-
1
-
-
85005965070
-
The human intestinal microbiome in health and disease
-
Lynch, S.V., Pedersen, O., The human intestinal microbiome in health and disease. N Engl J Med 375 (2016), 2369–2379.
-
(2016)
N Engl J Med
, vol.375
, pp. 2369-2379
-
-
Lynch, S.V.1
Pedersen, O.2
-
2
-
-
20044374023
-
Design and validation of a histological scoring system for nonalcoholic fatty liver disease
-
Kleiner, D.E., Brunt, E.M., Van Natta, M., et al. Design and validation of a histological scoring system for nonalcoholic fatty liver disease. Hepatology 41 (2005), 1313–1321.
-
(2005)
Hepatology
, vol.41
, pp. 1313-1321
-
-
Kleiner, D.E.1
Brunt, E.M.2
Van Natta, M.3
-
3
-
-
58149234737
-
Real-time DNA sequencing from single polymerase molecules
-
Eid, J., Fehr, A., Gray, J., et al. Real-time DNA sequencing from single polymerase molecules. Science 323 (2009), 133–138.
-
(2009)
Science
, vol.323
, pp. 133-138
-
-
Eid, J.1
Fehr, A.2
Gray, J.3
-
4
-
-
84862182131
-
Next-generation sequencing technologies and applications for human genetic history and forensics
-
Berglund, E.C., Kiialainen, A., Syvanen, A.C., Next-generation sequencing technologies and applications for human genetic history and forensics. Investig Genet, 2, 2011, 23.
-
(2011)
Investig Genet
, vol.2
, pp. 23
-
-
Berglund, E.C.1
Kiialainen, A.2
Syvanen, A.C.3
-
5
-
-
34548293679
-
Naïve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang, Q., Garrity, G.M., Tiedje, J.M., et al. Naïve 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
-
6
-
-
77952768782
-
Analysis of multitag pyrosequence data from human cervical lavage samples
-
Naqvi, A., Rangwala, H., Spear, G., et al. Analysis of multitag pyrosequence data from human cervical lavage samples. Chem Biodivers 7 (2010), 1076–1085.
-
(2010)
Chem Biodivers
, vol.7
, pp. 1076-1085
-
-
Naqvi, A.1
Rangwala, H.2
Spear, G.3
-
7
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso, J.G., Kuczynski, J., Stombaugh, J., 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
-
8
-
-
72949107142
-
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss, P.D., Westcott, S.L., Ryabin, T., et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75 (2009), 7537–7541.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
-
9
-
-
84884127512
-
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
-
Langille, M.G.I., Zaneveld, J., Caporaso, J.G., et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotech 31 (2013), 814–821.
-
(2013)
Nat Biotech
, vol.31
, pp. 814-821
-
-
Langille, M.G.I.1
Zaneveld, J.2
Caporaso, J.G.3
-
10
-
-
0033982936
-
KEGG: kyoto encyclopedia of genes and genomes
-
Kanehisa, M., Goto, S., KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28 (2000), 27–30.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
11
-
-
79959383523
-
Metagenomic biomarker discovery and explanation
-
Segata, N., Izard, J., Walron, L., et al. Metagenomic biomarker discovery and explanation. Genome Biol, 12, 2011, R60.
-
(2011)
Genome Biol
, vol.12
, pp. R60
-
-
Segata, N.1
Izard, J.2
Walron, L.3
-
12
-
-
66249145772
-
Statistical methods for detecting differentially abundant features in clinical metagenomic samples
-
White, J.R., Nagarajan, N., Pop, M., Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol, 5, 2009, e1000352.
-
(2009)
PLoS Comput Biol
, vol.5
, pp. e1000352
-
-
White, J.R.1
Nagarajan, N.2
Pop, M.3
-
13
-
-
84888884475
-
Metagenomic species profiling using universal phylogenetic marker genes
-
Sunagawa, S., Mende, D.R., Zeller, G., et al. Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods 10 (2013), 1196–1199.
-
(2013)
Nat Methods
, vol.10
, pp. 1196-1199
-
-
Sunagawa, S.1
Mende, D.R.2
Zeller, G.3
-
14
-
-
84946781151
-
Library preparation methodology can influence genomic and functional predictions in human microbiome research
-
Jones, M.B., Highlander, S.K., Anderson, E.L., et al. Library preparation methodology can influence genomic and functional predictions in human microbiome research. Proc Natl Acad Sci USA 112 (2015), 14024–14029.
-
(2015)
Proc Natl Acad Sci USA
, vol.112
, pp. 14024-14029
-
-
Jones, M.B.1
Highlander, S.K.2
Anderson, E.L.3
-
15
-
-
77952779332
-
Network-based modeling of the human gut microbiome
-
Naqvi, A., Rangwale, H., Keshavarzian, A., et al. Network-based modeling of the human gut microbiome. Chem Biodiversity 7 (2010), 1040–1050.
-
(2010)
Chem Biodiversity
, vol.7
, pp. 1040-1050
-
-
Naqvi, A.1
Rangwale, H.2
Keshavarzian, A.3
-
16
-
-
0242490780
-
Cytoscape: a software environment for integrated models of biomolecular interaction networks
-
Shannon, P., Markiel, A., Ozier, O., et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13 (2003), 2498–2504.
-
(2003)
Genome Res
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
-
17
-
-
20444473800
-
Mechanisms of disease: pathogenesis of nonalcoholic fatty liver disease
-
Sanyal, A.J., Mechanisms of disease: pathogenesis of nonalcoholic fatty liver disease. Nat Clin Pract Gastroenterol Hepatol 2 (2005), 46–53.
-
(2005)
Nat Clin Pract Gastroenterol Hepatol
, vol.2
, pp. 46-53
-
-
Sanyal, A.J.1
-
18
-
-
0035084699
-
Nonalcoholic steatohepatitis: association of insulin resistance and mitochondrial abnormalities
-
Sanyal, A.J., Campbell-Sargent, C., Mirshahi, F., et al. Nonalcoholic steatohepatitis: association of insulin resistance and mitochondrial abnormalities. Gastroenterology 120 (2001), 1183–1192.
-
(2001)
Gastroenterology
, vol.120
, pp. 1183-1192
-
-
Sanyal, A.J.1
Campbell-Sargent, C.2
Mirshahi, F.3
-
19
-
-
41849127118
-
Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome
-
Turnbaugh, P.J., Backhed, F., Fulton, L., et al. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3 (2008), 213–223.
-
(2008)
Cell Host Microbe
, vol.3
, pp. 213-223
-
-
Turnbaugh, P.J.1
Backhed, F.2
Fulton, L.3
-
20
-
-
33845874101
-
An obesity-associated gut microbiome with increased capacity for energy harvest
-
Turnbaugh, P.J., Ley, R.E., Mahowald, M.A., et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444 (2006), 1027–1031.
-
(2006)
Nature
, vol.444
, pp. 1027-1031
-
-
Turnbaugh, P.J.1
Ley, R.E.2
Mahowald, M.A.3
-
21
-
-
84883179071
-
Clostridium scindens: a human gut microbe with a high potential to convert glucocorticoids into androgens
-
Ridlon, J.M., Ikegawa, S., Alves, J.M., et al. Clostridium scindens: a human gut microbe with a high potential to convert glucocorticoids into androgens. J Lipid Res 54 (2013), 2437–2449.
-
(2013)
J Lipid Res
, vol.54
, pp. 2437-2449
-
-
Ridlon, J.M.1
Ikegawa, S.2
Alves, J.M.3
-
22
-
-
69149083245
-
TGR5-mediated bile acid sensing controls glucose homeostasis
-
Thomas, C., Gioiello, A., Noriega, L., et al. TGR5-mediated bile acid sensing controls glucose homeostasis. Cell Metab 10 (2009), 167–177.
-
(2009)
Cell Metab
, vol.10
, pp. 167-177
-
-
Thomas, C.1
Gioiello, A.2
Noriega, L.3
-
23
-
-
84964896040
-
Activation of transmembrane bile acid receptor TGR5 modulates pancreatic islet alpha cells to promote glucose homeostasis
-
Kumar, D.P., Asgharpour, A., Mirshahi, F., et al. Activation of transmembrane bile acid receptor TGR5 modulates pancreatic islet alpha cells to promote glucose homeostasis. J Biol Chem 291 (2016), 6626–6640.
-
(2016)
J Biol Chem
, vol.291
, pp. 6626-6640
-
-
Kumar, D.P.1
Asgharpour, A.2
Mirshahi, F.3
-
24
-
-
84860441011
-
Inflammation and lipid signaling in the etiology of insulin resistance
-
Glass, C.K., Olefsky, J.M., Inflammation and lipid signaling in the etiology of insulin resistance. Cell Metab 15 (2012), 635–645.
-
(2012)
Cell Metab
, vol.15
, pp. 635-645
-
-
Glass, C.K.1
Olefsky, J.M.2
-
25
-
-
84860483727
-
The role of endoplasmic reticulum in hepatic lipid homeostasis and stress signaling
-
Fu, S., Watkins, S.M., Hotamisligil, G.S., The role of endoplasmic reticulum in hepatic lipid homeostasis and stress signaling. Cell Metab 15 (2012), 623–634.
-
(2012)
Cell Metab
, vol.15
, pp. 623-634
-
-
Fu, S.1
Watkins, S.M.2
Hotamisligil, G.S.3
-
26
-
-
84943151832
-
Increased plasma levels of asymmetric dimethylarginine in nonalcoholic fatty liver disease: relation with insulin resistance, inflammation, and liver histology
-
Boga, S., Alkim, H., Koksal, A.R., et al. Increased plasma levels of asymmetric dimethylarginine in nonalcoholic fatty liver disease: relation with insulin resistance, inflammation, and liver histology. J Investig Med 63 (2015), 871–877.
-
(2015)
J Investig Med
, vol.63
, pp. 871-877
-
-
Boga, S.1
Alkim, H.2
Koksal, A.R.3
-
27
-
-
84908238878
-
Both bone marrow-derived and non-bone marrow-derived cells contribute to AIM2 and NLRP3 inflammasome activation in a MyD88-dependent manner in dietary steatohepatitis
-
Csak, T., Pillai, A., Ganz, M., et al. Both bone marrow-derived and non-bone marrow-derived cells contribute to AIM2 and NLRP3 inflammasome activation in a MyD88-dependent manner in dietary steatohepatitis. Liver Int 34 (2014), 1402–1413.
-
(2014)
Liver Int
, vol.34
, pp. 1402-1413
-
-
Csak, T.1
Pillai, A.2
Ganz, M.3
-
28
-
-
62649139025
-
Immunological and inflammatory functions of the interleukin-1 family
-
Dinarello, C.A., Immunological and inflammatory functions of the interleukin-1 family. Annu Rev Immunol 27 (2009), 519–550.
-
(2009)
Annu Rev Immunol
, vol.27
, pp. 519-550
-
-
Dinarello, C.A.1
-
29
-
-
84892149853
-
An update on PYRIN domain-containing pattern recognition receptors: from immunity to pathology
-
Ratsimandresy, R.A., Dorfleutner, A., Stehlik, C., An update on PYRIN domain-containing pattern recognition receptors: from immunity to pathology. Front Immunol, 4, 2013, 440.
-
(2013)
Front Immunol
, vol.4
, pp. 440
-
-
Ratsimandresy, R.A.1
Dorfleutner, A.2
Stehlik, C.3
-
30
-
-
82455205872
-
Lipopolysaccharide induces and activates the Nalp3 inflammasome in the liver
-
Ganz, M., Csak, T., Nath, B., et al. Lipopolysaccharide induces and activates the Nalp3 inflammasome in the liver. World J Gastroenterol 17 (2011), 4772–4778.
-
(2011)
World J Gastroenterol
, vol.17
, pp. 4772-4778
-
-
Ganz, M.1
Csak, T.2
Nath, B.3
-
31
-
-
35948958955
-
TLR4 enhances TGF-beta signaling and hepatic fibrosis
-
Seki, E., De Minicis, S., Osterreicher, C.H., et al. TLR4 enhances TGF-beta signaling and hepatic fibrosis. Nat Med 13 (2007), 1324–1332.
-
(2007)
Nat Med
, vol.13
, pp. 1324-1332
-
-
Seki, E.1
De Minicis, S.2
Osterreicher, C.H.3
-
32
-
-
0032934278
-
Monocyte chemotactic protein-1 as a chemoattractant for human hepatic stellate cells
-
Marra, F., Romanelli, R.G., Giannini, C., et al. Monocyte chemotactic protein-1 as a chemoattractant for human hepatic stellate cells. Hepatology 29 (1999), 140–148.
-
(1999)
Hepatology
, vol.29
, pp. 140-148
-
-
Marra, F.1
Romanelli, R.G.2
Giannini, C.3
-
33
-
-
84960110717
-
Efficacy and safety study of cenicriviroc for the treatment of non-alcoholic steatohepatitis in adult subjects with liver fibrosis: CENTAUR Phase 2b study design
-
Friedman, S., Sanyal, A., Goodman, Z., et al. Efficacy and safety study of cenicriviroc for the treatment of non-alcoholic steatohepatitis in adult subjects with liver fibrosis: CENTAUR Phase 2b study design. Contemp Clin Trials 47 (2016), 356–365.
-
(2016)
Contemp Clin Trials
, vol.47
, pp. 356-365
-
-
Friedman, S.1
Sanyal, A.2
Goodman, Z.3
-
34
-
-
84976487656
-
TGF-beta signalling and liver disease
-
Fabregat, I., Moreno-Caceres, J., Sanchez, A., et al. TGF-beta signalling and liver disease. FEBS J 283 (2016), 2219–2232.
-
(2016)
FEBS J
, vol.283
, pp. 2219-2232
-
-
Fabregat, I.1
Moreno-Caceres, J.2
Sanchez, A.3
-
35
-
-
71049139747
-
Human BAMBI cooperates with Smad7 to inhibit transforming growth factor-beta signaling
-
Yan, X., Lin, Z., Chen, F., et al. Human BAMBI cooperates with Smad7 to inhibit transforming growth factor-beta signaling. J Biol Chem 284 (2009), 30097–30104.
-
(2009)
J Biol Chem
, vol.284
, pp. 30097-30104
-
-
Yan, X.1
Lin, Z.2
Chen, F.3
-
36
-
-
33845901507
-
Microbial ecology: human gut microbes associated with obesity
-
Ley, R.E., Turnbaugh, P.J., Klein, S., et al. Microbial ecology: human gut microbes associated with obesity. Nature 444 (2006), 1022–1023.
-
(2006)
Nature
, vol.444
, pp. 1022-1023
-
-
Ley, R.E.1
Turnbaugh, P.J.2
Klein, S.3
-
37
-
-
58749112734
-
A core gut microbiome in obese and lean twins
-
Turnbaugh, P.J., Hamady, M., Yatsunenko, T., et al. A core gut microbiome in obese and lean twins. Nature 457 (2009), 480–484.
-
(2009)
Nature
, vol.457
, pp. 480-484
-
-
Turnbaugh, P.J.1
Hamady, M.2
Yatsunenko, T.3
-
38
-
-
84883110880
-
Richness of human gut microbiome correlates with metabolic markers
-
Le Chatelier, E., Nielsen, T., Qin, J., et al. Richness of human gut microbiome correlates with metabolic markers. Nature 500 (2013), 541–546.
-
(2013)
Nature
, vol.500
, pp. 541-546
-
-
Le Chatelier, E.1
Nielsen, T.2
Qin, J.3
-
39
-
-
85027927719
-
Enterotypes of the human gut microbiome
-
Arumugam, M., Raes, J., Pelletier, E., et al. Enterotypes of the human gut microbiome. Nature 473 (2011), 174–180.
-
(2011)
Nature
, vol.473
, pp. 174-180
-
-
Arumugam, M.1
Raes, J.2
Pelletier, E.3
-
40
-
-
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
-
-
Human Microbiome Project Consortium1
-
41
-
-
84897138661
-
A taxonomic signature of obesity in the microbiome? getting to the guts of the matter
-
Finucane, M.M., Sharpton, T.J., Laurent, T.J., et al. A taxonomic signature of obesity in the microbiome? getting to the guts of the matter. PLoS One, 9, 2014, e84689.
-
(2014)
PLoS One
, vol.9
, pp. e84689
-
-
Finucane, M.M.1
Sharpton, T.J.2
Laurent, T.J.3
-
42
-
-
79952316380
-
Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency
-
Spencer, M.D., Hamp, T.J., Reid, R.W., et al. Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency. Gastroenterology 140 (2011), 976–986.
-
(2011)
Gastroenterology
, vol.140
, pp. 976-986
-
-
Spencer, M.D.1
Hamp, T.J.2
Reid, R.W.3
-
43
-
-
84873296091
-
Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: a connection between endogenous alcohol and NASH
-
Zhu, L., Baker, S.S., Gill, C., et al. Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: a connection between endogenous alcohol and NASH. Hepatology 57 (2013), 601–609.
-
(2013)
Hepatology
, vol.57
, pp. 601-609
-
-
Zhu, L.1
Baker, S.S.2
Gill, C.3
-
44
-
-
84900538053
-
Endotoxemia unrequired in the pathogenesis of pediatric nonalcoholic steatohepatitis
-
Yuan, J., Baker, S.S., Liu, W., et al. Endotoxemia unrequired in the pathogenesis of pediatric nonalcoholic steatohepatitis. J Gastroenterol Hepatol 29 (2014), 1292–1298.
-
(2014)
J Gastroenterol Hepatol
, vol.29
, pp. 1292-1298
-
-
Yuan, J.1
Baker, S.S.2
Liu, W.3
-
45
-
-
84879604697
-
Intestinal microbiota in patients with nonalcoholic fatty liver disease
-
Mouzaki, M., Comelli, E.M., Arendt, B.M., et al. Intestinal microbiota in patients with nonalcoholic fatty liver disease. Hepatology 58 (2013), 120–127.
-
(2013)
Hepatology
, vol.58
, pp. 120-127
-
-
Mouzaki, M.1
Comelli, E.M.2
Arendt, B.M.3
-
46
-
-
84879245628
-
Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease
-
Raman, M., Ahmed, I., Gillevet, P.M., et al. Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease. Clin Gastroenterol Hepatol 11 (2013), 868–875.e1–3.
-
(2013)
Clin Gastroenterol Hepatol
, vol.11
, pp. 868-875.e13
-
-
Raman, M.1
Ahmed, I.2
Gillevet, P.M.3
-
47
-
-
84954288595
-
The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota
-
Boursier, J., Mueller, O., Barret, M., et al. The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota. Hepatology 63 (2016), 764–775.
-
(2016)
Hepatology
, vol.63
, pp. 764-775
-
-
Boursier, J.1
Mueller, O.2
Barret, M.3
-
48
-
-
85018954191
-
Gut microbiome-based metagenomic signature for non-invasive detection of advanced fibrosis in human nonalcoholic fatty liver disease
-
Loomba, R., Seguritan, V., Li, W., et al. Gut microbiome-based metagenomic signature for non-invasive detection of advanced fibrosis in human nonalcoholic fatty liver disease. Cell Metab 25 (2017), 1054–1062.e5.
-
(2017)
Cell Metab
, vol.25
, pp. 1054-1062.e5
-
-
Loomba, R.1
Seguritan, V.2
Li, W.3
|