-
1
-
-
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 (2015), 166–169.
-
(2015)
Bioinformatics
, vol.31
, pp. 166-169
-
-
Anders, S.1
Pyl, P.T.2
Huber, W.3
-
2
-
-
84922607138
-
The biology of innate lymphoid cells
-
Artis, D., Spits, H., The biology of innate lymphoid cells. Nature 517 (2015), 293–301.
-
(2015)
Nature
, vol.517
, pp. 293-301
-
-
Artis, D.1
Spits, H.2
-
3
-
-
4544300682
-
RELMbeta/FIZZ2 is a goblet cell-specific immune-effector molecule in the gastrointestinal tract
-
Artis, D., Wang, M.L., Keilbaugh, S.A., He, W., Brenes, M., Swain, G.P., Knight, P.A., Donaldson, D.D., Lazar, M.A., Miller, H.R., et al. RELMbeta/FIZZ2 is a goblet cell-specific immune-effector molecule in the gastrointestinal tract. Proc. Natl. Acad. Sci. USA 101 (2004), 13596–13600.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 13596-13600
-
-
Artis, D.1
Wang, M.L.2
Keilbaugh, S.A.3
He, W.4
Brenes, M.5
Swain, G.P.6
Knight, P.A.7
Donaldson, D.D.8
Lazar, M.A.9
Miller, H.R.10
-
4
-
-
84958078627
-
The heterogeneity of human CD127(+) innate lymphoid cells revealed by single-cell RNA sequencing
-
Björklund, A.K., Forkel, M., Picelli, S., Konya, V., Theorell, J., Friberg, D., Sandberg, R., Mjösberg, J., The heterogeneity of human CD127(+) innate lymphoid cells revealed by single-cell RNA sequencing. Nat. Immunol. 17 (2016), 451–460.
-
(2016)
Nat. Immunol.
, vol.17
, pp. 451-460
-
-
Björklund, A.K.1
Forkel, M.2
Picelli, S.3
Konya, V.4
Theorell, J.5
Friberg, D.6
Sandberg, R.7
Mjösberg, J.8
-
5
-
-
84888877924
-
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
-
Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y., Greenleaf, W.J., Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10 (2013), 1213–1218.
-
(2013)
Nat. Methods
, vol.10
, pp. 1213-1218
-
-
Buenrostro, J.D.1
Giresi, P.G.2
Zaba, L.C.3
Chang, H.Y.4
Greenleaf, W.J.5
-
6
-
-
84941006177
-
Transcription factor Bcl11b controls identity and function of mature type 2 innate lymphoid cells
-
Califano, D., Cho, J.J., Uddin, M.N., Lorentsen, K.J., Yang, Q., Bhandoola, A., Li, H., Avram, D., Transcription factor Bcl11b controls identity and function of mature type 2 innate lymphoid cells. Immunity 43 (2015), 354–368.
-
(2015)
Immunity
, vol.43
, pp. 354-368
-
-
Califano, D.1
Cho, J.J.2
Uddin, M.N.3
Lorentsen, K.J.4
Yang, Q.5
Bhandoola, A.6
Li, H.7
Avram, D.8
-
7
-
-
84951866819
-
Aryl hydrocarbon receptor: linking environment to immunity
-
Cella, M., Colonna, M., Aryl hydrocarbon receptor: linking environment to immunity. Semin. Immunol. 27 (2015), 310–314.
-
(2015)
Semin. Immunol.
, vol.27
, pp. 310-314
-
-
Cella, M.1
Colonna, M.2
-
8
-
-
85048628201
-
Innate lymphoid cells: diversity, plasticity, and unique functions in immunity
-
Colonna, M., Innate lymphoid cells: diversity, plasticity, and unique functions in immunity. Immunity 48 (2018), 1104–1117.
-
(2018)
Immunity
, vol.48
, pp. 1104-1117
-
-
Colonna, M.1
-
9
-
-
84964828817
-
Transforming growth factor-β signaling guides the differentiation of innate lymphoid cells in salivary glands
-
Cortez, V.S., Cervantes-Barragan, L., Robinette, M.L., Bando, J.K., Wang, Y., Geiger, T.L., Gilfillan, S., Fuchs, A., Vivier, E., Sun, J.C., et al. Transforming growth factor-β signaling guides the differentiation of innate lymphoid cells in salivary glands. Immunity 44 (2016), 1127–1139.
-
(2016)
Immunity
, vol.44
, pp. 1127-1139
-
-
Cortez, V.S.1
Cervantes-Barragan, L.2
Robinette, M.L.3
Bando, J.K.4
Wang, Y.5
Geiger, T.L.6
Gilfillan, S.7
Fuchs, A.8
Vivier, E.9
Sun, J.C.10
-
10
-
-
84947423751
-
Pulmonary epithelial cell-derived cytokine TGF-β1 is a critical cofactor for enhanced innate lymphoid cell function
-
Denney, L., Byrne, A.J., Shea, T.J., Buckley, J.S., Pease, J.E., Herledan, G.M.F., Walker, S.A., Gregory, L.G., Lloyd, C.M., Pulmonary epithelial cell-derived cytokine TGF-β1 is a critical cofactor for enhanced innate lymphoid cell function. Immunity 43 (2015), 945–958.
-
(2015)
Immunity
, vol.43
, pp. 945-958
-
-
Denney, L.1
Byrne, A.J.2
Shea, T.J.3
Buckley, J.S.4
Pease, J.E.5
Herledan, G.M.F.6
Walker, S.A.7
Gregory, L.G.8
Lloyd, C.M.9
-
11
-
-
85032359621
-
Innate lymphoid cells: major players in inflammatory diseases
-
Ebbo, M., Crinier, A., Vély, F., Vivier, E., Innate lymphoid cells: major players in inflammatory diseases. Nat. Rev. Immunol. 17 (2017), 665–678.
-
(2017)
Nat. Rev. Immunol.
, vol.17
, pp. 665-678
-
-
Ebbo, M.1
Crinier, A.2
Vély, F.3
Vivier, E.4
-
12
-
-
3042720708
-
Thymic origin of intestinal alphabeta T cells revealed by fate mapping of RORgammat+ cells
-
Eberl, G., Littman, D.R., Thymic origin of intestinal alphabeta T cells revealed by fate mapping of RORgammat+ cells. Science 305 (2004), 248–251.
-
(2004)
Science
, vol.305
, pp. 248-251
-
-
Eberl, G.1
Littman, D.R.2
-
13
-
-
0029000839
-
Immune system impairment and hepatic fibrosis in mice lacking the dioxin-binding Ah receptor
-
Fernandez-Salguero, P., Pineau, T., Hilbert, D.M., McPhail, T., Lee, S.S., Kimura, S., Nebert, D.W., Rudikoff, S., Ward, J.M., Gonzalez, F.J., Immune system impairment and hepatic fibrosis in mice lacking the dioxin-binding Ah receptor. Science 268 (1995), 722–726.
-
(1995)
Science
, vol.268
, pp. 722-726
-
-
Fernandez-Salguero, P.1
Pineau, T.2
Hilbert, D.M.3
McPhail, T.4
Lee, S.S.5
Kimura, S.6
Nebert, D.W.7
Rudikoff, S.8
Ward, J.M.9
Gonzalez, F.J.10
-
14
-
-
84892482473
-
Induction of innate lymphoid cell-derived interleukin-22 by the transcription factor STAT3 mediates protection against intestinal infection
-
Guo, X., Qiu, J., Tu, T., Yang, X., Deng, L., Anders, R.A., Zhou, L., Fu, Y.X., Induction of innate lymphoid cell-derived interleukin-22 by the transcription factor STAT3 mediates protection against intestinal infection. Immunity 40 (2014), 25–39.
-
(2014)
Immunity
, vol.40
, pp. 25-39
-
-
Guo, X.1
Qiu, J.2
Tu, T.3
Yang, X.4
Deng, L.5
Anders, R.A.6
Zhou, L.7
Fu, Y.X.8
-
15
-
-
85044303941
-
Regulation of the immune response by the aryl hydrocarbon receptor
-
Gutiérrez-Vázquez, C., Quintana, F.J., Regulation of the immune response by the aryl hydrocarbon receptor. Immunity 48 (2018), 19–33.
-
(2018)
Immunity
, vol.48
, pp. 19-33
-
-
Gutiérrez-Vázquez, C.1
Quintana, F.J.2
-
16
-
-
84952637013
-
Group 2 innate lymphoid cells license dendritic cells to potentiate memory TH2 cell responses
-
Halim, T.Y., Hwang, Y.Y., Scanlon, S.T., Zaghouani, H., Garbi, N., Fallon, P.G., McKenzie, A.N., Group 2 innate lymphoid cells license dendritic cells to potentiate memory TH2 cell responses. Nat. Immunol. 17 (2016), 57–64.
-
(2016)
Nat. Immunol.
, vol.17
, pp. 57-64
-
-
Halim, T.Y.1
Hwang, Y.Y.2
Scanlon, S.T.3
Zaghouani, H.4
Garbi, N.5
Fallon, P.G.6
McKenzie, A.N.7
-
17
-
-
77952567987
-
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
-
Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y.C., Laslo, P., Cheng, J.X., Murre, C., Singh, H., Glass, C.K., Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38 (2010), 576–589.
-
(2010)
Mol. Cell
, vol.38
, pp. 576-589
-
-
Heinz, S.1
Benner, C.2
Spann, N.3
Bertolino, E.4
Lin, Y.C.5
Laslo, P.6
Cheng, J.X.7
Murre, C.8
Singh, H.9
Glass, C.K.10
-
18
-
-
84878737123
-
Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria
-
Hepworth, M.R., Monticelli, L.A., Fung, T.C., Ziegler, C.G., Grunberg, S., Sinha, R., Mantegazza, A.R., Ma, H.L., Crawford, A., Angelosanto, J.M., et al. Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria. Nature 498 (2013), 113–117.
-
(2013)
Nature
, vol.498
, pp. 113-117
-
-
Hepworth, M.R.1
Monticelli, L.A.2
Fung, T.C.3
Ziegler, C.G.4
Grunberg, S.5
Sinha, R.6
Mantegazza, A.R.7
Ma, H.L.8
Crawford, A.9
Angelosanto, J.M.10
-
19
-
-
84876996918
-
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., Salzberg, S.L., TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol., 14, 2013, R36.
-
(2013)
Genome Biol.
, vol.14
, pp. R36
-
-
Kim, D.1
Pertea, G.2
Trapnell, C.3
Pimentel, H.4
Kelley, R.5
Salzberg, S.L.6
-
20
-
-
47749107262
-
Aryl hydrocarbon receptor regulates Stat1 activation and participates in the development of Th17 cells
-
Kimura, A., Naka, T., Nohara, K., Fujii-Kuriyama, Y., Kishimoto, T., Aryl hydrocarbon receptor regulates Stat1 activation and participates in the development of Th17 cells. Proc. Natl. Acad. Sci. USA 105 (2008), 9721–9726.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 9721-9726
-
-
Kimura, A.1
Naka, T.2
Nohara, K.3
Fujii-Kuriyama, Y.4
Kishimoto, T.5
-
21
-
-
83855160821
-
Natural aryl hydrocarbon receptor ligands control organogenesis of intestinal lymphoid follicles
-
Kiss, E.A., Vonarbourg, C., Kopfmann, S., Hobeika, E., Finke, D., Esser, C., Diefenbach, A., Natural aryl hydrocarbon receptor ligands control organogenesis of intestinal lymphoid follicles. Science 334 (2011), 1561–1565.
-
(2011)
Science
, vol.334
, pp. 1561-1565
-
-
Kiss, E.A.1
Vonarbourg, C.2
Kopfmann, S.3
Hobeika, E.4
Finke, D.5
Esser, C.6
Diefenbach, A.7
-
22
-
-
84976336408
-
Innate lymphoid cells as regulators of immunity, inflammation and tissue homeostasis
-
Klose, C.S.N., Artis, D., Innate lymphoid cells as regulators of immunity, inflammation and tissue homeostasis. Nat. Immunol. 17 (2016), 765–774.
-
(2016)
Nat. Immunol.
, vol.17
, pp. 765-774
-
-
Klose, C.S.N.1
Artis, D.2
-
23
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B., Salzberg, S.L., Fast gapped-read alignment with Bowtie 2. Nat. Methods 9 (2012), 357–359.
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
24
-
-
84855917402
-
AHR drives the development of gut ILC22 cells and postnatal lymphoid tissues via pathways dependent on and independent of Notch
-
Lee, J.S., Cella, M., McDonald, K.G., Garlanda, C., Kennedy, G.D., Nukaya, M., Mantovani, A., Kopan, R., Bradfield, C.A., Newberry, R.D., Colonna, M., AHR drives the development of gut ILC22 cells and postnatal lymphoid tissues via pathways dependent on and independent of Notch. Nat. Immunol. 13 (2011), 144–151.
-
(2011)
Nat. Immunol.
, vol.13
, pp. 144-151
-
-
Lee, J.S.1
Cella, M.2
McDonald, K.G.3
Garlanda, C.4
Kennedy, G.D.5
Nukaya, M.6
Mantovani, A.7
Kopan, R.8
Bradfield, C.A.9
Newberry, R.D.10
Colonna, M.11
-
25
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25 (2009), 2078–2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
26
-
-
84990869187
-
Ikaros inhibits group 3 innate lymphoid cell development and function by suppressing the aryl hydrocarbon receptor pathway
-
Li, S., Heller, J.J., Bostick, J.W., Lee, A., Schjerven, H., Kastner, P., Chan, S., Chen, Z.E., Zhou, L., Ikaros inhibits group 3 innate lymphoid cell development and function by suppressing the aryl hydrocarbon receptor pathway. Immunity 45 (2016), 185–197.
-
(2016)
Immunity
, vol.45
, pp. 185-197
-
-
Li, S.1
Heller, J.J.2
Bostick, J.W.3
Lee, A.4
Schjerven, H.5
Kastner, P.6
Chan, S.7
Chen, Z.E.8
Zhou, L.9
-
27
-
-
85040082994
-
Regulation of innate lymphoid cells by aryl hydrocarbon receptor
-
Li, S., Bostick, J.W., Zhou, L., Regulation of innate lymphoid cells by aryl hydrocarbon receptor. Front. Immunol., 8, 2018, 1909.
-
(2018)
Front. Immunol.
, vol.8
, pp. 1909
-
-
Li, S.1
Bostick, J.W.2
Zhou, L.3
-
28
-
-
84994879643
-
IL-12 drives functional plasticity of human group 2 innate lymphoid cells
-
Lim, A.I., Menegatti, S., Bustamante, J., Le Bourhis, L., Allez, M., Rogge, L., Casanova, J.L., Yssel, H., Di Santo, J.P., IL-12 drives functional plasticity of human group 2 innate lymphoid cells. J. Exp. Med. 213 (2016), 569–583.
-
(2016)
J. Exp. Med.
, vol.213
, pp. 569-583
-
-
Lim, A.I.1
Menegatti, S.2
Bustamante, J.3
Le Bourhis, L.4
Allez, M.5
Rogge, L.6
Casanova, J.L.7
Yssel, H.8
Di Santo, J.P.9
-
29
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love, M.I., Huber, W., Anders, S., Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15, 2014, 550.
-
(2014)
Genome Biol.
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
30
-
-
84875404794
-
The UCSC Genome Browser database: extensions and updates 2013
-
Meyer, L.R., Zweig, A.S., Hinrichs, A.S., Karolchik, D., Kuhn, R.M., Wong, M., Sloan, C.A., Rosenbloom, K.R., Roe, G., Rhead, B., et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 41 (2013), D64–D69.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D64-D69
-
-
Meyer, L.R.1
Zweig, A.S.2
Hinrichs, A.S.3
Karolchik, D.4
Kuhn, R.M.5
Wong, M.6
Sloan, C.A.7
Rosenbloom, K.R.8
Roe, G.9
Rhead, B.10
-
31
-
-
84953284110
-
Group 2 innate lymphoid cells utilize the IRF4-IL-9 module to coordinate epithelial cell maintenance of lung homeostasis
-
Mohapatra, A., Van Dyken, S.J., Schneider, C., Nussbaum, J.C., Liang, H.E., Locksley, R.M., Group 2 innate lymphoid cells utilize the IRF4-IL-9 module to coordinate epithelial cell maintenance of lung homeostasis. Mucosal Immunol. 9 (2016), 275–286.
-
(2016)
Mucosal Immunol.
, vol.9
, pp. 275-286
-
-
Mohapatra, A.1
Van Dyken, S.J.2
Schneider, C.3
Nussbaum, J.C.4
Liang, H.E.5
Locksley, R.M.6
-
32
-
-
84940527399
-
IL-33 promotes an innate immune pathway of intestinal tissue protection dependent on amphiregulin-EGFR interactions
-
Monticelli, L.A., Osborne, L.C., Noti, M., Tran, S.V., Zaiss, D.M.W., Artis, D., IL-33 promotes an innate immune pathway of intestinal tissue protection dependent on amphiregulin-EGFR interactions. Proc. Natl. Acad. Sci. USA 112 (2015), 10762–10767.
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, pp. 10762-10767
-
-
Monticelli, L.A.1
Osborne, L.C.2
Noti, M.3
Tran, S.V.4
Zaiss, D.M.W.5
Artis, D.6
-
33
-
-
84899639879
-
Cytokines in inflammatory bowel disease
-
Neurath, M.F., Cytokines in inflammatory bowel disease. Nat. Rev. Immunol. 14 (2014), 329–342.
-
(2014)
Nat. Rev. Immunol.
, vol.14
, pp. 329-342
-
-
Neurath, M.F.1
-
34
-
-
84885572626
-
Type 2 innate lymphoid cells control eosinophil homeostasis
-
Nussbaum, J.C., Van Dyken, S.J., von Moltke, J., Cheng, L.E., Mohapatra, A., Molofsky, A.B., Thornton, E.E., Krummel, M.F., Chawla, A., Liang, H.E., Locksley, R.M., Type 2 innate lymphoid cells control eosinophil homeostasis. Nature 502 (2013), 245–248.
-
(2013)
Nature
, vol.502
, pp. 245-248
-
-
Nussbaum, J.C.1
Van Dyken, S.J.2
von Moltke, J.3
Cheng, L.E.4
Mohapatra, A.5
Molofsky, A.B.6
Thornton, E.E.7
Krummel, M.F.8
Chawla, A.9
Liang, H.E.10
Locksley, R.M.11
-
35
-
-
84907370454
-
MHCII-mediated dialog between group 2 innate lymphoid cells and CD4(+) T cells potentiates type 2 immunity and promotes parasitic helminth expulsion
-
Oliphant, C.J., Hwang, Y.Y., Walker, J.A., Salimi, M., Wong, S.H., Brewer, J.M., Englezakis, A., Barlow, J.L., Hams, E., Scanlon, S.T., et al. MHCII-mediated dialog between group 2 innate lymphoid cells and CD4(+) T cells potentiates type 2 immunity and promotes parasitic helminth expulsion. Immunity 41 (2014), 283–295.
-
(2014)
Immunity
, vol.41
, pp. 283-295
-
-
Oliphant, C.J.1
Hwang, Y.Y.2
Walker, J.A.3
Salimi, M.4
Wong, S.H.5
Brewer, J.M.6
Englezakis, A.7
Barlow, J.L.8
Hams, E.9
Scanlon, S.T.10
-
36
-
-
77952324145
-
Epithelial-derived IL-33 and its receptor ST2 are dysregulated in ulcerative colitis and in experimental Th1/Th2 driven enteritis
-
Pastorelli, L., Garg, R.R., Hoang, S.B., Spina, L., Mattioli, B., Scarpa, M., Fiocchi, C., Vecchi, M., Pizarro, T.T., Epithelial-derived IL-33 and its receptor ST2 are dysregulated in ulcerative colitis and in experimental Th1/Th2 driven enteritis. Proc. Natl. Acad. Sci. USA 107 (2010), 8017–8022.
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 8017-8022
-
-
Pastorelli, L.1
Garg, R.R.2
Hoang, S.B.3
Spina, L.4
Mattioli, B.5
Scarpa, M.6
Fiocchi, C.7
Vecchi, M.8
Pizarro, T.T.9
-
37
-
-
84856468953
-
NGS QC Toolkit: a toolkit for quality control of next generation sequencing data
-
Patel, R.K., Jain, M., NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS ONE, 7, 2012, e30619.
-
(2012)
PLoS ONE
, vol.7
, pp. e30619
-
-
Patel, R.K.1
Jain, M.2
-
38
-
-
84991608456
-
H2 cells following Heligmosomoides polygyrus infection
-
H2 cells following Heligmosomoides polygyrus infection. Mucosal Immunol. 9 (2016), 1407–1417.
-
(2016)
Mucosal Immunol.
, vol.9
, pp. 1407-1417
-
-
Pelly, V.S.1
Kannan, Y.2
Coomes, S.M.3
Entwistle, L.J.4
Rückerl, D.5
Seddon, B.6
MacDonald, A.S.7
McKenzie, A.8
Wilson, M.S.9
-
39
-
-
84859378165
-
Endogenous IL-33 is highly expressed in mouse epithelial barrier tissues, lymphoid organs, brain, embryos, and inflamed tissues: in situ analysis using a novel Il-33-LacZ gene trap reporter strain
-
Pichery, M., Mirey, E., Mercier, P., Lefrancais, E., Dujardin, A., Ortega, N., Girard, J.P., Endogenous IL-33 is highly expressed in mouse epithelial barrier tissues, lymphoid organs, brain, embryos, and inflamed tissues: in situ analysis using a novel Il-33-LacZ gene trap reporter strain. J. Immunol. 188 (2012), 3488–3495.
-
(2012)
J. Immunol.
, vol.188
, pp. 3488-3495
-
-
Pichery, M.1
Mirey, E.2
Mercier, P.3
Lefrancais, E.4
Dujardin, A.5
Ortega, N.6
Girard, J.P.7
-
40
-
-
84856237141
-
The aryl hydrocarbon receptor regulates gut immunity through modulation of innate lymphoid cells
-
Qiu, J., Heller, J.J., Guo, X., Chen, Z.M.E., Fish, K., Fu, Y.X., Zhou, L., The aryl hydrocarbon receptor regulates gut immunity through modulation of innate lymphoid cells. Immunity 36 (2012), 92–104.
-
(2012)
Immunity
, vol.36
, pp. 92-104
-
-
Qiu, J.1
Heller, J.J.2
Guo, X.3
Chen, Z.M.E.4
Fish, K.5
Fu, Y.X.6
Zhou, L.7
-
41
-
-
84882668842
-
Group 3 innate lymphoid cells inhibit T-cell-mediated intestinal inflammation through aryl hydrocarbon receptor signaling and regulation of microflora
-
Qiu, J., Guo, X., Chen, Z.M., He, L., Sonnenberg, G.F., Artis, D., Fu, Y.X., Zhou, L., Group 3 innate lymphoid cells inhibit T-cell-mediated intestinal inflammation through aryl hydrocarbon receptor signaling and regulation of microflora. Immunity 39 (2013), 386–399.
-
(2013)
Immunity
, vol.39
, pp. 386-399
-
-
Qiu, J.1
Guo, X.2
Chen, Z.M.3
He, L.4
Sonnenberg, G.F.5
Artis, D.6
Fu, Y.X.7
Zhou, L.8
-
42
-
-
77951770756
-
BEDTools: a flexible suite of utilities for comparing genomic features
-
Quinlan, A.R., Hall, I.M., BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26 (2010), 841–842.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
43
-
-
42649095378
-
Control of T(reg) and T(H)17 cell differentiation by the aryl hydrocarbon receptor
-
Quintana, F.J., Basso, A.S., Iglesias, A.H., Korn, T., Farez, M.F., Bettelli, E., Caccamo, M., Oukka, M., Weiner, H.L., Control of T(reg) and T(H)17 cell differentiation by the aryl hydrocarbon receptor. Nature 453 (2008), 65–71.
-
(2008)
Nature
, vol.453
, pp. 65-71
-
-
Quintana, F.J.1
Basso, A.S.2
Iglesias, A.H.3
Korn, T.4
Farez, M.F.5
Bettelli, E.6
Caccamo, M.7
Oukka, M.8
Weiner, H.L.9
-
44
-
-
84923436228
-
Transcriptional programs define molecular characteristics of innate lymphoid cell classes and subsets
-
Robinette, M.L., Fuchs, A., Cortez, V.S., Lee, J.S., Wang, Y., Durum, S.K., Gilfillan, S., Colonna, M., Immunological Genome Consortium. Transcriptional programs define molecular characteristics of innate lymphoid cell classes and subsets. Nat. Immunol. 16 (2015), 306–317.
-
(2015)
Nat. Immunol.
, vol.16
, pp. 306-317
-
-
Robinette, M.L.1
Fuchs, A.2
Cortez, V.S.3
Lee, J.S.4
Wang, Y.5
Durum, S.K.6
Gilfillan, S.7
Colonna, M.8
-
45
-
-
84866975037
-
Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification
-
Samstein, R.M., Arvey, A., Josefowicz, S.Z., Peng, X., Reynolds, A., Sandstrom, R., Neph, S., Sabo, P., Kim, J.M., Liao, W., et al. Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification. Cell 151 (2012), 153–166.
-
(2012)
Cell
, vol.151
, pp. 153-166
-
-
Samstein, R.M.1
Arvey, A.2
Josefowicz, S.Z.3
Peng, X.4
Reynolds, A.5
Sandstrom, R.6
Neph, S.7
Sabo, P.8
Kim, J.M.9
Liao, W.10
-
46
-
-
85047291496
-
A metabolite-triggered tuft cell-ILC2 circuit drives small intestinal remodeling
-
Schneider, C., O'Leary, C.E., von Moltke, J., Liang, H.E., Ang, Q.Y., Turnbaugh, P.J., Radhakrishnan, S., Pellizzon, M., Ma, A., Locksley, R.M., A metabolite-triggered tuft cell-ILC2 circuit drives small intestinal remodeling. Cell 174 (2018), 271–284.e14.
-
(2018)
Cell
, vol.174
, pp. 271-284.e14
-
-
Schneider, C.1
O'Leary, C.E.2
von Moltke, J.3
Liang, H.E.4
Ang, Q.Y.5
Turnbaugh, P.J.6
Radhakrishnan, S.7
Pellizzon, M.8
Ma, A.9
Locksley, R.M.10
-
47
-
-
84887459057
-
Neutralisation of the interleukin-33/ST2 pathway ameliorates experimental colitis through enhancement of mucosal healing in mice
-
Sedhom, M.A.K., Pichery, M., Murdoch, J.R., Foligné, B., Ortega, N., Normand, S., Mertz, K., Sanmugalingam, D., Brault, L., Grandjean, T., et al. Neutralisation of the interleukin-33/ST2 pathway ameliorates experimental colitis through enhancement of mucosal healing in mice. Gut 62 (2013), 1714–1723.
-
(2013)
Gut
, vol.62
, pp. 1714-1723
-
-
Sedhom, M.A.K.1
Pichery, M.2
Murdoch, J.R.3
Foligné, B.4
Ortega, N.5
Normand, S.6
Mertz, K.7
Sanmugalingam, D.8
Brault, L.9
Grandjean, T.10
-
48
-
-
84899493057
-
ngs.plot: quick mining and visualization of next-generation sequencing data by integrating genomic databases
-
Shen, L., Shao, N., Liu, X., Nestler, E., ngs.plot: quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics, 15, 2014, 284.
-
(2014)
BMC Genomics
, vol.15
, pp. 284
-
-
Shen, L.1
Shao, N.2
Liu, X.3
Nestler, E.4
-
49
-
-
84964922317
-
Developmental acquisition of regulomes underlies innate lymphoid cell functionality
-
Shih, H.Y., Sciumè, G., Mikami, Y., Guo, L., Sun, H.W., Brooks, S.R., Urban, J.F. Jr., Davis, F.P., Kanno, Y., O'Shea, J.J., Developmental acquisition of regulomes underlies innate lymphoid cell functionality. Cell 165 (2016), 1120–1133.
-
(2016)
Cell
, vol.165
, pp. 1120-1133
-
-
Shih, H.Y.1
Sciumè, G.2
Mikami, Y.3
Guo, L.4
Sun, H.W.5
Brooks, S.R.6
Urban, J.F.7
Davis, F.P.8
Kanno, Y.9
O'Shea, J.J.10
-
50
-
-
85038925587
-
Dissecting human ILC heterogeneity: more than just three subsets
-
Simoni, Y., Newell, E.W., Dissecting human ILC heterogeneity: more than just three subsets. Immunology 153 (2018), 297–303.
-
(2018)
Immunology
, vol.153
, pp. 297-303
-
-
Simoni, Y.1
Newell, E.W.2
-
51
-
-
84936892270
-
Innate lymphoid cells in the initiation, regulation and resolution of inflammation
-
Sonnenberg, G.F., Artis, D., Innate lymphoid cells in the initiation, regulation and resolution of inflammation. Nat. Med. 21 (2015), 698–708.
-
(2015)
Nat. Med.
, vol.21
, pp. 698-708
-
-
Sonnenberg, G.F.1
Artis, D.2
-
52
-
-
84888000653
-
Specification of type 2 innate lymphocytes by the transcriptional determinant Gfi1
-
Spooner, C.J., Lesch, J., Yan, D., Khan, A.A., Abbas, A., Ramirez-Carrozzi, V., Zhou, M., Soriano, R., Eastham-Anderson, J., Diehl, L., et al. Specification of type 2 innate lymphocytes by the transcriptional determinant Gfi1. Nat. Immunol. 14 (2013), 1229–1236.
-
(2013)
Nat. Immunol.
, vol.14
, pp. 1229-1236
-
-
Spooner, C.J.1
Lesch, J.2
Yan, D.3
Khan, A.A.4
Abbas, A.5
Ramirez-Carrozzi, V.6
Zhou, M.7
Soriano, R.8
Eastham-Anderson, J.9
Diehl, L.10
-
53
-
-
84907000772
-
Commensal bacteria protect against food allergen sensitization
-
Stefka, A.T., Feehley, T., Tripathi, P., Qiu, J., McCoy, K., Mazmanian, S.K., Tjota, M.Y., Seo, G.Y., Cao, S., Theriault, B.R., et al. Commensal bacteria protect against food allergen sensitization. Proc. Natl. Acad. Sci. USA 111 (2014), 13145–13150.
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. 13145-13150
-
-
Stefka, A.T.1
Feehley, T.2
Tripathi, P.3
Qiu, J.4
McCoy, K.5
Mazmanian, S.K.6
Tjota, M.Y.7
Seo, G.Y.8
Cao, S.9
Theriault, B.R.10
-
54
-
-
84896935541
-
The aryl hydrocarbon receptor: multitasking in the immune system
-
Stockinger, B., Di Meglio, P., Gialitakis, M., Duarte, J.H., The aryl hydrocarbon receptor: multitasking in the immune system. Annu. Rev. Immunol. 32 (2014), 403–432.
-
(2014)
Annu. Rev. Immunol.
, vol.32
, pp. 403-432
-
-
Stockinger, B.1
Di Meglio, P.2
Gialitakis, M.3
Duarte, J.H.4
-
55
-
-
27344435774
-
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S., Mesirov, J.P., Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102 (2005), 15545–15550.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
Paulovich, A.7
Pomeroy, S.L.8
Golub, T.R.9
Lander, E.S.10
Mesirov, J.P.11
-
56
-
-
0034733039
-
Requirement for RORgamma in thymocyte survival and lymphoid organ development
-
Sun, Z., Unutmaz, D., Zou, Y.R., Sunshine, M.J., Pierani, A., Brenner-Morton, S., Mebius, R.E., Littman, D.R., Requirement for RORgamma in thymocyte survival and lymphoid organ development. Science 288 (2000), 2369–2373.
-
(2000)
Science
, vol.288
, pp. 2369-2373
-
-
Sun, Z.1
Unutmaz, D.2
Zou, Y.R.3
Sunshine, M.J.4
Pierani, A.5
Brenner-Morton, S.6
Mebius, R.E.7
Littman, D.R.8
-
57
-
-
85030094038
-
Immunology of food allergy
-
Tordesillas, L., Berin, M.C., Sampson, H.A., Immunology of food allergy. Immunity 47 (2017), 32–50.
-
(2017)
Immunity
, vol.47
, pp. 32-50
-
-
Tordesillas, L.1
Berin, M.C.2
Sampson, H.A.3
-
58
-
-
77952123055
-
Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell, C., Williams, B.A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M.J., Salzberg, S.L., Wold, B.J., Pachter, L., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28 (2010), 511–515.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
59
-
-
84887315051
-
IL-22 mediates goblet cell hyperplasia and worm expulsion in intestinal helminth infection
-
Turner, J.E., Stockinger, B., Helmby, H., IL-22 mediates goblet cell hyperplasia and worm expulsion in intestinal helminth infection. PLoS Pathog., 9, 2013, e1003698.
-
(2013)
PLoS Pathog.
, vol.9
, pp. e1003698
-
-
Turner, J.E.1
Stockinger, B.2
Helmby, H.3
-
60
-
-
42649106556
-
The aryl hydrocarbon receptor links TH17-cell-mediated autoimmunity to environmental toxins
-
Veldhoen, M., Hirota, K., Westendorf, A.M., Buer, J., Dumoutier, L., Renauld, J.C., Stockinger, B., The aryl hydrocarbon receptor links TH17-cell-mediated autoimmunity to environmental toxins. Nature 453 (2008), 106–109.
-
(2008)
Nature
, vol.453
, pp. 106-109
-
-
Veldhoen, M.1
Hirota, K.2
Westendorf, A.M.3
Buer, J.4
Dumoutier, L.5
Renauld, J.C.6
Stockinger, B.7
-
61
-
-
84870017183
-
Designing an enhancer landscape
-
Xu, J., Smale, S.T., Designing an enhancer landscape. Cell 151 (2012), 929–931.
-
(2012)
Cell
, vol.151
, pp. 929-931
-
-
Xu, J.1
Smale, S.T.2
-
62
-
-
84896396519
-
The transcription factor GATA3 is critical for the development of all IL-7Rα-expressing innate lymphoid cells
-
Yagi, R., Zhong, C., Northrup, D.L., Yu, F., Bouladoux, N., Spencer, S., Hu, G., Barron, L., Sharma, S., Nakayama, T., et al. The transcription factor GATA3 is critical for the development of all IL-7Rα-expressing innate lymphoid cells. Immunity 40 (2014), 378–388.
-
(2014)
Immunity
, vol.40
, pp. 378-388
-
-
Yagi, R.1
Zhong, C.2
Northrup, D.L.3
Yu, F.4
Bouladoux, N.5
Spencer, S.6
Hu, G.7
Barron, L.8
Sharma, S.9
Nakayama, T.10
-
63
-
-
85034865881
-
The aryl hydrocarbon receptor preferentially marks and promotes gut regulatory T cells
-
Ye, J., Qiu, J., Bostick, J.W., Ueda, A., Schjerven, H., Li, S., Jobin, C., Chen, Z.E., Zhou, L., The aryl hydrocarbon receptor preferentially marks and promotes gut regulatory T cells. Cell Rep. 21 (2017), 2277–2290.
-
(2017)
Cell Rep.
, vol.21
, pp. 2277-2290
-
-
Ye, J.1
Qiu, J.2
Bostick, J.W.3
Ueda, A.4
Schjerven, H.5
Li, S.6
Jobin, C.7
Chen, Z.E.8
Zhou, L.9
-
64
-
-
84994673999
-
The aryl hydrocarbon receptor is required for the maintenance of liver-resident natural killer cells
-
Zhang, L.H., Shin, J.H., Haggadone, M.D., Sunwoo, J.B., The aryl hydrocarbon receptor is required for the maintenance of liver-resident natural killer cells. J. Exp. Med. 213 (2016), 2249–2257.
-
(2016)
J. Exp. Med.
, vol.213
, pp. 2249-2257
-
-
Zhang, L.H.1
Shin, J.H.2
Haggadone, M.D.3
Sunwoo, J.B.4
-
65
-
-
84955200559
-
Group 3 innate lymphoid cells continuously require the transcription factor GATA-3 after commitment
-
Zhong, C., Cui, K., Wilhelm, C., Hu, G., Mao, K., Belkaid, Y., Zhao, K., Zhu, J., Group 3 innate lymphoid cells continuously require the transcription factor GATA-3 after commitment. Nat. Immunol. 17 (2016), 169–178.
-
(2016)
Nat. Immunol.
, vol.17
, pp. 169-178
-
-
Zhong, C.1
Cui, K.2
Wilhelm, C.3
Hu, G.4
Mao, K.5
Belkaid, Y.6
Zhao, K.7
Zhu, J.8
-
66
-
-
84952864852
-
AHR function in lymphocytes: emerging concepts
-
Zhou, L., AHR function in lymphocytes: emerging concepts. Trends Immunol. 37 (2016), 17–31.
-
(2016)
Trends Immunol.
, vol.37
, pp. 17-31
-
-
Zhou, L.1
-
67
-
-
34147206377
-
An inducible enhancer required for Il12b promoter activity in an insulated chromatin environment
-
Zhou, L., Nazarian, A.A., Xu, J., Tantin, D., Corcoran, L.M., Smale, S.T., An inducible enhancer required for Il12b promoter activity in an insulated chromatin environment. Mol. Cell. Biol. 27 (2007), 2698–2712.
-
(2007)
Mol. Cell. Biol.
, vol.27
, pp. 2698-2712
-
-
Zhou, L.1
Nazarian, A.A.2
Xu, J.3
Tantin, D.4
Corcoran, L.M.5
Smale, S.T.6
-
68
-
-
84935871666
-
IL-33 aggravates DSS-induced acute colitis in mouse colon lamina propria by enhancing Th2 cell responses
-
Zhu, J., Yang, F., Sang, L., Zhai, J., Zhang, X., Yue, D., Li, S., Li, Y., Lu, C., Sun, X., IL-33 aggravates DSS-induced acute colitis in mouse colon lamina propria by enhancing Th2 cell responses. Mediators Inflamm., 2015, 2015, 913041.
-
(2015)
Mediators Inflamm.
, vol.2015
, pp. 913041
-
-
Zhu, J.1
Yang, F.2
Sang, L.3
Zhai, J.4
Zhang, X.5
Yue, D.6
Li, S.7
Li, Y.8
Lu, C.9
Sun, X.10
|