-
1
-
-
84871454511
-
Gut microbiota composition and activity in relation to host metabolic phenotype and disease risk
-
Holmes, E., Li, J. V., Marchesi, J. R. & Nicholson, J. K. Gut microbiota composition and activity in relation to host metabolic phenotype and disease risk. Cell Metab. 16, 559-564 (2012).
-
(2012)
Cell Metab.
, vol.16
, pp. 559-564
-
-
Holmes, E.1
Li, J.V.2
Marchesi, J.R.3
Nicholson, J.K.4
-
2
-
-
84877248514
-
The complex interplay between inflammation, the microbiota and colorectal cancer
-
Arthur, J. C. & Jobin, C. The complex interplay between inflammation, the microbiota and colorectal cancer. Gut Microbes 4, 253-258 (2013).
-
(2013)
Gut Microbes
, vol.4
, pp. 253-258
-
-
Arthur, J.C.1
Jobin, C.2
-
3
-
-
84873372079
-
NOD2-mediated dysbiosis predisposes mice to transmissible colitis and colorectal cancer
-
Couturier-Maillard, A. et al. NOD2-mediated dysbiosis predisposes mice to transmissible colitis and colorectal cancer. J. Clin. Invest. 123, 700-711 (2013).
-
(2013)
J. Clin. Invest.
, vol.123
, pp. 700-711
-
-
Couturier-Maillard, A.1
-
4
-
-
84891585929
-
The gut microbiome modulates colon tumorigenesis
-
Zackular, J. P. et al. The gut microbiome modulates colon tumorigenesis. mBio 4, e00692-13 (2013).
-
(2013)
mBio
, vol.4
-
-
Zackular, J.P.1
-
5
-
-
84888638819
-
The microbiome and cancer
-
Schwabe, R. F. & Jobin, C. The microbiome and cancer. Nat. Rev. Cancer 13, 800-812 (2013).
-
(2013)
Nat. Rev. Cancer
, vol.13
, pp. 800-812
-
-
Schwabe, R.F.1
Jobin, C.2
-
6
-
-
84867192879
-
Intestinal inflammation targets cancer-inducing activity of the microbiota
-
Arthur, J. C. et al. Intestinal inflammation targets cancer-inducing activity of the microbiota. Science 338, 120-123 (2012).
-
(2012)
Science
, vol.338
, pp. 120-123
-
-
Arthur, J.C.1
-
7
-
-
84882354326
-
Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment
-
Kostic, A. D. et al. Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe 14, 207-215 (2013).
-
(2013)
Cell Host Microbe
, vol.14
, pp. 207-215
-
-
Kostic, A.D.1
-
8
-
-
84882334105
-
Fusobacterium nucleatum promotes colorectal carcinogenesis by modulating E-cadherin/beta-catenin signaling via its FadA adhesin
-
Rubinstein, M. R. et al. Fusobacterium nucleatum promotes colorectal carcinogenesis by modulating E-cadherin/beta-catenin signaling via its FadA adhesin. Cell Host Microbe 14, 195-206 (2013).
-
(2013)
Cell Host Microbe
, vol.14
, pp. 195-206
-
-
Rubinstein, M.R.1
-
9
-
-
84866146940
-
Diversity, stability and resilience of the human gut microbiota
-
Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K. & Knight, R. Diversity, stability and resilience of the human gut microbiota. Nature 489, 220-230 (2012).
-
(2012)
Nature
, vol.489
, pp. 220-230
-
-
Lozupone, C.A.1
Stombaugh, J.I.2
Gordon, J.I.3
Jansson, J.K.4
Knight, R.5
-
10
-
-
84888633713
-
Inflammation-induced cancer: Crosstalk between tumours, immune cells and microorganisms
-
Elinav, E. et al. Inflammation-induced cancer: crosstalk between tumours, immune cells and microorganisms. Nat. Rev. Cancer 13, 759-771 (2013).
-
(2013)
Nat. Rev. Cancer
, vol.13
, pp. 759-771
-
-
Elinav, E.1
-
11
-
-
84866549438
-
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
-
Morgan, X. C. et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 13, R79 (2012).
-
(2012)
Genome Biol.
, vol.13
-
-
Morgan, X.C.1
-
12
-
-
0031758230
-
Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn's disease
-
Darfeuille-Michaud, A. et al. Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn's disease. Gastroenterology 115, 1405-1413 (1998).
-
(1998)
Gastroenterology
, vol.115
, pp. 1405-1413
-
-
Darfeuille-Michaud, A.1
-
13
-
-
3242737791
-
Enhanced Escherichia coli adherence and invasion in Crohn's disease and colon cancer
-
Martin, H. M. et al. Enhanced Escherichia coli adherence and invasion in Crohn's disease and colon cancer. Gastroenterology 127, 80-93 (2004).
-
(2004)
Gastroenterology
, vol.127
, pp. 80-93
-
-
Martin, H.M.1
-
14
-
-
77954821323
-
Molecular characterization of mucosal adherent bacteria and associations with colorectal adenomas
-
Shen, X. J. et al. Molecular characterization of mucosal adherent bacteria and associations with colorectal adenomas. Gut Microbes 1, 138-147 (2010).
-
(2010)
Gut Microbes
, vol.1
, pp. 138-147
-
-
Shen, X.J.1
-
15
-
-
0031928730
-
Association between intraepithelial Escherichia coli and colorectal cancer
-
Swidsinski, A. et al. Association between intraepithelial Escherichia coli and colorectal cancer. Gastroenterology 115, 281-286 (1998).
-
(1998)
Gastroenterology
, vol.115
, pp. 281-286
-
-
Swidsinski, A.1
-
16
-
-
84874007506
-
High prevalence of mucosa-associated E. coli producing cyclomodulin and genotoxin in colon cancer
-
Buc, E. et al. High prevalence of mucosa-associated E. coli producing cyclomodulin and genotoxin in colon cancer. PLoS ONE 8, e56964 (2013).
-
(2013)
PLoS ONE
, vol.8
-
-
Buc, E.1
-
17
-
-
84897964236
-
Colonic mucosa-associated diffusely adherent afaC + Escherichia coli expressing lpfA and pks are increased in inflammatory bowel disease and colon cancer
-
Prorok-Hamon, M. et al. Colonic mucosa-associated diffusely adherent afaC + Escherichia coli expressing lpfA and pks are increased in inflammatory bowel disease and colon cancer. Gut 63, 761-770 (2014).
-
(2014)
Gut
, vol.63
, pp. 761-770
-
-
Prorok-Hamon, M.1
-
18
-
-
33747137269
-
Escherichia coli induces DNA double-strand breaks in eukaryotic cells
-
Nougayrede, J. P. et al. Escherichia coli induces DNA double-strand breaks in eukaryotic cells. Science 313, 848-851 (2006).
-
(2006)
Science
, vol.313
, pp. 848-851
-
-
Nougayrede, J.P.1
-
19
-
-
77954730486
-
Escherichia coli induces DNA damage in vivo and triggers genomic instability in mammalian cells
-
Cuevas-Ramos, G. et al. Escherichia coli induces DNA damage in vivo and triggers genomic instability in mammalian cells. Proc. Natl Acad. Sci. USA 107, 11537-11542 (2010).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 11537-11542
-
-
Cuevas-Ramos, G.1
-
20
-
-
84868607652
-
Genotoxicity of Escherichia coli Nissle 1917 strain cannot be dissociated from its probiotic activity
-
Olier, M. et al. Genotoxicity of Escherichia coli Nissle 1917 strain cannot be dissociated from its probiotic activity. Gut Microbes 3, 501-509 (2012).
-
(2012)
Gut Microbes
, vol.3
, pp. 501-509
-
-
Olier, M.1
-
21
-
-
80054806900
-
Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota
-
Thiennimitr, P. et al. Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota. Proc. Natl Acad. Sci. USA 108, 17480-17485 (2011).
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 17480-17485
-
-
Thiennimitr, P.1
-
22
-
-
84873513423
-
Host-derived nitrate boosts growth of E. coli in the inflamed gut
-
Winter, S. E. et al. Host-derived nitrate boosts growth of E. coli in the inflamed gut. Science 339, 708-711 (2013).
-
(2013)
Science
, vol.339
, pp. 708-711
-
-
Winter, S.E.1
-
23
-
-
84886723193
-
Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model
-
McCafferty, J. et al. Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model. ISME J. 7, 2116-2125 (2013).
-
(2013)
ISME J.
, vol.7
, pp. 2116-2125
-
-
McCafferty, J.1
-
24
-
-
84880199410
-
Pathview: An R/Bioconductor package for pathway-based data integration and visualization
-
Luo, W. & Brouwer, C. Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics 29, 1830-1831 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 1830-1831
-
-
Luo, W.1
Brouwer, C.2
-
25
-
-
80051486126
-
Antigen-presenting cell production of IL-10 inhibits T-helper 1 and 17 cell responses and suppresses colitis in mice
-
Liu, B., Tonkonogy, S. L. & Sartor, R. B. Antigen-presenting cell production of IL-10 inhibits T-helper 1 and 17 cell responses and suppresses colitis in mice. Gastroenterology 141, 653-662 (2011).
-
(2011)
Gastroenterology
, vol.141
, pp. 653-662
-
-
Liu, B.1
Tonkonogy, S.L.2
Sartor, R.B.3
-
26
-
-
79952763661
-
Succession of microbial consortia in the developing infant gut microbiome
-
Koenig, J. E. et al. Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl Acad. Sci. USA 108(Suppl 1): 4578-4585 (2011).
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, Issue.SUPPL. 1
, pp. 4578-4585
-
-
Koenig, J.E.1
-
27
-
-
84861139714
-
Ecological succession of bacterial communities during conventionalization of germ-free mice
-
Gillilland, 3rd M. G. et al. Ecological succession of bacterial communities during conventionalization of germ-free mice. Appl. Environ. Microbiol. 78, 2359-2366 (2012).
-
(2012)
Appl. Environ. Microbiol.
, vol.78
, pp. 2359-2366
-
-
Gillilland III, M.G.1
-
28
-
-
77956569409
-
Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis
-
Garrett, W. S. et al. Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe 8, 292-300 (2010).
-
(2010)
Cell Host Microbe
, vol.8
, pp. 292-300
-
-
Garrett, W.S.1
-
29
-
-
84865134857
-
Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice
-
Carvalho, F. A. et al. Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. Cell Host Microbe 12, 139-152 (2012).
-
(2012)
Cell Host Microbe
, vol.12
, pp. 139-152
-
-
Carvalho, F.A.1
-
30
-
-
84893560224
-
Intestinal microbial ecology and environmental factors affecting necrotizing enterocolitis
-
Torrazza, R. M. et al. Intestinal microbial ecology and environmental factors affecting necrotizing enterocolitis. PLoS ONE 8, e83304 (2013).
-
(2013)
PLoS ONE
, vol.8
-
-
Torrazza, R.M.1
-
31
-
-
34447104759
-
Induction of inducible nitric oxide synthase: A protective mechanism in colitis-induced adenocarcinoma
-
Zhang, R., Ma, A., Urbanski, S. J. & McCafferty, D. M. Induction of inducible nitric oxide synthase: a protective mechanism in colitis-induced adenocarcinoma. Carcinogenesis 28, 1122-1130 (2007).
-
(2007)
Carcinogenesis
, vol.28
, pp. 1122-1130
-
-
Zhang, R.1
Ma, A.2
Urbanski, S.J.3
McCafferty, D.M.4
-
32
-
-
0141731259
-
CD4(+)CD25(+) regulatory lymphocytes require interleukin 10 to interrupt colon carcinogenesis in mice
-
Erdman, S. E. et al. CD4(+)CD25(+) regulatory lymphocytes require interleukin 10 to interrupt colon carcinogenesis in mice. Cancer Res. 63, 6042-6050 (2003).
-
(2003)
Cancer Res.
, vol.63
, pp. 6042-6050
-
-
Erdman, S.E.1
-
33
-
-
0035953308
-
IFNgamma and lymphocytes prevent primary tumour development and shape tumour immunogenicity
-
Shankaran, V. et al. IFNgamma and lymphocytes prevent primary tumour development and shape tumour immunogenicity. Nature 410, 1107-1111 (2001).
-
(2001)
Nature
, vol.410
, pp. 1107-1111
-
-
Shankaran, V.1
-
34
-
-
80054846602
-
Chronic intestinal inflammation induces stress-response genes in commensal Escherichia coli
-
Patwa, L. G. et al. Chronic intestinal inflammation induces stress-response genes in commensal Escherichia coli. Gastroenterology 141, 1842-1851 (2011).
-
(2011)
Gastroenterology
, vol.141
, pp. 1842-1851
-
-
Patwa, L.G.1
-
35
-
-
55949120483
-
The two-component network and the general stress sigma factor RpoS (sigma S) in Escherichia coli
-
Hengge, R. The two-component network and the general stress sigma factor RpoS (sigma S) in Escherichia coli. Adv. Exp. Med. Biol. 631, 40-53 (2008).
-
(2008)
Adv. Exp. Med. Biol.
, vol.631
, pp. 40-53
-
-
Hengge, R.1
-
36
-
-
55949119280
-
The roles of two-component systems in virulence of pathogenic Escherichia coli and Shigella spp
-
Tobe, T. The roles of two-component systems in virulence of pathogenic Escherichia coli and Shigella spp. Adv. Exp. Med. Biol. 631, 189-199 (2008).
-
(2008)
Adv. Exp. Med. Biol.
, vol.631
, pp. 189-199
-
-
Tobe, T.1
-
37
-
-
84870208079
-
Second messenger regulation of biofilm formation: Breakthroughs in understanding c-di-GMP effector systems
-
Boyd, C. D. & O'Toole, G. A. Second messenger regulation of biofilm formation: breakthroughs in understanding c-di-GMP effector systems. Annu. Rev. Cell Dev. Biol. 28, 439-462 (2012).
-
(2012)
Annu. Rev. Cell Dev. Biol.
, vol.28
, pp. 439-462
-
-
Boyd, C.D.1
O'Toole, G.A.2
-
38
-
-
33644517930
-
Bacterial small-molecule signaling pathways
-
Camilli, A. & Bassler, B. L. Bacterial small-molecule signaling pathways. Science 311, 1113-1116 (2006).
-
(2006)
Science
, vol.311
, pp. 1113-1116
-
-
Camilli, A.1
Bassler, B.L.2
-
39
-
-
84906944891
-
Mild gut inflammation modulates the proteome of intestinal Escherichia coli
-
Schumann, S. et al. Mild gut inflammation modulates the proteome of intestinal Escherichia coli. Environ. Microbiol. http://onlinelibrary.wiley.com/ doi/10.1111/1462-2920.12192/abstractdoi: (2013).
-
(2013)
Environ. Microbiol.
-
-
Schumann, S.1
-
40
-
-
84891736162
-
Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis
-
Johansson, M. E. et al. Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis. Gut 63, 281-291 (2014).
-
(2014)
Gut
, vol.63
, pp. 281-291
-
-
Johansson, M.E.1
-
41
-
-
34047167850
-
Comparative study of the intestinal mucus barrier in normal and inflamed colon
-
Swidsinski, A. et al. Comparative study of the intestinal mucus barrier in normal and inflamed colon. Gut 56, 343-350 (2007).
-
(2007)
Gut
, vol.56
, pp. 343-350
-
-
Swidsinski, A.1
-
42
-
-
9144231385
-
Interleukin 10-deficient mice exhibit defective colonic Muc2 synthesis before and after induction of colitis by commensal bacteria
-
Schwerbrock, N. M. et al. Interleukin 10-deficient mice exhibit defective colonic Muc2 synthesis before and after induction of colitis by commensal bacteria. Inflamm. Bowel Dis. 10, 811-823 (2004).
-
(2004)
Inflamm. Bowel Dis.
, vol.10
, pp. 811-823
-
-
Schwerbrock, N.M.1
-
43
-
-
84866461477
-
Familial transmission rather than defective innate immunity shapes the distinct intestinal microbiota of TLR-deficient mice
-
Ubeda, C. et al. Familial transmission rather than defective innate immunity shapes the distinct intestinal microbiota of TLR-deficient mice. J. Exp. Med. 209, 1445-1456 (2012).
-
(2012)
J. Exp. Med.
, vol.209
, pp. 1445-1456
-
-
Ubeda, C.1
-
44
-
-
67650299380
-
Modulation of the intestinal microbiota alters colitisassociated colorectal cancer susceptibility
-
Uronis, J. M. et al. Modulation of the intestinal microbiota alters colitisassociated colorectal cancer susceptibility. PLoS ONE 4, e6026 (2009).
-
(2009)
PLoS ONE
, vol.4
-
-
Uronis, J.M.1
-
45
-
-
17144383927
-
Variable phenotypes of enterocolitis in interleukin 10-deficient mice monoassociated with two different commensal bacteria
-
Kim, S. C. et al. Variable phenotypes of enterocolitis in interleukin 10-deficient mice monoassociated with two different commensal bacteria. Gastroenterology 128, 891-906 (2005).
-
(2005)
Gastroenterology
, vol.128
, pp. 891-906
-
-
Kim, S.C.1
-
46
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-2200 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 2194-2200
-
-
Edgar, R.C.1
Haas, B.J.2
Clemente, J.C.3
Quince, C.4
Knight, R.5
-
47
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
-
48
-
-
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, 5261-5267 (2007).
-
(2007)
Appl. Environ. Microbiol.
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
49
-
-
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
-
50
-
-
34548785562
-
Expression analysis of the colibactin gene cluster coding for a novel polyketide in Escherichia coli
-
Homburg, S., Oswald, E., Hacker, J. & Dobrindt, U. Expression analysis of the colibactin gene cluster coding for a novel polyketide in Escherichia coli. FEMS Microbiol. Lett. 275, 255-262 (2007).
-
(2007)
FEMS Microbiol. Lett.
, vol.275
, pp. 255-262
-
-
Homburg, S.1
Oswald, E.2
Hacker, J.3
Dobrindt, U.4
-
51
-
-
84856534859
-
Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma
-
Castellarin, M. et al. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res. 22, 299-306 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 299-306
-
-
Castellarin, M.1
-
52
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
53
-
-
84864440400
-
Metagenomic microbial community profiling using unique clade-specific marker genes
-
Segata, N. et al. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods 9, 811-814 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 811-814
-
-
Segata, N.1
-
54
-
-
78650050018
-
Scaffolding a Caenorhabditis nematode genome with RNA-seq
-
Mortazavi, A. et al. Scaffolding a Caenorhabditis nematode genome with RNA-seq. Genome Res. 20, 1740-1747 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 1740-1747
-
-
Mortazavi, A.1
-
55
-
-
80054913451
-
FLASH: Fast length adjustment of short reads to improve genome assemblies
-
Magoc, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957-2963 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 2957-2963
-
-
Magoc, T.1
Salzberg, S.L.2
-
56
-
-
84865176493
-
Scaling metagenome sequence assembly with probabilistic de Bruijn graphs
-
Pell, J. et al. Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. Proc. Natl Acad. Sci. USA 109, 13272-13277 (2012).
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. 13272-13277
-
-
Pell, J.1
-
57
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380 (2005).
-
(2005)
Nature
, vol.437
, pp. 376-380
-
-
Margulies, M.1
-
58
-
-
84901417347
-
Prokka: Rapid prokaryotic genome annotation
-
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068-2069 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 2068-2069
-
-
Seemann, T.1
-
59
-
-
84883644707
-
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
-
Rapaport, F. et al. Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol. 14, R95 (2013).
-
(2013)
Genome Biol.
, vol.14
-
-
Rapaport, F.1
-
60
-
-
84893242996
-
RNA-seq differential expression studies: More sequence, or more replication?
-
Liu, Y., Zhou, J. & White, K. P. RNA-seq differential expression studies: more sequence, or more replication? Bioinformatics 30, 301-304 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 301-304
-
-
Liu, Y.1
Zhou, J.2
White, K.P.3
-
61
-
-
75249087100
-
edgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
62
-
-
84881504578
-
Computational analysis of bacterial RNA-Seq data
-
McClure, R. et al. Computational analysis of bacterial RNA-Seq data. Nucleic Acids Res. 41, e140 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
McClure, R.1
-
63
-
-
67649202800
-
GAGE: Generally applicable gene set enrichment for pathway analysis
-
Luo, W., Friedman, M. S., Shedden, K., Hankenson, K. D. &Woolf, P. J. GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics 10, 161 (2009).
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 161
-
-
Luo, W.1
Friedman, M.S.2
Shedden, K.3
Hankenson, K.D.4
Woolf, P.J.5
-
64
-
-
84891765377
-
DOOR 2.0: Presenting operons and their functions through dynamic and integrated views
-
Mao, X. et al. DOOR 2.0: presenting operons and their functions through dynamic and integrated views. Nucleic Acids Res. 42, D654-D659 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
-
-
Mao, X.1
-
65
-
-
70350439157
-
Genetic structure and distribution of the colibactin genomic island among members of the family Enterobacteriaceae
-
Putze, J. et al. Genetic structure and distribution of the colibactin genomic island among members of the family Enterobacteriaceae . Infect. Immun. 77, 4696-4703 (2009).
-
(2009)
Infect. Immun.
, vol.77
, pp. 4696-4703
-
-
Putze, J.1
-
66
-
-
0001677717
-
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 57, 289-300 (1995).
-
(1995)
J. R Stat. Soc. Ser. B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
|