-
1
-
-
43849089834
-
Microbial diversity and the genetic nature of microbial species
-
Achtman M, Wagner M. (2008). Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol 6: 431-440.
-
(2008)
Nat Rev Microbiol
, vol.6
, pp. 431-440
-
-
Achtman, M.1
Wagner, M.2
-
2
-
-
1942443733
-
Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons
-
Acinas SG, Marcelino LA, Klepac-Ceraj V, Polz MF. (2004). Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186: 2629-2635.
-
(2004)
J Bacteriol
, vol.186
, pp. 2629-2635
-
-
Acinas, S.G.1
Marcelino, L.A.2
Klepac-Ceraj, V.3
Polz, M.F.4
-
3
-
-
0035997908
-
T-bet is a STAT 1-induced regulator of IL-12 R expression in naive CD 4 + T cells
-
Afkarian M, Sedy JR, Yang J, Jacobson NG, Cereb N, Yang SY et al. (2002). T-bet is a STAT 1-induced regulator of IL-12 R expression in naive CD 4 + T cells. Nat Immunol 3: 549-557.
-
(2002)
Nat Immunol
, vol.3
, pp. 549-557
-
-
Afkarian, M.1
Sedy, J.R.2
Yang, J.3
Jacobson, N.G.4
Cereb, N.5
Yang, S.Y.6
-
4
-
-
70349631208
-
Monitoring bacterial community of human gut microbiota reveals an increase in Lactobacillus in obese patients and Methanogens in anorexic patients
-
Armougom F, Henry M, Vialettes B, Raccah D, Raoult D. (2009). Monitoring bacterial community of human gut microbiota reveals an increase in Lactobacillus in obese patients and Methanogens in anorexic patients. PLoS One 4: e7125.
-
(2009)
PLoS One
, vol.4
-
-
Armougom, F.1
Henry, M.2
Vialettes, B.3
Raccah, D.4
Raoult, D.5
-
5
-
-
55349134911
-
Hyaluronan-mediated leukocyte adhesion and dextran sulfate sodiuminduced colitis are attenuated in the absence of signal transducer and activator of transcription 1
-
Bandyopadhyay SK, CAdl Motte, Kessler SP, Hascall VC, Hill DR, Strong SA. (2008). Hyaluronan-mediated leukocyte adhesion and dextran sulfate sodiuminduced colitis are attenuated in the absence of signal transducer and activator of transcription 1. Am J Pathol 173: 1361-1368.
-
(2008)
Am J Pathol
, vol.173
, pp. 1361-1368
-
-
Bandyopadhyay, S.K.1
Motte, C.A.2
Kessler, S.P.3
Hascall, V.C.4
Hill, D.R.5
Strong, S.A.6
-
6
-
-
0018424447
-
Movement of microorganisms in viscous environments
-
Berg HC, Turner L. (1979). Movement of microorganisms in viscous environments. Nature 278: 349-351.
-
(1979)
Nature
, vol.278
, pp. 349-351
-
-
Berg, H.C.1
Turner, L.2
-
7
-
-
83155178360
-
Barcoded pyrosequencing primers used in multiplex amplicon sequencing bias amplification
-
Berry D, Ben Mahfoudh K, Wagner M, Loy A. (2011). Barcoded pyrosequencing primers used in multiplex amplicon sequencing bias amplification. Appl Environ Microbiol 77: 7846-7849.
-
(2011)
Appl Environ Microbiol
, vol.77
, pp. 7846-7849
-
-
Berry, D.1
Ben Mahfoudh, K.2
Wagner, M.3
Loy, A.4
-
8
-
-
79956078164
-
Commensal Bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease
-
Bloom SM, Bijanki VN, Nava GM, Sun L, Malvin NP, Donermeyer DL et al. (2011). Commensal Bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease. Cell Host Microbe 9: 390-403.
-
(2011)
Cell Host Microbe
, vol.9
, pp. 390-403
-
-
Bloom, S.M.1
Bijanki, V.N.2
Nava, G.M.3
Sun, L.4
Malvin, N.P.5
Donermeyer, D.L.6
-
9
-
-
33947416195
-
Body traffic: Ecology, genetics, and immunity in inflammatory bowel disease
-
Braun J, Wei B. (2007). Body traffic: Ecology, genetics, and immunity in inflammatory bowel disease. Annu Rev Pathol: Mech Dis 2: 401-429.
-
(2007)
Annu Rev Pathol: Mech Dis
, vol.2
, pp. 401-429
-
-
Braun, J.1
Wei, B.2
-
10
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
-
(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
-
11
-
-
0036137277
-
DNA sequence quality trimming and vector removal
-
Chou H-H, Holmes MH. (2001). DNA sequence quality trimming and vector removal. Bioinformatics 17: 1093-1104.
-
(2001)
Bioinformatics
, vol.17
, pp. 1093-1104
-
-
Chou, H.-H.1
Holmes, M.H.2
-
12
-
-
77958490531
-
Postprandial remodeling of the gut microbiota in Burmese pythons
-
Costello EK, Gordon JI, Secor SM, Knight R. (2010). Postprandial remodeling of the gut microbiota in Burmese pythons. ISME J 4: 1375-1385.
-
(2010)
ISME J
, vol.4
, pp. 1375-1385
-
-
Costello, E.K.1
Gordon, J.I.2
Secor, S.M.3
Knight, R.4
-
13
-
-
33644868597
-
Daime, a novel image analysis program for microbial ecology and biofilm research
-
Daims H, Lücker S, Wagner M. (2006). daime, a novel image analysis program for microbial ecology and biofilm research. Environ Microbiol 8: 200-213.
-
(2006)
Environ Microbiol
, vol.8
, pp. 200-213
-
-
Daims, H.1
Lücker, S.2
Wagner, M.3
-
14
-
-
13444308853
-
Fluorescence in situ hybridisation for the detection of prokaryotes
-
Osborn A, Smith C (eds Bios-Garland: Abingdon, UK
-
Daims H, Stoecker K, Wagner M. (2005). Fluorescence in situ hybridisation for the detection of prokaryotes. In: Osborn A, Smith C (eds) Advanced Methods in Molecular Microbial Ecology. Bios-Garland: Abingdon, UK, pp 213-239.
-
(2005)
Advanced Methods in Molecular Microbial Ecology
, pp. 213-239
-
-
Daims, H.1
Stoecker, K.2
Wagner, M.3
-
15
-
-
72949118701
-
Associations between species and groups of sites: Indices and statistical inference
-
De Cáceres M, Legendre P. (2009). Associations between species and groups of sites: indices and statistical inference. Ecology 90: 3566-3574.
-
(2009)
Ecology
, vol.90
, pp. 3566-3574
-
-
De Cáceres, M.1
Legendre, P.2
-
16
-
-
25444495693
-
The yin and yang of type i interferon activity in bacterial infection
-
Decker T, Müller M, Stockinger S. (2005). The yin and yang of type I interferon activity in bacterial infection. Nat Rev Immunol 5: 675-687.
-
(2005)
Nat Rev Immunol
, vol.5
, pp. 675-687
-
-
Decker, T.1
Müller, M.2
Stockinger, S.3
-
17
-
-
40549106737
-
The mucin degrader Akkermansia muciniphila is an abundant resident of the human intestinal tract
-
Derrien M, Collado MC, Ben-Amor K, Salminen S, de Vos WM. (2008). The mucin degrader Akkermansia muciniphila is an abundant resident of the human intestinal tract. Appl Environ Microbiol 74: 1646-1648.
-
(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
-
18
-
-
5444248493
-
Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium
-
Derrien M, Vaughan EE, Plugge CM, de Vos WM. (2004). Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int J Syst Evol Microbiol 54: 1469-1476.
-
(2004)
Int J Syst Evol Microbiol
, vol.54
, pp. 1469-1476
-
-
Derrien, M.1
Vaughan, E.E.2
Plugge, C.M.3
De Vos, W.M.4
-
19
-
-
0032803862
-
Phylogeny of the defined murine microbiota: Altered Schaedler flora
-
Dewhirst FE, Chien C-C, Paster BJ, Ericson RL, Orcutt RP, Schauer DB et al. (1999). Phylogeny of the defined murine microbiota: Altered Schaedler flora. Appl Environ Microbiol 65: 3287-3292.
-
(1999)
Appl Environ Microbiol
, vol.65
, pp. 3287-3292
-
-
Dewhirst, F.E.1
Chien, C.-C.2
Paster, B.J.3
Ericson, R.L.4
Orcutt, R.P.5
Schauer, D.B.6
-
20
-
-
0031012926
-
T cell receptor-alpha betadeficient mice fail to develop colitis in the absence of a microbial environment
-
Dianda L, Hanby AM, Wright NA, Sebesteny A, Hayday AC, Owen MJ. (1997). T cell receptor-alpha betadeficient mice fail to develop colitis in the absence of a microbial environment. Am J Pathol 150: 91-97.
-
(1997)
Am J Pathol
, vol.150
, pp. 91-97
-
-
Dianda, L.1
Hanby, A.M.2
Wright, N.A.3
Sebesteny, A.4
Hayday, A.C.5
Owen, M.J.6
-
21
-
-
35349019357
-
Isolation of flagellated bacteria implicated in Crohn's disease
-
Duck LW, Walter MR, Novak J, Kelly D, Tomasi M, Cong Y et al. (2007). Isolation of flagellated bacteria implicated in Crohn's disease. Inflamm Bowel Dis 13: 1191-1201.
-
(2007)
Inflamm Bowel Dis
, vol.13
, pp. 1191-1201
-
-
Duck, L.W.1
Walter, M.R.2
Novak, J.3
Kelly, D.4
Tomasi, M.5
Cong, Y.6
-
22
-
-
0030024563
-
Targeted disruption of the mouse stat1 gene results in compromised innate immunity to viral disease
-
Durbin JE, Hackenmiller R, Simon MC, Levy DE. (1996). Targeted disruption of the mouse stat1 gene results in compromised innate immunity to viral disease. Cell 84: 443-450.
-
(1996)
Cell
, vol.84
, pp. 443-450
-
-
Durbin, J.E.1
Hackenmiller, R.2
Simon, M.C.3
Levy, D.E.4
-
23
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar RC. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
24
-
-
0020026375
-
Mucin secretion in inflammatory bowel disease: Correlation with disease activity and dysplasia
-
Ehsanullah M, Filipe MI, Gazzard B. (1982). Mucin secretion in inflammatory bowel disease: Correlation with disease activity and dysplasia. Gut 23: 485-489.
-
(1982)
Gut
, vol.23
, pp. 485-489
-
-
Ehsanullah, M.1
Filipe, M.I.2
Gazzard, B.3
-
25
-
-
0036313949
-
Role of mucins in inflammatory bowel disease: Important lessons from experimental models
-
Einerhand AWC, Renes IB, Makkink MK, van der Sluis M, Büller HA, Dekker J. (2002). Role of mucins in inflammatory bowel disease: Important lessons from experimental models. Eur J Gastroenterol Hepatol 14: 757-765.
-
(2002)
Eur J Gastroenterol Hepatol
, vol.14
, pp. 757-765
-
-
Einerhand, A.W.C.1
Renes, I.B.2
Makkink, M.K.3
Van Der Sluis, M.4
Büller, H.A.5
Dekker, J.6
-
26
-
-
35348857386
-
Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases
-
Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. (2007). Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci USA 104: 13780-13785.
-
(2007)
Proc Natl Acad Sci USA
, 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
-
27
-
-
0036701963
-
Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence
-
Fukushima M, Kakinuma K, Kawaguchi R. (2002). Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence. J Clin Microbiol 40: 2779-2785.
-
(2002)
J Clin Microbiol
, vol.40
, pp. 2779-2785
-
-
Fukushima, M.1
Kakinuma, K.2
Kawaguchi, R.3
-
28
-
-
34848889673
-
Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system
-
Garrett WS, Lord GM, Punit S, Lugo-Villarino G, Mazmanian SK, Ito S et al. (2007). Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system. Cell 131: 33-45.
-
(2007)
Cell
, vol.131
, pp. 33-45
-
-
Garrett, W.S.1
Lord, G.M.2
Punit, S.3
Lugo-Villarino, G.4
Mazmanian, S.K.5
Ito, S.6
-
29
-
-
70350294348
-
Systematic artifacts in metagenomes from complex microbial communities
-
Gomez-Alvarez V, Teal TK, Schmidt TM. (2009). Systematic artifacts in metagenomes from complex microbial communities. ISME J 3: 1314-1317.
-
(2009)
ISME J
, vol.3
, pp. 1314-1317
-
-
Gomez-Alvarez, V.1
Teal, T.K.2
Schmidt, T.M.3
-
30
-
-
79952401369
-
Metatranscriptomic approach to analyze the functional human gut microbiota
-
Gosalbes MJ, Durbán A, Pignatelli M, Abellan JJ, Jiménez-Hernández N, Pérez-Cobas AE et al. (2011). Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS One 6: e17447.
-
(2011)
PLoS One
, vol.6
-
-
Gosalbes, M.J.1
Durbán, A.2
Pignatelli, M.3
Abellan, J.J.4
Jiménez-Hernández, N.5
Pérez-Cobas, A.E.6
-
31
-
-
0034468557
-
Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA-and rRNA-based microbial community composition
-
Griffiths RI, Whiteley AS, O'Donnell AG, Bailey MJ. (2000). Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA-and rRNA-based microbial community composition. Appl Environ Microbiol 66: 5488-5491.
-
(2000)
Appl Environ Microbiol
, vol.66
, pp. 5488-5491
-
-
Griffiths, R.I.1
Whiteley, A.S.2
O'Donnell, A.G.3
Bailey, M.J.4
-
32
-
-
40149103278
-
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
-
Hamady M,Walker JJ, Harris JK, Gold NJ, Knight R. (2008). Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 5: 235-237.
-
(2008)
Nat Methods
, vol.5
, pp. 235-237
-
-
Hamady Mwalker, J.J.1
Harris, J.K.2
Gold, N.J.3
Knight, R.4
-
33
-
-
0035953543
-
The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5
-
Hayashi F, Smith KD, Ozinsky A, Hawn TR, Yi EC, Goodlett DR et al. (2001). The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5. Nature 410: 1099-1103.
-
(2001)
Nature
, vol.410
, pp. 1099-1103
-
-
Hayashi, F.1
Smith, K.D.2
Ozinsky, A.3
Hawn, T.R.4
Yi, E.C.5
Goodlett, D.R.6
-
34
-
-
41549092745
-
Aberrant mucin assembly in mice causes endoplasmic reticulum stress and spontaneous inflammation resembling ulcerative colitis
-
Heazlewood CK, Cook MC, Eri R, Price GR, Tauro SB, Taupin D et al. (2008). Aberrant mucin assembly in mice causes endoplasmic reticulum stress and spontaneous inflammation resembling ulcerative colitis. PLoS Medicine 5: e54.
-
(2008)
PLoS Medicine
, vol.5
-
-
Heazlewood, C.K.1
Cook, M.C.2
Eri, R.3
Price, G.R.4
Tauro, S.B.5
Taupin, D.6
-
35
-
-
38649129512
-
Shift towards proinflammatory intestinal bacteria aggravates acute murine colitis via Toll-like Receptors 2 and 4
-
Heimesaat MM, Fischer A, Siegmund B, Kupz A, Niebergall J, Fuchs D et al. (2007). Shift towards proinflammatory intestinal bacteria aggravates acute murine colitis via Toll-like Receptors 2 and 4. PLoS One 2: e662.
-
(2007)
PLoS One
, vol.2
-
-
Heimesaat, M.M.1
Fischer, A.2
Siegmund, B.3
Kupz, A.4
Niebergall, J.5
Fuchs, D.6
-
36
-
-
77249163771
-
Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis
-
Hill DA, Hoffmann C, Abt MC, Du Y, Kobuley D Kirn TJ et al. (2010). Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis. Mucosal Immunol 3: 148.
-
(2010)
Mucosal Immunol
, vol.3
, pp. 148
-
-
Hill, D.A.1
Hoffmann, C.2
Abt, M.C.3
Du, Y.4
Kobuley Kirn D, T.J.5
-
37
-
-
0019511383
-
Mucin degradation in human colon ecosystems: Evidence for the existence and role of bacterial subpopulations producing glycosidases as extracellular enzymes
-
Hoskins LC, Boulding ET. (1981). Mucin degradation in human colon ecosystems: evidence for the existence and role of bacterial subpopulations producing glycosidases as extracellular enzymes. J Clin Invest 67: 163.
-
(1981)
J Clin Invest
, vol.67
, pp. 163
-
-
Hoskins, L.C.1
Boulding, E.T.2
-
39
-
-
77957906400
-
Bacteria penetrate the inner mucus layer before inflammation in the dextran sulfate colitis model
-
Johansson MEV, Gustafsson JK, Sjöberg KE, Petersson J, Holm L, Sjövall H et al. (2010). Bacteria penetrate the inner mucus layer before inflammation in the dextran sulfate colitis model. PLoS One 5: e12238.
-
(2010)
PLoS One
, vol.5
-
-
Johansson, M.E.V.1
Gustafsson, J.K.2
Sjöberg, K.E.3
Petersson, J.4
Holm, L.5
Sjövall, H.6
-
40
-
-
0036547571
-
A model for dextran sodium sulfate (DSS)-induced mouse colitis: Bacterial degradation of DSS does not occur after incubation with mouse cecal contents
-
Kitajima S, Morimoto M, Sagara E. (2002). A model for dextran sodium sulfate (DSS)-induced mouse colitis: bacterial degradation of DSS does not occur after incubation with mouse cecal contents. Exp Anim 51: 203-206.
-
(2002)
Exp Anim
, vol.51
, pp. 203-206
-
-
Kitajima, S.1
Morimoto, M.2
Sagara, E.3
-
41
-
-
0033158529
-
Changes in colonic mucosal permeability in mouse colitis induced with dextran sulfate sodium
-
Kitakima S, Takuma S, Morimoto M. (1999). Changes in colonic mucosal permeability in mouse colitis induced with dextran sulfate sodium. Exp Anim 48: 137-143.
-
(1999)
Exp Anim
, vol.48
, pp. 137-143
-
-
Kitakima, S.1
Takuma, S.2
Morimoto, M.3
-
42
-
-
0027521572
-
Interleukin-10-deficient mice develop chronic enterocolitis
-
Kühn R, Löhler J, Rennick D, Rajewsky K, Müller W. (1993). Interleukin-10-deficient mice develop chronic enterocolitis. Cell 75: 263-274.
-
(1993)
Cell
, vol.75
, pp. 263-274
-
-
Kühn, R.1
Löhler, J.2
Rennick, D.3
Rajewsky, K.4
Müller, W.5
-
43
-
-
23344442120
-
Obesity alters gut microbial ecology
-
Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. (2005). Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 102: 11070.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 11070
-
-
Ley, R.E.1
Bäckhed, F.2
Turnbaugh, P.3
Lozupone, C.A.4
Knight, R.D.5
Gordon, J.I.6
-
44
-
-
2442563304
-
Clinical epidemiology of inflammatory bowel disease: Incidence, prevalence, and environmental influences
-
Loftus EVJ. (2004). Clinical epidemiology of inflammatory bowel disease: incidence, prevalence, and environmental influences. Gastroenterology 126: 1504-1517.
-
(2004)
Gastroenterology
, vol.126
, pp. 1504-1517
-
-
Loftus, E.V.J.1
-
45
-
-
29144464937
-
UniFrac: A new phylogenetic method for comparing microbial communities
-
Lozupone C, Knight R. (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 8228-8235
-
-
Lozupone, C.1
Knight, R.2
-
46
-
-
78751575501
-
UniFrac: An effective distance metric for microbial community comparison
-
Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. (2011). UniFrac: an effective distance metric for microbial community comparison. ISME J 5: 169-172.
-
(2011)
ISME J
, vol.5
, pp. 169-172
-
-
Lozupone, C.1
Lladser, M.E.2
Knights, D.3
Stombaugh, J.4
Knight, R.5
-
47
-
-
34547684651
-
Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae
-
Lupp C, Robertson ML, Wickham ME, Sekirov I, Champion OL, Gaynor EC et al. (2007). Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe 2: 119-129.
-
(2007)
Cell Host Microbe
, vol.2
, pp. 119-129
-
-
Lupp, C.1
Robertson, M.L.2
Wickham, M.E.3
Sekirov, I.4
Champion, O.L.5
Gaynor, E.C.6
-
48
-
-
30944466824
-
Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach
-
Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L et al. (2006). Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 55: 205-211.
-
(2006)
Gut
, vol.55
, pp. 205-211
-
-
Manichanh, C.1
Rigottier-Gois, L.2
Bonnaud, E.3
Gloux, K.4
Pelletier, E.5
Frangeul, L.6
-
49
-
-
13344282731
-
Targeted disruption of the stat1 gene in mice reveals unexpected physiologic specificity in the JAK-STAT signaling pathway
-
Meraz MA, White JM, Sheehan KCF, Bach EA, Rodig SJ, Dighe AS et al. (1996). Targeted disruption of the stat1 gene in mice reveals unexpected physiologic specificity in the JAK-STAT signaling pathway. Cell 84: 431-442.
-
(1996)
Cell
, vol.84
, pp. 431-442
-
-
Meraz, M.A.1
White, J.M.2
Sheehan, K.C.F.3
Bach, E.A.4
Rodig, S.J.5
Dighe, A.S.6
-
50
-
-
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 Kubal M et al. (2008). The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinf 9: 386.
-
(2008)
BMC Bioinf
, vol.9
, pp. 386
-
-
Meyer, F.1
Paarmann, D.2
D'Souza, M.3
Olson, R.4
Glass, E.5
Kubal, M.6
-
51
-
-
0019472728
-
Mucin degradation in human colon ecosystems. Fecal population densities of mucin-degrading bacteria estimated by 'most probable number' method
-
Miller R, Hoskins L. (1981). Mucin degradation in human colon ecosystems. Fecal population densities of mucin-degrading bacteria estimated by a 'most probable number' method. Gastroenterology 81: 759-765.
-
(1981)
Gastroenterology
, vol.81
, pp. 759-765
-
-
Miller, R.1
Hoskins, L.2
-
52
-
-
30944458581
-
Layers of mutualism with commensal bacteria protect us from intestinal inflammation
-
Mueller C, Macpherson AJ. (2006). Layers of mutualism with commensal bacteria protect us from intestinal inflammation. Gut 55: 276-284.
-
(2006)
Gut
, vol.55
, pp. 276-284
-
-
Mueller, C.1
MacPherson, A.J.2
-
53
-
-
78649887273
-
Composition and energy harvesting capacity of the gut microbiota: Relationship to diet, obesity and time in mouse models
-
Murphy EF, Cotter PD, Healy S, Marques TM, O'Sullivan O, Fouhy F et al. (2010). Composition and energy harvesting capacity of the gut microbiota: relationship to diet, obesity and time in mouse models. Gut 59: 1635-1642.
-
(2010)
Gut
, vol.59
, pp. 1635-1642
-
-
Murphy, E.F.1
Cotter, P.D.2
Healy, S.3
Marques, T.M.4
O'Sullivan, O.5
Fouhy, F.6
-
54
-
-
79952478107
-
Microbial ecology of the murine gut associated with the development of dextran sodium sulfate-induced colitis
-
Nagalingam NA, Kao JY, Young VB. (2011). Microbial ecology of the murine gut associated with the development of dextran sodium sulfate-induced colitis. Inflamm Bowel Dis 17: 917-926.
-
(2011)
Inflamm Bowel Dis
, vol.17
, pp. 917-926
-
-
Nagalingam, N.A.1
Kao, J.Y.2
Young, V.B.3
-
55
-
-
77954758654
-
The impact of the microbiota on the pathogenesis of IBD: Lessons from mouse infection models
-
Nell S, Suerbaum S, Josenhans C. (2010). The impact of the microbiota on the pathogenesis of IBD: lessons from mouse infection models. Nat Rev Micro 8: 564-577.
-
(2010)
Nat Rev Micro
, vol.8
, pp. 564-577
-
-
Nell, S.1
Suerbaum, S.2
Josenhans, C.3
-
56
-
-
0025181580
-
A novel method in the induction of reliable experimental acute and chronic ulcerative colitis in mice
-
Okayasu I, Hatakeyama S, Yamada M, Ohkusa T, Inagaki Y, Nakaya R. (1990). A novel method in the induction of reliable experimental acute and chronic ulcerative colitis in mice. Gastroenterology 98: 694-702.
-
(1990)
Gastroenterology
, vol.98
, pp. 694-702
-
-
Okayasu, I.1
Hatakeyama, S.2
Yamada, M.3
Ohkusa, T.4
Inagaki, Y.5
Nakaya, R.6
-
57
-
-
70349255569
-
-
R package version 1.17-4
-
Oksanen J, Blanchet FG, Kindt R, Legendre P, O'Hara RB, Simpson GL et al. (2010). Vegan: community ecology package, R package version 1.17-4 (http://cran.r-project.org/).
-
(2010)
Vegan: Community Ecology Package
-
-
Oksanen, J.1
Blanchet, F.G.2
Kindt, R.3
Legendre, P.4
O'Hara, R.B.5
Simpson, G.L.6
-
58
-
-
65549129496
-
Commensal bacteria, traditional and opportunistic pathogens, dysbiosis and bacterial killing in inflammatory bowel diseases
-
Packey C, Sartor D, Balfour R. (2009). Commensal bacteria, traditional and opportunistic pathogens, dysbiosis and bacterial killing in inflammatory bowel diseases. Curr Opin Infect Dis 22: 292-301.
-
(2009)
Curr Opin Infect Dis
, vol.22
, pp. 292-301
-
-
Packey, C.1
Sartor, D.2
Balfour, R.3
-
59
-
-
66349091311
-
The protein disulfide isomerase AGR2 is essential for production of intestinal mucus
-
Park SW, Zhen G, Verhaeghe C, Nakagami Y, Nguyenvu LT, Barczak AJ et al. (2009). The protein disulfide isomerase AGR2 is essential for production of intestinal mucus. Proc Natl Acad Sci USA 106: 6950-6955.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 6950-6955
-
-
Park, S.W.1
Zhen, G.2
Verhaeghe, C.3
Nakagami, Y.4
Nguyenvu, L.T.5
Barczak, A.J.6
-
60
-
-
77951945504
-
Identifying biologically relevant differences between metagenomic communities
-
Parks DH, Beiko RG. (2010). Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26: 715-721.
-
(2010)
Bioinformatics
, vol.26
, pp. 715-721
-
-
Parks, D.H.1
Beiko, R.G.2
-
61
-
-
73949099325
-
Epidermal loss of JunB leads to a SLE phenotype due to hyper IL-6 signaling
-
Pflegerl P, Vesely P, Hantusch B, Schlederer M, Zenz R, Janig E et al. (2009). Epidermal loss of JunB leads to a SLE phenotype due to hyper IL-6 signaling. Proc Natl Acad Sci USA 106: 20423-20428.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 20423-20428
-
-
Pflegerl, P.1
Vesely, P.2
Hantusch, B.3
Schlederer, M.4
Zenz, R.5
Janig, E.6
-
62
-
-
77953619002
-
The ecological coherence of high bacterial taxonomic ranks
-
Philippot L, Andersson SGE, Battin TJ, Prosser JI, Schimel JP, Whitman WB et al. (2010). The ecological coherence of high bacterial taxonomic ranks. Nat Rev Micro 8: 523-529.
-
(2010)
Nat Rev Micro
, vol.8
, pp. 523-529
-
-
Philippot, L.1
Andersson, S.G.E.2
Battin, T.J.3
Prosser, J.I.4
Schimel, J.P.5
Whitman, W.B.6
-
63
-
-
78149283854
-
Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria
-
Png CW, Linden SK, Gilshenan KS, Zoetendal EG, McSweeney CS, Sly LI et al. (2010). Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria. Am J Gastroenterol 105: 2420-2428.
-
(2010)
Am J Gastroenterol
, vol.105
, pp. 2420-2428
-
-
Png, C.W.1
Linden, S.K.2
Gilshenan, K.S.3
Zoetendal, E.G.4
McSweeney, C.S.5
Sly, L.I.6
-
64
-
-
0031711754
-
Bias in template-toproduct ratios in multitemplate PCR
-
Polz MF, Cavanaugh CM. (1998). Bias in template-toproduct ratios in multitemplate PCR. Appl Environ Microbiol 64: 3724-3730.
-
(1998)
Appl Environ Microbiol
, vol.64
, pp. 3724-3730
-
-
Polz, M.F.1
Cavanaugh, C.M.2
-
65
-
-
77957927457
-
Gut microbial gene expression in mother-fed and formula-fed piglets
-
Poroyko V, White JR, Wang M, Donovan S, Alverdy J, Liu DC et al. (2010). Gut microbial gene expression in mother-fed and formula-fed piglets. PLoS One 5: e12459.
-
(2010)
PLoS One
, vol.5
-
-
Poroyko, V.1
White, J.R.2
Wang, M.3
Donovan, S.4
Alverdy, J.5
Liu, D.C.6
-
66
-
-
0035082973
-
Different subsets of enteric bacteria induce and perpetuate experimental colitis in rats and mice
-
Rath HC, Schultz M, Freitag R, Dieleman LA, Li F, Linde H-J et al. (2001). Different subsets of enteric bacteria induce and perpetuate experimental colitis in rats and mice. Infect Immun 69: 2277-2285.
-
(2001)
Infect Immun
, vol.69
, pp. 2277-2285
-
-
Rath, H.C.1
Schultz, M.2
Freitag, R.3
Dieleman, L.A.4
Li, F.5
Linde, H.-J.6
-
67
-
-
77952679997
-
Thuricin CD, a posttranslationally modified bacteriocin with a narrow spectrum of activity against Clostridium difficile
-
Rea MC, Sit CS, Clayton E, O'Connor PM, Whittal RM, Zheng J et al. (2010). Thuricin CD, a posttranslationally modified bacteriocin with a narrow spectrum of activity against Clostridium difficile. Proc Natl Acad Sci USA 107: 9352-9357.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 9352-9357
-
-
Rea, M.C.1
Sit, C.S.2
Clayton, E.3
O'Connor, P.M.4
Whittal, R.M.5
Zheng, J.6
-
68
-
-
71949112397
-
Inflammatory bowel disease, gut bacteria and probiotic therapy
-
Reiff C, Kelly D. (2010). Inflammatory bowel disease, gut bacteria and probiotic therapy. Int J Med Microbiol 300: 25-33.
-
(2010)
Int J Med Microbiol
, vol.300
, pp. 25-33
-
-
Reiff, C.1
Kelly, D.2
-
69
-
-
19544388278
-
Mucispirillum schaedleri gen. nov., sp. nov., a spiral-shaped bacterium colonizing the mucus layer of the gastrointestinal tract of laboratory rodents
-
Robertson BR, O'Rourke JL, Neilan BA, Vandamme P, On SLW, Fox JG et al. (2005). Mucispirillum schaedleri gen. nov., sp. nov., a spiral-shaped bacterium colonizing the mucus layer of the gastrointestinal tract of laboratory rodents. Int J Syst Evol Microbiol 55: 1199-1204.
-
(2005)
Int J Syst Evol Microbiol
, vol.55
, pp. 1199-1204
-
-
Robertson, B.R.1
O'Rourke, J.L.2
Neilan, B.A.3
Vandamme, P.4
On, S.L.W.5
Fox, J.G.6
-
70
-
-
0036716702
-
Activation of signal transducer and activator of transcription (STAT) 1 in human chronic inflammatory bowel disease
-
Schreiber S, Rosenstiel P, Hampe J, Nikolaus S, Groessner B, Schottelius A et al. (2002). Activation of signal transducer and activator of transcription (STAT) 1 in human chronic inflammatory bowel disease. Gut 51: 379-385.
-
(2002)
Gut
, vol.51
, pp. 379-385
-
-
Schreiber, S.1
Rosenstiel, P.2
Hampe, J.3
Nikolaus, S.4
Groessner, B.5
Schottelius, A.6
-
72
-
-
70349905090
-
Response of gut microbiota to fasting and hibernation in Syrian hamsters
-
Sonoyama K, Fujiwara R, Takemura N, Ogasawara T, Watanabe J, Ito H et al. (2009). Response of gut microbiota to fasting and hibernation in Syrian hamsters. Appl Environ Microbiol 75: 6451-6456.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 6451-6456
-
-
Sonoyama, K.1
Fujiwara, R.2
Takemura, N.3
Ogasawara, T.4
Watanabe, J.5
Ito, H.6
-
73
-
-
79952748287
-
Unravelling the effects of the environment and host genotype on the gut microbiome
-
Spor A, Koren O, Ley R. (2011). Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Micro 9: 279-290.
-
(2011)
Nat Rev Micro
, vol.9
, pp. 279-290
-
-
Spor, A.1
Koren, O.2
Ley, R.3
-
74
-
-
77649209317
-
Like will to like: Abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria
-
Stecher B, Chaffron S, Käppeli R, Hapfelmeier S, Freedrich S, Weber TC et al. (2010). Like will to like: Abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog 6: e1000711.
-
(2010)
PLoS Pathog
, vol.6
-
-
Stecher, B.1
Chaffron, S.2
Käppeli, R.3
Hapfelmeier, S.4
Freedrich, S.5
Weber, T.C.6
-
75
-
-
0032981583
-
Dextran sodium sulphate induced colitis activity varies with mouse strain but develops in lipopolysaccharide unresponsive mice
-
Stevceva L, Pavli P, Buffinton G, Wozniak A, Doe W. (1999). Dextran sodium sulphate induced colitis activity varies with mouse strain but develops in lipopolysaccharide unresponsive mice. J Gastroen Hepatol 14: 54-60.
-
(1999)
J Gastroen Hepatol
, vol.14
, pp. 54-60
-
-
Stevceva, L.1
Pavli, P.2
Buffinton, G.3
Wozniak, A.4
Doe, W.5
-
76
-
-
49649087440
-
Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome
-
Urich T, Lanzén A, Qi J, Huson DH, Schleper C, Schuster SC. (2008). Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One 3: e2527.
-
(2008)
PLoS One
, vol.3
-
-
Urich, T.1
Lanzén, A.2
Qi, J.3
Huson, D.H.4
Schleper, C.5
Schuster, S.C.6
-
77
-
-
33745746660
-
Muc2-deficient mice spontaneously develop colitis, indicating that MUC2 is critical for colonic protection
-
Van der Sluis M, De Koning BAE, De Bruijn ACJM, Velcich A, Meijerink JPP, Van Goudoever JB et al. (2006). Muc2-deficient mice spontaneously develop colitis, indicating that MUC2 is critical for colonic protection. Gastroenterology 131: 117-129.
-
(2006)
Gastroenterology
, vol.131
, pp. 117-129
-
-
Van Der Sluis, M.1
De Koning, B.A.E.2
De Bruijn, A.C.J.M.3
Velcich, A.4
Meijerink, J.P.P.5
Van Goudoever, J.B.6
-
78
-
-
78650973052
-
High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and noninflamed regions of the intestine in inflammatory bowel disease
-
Walker A, Sanderson J, Churcher C, Parkes G, Hudspith B, Rayment N et al. (2011). High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and noninflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol 11: 7.
-
(2011)
BMC Microbiol
, vol.11
, pp. 7
-
-
Walker, A.1
Sanderson, J.2
Churcher, C.3
Parkes, G.4
Hudspith, B.5
Rayment, N.6
-
79
-
-
34548293679
-
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang Q, Garrity GM, Tiedje JM, Cole Jr. (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, Jr.4
-
81
-
-
0035123651
-
Enhanced survival and mucosal repair after dextran sodium sulfateinduced colitis in transgenic mice that overexpress growth hormone
-
Williams KL, Randall Fuller C, Dieleman LA, DaCosta CM, Haldeman KM, Balfour Sartor R et al. (2001). Enhanced survival and mucosal repair after dextran sodium sulfateinduced colitis in transgenic mice that overexpress growth hormone. Gastroenterology 120: 925-937.
-
(2001)
Gastroenterology
, vol.120
, pp. 925-937
-
-
Williams, K.L.1
Randall Fuller, C.2
Dieleman, L.A.3
Dacosta, C.M.4
Haldeman, K.M.5
Balfour Sartor, R.6
-
82
-
-
78649686679
-
A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes
-
Willing BP, Dicksved J, Halfvarson J, Andersson AF, Lucio M, Zheng Z et al. (2010). A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 139: 1844-1854.
-
(2010)
Gastroenterology
, vol.139
, pp. 1844-1854
-
-
Willing, B.P.1
Dicksved, J.2
Halfvarson, J.3
Andersson, A.F.4
Lucio, M.5
Zheng, Z.6
-
83
-
-
33745282930
-
Sex and virulence in Escherichia coli: An evolutionary perspective
-
Wirth T, Falush D, Lan R, Colles F, Mensa P, Wieler LH et al. (2006). Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol 60: 1136-1151.
-
(2006)
Mol Microbiol
, vol.60
, pp. 1136-1151
-
-
Wirth, T.1
Falush, D.2
Lan, R.3
Colles, F.4
Mensa, P.5
Wieler, L.H.6
-
84
-
-
52149085893
-
The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains
-
Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH et al. (2008). The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31: 241-250.
-
(2008)
Syst Appl Microbiol
, vol.31
, pp. 241-250
-
-
Yarza, P.1
Richter, M.2
Peplies, J.3
Euzeby, J.4
Amann, R.5
Schleifer, K.H.6
-
85
-
-
49749147158
-
Bacteria and bacterial rRNA genes associated with the development of colitis in IL-10-/-mice
-
Ye J, Lee JW, Presley LL, Bent E, Wei B, Braun J et al. (2008). Bacteria and bacterial rRNA genes associated with the development of colitis in IL-10-/-mice. Inflamm Bowel Dis 14: 1041-1050.
-
(2008)
Inflamm Bowel Dis
, vol.14
, pp. 1041-1050
-
-
Ye, J.1
Lee, J.W.2
Presley, L.L.3
Bent, E.4
Wei, B.5
Braun, J.6
|