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2011 Journal Article Histone deacetylases as regulators of inflammation and immunityShakespear, Melanie R., Halili, Maria A., Irvine, Katharine M., Fairlie, David P. and Sweet, Matthew J. (2011). Histone deacetylases as regulators of inflammation and immunity. Trends in Immunology, 32 (7), 335-343. doi: 10.1016/j.it.2011.04.001 |
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2011 Journal Article Update of the FANTOM web resource: From mammalian transcriptional landscape to its dynamic regulationKawaji, H, Severin, J, Lizio, M, Forrest, ARR, van Nimwegen, E, Rehli, M, Schroder, K, Irvine, K, Suzuki, H, Carninci, P, Hayashizaki, Y and Daub, CO (2011). Update of the FANTOM web resource: From mammalian transcriptional landscape to its dynamic regulation. Nucleic Acids Research, 39 (Supp. 1), D856-D860. doi: 10.1093/nar/gkq1112 |
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2011 Journal Article Macrophage activation and differentiation signals regulate Schlafen-4 gene expression: Evidence for Schlafen-4 as a modulator of myelopoiesisVan Zuylen, Wendy J., Garceau, Valerie, Idris, Adi, Schroder, Kate, Irvine, Katharine M., Lattin, Jane E., Ovchinnikov, Dmitry A., Perkins, Andrew C., Cook, Andrew D., Hamilton, John A., Hertzog, Paul J., Stacey, Katryn J., Kellie, Stuart, Hume, David A. and Sweet, Matthew J. (2011). Macrophage activation and differentiation signals regulate Schlafen-4 gene expression: Evidence for Schlafen-4 as a modulator of myelopoiesis. PLoS One, 6 (1) e15723, e15723-1-e15723-13. doi: 10.1371/journal.pone.0015723 |
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2010 Journal Article The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cellsKubosaki, A, Lindgren, G, Tagami, M, Simon, C, Tomaru, Y, Miura, H, Suzuki, T, Arner, E, Forrest, ARR, Irvine, KM, Schroder, K, Hasegawa, Y, Kanamori-Katayama, M, Rehli, M, Hume, DA, Kawai, J, Suzuki, M, Suzuki, H and Hayashizaki, Y (2010). The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells. Molecular Immunology, 47 (14), 2295-2302. doi: 10.1016/j.molimm.2010.05.289 |
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2010 Journal Article Differential effects of selective HDAC inhibitors on macrophage inflammatory responses to the Toll-like receptor 4 agonist LPSHalili, Maria A., Andrews, Melanie R., Labzin, Larisa I., Schroder, Kate, Matthias, Gabriele, Cao, Chun, Lovelace, Erica, Reid, Robert C., Le, Giang T., Hume, David A., Irvine, Katharine M., Matthias, Patrick, Fairlie, David P. and Sweet, Matthew J. (2010). Differential effects of selective HDAC inhibitors on macrophage inflammatory responses to the Toll-like receptor 4 agonist LPS. Journal of Leukocyte Biology, 87 (6), 1103-1114. doi: 10.1189/jlb.0509363 |
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2009 Book Chapter The impact of CAGE data on understanding macrophage transcriptional biologyHume, David A., Schroder, Kate and Irvine, Katharine M. (2009). The impact of CAGE data on understanding macrophage transcriptional biology. Cap-Analysis Gene Expression (CAGE): The Science of Decoding Genes Transcription. (pp. 227-243) Pan Stanford Publishing Pte. Ltd.. doi: 10.4032/9789814241359 |
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2009 Journal Article Selective induction of the Notch ligand Jagged -1 in macrophages by soluble egg antigen from Schistosoma mansoni involves ERK signalingGoh, Felicia, Irvine, Katharine M., Lovelace, Erica, Donnelly, Sheila, Jones, Malcolm K ., Brion, Kristian, Hume, David A., Kotze, Andrew C., Dalton John P., Ingham, Aaron and Sweet, Matthew J. (2009). Selective induction of the Notch ligand Jagged -1 in macrophages by soluble egg antigen from Schistosoma mansoni involves ERK signaling. Immunology, 127 (3), 326-337. doi: 10.1111/j.1365-2567.2008.02979.x |
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2009 Journal Article Corrigendum: Tiny RNAs associated with transcription start sites in animals (vol 41, pg 572, 2009)Taft, Ryan J., Glazov, Evgeny A., Cloonan, Nicole, Simons, Cas, Stephen, Stuart, Faulkner, Geoffrey J., Lassmann, Timo, Forrest, Alistair R. R., Grimmond, Sean M., Schroder, Kate, Irvine, Katharine, Arakawa, Takahiro, Nakamura, Mari, Kubosaki, Atsutaka, Hayashida, Kengo, Kawazu, Chika, Murata, Mitsuyoshi, Nishiyori, Hiromi, Fukuda, Shiro, Kawai, Jun, Daub, Carsten O., Hume, David A., Suzuki, Harukazu, Orlando, Valerio, Carninci, Piero, Hayashizaki, Yoshihide and Mattick, John S. (2009). Corrigendum: Tiny RNAs associated with transcription start sites in animals (vol 41, pg 572, 2009). Nature Genetics, 41 (7), 859-859. doi: 10.1038/ng0709-859a |
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2009 Journal Article Tiny RNAs associated with transcription start sites in animalsTaft, RJ, Glazov, EA, Cloonan, N, Simons, C, Stephen, S, Faulkner, GJ, Lassmann, T, Forrest, ARR, Grimmond, SM, Schroder, K, Irvine, K, Arakawa, T, Nakamura, M, Kubosaki, A, Hayashida, K, Kawazu, C, Murata, M, Nishiyori, H, Fukuda, S, Kawai, J, Daub, CO, Hume, DA, Suzuki, H, Orlando, V, Carninci, P, Hayashizaki, Y and Mattick, JS (2009). Tiny RNAs associated with transcription start sites in animals. Nature Genetics, 41 (5), 572-578. doi: 10.1038/ng.312 |
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2009 Journal Article The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell lineSuzuki, H, Forrest, ARR, van Nimwegen, E, Daub, CO, Balwierz, PJ, Irvine, KM, Lassmann, T, Ravasi, T, Hasegawa, Y, de Hoon, MJL, Katayama, S, Schroder, K, Carninci, P, Tomaru, Y, Kanamori-Katayama, M, Kubosaki, A, Akalin, A, Ando, Y, Arner, E, Asada, M, Asahara, H, Bailey, T, Bajic, VB, Bauer, D, Beckhouse, AG, Bertin, N, Bjorkegren, J, Brombacher, F, Bulger, E ... Riken Omics Science Center (2009). The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics, 41 (5), 553-562. doi: 10.1038/ng.375 |
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2009 Journal Article The regulated retrotransposon transcriptome of mammalian cellsFaulkner, Geoffrey J., Kimura, Yasumasa, Daub, Carsten O., Wani, Shivangi, Plessy, Charles, Irvine, Katharine M., Schroder, Kate, Cloonan, Nicole, Steptoe, Anita L., Lassmann, Timo, Waki, Kazunori, Hornig, Nadine, Arakawa, Takahiro, Takahashi, Hazuki, Kawai, Jun, Forrest, Alistair R. R., Suzuki, Harukazu, Hayashizaki, Yoshihide, Hume, David A., Orlando, Valerio, Grimmond, Sean M. and Carninci, Piero (2009). The regulated retrotransposon transcriptome of mammalian cells. Nature Genetics, 41 (5), 563-571. doi: 10.1038/ng.368 |
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2009 Journal Article Data-driven normalization strategies for high-throughput quantitative RT-PCRMar, Jessica C., Kimura, Yasumasa, Schroder, Kate, Irvine, Katherine M., Hayashizaki, Yoshihide, Suzuki, Harukazu, Hume, David and Quackenbush, John (2009). Data-driven normalization strategies for high-throughput quantitative RT-PCR. BMC Bioinformatics, 10 (1) 110, 110.1-110.10. doi: 10.1186/1471-2105-10-110 |
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2009 Journal Article The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulationKawaji, H, Severin, J, Lizio, M, Waterhouse, A, Katayama, S, Irvine, K. M., Hume, D. A., Forrest, A. R. R., Suzuki, H, Carninci, P, Hayashizaki, Y and Daub, C. O. (2009). The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Genome Biology, 10 (4) R40. doi: 10.1186/gb-2009-10-4-r40 |
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2009 Journal Article Colony-stimulating factor-1 (CSF-1) delivers a proatherogenic signal to human macrophagesIrvine, Katharine M., Andrews, Melanie R., Fernandez-Rojo, Manuel A., Schroder, Kate, Burns, Christopher J., Su, Stephen, Wilks, Andrew F., Parton, Robert G., Hume, David A. and Sweet, Matthew J. (2009). Colony-stimulating factor-1 (CSF-1) delivers a proatherogenic signal to human macrophages. Journal of Leukocyte Biology, 85 (2), 278-288. doi: 10.1189/jlb.0808497 |
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2009 Book Chapter The impact of CAGE data on the understanding of macrophage transcriptional biologyHume, D. A., Irvine, K. M. and Schroder, K. (2009). The impact of CAGE data on the understanding of macrophage transcriptional biology. Cap- Analysis Gene Expression (Cage): The Science of Decoding Gene Transcription. (pp. 227-244) edited by Piero Carninci. Singapore: Pan Stanford Publishing. |
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2008 Conference Publication The identification of novel CSF-1 target genes in human macrophagesIrvine, Katharine M., Andrews, Melanie R., Fernandez, Manuel A., Parton, Robert G., Burns, Christopher J., Su, Stephen, Wilks, Andrew F., Hume, David A. and Sweet, M. J. (2008). The identification of novel CSF-1 target genes in human macrophages. 7th Joint Conference of the International-Cytokine-Society/International-Society-for-Interferon-and-Cytoklin-Research, Montreal Canada, Oct 12-16, 2008. LONDON: ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD. doi: 10.1016/j.cyto.2008.07.078 |
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2008 Journal Article Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencerMaeda, Norihiro, Nishiyori, Hiromi , Nakamura, Mari , Kawazu, Chika, Murata, Mitsuyoshi , Sano, Hiromi, Hayashida, Kengo, Fukuda, Shiro, Tagami, Michihira, Hasegawa, Akira, Murakami, Kayoko, Schroder, Kate, Irvine, Katharine, Hume, David A., Hayashizaki, Yoshihide, Carninci, Piero and Suzuki, Harukazu (2008). Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer. BioTechniques, 45 (1), 95-97. doi: 10.2144/000112814 |
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2007 Journal Article Differential effects of CpG DNA on IFN-beta induction and STAT1 activation in murine macrophages versus dendritic cells: Alternatively activated STAT1 negatively regulates TLR signaling in macrophagesSchroder, K., Spille, M., Pilz, A., Lattin, J., Bode, K. A., Irvine, K. M., Burrows, A. D., Ravasi, T., Weighardt, H., Stacey, K. J., Decker, T., Hume, D. A., Dalpke, A. H. and Sweet, M. J. (2007). Differential effects of CpG DNA on IFN-beta induction and STAT1 activation in murine macrophages versus dendritic cells: Alternatively activated STAT1 negatively regulates TLR signaling in macrophages. Journal of Immunology, 179 (6), 3495-3503. doi: 10.4049/jimmunol.179.6.3495 |
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2007 Journal Article PU.1 and ICSBP control constitutive and IFN-gamma-regulated Tlr9 gene expression in mouse macrophagesSchroder, Kate, Lichtinger, Monika, Irvine, Katharine M., Brion, Kristian, Trieu, Angela, Ross, Ian L., Ravasi, Timothy, Stacey, Katryn J., Rehli, Michael, Hume, David A. and Sweet, Matthew J. (2007). PU.1 and ICSBP control constitutive and IFN-gamma-regulated Tlr9 gene expression in mouse macrophages. Journal of Leukocyte Biology, 81 (6), 1577-1590. doi: 10.1189/jlb.0107036 |
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2007 Journal Article Gpnmb is induced in macrophages by IFN-gamma and lipopolysaccharide and acts as a feedback regulator of proinflammatory responsesRipoll, Vera M., Irvine, Katharine M., Ravasi, Timothy, Sweet, Matthew J. and Hume, David A. (2007). Gpnmb is induced in macrophages by IFN-gamma and lipopolysaccharide and acts as a feedback regulator of proinflammatory responses. Journal of Immunology, 178 (10), 6557-6566. doi: 10.4049/jimmunol.178.10.6557 |
