.2676 PMID: 23975157
-
(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
-
9
-
-
84902336218
-
Changes in abundance of oral microbiota associated with oral cancer
-
PMID: 24887397
-
Schmidt BL, Kuczynski J, Bhattacharya A, Huey B, Corby PM, Queiroz ELS, et al. Changes in abundance of oral microbiota associated with oral cancer. PLoS One. 2014; 9: e98741. doi: 10.1371/journal.pone.0098741 PMID: 24887397
-
(2014)
PLoS One
, vol.9
, pp. e98741
-
-
Schmidt, B.L.1
Kuczynski, J.2
Bhattacharya, A.3
Huey, B.4
Corby, P.M.5
Queiroz, E.L.S.6
-
10
-
-
84871383437
-
Phylogenetic stratigraphy in the guerrero negro hypersaline microbial mat
-
PMID: 22832344
-
Harris JK, Caporaso JG, Walker JJ, Spear JR, Gold NJ, Robertson CE, et al. Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. ISME J. 2012; 7: 50-60. doi: 10.1038/ismej.2012.79 PMID: 22832344
-
(2012)
ISME J.
, vol.7
, pp. 50-60
-
-
Harris, J.K.1
Caporaso, J.G.2
Walker, J.J.3
Spear, J.R.4
Gold, N.J.5
Robertson, C.E.6
-
11
-
-
44649171625
-
Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat
-
PMID: 18523433
-
Kunin V, Raes J, Harris JK, Spear JR, Walker JJ, Ivanova N, et al. Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol Syst Biol. 2008; 4: 198. doi: 10.1038/msb.2008.35 PMID: 18523433
-
(2008)
Mol Syst Biol.
, vol.4
, pp. 198
-
-
Kunin, V.1
Raes, J.2
Harris, J.K.3
Spear, J.R.4
Walker, J.J.5
Ivanova, N.6
-
12
-
-
84873739311
-
The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools
-
PMID: 23193283
-
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 2013; 41: 590-596. doi: 10.1093/nar/gks1219 PMID: 23193283
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 590-596
-
-
Quast, C.1
Pruesse, E.2
Yilmaz, P.3
Gerken, J.4
Schweer, T.5
Yarza, P.6
-
13
-
-
84960483410
-
Microbiota studies in the bile duct strongly suggest a role for helicobacter pylori in extrahepatic cholangiocarcinoma
-
PMID: 26493848
-
Avilés-Jiménez F, Guitron A, Segura-López F, Méndez-Tenorio A, Iwai S, Hernández-Guerrero A, et al. Microbiota studies in the bile duct strongly suggest a role for Helicobacter pylori in extrahepatic cholangiocarcinoma. Clin Microbiol Infect. 2015; 22: 178.e11-178.e22. doi: 10.1016/j.cmi.2015.10.008 PMID: 26493848
-
(2015)
Clin Microbiol Infect
, vol.22
, pp. e11-e22
-
-
Avilés-Jiménez, F.1
Guitron, A.2
Segura-López, F.3
Méndez-Tenorio, A.4
Iwai, S.5
Hernández-Guerrero, A.6
-
14
-
-
84994570548
-
DNA copy number analysis of fresh and formalin-fixed specimens by whole-genome sequencing: Improved correction of systematic biases and exclusion of problematic regions
-
Scheinin I, Olshen AB, Thuijl HF Van, Wesseling P, Pinkel D, Albertson DG. DNA copy number analysis of fresh and formalin-fixed specimens by whole-genome sequencing: improved correction of systematic biases and exclusion of problematic regions. Genome Res. 2014; 1-24.
-
(2014)
Genome Res.
, pp. 1-24
-
-
Scheinin, I.1
Olshen, A.B.2
Van Thuijl, H.F.3
Wesseling, P.4
Pinkel, D.5
Albertson, D.G.6
-
15
-
-
84922784300
-
-
Wortman J, Giglio M, Creasy H, Chen A, Liolios K, Chu K, et al. A data analysis and coordination center for the human microbiome project. 2010; 11: 2010. doi: 10.1186/gb-2010-11-S1-O13
-
(2010)
A Data Analysis and Coordination Center for the Human Microbiome Project
, vol.11
, pp. 2010
-
-
Wortman, J.1
Giglio, M.2
Creasy, H.3
Chen, A.4
Liolios, K.5
Chu, K.6
-
16
-
-
79952422304
-
Quality control and preprocessing of metagenomic datasets
-
PMID: 21278185
-
Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011; 27: 863-864. doi: 10.1093/bioinformatics/btr026 PMID: 21278185
-
(2011)
Bioinformatics.
, vol.27
, pp. 863-864
-
-
Schmieder, R.1
Edwards, R.2
-
17
-
-
84859210032
-
Fast gapped-read alignment with bowtie 2
-
PMID: 22388286
-
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9: 357-360. doi: 10.1038/nmeth.1923 PMID: 22388286
-
(2012)
Nat Methods
, vol.9
, pp. 357-360
-
-
Langmead, B.1
Salzberg, S.L.2
-
18
-
-
84870814915
-
SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
-
PMID: 23071270
-
Kopylova E, Noé L, Touzet H. SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012; 28: 3211-3217. doi: 10.1093/bioinformatics/bts611 PMID: 23071270
-
(2012)
Bioinformatics.
, vol.28
, pp. 3211-3217
-
-
Kopylova, E.1
Noé, L.2
Touzet, H.3
-
19
-
-
79955877212
-
RAPSearch: A fast protein similarity search tool for short reads
-
PMID: 21575167
-
Ye Y, Choi J-H, Tang H. RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinformatics. 2011; 12: 159. doi: 10.1186/1471-2105-12-159 PMID: 21575167
-
(2011)
BMC Bioinformatics.
, vol.12
, pp. 159
-
-
Ye, Y.1
Choi, J.-H.2
Tang, H.3
-
20
-
-
84855167751
-
RAPSearch2: A fast and memory-efficient protein similarity search tool for nextgeneration sequencing data
-
PMID: 22039206
-
Zhao Y, Tang H, Ye Y. RAPSearch2: A fast and memory-efficient protein similarity search tool for nextgeneration sequencing data. Bioinformatics. 2012; 28: 125-126. doi: 10.1093/bioinformatics/btr595 PMID: 22039206
-
(2012)
Bioinformatics.
, vol.28
, pp. 125-126
-
-
Zhao, Y.1
Tang, H.2
Ye, Y.3
-
21
-
-
84891774001
-
The metacyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome databases
-
PMID: 24225315
-
Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher C a., et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res. 2014; 42: 459-471. doi: 10.1093/nar/gkt1103 PMID: 24225315
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 459-471
-
-
Caspi, R.1
Altman, T.2
Billington, R.3
Dreher, K.4
Foerster, H.5
Fulcher, C.A.6
-
22
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data intensity normalization improves color calling in SOLiD sequencing
-
PMID: 20383131
-
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data Intensity normalization improves color calling in SOLiD sequencing. Nat Methods. 2010; 7: 335-336. doi: 10.1038/nmeth0510-335 PMID: 20383131
-
(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
-
23
-
-
70349866695
-
Upcoming challenges for multiple sequence alignment methods in the highthroughput era
-
PMID: 19648142
-
Kemena C, Notredame C. Upcoming challenges for multiple sequence alignment methods in the highthroughput era. Bioinformatics. 2009; 25: 2455-2465. doi: 10.1093/bioinformatics/btp452 PMID: 19648142
-
(2009)
Bioinformatics.
, vol.25
, pp. 2455-2465
-
-
Kemena, C.1
Notredame, C.2
-
24
-
-
84934441554
-
Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment
-
Russell DJ, editor. (Clifton, NJ). Humana Press
-
Iantorno S, Gori K, Goldman N, Gil M, Dessimoz C. Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment. In: Russell DJ, editor. Methods in molecular biology (Clifton, NJ). Humana Press; 2014. pp. 59-73. doi: 10.1007/978-1-62703-646-7
-
(2014)
Methods in Molecular Biology
, pp. 59-73
-
-
Iantorno, S.1
Gori, K.2
Goldman, N.3
Gil, M.4
Dessimoz, C.5
-
25
-
-
84861347752
-
Phylogenetic reconstruction
-
Barton NH, Briggs DEG, Eisen JA, Goldstein DB, Patel NH, editors. Cold Spring Harbor Laboratory Press
-
Barton NH, Griggs DEG. Phylogenetic reconstruction. In: Barton NH, Briggs DEG, Eisen JA, Goldstein DB, Patel NH, editors. Evolution. Cold Spring Harbor Laboratory Press; 2007. pp. 1-55.
-
(2007)
Evolution
, pp. 1-55
-
-
Barton, N.H.1
Griggs, D.E.G.2
-
26
-
-
0033442555
-
Some limitations of ancestral character-state reconstruction when testing evolutionary hypotheses
-
Cunningham CW. Some limitations of ancestral character-state reconstruction when testing evolutionary hypotheses. Syst Biol. 1999; 48: 665-674. doi: 10.1080/106351599260238
-
(1999)
Syst Biol.
, vol.48
, pp. 665-674
-
-
Cunningham, C.W.1
-
27
-
-
84860161961
-
Effects of phylogenetic signal on ancestral state reconstruction
-
PMID: 22223447
-
Litsios G, Salamin N. Effects of phylogenetic signal on ancestral state reconstruction. Syst Biol. 2012; 61: 533-538. doi: 10.1093/sysbio/syr124 PMID: 22223447
-
(2012)
Syst Biol.
, vol.61
, pp. 533-538
-
-
Litsios, G.1
Salamin, N.2
-
28
-
-
84946130803
-
Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference
-
PMID: 26031838
-
Tan G, Muffato M, Ledergerber C, Herrero J, Goldman N, Gil M, et al. Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference. Syst Biol. 2015; 64: 778-791. doi: 10.1093/sysbio/syv033 PMID: 26031838
-
(2015)
Syst Biol.
, vol.64
, pp. 778-791
-
-
Tan, G.1
Muffato, M.2
Ledergerber, C.3
Herrero, J.4
Goldman, N.5
Gil, M.6
-
29
-
-
84960875114
-
Reconstruction of ancestral genomes in presence of gene gain and loss
-
PMID: 26885568
-
Avdeyev P, Jiang S, Aganezov S, Hu F, Alekseyev MA. Reconstruction of ancestral genomes in presence of gene gain and loss. J Comput. 2016; 23: 150-164. doi: 10.1089/cmb.2015.0160 PMID: 26885568
-
(2016)
J Comput.
, vol.23
, pp. 150-164
-
-
Avdeyev, P.1
Jiang, S.2
Aganezov, S.3
Hu, F.4
Alekseyev, M.A.5
-
30
-
-
33746061683
-
Greengenes, a chimerachecked 16S rRNA gene database and workbench compatible with ARB
-
PMID: 16820507
-
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Greengenes, a chimerachecked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006; 72: 5069-5072. doi: 10.1128/AEM.03006-05 PMID: 16820507
-
(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
-
31
-
-
72949107142
-
Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
PMID: 19801464
-
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009; 75: 7537-7541. doi: 10.1128/AEM.01541-09 PMID: 19801464
-
(2009)
Appl Environ Microbiol.
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
Hall, J.R.4
Hartmann, M.5
Hollister, E.B.6
-
32
-
-
84891787231
-
Ribosomal database project: Data and tools for high throughput rRNA analysis
-
PMID: 24288368
-
Cole JR, Wang Q, Fish J a., Chai B, McGarrell DM, Sun Y, et al. Ribosomal Database Project: Data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014; 42: 633-642. doi: 10.1093/nar/gkt1244 PMID: 24288368
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 633-642
-
-
Cole, J.R.1
Wang, Q.2
Fish, J.A.3
Chai, B.4
McGarrell, D.M.5
Sun, Y.6
-
33
-
-
84992374978
-
DADA2: High resolution sample inference from amplicon data
-
Callahan BJ, Mcmurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High resolution sample inference from amplicon data. bioRxiv. 2015; 0-14. doi: 10.1101/024034
-
(2015)
BioRxiv.
, pp. 0-14
-
-
Callahan, B.J.1
Mcmurdie, P.J.2
Rosen, M.J.3
Han, A.W.4
Johnson, A.J.5
Holmes, S.P.6
-
34
-
-
84884904719
-
UPARSE: Highly accurate OTU sequences from microbial amplicon reads
-
PMID: 23955772
-
Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013; 10: 996-8. doi: 10.1038/nmeth.2604 PMID: 23955772
-
(2013)
Nat Methods
, vol.10
, pp. 996-998
-
-
Edgar, R.C.1
-
35
-
-
84901363655
-
Waste not, want not: Why rarefying microbiome data is inadmissible
-
PMID: 24699258
-
McMurdie PJ, Holmes S. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol. 2014; 10: e1003531. doi: 10.1371/journal.pcbi.1003531 PMID: 24699258
-
(2014)
PLoS Comput Biol.
, vol.10
, pp. e1003531
-
-
McMurdie, P.J.1
Holmes, S.2
-
36
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Artn 550\r PMID: 25516281
-
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15: 550. Artn 550\r doi: 10.1186/S13059-014-0550-8 PMID: 25516281
-
(2014)
Genome Biol.
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
37
-
-
84876996918
-
TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
PMID: 23618408
-
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013; 14: R36. doi: 10.1186/gb-2013-14-4-r36 PMID: 23618408
-
(2013)
Genome Biol.
, vol.14
, pp. R36
-
-
Kim, D.1
Pertea, G.2
Trapnell, C.3
Pimentel, H.4
Kelley, R.5
Salzberg, S.L.6
-
38
-
-
84899694091
-
Points of significance: Nonparametric tests
-
PMID: 24820360
-
Krzywinski M, Altman N. Points of significance: Nonparametric tests. Nat Methods. 2014; 11: 467-469. doi: 10.1038/nmeth.2937 PMID: 24820360
-
(2014)
Nat Methods
, vol.11
, pp. 467-469
-
-
Krzywinski, M.1
Altman, N.2
-
39
-
-
84910107735
-
Genome resolved analysis of a premature infant gut microbial community reveals a varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life
-
PMID: 24451181
-
Brown CT, Sharon I, Thomas BC, Castelle CJ, Morowitz MJ, Banfield JF. Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life. Microbiome. 2013; 1: 30. doi: 10.1186/2049-2618-1-30 PMID: 24451181
-
(2013)
Microbiome.
, vol.1
, pp. 30
-
-
Brown, C.T.1
Sharon, I.2
Thomas, B.C.3
Castelle, C.J.4
Morowitz, M.J.5
Banfield, J.F.6
|