-
1
-
-
7644231561
-
The chemokine system in diverse forms of macrophage activation and polarization
-
Mantovani, A., A. Sica, S. Sozzani, P. Allavena, A. Vecchi, and M. Locati. 2004. The chemokine system in diverse forms of macrophage activation and polarization. Trends Immunol. 25: 677-686.
-
(2004)
Trends Immunol
, vol.25
, pp. 677-686
-
-
Mantovani, A.1
Sica, A.2
Sozzani, S.3
Allavena, P.4
Vecchi, A.5
Locati, M.6
-
2
-
-
84875544506
-
Interleukin-4- and interleukin-13- mediated alternatively activated macrophages: Roles in homeostasis and disease
-
Van Dyken, S. J., and R. M. Locksley. 2013. Interleukin-4- and interleukin-13- mediated alternatively activated macrophages: Roles in homeostasis and disease. Annu. Rev. Immunol. 31: 317-343.
-
(2013)
Annu. Rev. Immunol
, vol.31
, pp. 317-343
-
-
Van Dyken, S.J.1
Locksley, R.M.2
-
3
-
-
84894102230
-
Transcriptomebased network analysis reveals a spectrum model of human macrophage activation
-
Xue, J., S. V. Schmidt, J. Sander, A. Draffehn, W. Krebs, I. Quester, D. De Nardo, T. D. Gohel, M. Emde, L. Schmidleithner, et al. 2014. Transcriptomebased network analysis reveals a spectrum model of human macrophage activation. Immunity 40: 274-288.
-
(2014)
Immunity
, vol.40
, pp. 274-288
-
-
Xue, J.1
Schmidt, S.V.2
Sander, J.3
Draffehn, A.4
Krebs, W.5
Quester, I.6
De Nardo, D.7
Gohel, T.D.8
Emde, M.9
Schmidleithner, L.10
-
4
-
-
33947305781
-
ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
-
Margolin, A. A., I. Nemenman, K. Basso, C. Wiggins, G. Stolovitzky, R. Dalla Favera, and A. Califano. 2006. ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 7(Suppl 1): S7.
-
(2006)
BMC Bioinformatics
, vol.7 S7
-
-
Margolin, A.A.1
Nemenman, I.2
Basso, K.3
Wiggins, C.4
Stolovitzky, G.5
Dalla Favera, R.6
Califano, A.7
-
5
-
-
33750353888
-
Reverse engineering cellular networks
-
Margolin, A. A., K. Wang, W. K. Lim, M. Kustagi, I. Nemenman, and A. Califano. 2006. Reverse engineering cellular networks. Nat. Protoc. 1: 662-671.
-
(2006)
Nat. Protoc
, vol.1
, pp. 662-671
-
-
Margolin, A.A.1
Wang, K.2
Lim, W.K.3
Kustagi, M.4
Nemenman, I.5
Califano, A.6
-
6
-
-
16844376909
-
Reverse engineering of regulatory networks in human B cells
-
Basso, K., A. A. Margolin, G. Stolovitzky, U. Klein, R. Dalla-Favera, and A. Califano. 2005. Reverse engineering of regulatory networks in human B cells. Nat. Genet. 37: 382-390.
-
(2005)
Nat. Genet
, vol.37
, pp. 382-390
-
-
Basso, K.1
Margolin, A.A.2
Stolovitzky, G.3
Klein, U.4
Califano, A.5
-
7
-
-
36248940715
-
Reconstruction of metabolic networks from high-throughput metabolite profiling data: In silico analysis of red blood cell metabolism
-
Nemenman, I., G. S. Escola, W. S. Hlavacek, P. J. Unkefer, C. J. Unkefer, and M. E. Wall. 2007. Reconstruction of metabolic networks from high-throughput metabolite profiling data: In silico analysis of red blood cell metabolism. Ann. N. Y. Acad. Sci. 1115: 102-115.
-
(2007)
Ann. N. Y. Acad. Sci
, vol.1115
, pp. 102-115
-
-
Nemenman, I.1
Escola, G.S.2
Hlavacek, W.S.3
Unkefer, P.J.4
Unkefer, C.J.5
Wall, M.E.6
-
8
-
-
50949117527
-
Network inference algorithms elucidate Nrf2 regulation of mouse lung oxidative stress
-
Taylor, R. C., G. Acquaah-Mensah, M. Singhal, D. Malhotra, and S. Biswal. 2008. Network inference algorithms elucidate Nrf2 regulation of mouse lung oxidative stress. PLOS Comput. Biol. 4: E1000166.
-
(2008)
PLOS Comput. Biol
, vol.4
, pp. e1000166
-
-
Taylor, R.C.1
Singhal, M.2
Malhotra, D.3
Biswal, S.4
-
9
-
-
84866303839
-
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals
-
Garber, M., N. Yosef, A. Goren, R. Raychowdhury, A. Thielke, M. Guttman, J. Robinson, B. Minie, N. Chevrier, Z. Itzhaki, et al. 2012. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol. Cell 47: 810-822.
-
(2012)
Mol. Cell
, vol.47
, pp. 810-822
-
-
Garber, M.1
Yosef, N.2
Goren, A.3
Raychowdhury, R.4
Thielke, A.5
Guttman, M.6
Robinson, J.7
Minie, B.8
Chevrier, N.9
Itzhaki, Z.10
-
10
-
-
84904394690
-
Macrophage activation and polarization: Nomenclature and experimental guidelines
-
Murray, P. J., J. E. Allen, S. K. Biswas, E. A. Fisher, D. W. Gilroy, S. Goerdt, S. Gordon, J. A. Hamilton, L. B. Ivashkiv, T. Lawrence, et al. 2014. Macrophage activation and polarization: Nomenclature and experimental guidelines. Immunity 41: 14-20.
-
(2014)
Immunity
, vol.41
, pp. 14-20
-
-
Murray, P.J.1
Allen, J.E.2
Biswas, S.K.3
Fisher, E.A.4
Gilroy, D.W.5
Goerdt, S.6
Gordon, S.7
Hamilton, J.A.8
Ivashkiv, L.B.9
Lawrence, T.10
-
11
-
-
84876581893
-
InnateDB: Systems biology of innate immunity and beyond-recent updates and continuing curation
-
Breuer, K., A. K. Foroushani, M. R. Laird, C. Chen, A. Sribnaia, R. Lo, G. L. Winsor, R. E. W. Hancock, F. S. L. Brinkman, and D. J. Lynn. 2013. InnateDB: Systems biology of innate immunity and beyond-recent updates and continuing curation. Nucleic Acids Res. 41: D1228-D1233.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D1228-D1233
-
-
Breuer, K.1
Foroushani, A.K.2
Laird, M.R.3
Chen, C.4
Sribnaia, A.5
Lo, R.6
Winsor, G.L.7
Hancock, R.E.W.8
Brinkman, F.S.L.9
Lynn, D.J.10
-
12
-
-
84874947727
-
The Bio- GRID interaction database: 2013 update
-
Chatr-Aryamontri, A., B.-J. Breitkreutz, S. Heinicke, L. Boucher, A. Winter, C. Stark, J. Nixon, L. Ramage, N. Kolas, L. O'Donnell, et al. 2013. The Bio- GRID interaction database: 2013 update. Nucleic Acids Res. 41: D816-D823.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D816-D823
-
-
Chatr-Aryamontri, A.1
Breitkreutz, B.-J.2
Heinicke, S.3
Boucher, L.4
Winter, A.5
Stark, C.6
Nixon, J.7
Ramage, L.8
Kolas, N.9
-
13
-
-
4444222696
-
A genome-wide and nonredundant mouse transcription factor database
-
Kanamori, M., H. Konno, N. Osato, J. Kawai, Y. Hayashizaki, and H. Suzuki. 2004. A genome-wide and nonredundant mouse transcription factor database. Biochem. Biophys. Res. Commun. 322: 787-793.
-
(2004)
Biochem. Biophys. Res. Commun
, vol.322
, pp. 787-793
-
-
Kanamori, M.1
Konno, H.2
Osato, N.3
Kawai, J.4
Hayashizaki, Y.5
Suzuki, H.6
-
14
-
-
84865049521
-
HTRIdb: An open-Access database for experimentally verified human transcriptional regulation interactions
-
Bovolenta, L. A., M. L. Acencio, and N. Lemke. 2012. HTRIdb: An open-Access database for experimentally verified human transcriptional regulation interactions. BMC Genomics 13: 405.
-
(2012)
BMC Genomics
, vol.13
, pp. 405
-
-
Bovolenta, L.A.1
Acencio, M.L.2
Lemke, N.3
-
15
-
-
79551587720
-
Cytoscape 2.8: New features for data integration and network visualization
-
Smoot, M. E., K. Ono, J. Ruscheinski, P.-L. Wang, and T. Ideker. 2011. Cytoscape 2.8: New features for data integration and network visualization. Bioinformatics 27: 431-432.
-
(2011)
Bioinformatics
, vol.27
, pp. 431-432
-
-
Smoot, M.E.1
Ono, K.2
Ruscheinski, J.3
Wang, P.-L.4
Ideker, T.5
-
16
-
-
84868116568
-
Splenic red pulp macrophages produce type I interferons as early sentinels of malaria infection but are dispensable for control
-
Kim, C. C., C. S. Nelson, E. B. Wilson, B. Hou, A. L. DeFranco, and J. L. DeRisi. 2012. Splenic red pulp macrophages produce type I interferons as early sentinels of malaria infection but are dispensable for control. PLoS ONE 7: E48126.
-
(2012)
PLoS ONE
, vol.7
, pp. e48126
-
-
Kim, C.C.1
Nelson, C.S.2
Wilson, E.B.3
Hou, B.4
DeFranco, A.L.5
DeRisi, J.L.6
-
17
-
-
0242333835
-
Normalization of cDNA microarray data
-
Smyth, G. K., and T. Speed. 2003. Normalization of cDNA microarray data. Methods 31: 265-273.
-
(2003)
Methods
, vol.31
, pp. 265-273
-
-
Smyth, G.K.1
Speed, T.2
-
18
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
Tusher, V. G., R. Tibshirani, and G. Chu. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98: 5116-5121.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
19
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B., and S. L. Salzberg. 2012. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9: 357-359.
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
20
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
1000 Genome Project Data Processing Subgroup
-
Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, and R. Durbin, 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 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
-
21
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS
-
Zhang, Y., T. Liu, C. A. Meyer, J. Eeckhoute, D. S. Johnson, B. E. Bernstein, C. Nusbaum, R. M. Myers, M. Brown, W. Li, and X. S. Liu. 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9: R137.
-
(2008)
Genome Biol
, vol.9
, pp. R137
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
Bernstein, B.E.6
Nusbaum, C.7
Myers, R.M.8
Brown, M.9
Li, W.10
Liu, X.S.11
-
22
-
-
78649421803
-
IkappaBbeta is an essential co-Activator for LPS-induced IL-1b transcription in vivo
-
Scheibel, M., B. Klein, H. Merkle, M. Schulz, R. Fritsch, F. R. Greten, M. C. Arkan, G. Schneider, and R. M. Schmid. 2010. IkappaBbeta is an essential co-Activator for LPS-induced IL-1b transcription in vivo. J. Exp. Med. 207: 2621-2630.
-
(2010)
J. Exp. Med
, vol.207
, pp. 2621-2630
-
-
Scheibel, M.1
Klein, B.2
Merkle, H.3
Schulz, M.4
Fritsch, R.5
Greten, F.R.6
Arkan, M.C.7
Schneider, G.8
Schmid, R.M.9
-
23
-
-
0035971432
-
AP-1 in mouse development and tumorigenesis
-
Jochum, W., E. Passegué, and E. F. Wagner. 2001. AP-1 in mouse development and tumorigenesis. Oncogene 20: 2401-2412.
-
(2001)
Oncogene
, vol.20
, pp. 2401-2412
-
-
Jochum, W.1
Passegué, E.2
Wagner, E.F.3
-
24
-
-
0030858764
-
Lipopolysaccharide induction of the tumor necrosis factor-Alpha promoter in human monocytic cells. Regulation by Egr-1, c-Jun, and NF-kappaB transcription factors
-
Yao, J., N. Mackman, T. S. Edgington, and S. T. Fan. 1997. Lipopolysaccharide induction of the tumor necrosis factor-Alpha promoter in human monocytic cells. Regulation by Egr-1, c-Jun, and NF-kappaB transcription factors. J. Biol. Chem. 272: 17795-17801.
-
(1997)
J. Biol. Chem
, vol.272
, pp. 17795-17801
-
-
Yao, J.1
Mackman, N.2
Edgington, T.S.3
Fan, S.T.4
-
25
-
-
0242335086
-
Activation of src-family tyrosine kinases by LPS regulates cytokine production in dendritic cells by controlling AP-1 formation
-
Napolitani, G., N. Bortoletto, L. Racioppi, A. Lanzavecchia, and U. D'Oro. 2003. Activation of src-family tyrosine kinases by LPS regulates cytokine production in dendritic cells by controlling AP-1 formation. Eur. J. Immunol. 33: 2832-2841.
-
(2003)
Eur J. Immunol
, vol.33
, pp. 2832-2841
-
-
Napolitani, G.1
Bortoletto, N.2
Racioppi, L.3
Lanzavecchia, A.4
D'Oro, U.5
-
26
-
-
10844273239
-
Role of c-Jun N-terminal kinase on lipopolysaccharide induced maturation of human monocyte-derived dendritic cells
-
Nakahara, T., H. Uchi, K. Urabe, Q. Chen, M. Furue, and Y. Moroi. 2004. Role of c-Jun N-terminal kinase on lipopolysaccharide induced maturation of human monocyte-derived dendritic cells. Int. Immunol. 16: 1701-1709.
-
(2004)
Int. Immunol
, vol.16
, pp. 1701-1709
-
-
Nakahara, T.1
Uchi, H.2
Urabe, K.3
Chen, Q.4
Furue, M.5
Moroi, Y.6
-
27
-
-
0033557740
-
JunB is essential for mammalian placentation
-
Schorpp-Kistner, M., Z.-Q. Wang, P. Angel, and E. F. Wagner. 1999. JunB is essential for mammalian placentation. EMBO J. 18: 934-948.
-
(1999)
EMBO J
, vol.18
, pp. 934-948
-
-
Schorpp-Kistner, M.1
Wang, Z.-Q.2
Angel, P.3
Wagner, E.F.4
-
28
-
-
0033177995
-
Conditional gene targeting in macrophages and granulocytes using LysMcre mice
-
Clausen, B. E., C. Burkhardt, W. Reith, R. Renkawitz, and I. Förster. 1999. Conditional gene targeting in macrophages and granulocytes using LysMcre mice. Transgenic Res. 8: 265-277.
-
(1999)
Transgenic Res
, vol.8
, pp. 265-277
-
-
Clausen, B.E.1
Burkhardt, C.2
Reith, W.3
Renkawitz, R.4
Förster, I.5
-
29
-
-
7044269527
-
JunB deficiency leads to a myeloproliferative disorder arising from hematopoietic stem cells
-
Passegué, E., E. F. Wagner, and I. L. Weissman. 2004. JunB deficiency leads to a myeloproliferative disorder arising from hematopoietic stem cells. Cell 119: 431-443.
-
(2004)
Cell
, vol.119
, pp. 431-443
-
-
Passegué, E.1
Wagner, E.F.2
Weissman, I.L.3
-
30
-
-
77949661217
-
An NF-kappaB-dependent role for JunB in the induction of proinflammatory cytokines in LPS-Activated bone marrow-derived dendritic cells
-
Gomard, T., H.-A. Michaud, D. Tempé, K. Thiolon, M. Pelegrin, and M. Piechaczyk. 2010. An NF-kappaB-dependent role for JunB in the induction of proinflammatory cytokines in LPS-Activated bone marrow-derived dendritic cells. PLoS ONE 5: E9585.
-
(2010)
PLoS ONE
, vol.5
, pp. e9585
-
-
Gomard, T.1
Michaud, H.-A.2
Tempé, D.3
Thiolon, K.4
Pelegrin, M.5
Piechaczyk, M.6
-
31
-
-
0035947732
-
Characterization of an activation protein-1-binding site in the murine interleukin-12 p40 promoter. Demonstration of novel functional elements by a reductionist approach
-
Zhu, C., K. Gagnidze, J. H. Gemberling, and S. E. Plevy. 2001. Characterization of an activation protein-1-binding site in the murine interleukin-12 p40 promoter. Demonstration of novel functional elements by a reductionist approach. J. Biol. Chem. 276: 18519-18528.
-
(2001)
J. Biol. Chem
, vol.276
, pp. 18519-18528
-
-
Zhu, C.1
Gagnidze, K.2
Gemberling, J.H.3
Plevy, S.E.4
-
32
-
-
0344196985
-
Regulation of IL-4 expression by the transcription factor JunB during T helper cell differentiation
-
Li, B., C. Tournier, R. J. Davis, and R. A. Flavell. 1999. Regulation of IL-4 expression by the transcription factor JunB during T helper cell differentiation. EMBO J. 18: 420-432.
-
(1999)
EMBO J
, vol.18
, pp. 420-432
-
-
Li, B.1
Tournier, C.2
Davis, R.J.3
Flavell, R.A.4
-
33
-
-
34347324118
-
Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor
-
So, A. Y.-L., C. Chaivorapol, E. C. Bolton, H. Li, and K. R. Yamamoto. 2007. Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor. PLoS Genet. 3: E94.
-
(2007)
PLoS Genet
, vol.3
, pp. e94
-
-
So, A.Y.-L.1
Chaivorapol, C.2
Bolton, E.C.3
Li, H.4
Yamamoto, K.R.5
-
34
-
-
32044439558
-
Selective and antagonistic functions of SWI/SNF and Mi-2beta nucleosome remodeling complexes during an inflammatory response
-
Ramirez-Carrozzi, V. R., A. A. Nazarian, C. C. Li, S. L. Gore, R. Sridharan, A. N. Imbalzano, and S. T. Smale. 2006. Selective and antagonistic functions of SWI/SNF and Mi-2beta nucleosome remodeling complexes during an inflammatory response. Genes Dev. 20: 282-296.
-
(2006)
Genes Dev
, vol.20
, pp. 282-296
-
-
Ramirez-Carrozzi, V.R.1
Nazarian, A.A.2
Li, C.C.3
Gore, S.L.4
Sridharan, R.5
Imbalzano, A.N.6
Smale, S.T.7
-
35
-
-
67649669255
-
A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling
-
Ramirez-Carrozzi, V. R., D. Braas, D. M. Bhatt, C. S. Cheng, C. Hong, K. R. Doty, J. C. Black, A. Hoffmann, M. Carey, and S. T. Smale. 2009. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell 138: 114-128.
-
(2009)
Cell
, vol.138
, pp. 114-128
-
-
Ramirez-Carrozzi, V.R.1
Braas, D.2
Bhatt, D.M.3
Cheng, C.S.4
Hong, C.5
Doty, K.R.6
Black, J.C.7
Hoffmann, A.8
Carey, M.9
Smale, S.T.10
-
36
-
-
34250823515
-
Gene-specific control of inflammation by TLR-induced chromatin modifications
-
Foster, S. L., D. C. Hargreaves, and R. Medzhitov. 2007. Gene-specific control of inflammation by TLR-induced chromatin modifications. Nature 447: 972-978.
-
(2007)
Nature
, vol.447
, pp. 972-978
-
-
Foster, S.L.1
Hargreaves, D.C.2
Medzhitov, R.3
-
37
-
-
80054966913
-
STING is a direct innate immune sensor of cyclic di-GMP
-
Burdette, D. L., K. M. Monroe, K. Sotelo-Troha, J. S. Iwig, B. Eckert, M. Hyodo, Y. Hayakawa, and R. E. Vance. 2011. STING is a direct innate immune sensor of cyclic di-GMP. Nature 478: 515-518.
-
(2011)
Nature
, vol.478
, pp. 515-518
-
-
Burdette, D.L.1
Monroe, K.M.2
Iwig, J.S.3
Eckert, B.4
Hyodo, M.5
Hayakawa, Y.6
Vance, R.E.7
-
38
-
-
84900533241
-
C/EBPa regulates macrophage activation and systemic metabolism
-
Lee, B., L. Qiao, M. Lu, H. S. Yoo, W. W. Cheung, R. Mak, J. Schaack, G.-S. Feng, N.-W. Chi, J. M. Olefsky, and J. Shao. 2014. C/EBPa regulates macrophage activation and systemic metabolism. Am. J. Physiol. Endocrinol. Metab. 306: E1144-E1154.
-
(2014)
Am. J. Physiol. Endocrinol. Metab
, vol.306
, pp. E1144-E1154
-
-
Lee, B.1
Qiao, L.2
Lu, M.3
Yoo, H.S.4
Cheung, W.W.5
Mak, R.6
Schaack, J.7
Feng, G.-S.8
Chi, N.-W.9
Olefsky, J.M.10
Shao, J.11
-
39
-
-
67749117934
-
Signal integration by JNK and p38 MAPK pathways in cancer development
-
Wagner, E. F., and A. R. Nebreda. 2009. Signal integration by JNK and p38 MAPK pathways in cancer development. Nat. Rev. Cancer 9: 537-549.
-
(2009)
Nat. Rev. Cancer
, vol.9
, pp. 537-549
-
-
Wagner, E.F.1
Nebreda, A.R.2
-
40
-
-
0036463679
-
JunB can substitute for Jun in mouse development and cell proliferation
-
Passegué, E., W. Jochum, A. Behrens, R. Ricci, and E. F. Wagner. 2002. JunB can substitute for Jun in mouse development and cell proliferation. Nat. Genet. 30: 158-166.
-
(2002)
Nat. Genet
, vol.30
, pp. 158-166
-
-
Passegué, E.1
Jochum, W.2
Behrens, A.3
Ricci, R.4
Wagner, E.F.5
|