-
1
-
-
79151478555
-
Type 2 diabetes as an inflammatory disease
-
Donath, M. Y. & Shoelson, S. E. Type 2 diabetes as an inflammatory disease. Nat. Rev. Immunol. 11, 98-107 (2011).
-
(2011)
Nat. Rev. Immunol.
, vol.11
, pp. 98-107
-
-
Donath, M.Y.1
Shoelson, S.E.2
-
2
-
-
68349150756
-
CD8+ effector T cells contribute to macrophage recruitment and adipose tissue inflammation in obesity
-
Nishimura, S. et al. CD8+ effector T cells contribute to macrophage recruitment and adipose tissue inflammation in obesity. Nat. Med. 15, 914-920 (2009).
-
(2009)
Nat. Med.
, vol.15
, pp. 914-920
-
-
Nishimura, S.1
-
3
-
-
33846026712
-
Obesity induces a phenotypic switch in adipose tissue macrophage polarization
-
Lumeng, C. N., Bodzin, J. L. & Saltiel, A. R. Obesity induces a phenotypic switch in adipose tissue macrophage polarization. J. Clin. Invest. 117, 175-184 (2007).
-
(2007)
J. Clin. Invest
, vol.117
, pp. 175-184
-
-
Lumeng, C.N.1
Bodzin, J.L.2
Saltiel, A.R.3
-
4
-
-
68349148211
-
Lean, but not obese, fat is enriched for a unique population of regulatory T cells that affect metabolic parameters
-
Feuerer, M. et al. Lean, but not obese, fat is enriched for a unique population of regulatory T cells that affect metabolic parameters. Nat. Med. 15, 930-939 (2009).
-
(2009)
Nat. Med.
, vol.15
, pp. 930-939
-
-
Feuerer, M.1
-
5
-
-
65649117802
-
Unexpected trafficking of immune cells within the adipose tissue during the onset of obesity
-
Duffaut, C., Galitzky, J., Lafontan, M. & Bouloumie, A. Unexpected trafficking of immune cells within the adipose tissue during the onset of obesity. Biochem. Biophys. Res. Commun. 384, 482-485 (2009).
-
(2009)
Biochem. Biophys. Res. Commun.
, vol.384
, pp. 482-485
-
-
Duffaut, C.1
Galitzky, J.2
Lafontan, M.3
Bouloumie, A.4
-
6
-
-
80053148046
-
Deficiency in interferon-gamma results in reduced body weight and better glucose tolerance in mice
-
Wong, N. et al. Deficiency in interferon-gamma results in reduced body weight and better glucose tolerance in mice. Endocrinology 152, 3690-3699 (2011).
-
(2011)
Endocrinology
, vol.152
, pp. 3690-3699
-
-
Wong, N.1
-
7
-
-
54049086276
-
Interferon-gamma, a Th1 cytokine, regulates fat inflammation: A role for adaptive immunity in obesity
-
Rocha, V. Z. et al. Interferon-gamma, a Th1 cytokine, regulates fat inflammation: a role for adaptive immunity in obesity. Circ. Res. 103, 467-476 (2008).
-
(2008)
Circ. Res.
, vol.103
, pp. 467-476
-
-
Rocha, V.Z.1
-
8
-
-
84864286000
-
Systemic inflammation and insulin sensitivity in obese IFN-gamma knockout mice
-
O'Rourke, R. W. et al. Systemic inflammation and insulin sensitivity in obese IFN-gamma knockout mice. Metabolism 61, 1152-1161 (2012).
-
(2012)
Metabolism
, vol.61
, pp. 1152-1161
-
-
O'Rourke, R.W.1
-
9
-
-
8144226856
-
The gut microbiota as an environmental factor that regulates fat storage
-
Backhed, F. et al. The gut microbiota as an environmental factor that regulates fat storage. Proc. Natl Acad. Sci. USA 101, 15718-15723 (2004).
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 15718-15723
-
-
Backhed, F.1
-
10
-
-
33845874101
-
An obesity-associated gut microbiome with increased capacity for energy harvest
-
Turnbaugh, P. J. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027-1131 (2006).
-
(2006)
Nature
, vol.444
, pp. 1027-1131
-
-
Turnbaugh, P.J.1
-
11
-
-
77950250064
-
Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5
-
Vijay-Kumar, M. et al. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 328, 228-231 (2010).
-
(2010)
Science
, vol.328
, pp. 228-231
-
-
Vijay-Kumar, M.1
-
12
-
-
84855174006
-
Gut microbiota is a key modulator of insulin resistance in TLR 2 knockout mice
-
Caricilli, A. M. et al. Gut microbiota is a key modulator of insulin resistance in TLR 2 knockout mice. PLoS Biol. 9, e1001212 (2011).
-
(2011)
PLoS Biol.
, vol.9
, pp. e1001212
-
-
Caricilli, A.M.1
-
13
-
-
84856083002
-
Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut
-
Shulzhenko, N. et al. Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut. Nat. Med. 17, 1585-1593 (2011).
-
(2011)
Nat. Med.
, vol.17
, pp. 1585-1593
-
-
Shulzhenko, N.1
-
14
-
-
84923261268
-
Intestinal epithelial MyD88 is a sensor switching host metabolism towards obesity according to nutritional status
-
Everard, A. et al. Intestinal epithelial MyD88 is a sensor switching host metabolism towards obesity according to nutritional status. Nat. Commun. 5, 5648 (2014).
-
(2014)
Nat. Commun.
, vol.5
, pp. 5648
-
-
Everard, A.1
-
15
-
-
84947552418
-
Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks
-
Morgun, A. et al. Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks. Gut 64, 1732-1743 (2015).
-
(2015)
Gut
, vol.64
, pp. 1732-1743
-
-
Morgun, A.1
-
16
-
-
84888049920
-
Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment
-
Iida, N. et al. Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment. Science 342, 967-970 (2013).
-
(2013)
Science
, vol.342
, pp. 967-970
-
-
Iida, N.1
-
17
-
-
3242664636
-
Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis
-
Rakoff-Nahoum, S., Paglino, J., Eslami-Varzaneh, F., Edberg, S. & Medzhitov, R. Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell 118, 229-241 (2004).
-
(2004)
Cell
, vol.118
, pp. 229-241
-
-
Rakoff-Nahoum, S.1
Paglino, J.2
Eslami-Varzaneh, F.3
Edberg, S.4
Medzhitov, R.5
-
18
-
-
84868687011
-
Gut-derived lipopolysaccharide augments adipose macrophage accumulation but is not essential for impaired glucose or insulin tolerance in mice
-
Caesar, R. et al. Gut-derived lipopolysaccharide augments adipose macrophage accumulation but is not essential for impaired glucose or insulin tolerance in mice. Gut 61, 1701-1707 (2012).
-
(2012)
Gut
, vol.61
, pp. 1701-1707
-
-
Caesar, R.1
-
19
-
-
84933505154
-
Alteration of gut microbiota by vancomycin and bacitracin improves insulin resistance via glucagon-like peptide 1 in diet-induced obesity
-
Hwang, I. et al. Alteration of gut microbiota by vancomycin and bacitracin improves insulin resistance via glucagon-like peptide 1 in diet-induced obesity. FASEB J. 29, 2397-2411 (2015).
-
(2015)
FASEB J.
, vol.29
, pp. 2397-2411
-
-
Hwang, I.1
-
20
-
-
84866141702
-
Modulation of gut microbiota by antibiotics improves insulin signalling in high-fat fed mice
-
Carvalho, B. M. et al. Modulation of gut microbiota by antibiotics improves insulin signalling in high-fat fed mice. Diabetologia 55, 2823-2834 (2012).
-
(2012)
Diabetologia
, vol.55
, pp. 2823-2834
-
-
Carvalho, B.M.1
-
21
-
-
46749098265
-
Gut microbiota modulation with norfloxacin and ampicillin enhances glucose tolerance in mice
-
Membrez, M. et al. Gut microbiota modulation with norfloxacin and ampicillin enhances glucose tolerance in mice. FASEB J. 22, 2416-2426 (2008).
-
(2008)
FASEB J.
, vol.22
, pp. 2416-2426
-
-
Membrez, M.1
-
22
-
-
84865369416
-
Temporal and spatial interplay of microbiota and intestinal mucosa drive establishment of immune homeostasis in conventionalized mice
-
El Aidy, S. et al. Temporal and spatial interplay of microbiota and intestinal mucosa drive establishment of immune homeostasis in conventionalized mice. Mucosal Immunol. 5, 567-579 (2012).
-
(2012)
Mucosal Immunol.
, vol.5
, pp. 567-579
-
-
El Aidy, S.1
-
23
-
-
84992128547
-
Unexpected links reflect the noise in networks
-
Yambartsev, A. et al. Unexpected links reflect the noise in networks. Biol. Direct. doi: 10.1186/s13062-016-0155-0 (2016).
-
(2016)
Biol. Direct.
-
-
Yambartsev, A.1
-
24
-
-
40549106737
-
The Mucin degrader Akkermansia muciniphila is an abundant resident of the human intestinal tract
-
Derrien, M., Collado, M. C., Ben-Amor, K., Salminen, S. & de Vos, W. M. The Mucin degrader Akkermansia muciniphila is an abundant resident of the human intestinal tract. Appl. Environ. Microbiol. 74, 1646-1648 (2008).
-
(2008)
Appl. Environ. Microbiol.
, vol.74
, pp. 1646-1648
-
-
Derrien, M.1
Collado, M.C.2
Ben-Amor, K.3
Salminen, S.4
De Vos, W.M.5
-
25
-
-
84868197954
-
The microbiota of the gut in preschool children with normal and excessive body weight
-
Karlsson, C. L. et al. The microbiota of the gut in preschool children with normal and excessive body weight. Obesity 20, 2257-2261 (2012).
-
(2012)
Obesity
, vol.20
, pp. 2257-2261
-
-
Karlsson, C.L.1
-
26
-
-
84878465280
-
Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity
-
Everard, A. et al. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc. Natl Acad. Sci. USA 110, 9066-9071 (2013).
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. 9066-9071
-
-
Everard, A.1
-
27
-
-
84897960120
-
An increase in the Akkermansia spp. Population induced by metformin treatment improves glucose homeostasis in diet-induced obese mice
-
Shin, N. R. et al. An increase in the Akkermansia spp. population induced by metformin treatment improves glucose homeostasis in diet-induced obese mice. Gut 63, 727-735 (2014).
-
(2014)
Gut
, vol.63
, pp. 727-735
-
-
Shin, N.R.1
-
29
-
-
84878571547
-
Gene network reconstruction reveals cell cycle and antiviral genes as major drivers of cervical cancer
-
Mine, K. L. et al. Gene network reconstruction reveals cell cycle and antiviral genes as major drivers of cervical cancer. Nat. Commun. 4, 1806 (2013).
-
(2013)
Nat. Commun.
, vol.4
, pp. 1806
-
-
Mine, K.L.1
-
30
-
-
78649976005
-
An integrated approach to uncover drivers of cancer
-
Akavia, U. D. et al. An integrated approach to uncover drivers of cancer. Cell 143, 1005-1017 (2010).
-
(2010)
Cell
, vol.143
, pp. 1005-1017
-
-
Akavia, U.D.1
-
31
-
-
84865739425
-
Architecture of the human regulatory network derived from ENCODE data
-
Gerstein, M. B. et al. Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91-100 (2012).
-
(2012)
Nature
, vol.489
, pp. 91-100
-
-
Gerstein, M.B.1
-
32
-
-
77954672686
-
Gut microbiota composition is associated with body weight, weight gain and biochemical parameters in pregnant women
-
Santacruz, A. et al. Gut microbiota composition is associated with body weight, weight gain and biochemical parameters in pregnant women. Br J. Nutr. 104, 83-92 (2010).
-
(2010)
Br J. Nutr.
, vol.104
, pp. 83-92
-
-
Santacruz, A.1
-
33
-
-
84887621987
-
Faecal levels of Bifidobacterium and Clostridium coccoides but not plasma lipopolysaccharide are inversely related to insulin and HOMA index in women
-
Teixeira, F. S. et al. Faecal levels of Bifidobacterium and Clostridium coccoides but not plasma lipopolysaccharide are inversely related to insulin and HOMA index in women. Clin. Nutr. 32, 1017-1022 (2013).
-
(2013)
Clin. Nutr.
, vol.32
, pp. 1017-1022
-
-
Teixeira, F.S.1
-
34
-
-
84883181684
-
Human gut microbiota changes reveal the progression of glucose intolerance
-
Zhang, X. et al. Human gut microbiota changes reveal the progression of glucose intolerance. PLoS ONE 8, e71108 (2013).
-
(2013)
PLoS ONE
, vol.8
, pp. e71108
-
-
Zhang, X.1
-
35
-
-
84867074831
-
A metagenome-wide association study of gut microbiota in type 2 diabetes
-
Qin, J. et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490, 55-60 (2012).
-
(2012)
Nature
, vol.490
, pp. 55-60
-
-
Qin, J.1
-
36
-
-
84878709716
-
Gut metagenome in European women with normal, impaired and diabetic glucose control
-
Karlsson, F. H. et al. Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature 498, 99-103 (2013).
-
(2013)
Nature
, vol.498
, pp. 99-103
-
-
Karlsson, F.H.1
-
37
-
-
84926338262
-
Classification and diagnosis of diabetes
-
American Diabetes Association. Classification and diagnosis of diabetes. Diabetes Care 38, S8-S16 (2015).
-
(2015)
Diabetes Care
, vol.38
, pp. S8-S16
-
-
-
38
-
-
84942808776
-
Type 2 diabetes in Brazil: Epidemiology and management
-
de Almeida-Pititto, B. et al. Type 2 diabetes in Brazil: epidemiology and management. Diabetes Metab. Syndr. Obes. 8, 17-28 (2015).
-
(2015)
Diabetes Metab. Syndr. Obes.
, vol.8
, pp. 17-28
-
-
De Almeida-Pititto, B.1
-
39
-
-
84907021154
-
Effect of metformin on metabolic improvement and gut microbiota
-
Lee, H. & Ko, G. Effect of metformin on metabolic improvement and gut microbiota. Appl. Environ. Microbiol. 80, 5935-5943 (2014).
-
(2014)
Appl. Environ. Microbiol.
, vol.80
, pp. 5935-5943
-
-
Lee, H.1
Ko, G.2
-
40
-
-
84981489040
-
Reverse enGENEering of regulatory networks from big data: A roadmap for biologists
-
Dong, X. et al. Reverse enGENEering of regulatory networks from big data: a roadmap for biologists. Bioinform. Biol. Insights 61, 61-74 (2015).
-
(2015)
Bioinform. Biol. Insights
, vol.61
, pp. 61-74
-
-
Dong, X.1
-
41
-
-
84923587206
-
Host adaptive immunity alters gut microbiota
-
Zhang, H., Sparks, J. B., Karyala, S. V., Settlage, R. & Luo, X. M. Host adaptive immunity alters gut microbiota. ISME J. 9, 770-781 (2015).
-
(2015)
ISME J.
, vol.9
, pp. 770-781
-
-
Zhang, H.1
Sparks, J.B.2
Karyala, S.V.3
Settlage, R.4
Luo, X.M.5
-
42
-
-
34047256441
-
IRG proteins: Key mediators of interferon-regulated host resistance to intracellular pathogens
-
Taylor, G. A. IRG proteins: key mediators of interferon-regulated host resistance to intracellular pathogens. Cell. Microbiol. 9, 1099-1107 (2007).
-
(2007)
Cell. Microbiol.
, vol.9
, pp. 1099-1107
-
-
Taylor, G.A.1
-
43
-
-
0035898464
-
Inactivation of LRG-47 and IRG-47 reveals a family of interferon gamma-inducible genes with essential, pathogen-specific roles in resistance to infection
-
Collazo, C. M. et al. Inactivation of LRG-47 and IRG-47 reveals a family of interferon gamma-inducible genes with essential, pathogen-specific roles in resistance to infection. J. Exp. Med. 194, 181-188 (2001).
-
(2001)
J. Exp. Med.
, vol.194
, pp. 181-188
-
-
Collazo, C.M.1
-
44
-
-
84885673740
-
Irgm1-deficient mice exhibit Paneth cell abnormalities and increased susceptibility to acute intestinal inflammation
-
Liu, B. et al. Irgm1-deficient mice exhibit Paneth cell abnormalities and increased susceptibility to acute intestinal inflammation. Am. J. Physiol. Gastrointest. Liver Physiol. 305, G573-G584 (2013).
-
(2013)
Am. J. Physiol. Gastrointest. Liver Physiol.
, vol.305
, pp. G573-G584
-
-
Liu, B.1
-
45
-
-
84903794978
-
Paneth cell extrusion and release of antimicrobial products is directly controlled by immune cell-derived IFN-g
-
Farin, H. F. et al. Paneth cell extrusion and release of antimicrobial products is directly controlled by immune cell-derived IFN-g. J. Exp. Med. 211, 1393-1405 (2014).
-
(2014)
J. Exp. Med.
, vol.211
, pp. 1393-1405
-
-
Farin, H.F.1
-
46
-
-
84898032485
-
Extended lifespan and reduced adiposity in mice lacking the FAT10 gene
-
Canaan, A. et al. Extended lifespan and reduced adiposity in mice lacking the FAT10 gene. Proc. Natl Acad. Sci. USA 111, 5313-5318 (2014).
-
(2014)
Proc. Natl Acad. Sci. USA
, vol.111
, pp. 5313-5318
-
-
Canaan, A.1
-
47
-
-
84878545299
-
Therapeutic improvement of glucoregulation in newly diagnosed type 2 diabetes patients is associated with a reduction of IL-17 levels
-
Sumarac-Dumanovic, M. et al. Therapeutic improvement of glucoregulation in newly diagnosed type 2 diabetes patients is associated with a reduction of IL-17 levels. Immunobiology 218, 1113-1118 (2013).
-
(2013)
Immunobiology
, vol.218
, pp. 1113-1118
-
-
Sumarac-Dumanovic, M.1
-
48
-
-
33744526526
-
Increased T-helper interferon-gamma-secreting cells in obese children
-
Pacifico, L. et al. Increased T-helper interferon-gamma-secreting cells in obese children. Eur. J. Endocrinol. 154, 691-697 (2006).
-
(2006)
Eur. J. Endocrinol.
, vol.154
, pp. 691-697
-
-
Pacifico, L.1
-
49
-
-
84947460237
-
Akkermansia muciniphila inversely correlates with the onset of inflammation, altered adipose tissue metabolism and metabolic disorders during obesity in mice
-
Schneeberger, M. et al. Akkermansia muciniphila inversely correlates with the onset of inflammation, altered adipose tissue metabolism and metabolic disorders during obesity in mice. Sci. Rep. 5, 16643 (2015).
-
(2015)
Sci. Rep.
, vol.5
, pp. 16643
-
-
Schneeberger, M.1
-
50
-
-
67649196932
-
Metformin attenuated the autoimmune disease of the central nervous system in animal models of multiple sclerosis
-
Nath, N. et al. Metformin attenuated the autoimmune disease of the central nervous system in animal models of multiple sclerosis. J. Immunol. 182, 8005-8014 (2009).
-
(2009)
J. Immunol.
, vol.182
, pp. 8005-8014
-
-
Nath, N.1
-
51
-
-
84949772416
-
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
-
Forslund, K. et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature 528, 262-266 (2015).
-
(2015)
Nature
, vol.528
, pp. 262-266
-
-
Forslund, K.1
-
52
-
-
38449104720
-
Intestinal integrity and Akkermansia muciniphila, a mucin-degrading member of the intestinal microbiota present in infants, adults, and the elderly
-
Collado, M. C., Derrien, M., Isolauri, E., de Vos, W. M. & Salminen, S. Intestinal integrity and Akkermansia muciniphila, a mucin-degrading member of the intestinal microbiota present in infants, adults, and the elderly. Appl. Environ. Microbiol. 73, 7767-7770 (2007).
-
(2007)
Appl. Environ. Microbiol.
, vol.73
, pp. 7767-7770
-
-
Collado, M.C.1
Derrien, M.2
Isolauri, E.3
De Vos, W.M.4
Salminen, S.5
-
53
-
-
0025294528
-
Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations
-
Amann, R. I. et al. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56, 1919-1925 (1990).
-
(1990)
Appl. Environ. Microbiol.
, vol.56
, pp. 1919-1925
-
-
Amann, R.I.1
-
54
-
-
46249088370
-
Lumi: A pipeline for processing Illumina microarray
-
Du, P., Kibbe, W. A. & Lin, S. M. Lumi: a pipeline for processing Illumina microarray. Bioinformatics 24, 1547-1548 (2008).
-
(2008)
Bioinformatics
, vol.24
, pp. 1547-1548
-
-
Du, P.1
Kibbe, W.A.2
Lin, S.M.3
-
55
-
-
84863981120
-
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
-
Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621-1624 (2012).
-
(2012)
ISME J.
, vol.6
, pp. 1621-1624
-
-
Caporaso, J.G.1
-
56
-
-
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
-
57
-
-
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
-
58
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
De Santis, 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
-
-
De Santis, T.Z.1
-
59
-
-
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
-
60
-
-
79952422304
-
Quality control and preprocessing of metagenomic datasets
-
Schmieder, R. & Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863-864 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 863-864
-
-
Schmieder, R.1
Edwards, R.2
-
61
-
-
84905049901
-
Trimmomatic: A flexible trimmer for Illumina sequence data
-
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
62
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-Seq
-
Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
63
-
-
84928987900
-
HTSeq-A Python framework to work with high-throughput sequencing data
-
Anders, S., Pyl, P. T. & Huber, W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169 (2014).
-
(2014)
Bioinformatics
, vol.31
, pp. 166-169
-
-
Anders, S.1
Pyl, P.T.2
Huber, W.3
-
64
-
-
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
-
65
-
-
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
-
66
-
-
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 (2011).
-
(2011)
ISME J.
, vol.6
, pp. 610-618
-
-
McDonald, D.1
-
67
-
-
33748106497
-
Excess IL-12 but not IL-23 accompanies the inflammatory bowel disease associated with common variable immunodeficiency
-
Mannon, P. J. et al. Excess IL-12 but not IL-23 accompanies the inflammatory bowel disease associated with common variable immunodeficiency. Gastroenterology 131, 748-756 (2006).
-
(2006)
Gastroenterology
, vol.131
, pp. 748-756
-
-
Mannon, P.J.1
-
68
-
-
84953776209
-
International Consensus Document (ICON): Common variable immunodeficiency disorders
-
Bonilla, F. A. et al. International Consensus Document (ICON): common variable immunodeficiency disorders. J. Allergy Clin. Immunol. Pract. 4, 38-59 (2016).
-
(2016)
J. Allergy Clin. Immunol. Pract.
, vol.4
, pp. 38-59
-
-
Bonilla, F.A.1
|