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Items: 31

1.

Codon bias confers stability to human mRNAs.

Hia F, Yang SF, Shichino Y, Yoshinaga M, Murakawa Y, Vandenbon A, Fukao A, Fujiwara T, Landthaler M, Natsume T, Adachi S, Iwasaki S, Takeuchi O.

EMBO Rep. 2019 Nov 5;20(11):e48220. doi: 10.15252/embr.201948220. Epub 2019 Sep 3.

PMID:
31482640
2.

Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation.

Vandenbon A, Kumagai Y, Lin M, Suzuki Y, Nakai K.

Genome Biol. 2018 Sep 19;19(1):138. doi: 10.1186/s13059-018-1524-z.

3.

Pulmonary Regnase-1 orchestrates the interplay of epithelium and adaptive immune systems to protect against pneumonia.

Nakatsuka Y, Vandenbon A, Mino T, Yoshinaga M, Uehata T, Cui X, Sato A, Tsujimura T, Suzuki Y, Sato A, Handa T, Chin K, Sawa T, Hirai T, Takeuchi O.

Mucosal Immunol. 2018 Jul;11(4):1203-1218. doi: 10.1038/s41385-018-0024-5. Epub 2018 Apr 25.

PMID:
29695841
4.

Addendum: Guidance of regulatory T cell development by Satb1-dependent super-enhancer establishment.

Kitagawa Y, Ohkura N, Kidani Y, Vandenbon A, Hirota K, Kawakami R, Yasuda K, Motooka D, Nakamura S, Kondo M, Taniuchi I, Kohwi-Shigematsu T, Sakaguchi S.

Nat Immunol. 2017 Oct 18;18(11):1270. doi: 10.1038/ni1117-1270a.

PMID:
29044238
5.

Modeling the cis-regulatory modules of genes expressed in developmental stages of Drosophila melanogaster.

López Y, Vandenbon A, Nose A, Nakai K.

PeerJ. 2017 May 30;5:e3389. doi: 10.7717/peerj.3389. eCollection 2017.

6.

Regnase-1 Maintains Iron Homeostasis via the Degradation of Transferrin Receptor 1 and Prolyl-Hydroxylase-Domain-Containing Protein 3 mRNAs.

Yoshinaga M, Nakatsuka Y, Vandenbon A, Ori D, Uehata T, Tsujimura T, Suzuki Y, Mino T, Takeuchi O.

Cell Rep. 2017 May 23;19(8):1614-1630. doi: 10.1016/j.celrep.2017.05.009.

7.

Erratum: Guidance of regulatory T cell development by Satb1-dependent super-enhancer establishment.

Kitagawa Y, Ohkura N, Kidani Y, Vandenbon A, Hirota K, Kawakami R, Yasuda K, Motooka D, Nakamura S, Kondo M, Taniuchi I, Kohwi-Shigematsu T, Sakaguchi S.

Nat Immunol. 2017 Mar 22;18(4):474. doi: 10.1038/ni0417-474d. No abstract available.

PMID:
28323270
8.

Microarray and gene co-expression analysis reveals that melatonin attenuates immune responses and modulates actin rearrangement in macrophages.

Kadena M, Kumagai Y, Vandenbon A, Matsushima H, Fukamachi H, Maruta N, Kataoka H, Arimoto T, Morisaki H, Funatsu T, Kuwata H.

Biochem Biophys Res Commun. 2017 Apr 1;485(2):414-420. doi: 10.1016/j.bbrc.2017.02.063. Epub 2017 Feb 13.

9.

Mapping circulating serum miRNAs to their immune-related target mRNAs.

Nosirov B, Billaud J, Vandenbon A, Diez D, Wijaya E, Ishii KJ, Teraguchi S, Standley DM.

Adv Appl Bioinform Chem. 2017 Feb 2;10:1-9. doi: 10.2147/AABC.S121598. eCollection 2017.

10.

Microarray analysis of macrophage response to infection with Streptococcus oralis reveals the immunosuppressive effect of hydrogen peroxide.

Matsushima H, Kumagai Y, Vandenbon A, Kataoka H, Kadena M, Fukamachi H, Arimoto T, Morisaki H, Fujiwara N, Okahashi N, Kuwata H.

Biochem Biophys Res Commun. 2017 Apr 1;485(2):461-467. doi: 10.1016/j.bbrc.2017.02.048. Epub 2017 Feb 13.

11.

Genome-wide map of RNA degradation kinetics patterns in dendritic cells after LPS stimulation facilitates identification of primary sequence and secondary structure motifs in mRNAs.

Kumagai Y, Vandenbon A, Teraguchi S, Akira S, Suzuki Y.

BMC Genomics. 2016 Dec 22;17(Suppl 13):1032. doi: 10.1186/s12864-016-3325-7.

12.

Guidance of regulatory T cell development by Satb1-dependent super-enhancer establishment.

Kitagawa Y, Ohkura N, Kidani Y, Vandenbon A, Hirota K, Kawakami R, Yasuda K, Motooka D, Nakamura S, Kondo M, Taniuchi I, Kohwi-Shigematsu T, Sakaguchi S.

Nat Immunol. 2017 Feb;18(2):173-183. doi: 10.1038/ni.3646. Epub 2016 Dec 19. Erratum in: Nat Immunol. 2017 Mar 22;18(4):474. Nat Immunol. 2017 Oct 18;18(11):1270.

13.

A rare subset of skin-tropic regulatory T cells expressing Il10/Gzmb inhibits the cutaneous immune response.

Ikebuchi R, Teraguchi S, Vandenbon A, Honda T, Shand FH, Nakanishi Y, Watanabe T, Tomura M.

Sci Rep. 2016 Oct 19;6:35002. doi: 10.1038/srep35002.

14.

Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system.

Vandenbon A, Dinh VH, Mikami N, Kitagawa Y, Teraguchi S, Ohkura N, Sakaguchi S.

Proc Natl Acad Sci U S A. 2016 Apr 26;113(17):E2393-402. doi: 10.1073/pnas.1604351113. Epub 2016 Apr 13.

15.

Regnase-1 and Roquin Regulate a Common Element in Inflammatory mRNAs by Spatiotemporally Distinct Mechanisms.

Mino T, Murakawa Y, Fukao A, Vandenbon A, Wessels HH, Ori D, Uehata T, Tartey S, Akira S, Suzuki Y, Vinuesa CG, Ohler U, Standley DM, Landthaler M, Fujiwara T, Takeuchi O.

Cell. 2015 May 21;161(5):1058-1073. doi: 10.1016/j.cell.2015.04.029.

16.

Hydroxypropyl-β-cyclodextrin spikes local inflammation that induces Th2 cell and T follicular helper cell responses to the coadministered antigen.

Onishi M, Ozasa K, Kobiyama K, Ohata K, Kitano M, Taniguchi K, Homma T, Kobayashi M, Sato A, Katakai Y, Yasutomi Y, Wijaya E, Igarashi Y, Nakatsu N, Ise W, Inoue T, Yamada H, Vandenbon A, Standley DM, Kurosaki T, Coban C, Aoshi T, Kuroda E, Ishii KJ.

J Immunol. 2015 Mar 15;194(6):2673-82. doi: 10.4049/jimmunol.1402027. Epub 2015 Feb 13.

17.

Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation.

Vandenbon A, Teraguchi S, Takeuchi O, Suzuki Y, Standley DM.

BMC Genomics. 2014;15 Suppl 10:S4. doi: 10.1186/1471-2164-15-S10-S4. Epub 2014 Dec 12.

18.

A set of structural features defines the cis-regulatory modules of antenna-expressed genes in Drosophila melanogaster.

López Y, Vandenbon A, Nakai K.

PLoS One. 2014 Aug 25;9(8):e104342. doi: 10.1371/journal.pone.0104342. eCollection 2014.

19.

Akirin2 is critical for inducing inflammatory genes by bridging IκB-ζ and the SWI/SNF complex.

Tartey S, Matsushita K, Vandenbon A, Ori D, Imamura T, Mino T, Standley DM, Hoffmann JA, Reichhart JM, Akira S, Takeuchi O.

EMBO J. 2014 Oct 16;33(20):2332-48. doi: 10.15252/embj.201488447. Epub 2014 Aug 8.

20.

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation.

Morikawa H, Ohkura N, Vandenbon A, Itoh M, Nagao-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Standley DM, Date H, Sakaguchi S; FANTOM Consortium.

Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5289-94. doi: 10.1073/pnas.1312717110. Epub 2014 Mar 27.

21.

Malt1-induced cleavage of regnase-1 in CD4(+) helper T cells regulates immune activation.

Uehata T, Iwasaki H, Vandenbon A, Matsushita K, Hernandez-Cuellar E, Kuniyoshi K, Satoh T, Mino T, Suzuki Y, Standley DM, Tsujimura T, Rakugi H, Isaka Y, Takeuchi O, Akira S.

Cell. 2013 May 23;153(5):1036-49. doi: 10.1016/j.cell.2013.04.034.

22.

A Parzen window-based approach for the detection of locally enriched transcription factor binding sites.

Vandenbon A, Kumagai Y, Teraguchi S, Amada KM, Akira S, Standley DM.

BMC Bioinformatics. 2013 Jan 21;14:26. doi: 10.1186/1471-2105-14-26.

23.

A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription.

Vandenbon A, Kumagai Y, Akira S, Standley DM.

BMC Genomics. 2012;13 Suppl 7:S11. doi: 10.1186/1471-2164-13-S7-S11. Epub 2012 Dec 13.

24.

The transcription factor Jdp2 controls bone homeostasis and antibacterial immunity by regulating osteoclast and neutrophil differentiation.

Maruyama K, Fukasaka M, Vandenbon A, Saitoh T, Kawasaki T, Kondo T, Yokoyama KK, Kidoya H, Takakura N, Standley D, Takeuchi O, Akira S.

Immunity. 2012 Dec 14;37(6):1024-36. doi: 10.1016/j.immuni.2012.08.022. Epub 2012 Nov 29.

25.

Systems biology approaches to toll-like receptor signaling.

Vandenbon A, Teraguchi S, Akira S, Takeda K, Standley DM.

Wiley Interdiscip Rev Syst Biol Med. 2012 Sep-Oct;4(5):497-507. doi: 10.1002/wsbm.1178. Epub 2012 Jun 19.

26.

Stochastic binary modeling of cells in continuous time as an alternative to biochemical reaction equations.

Teraguchi S, Kumagai Y, Vandenbon A, Akira S, Standley DM.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Dec;84(6 Pt 1):062903. Epub 2011 Dec 15.

PMID:
22304139
27.

IκBζ is essential for natural killer cell activation in response to IL-12 and IL-18.

Miyake T, Satoh T, Kato H, Matsushita K, Kumagai Y, Vandenbon A, Tani T, Muta T, Akira S, Takeuchi O.

Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17680-5. doi: 10.1073/pnas.1012977107. Epub 2010 Sep 27.

28.

The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection.

Satoh T, Takeuchi O, Vandenbon A, Yasuda K, Tanaka Y, Kumagai Y, Miyake T, Matsushita K, Okazaki T, Saitoh T, Honma K, Matsuyama T, Yui K, Tsujimura T, Standley DM, Nakanishi K, Nakai K, Akira S.

Nat Immunol. 2010 Oct;11(10):936-44. doi: 10.1038/ni.1920. Epub 2010 Aug 22.

PMID:
20729857
29.

Modeling tissue-specific structural patterns in human and mouse promoters.

Vandenbon A, Nakai K.

Nucleic Acids Res. 2010 Jan;38(1):17-25. doi: 10.1093/nar/gkp866. Epub 2009 Oct 22.

30.

Markov chain-based promoter structure modeling for tissue-specific expression pattern prediction.

Vandenbon A, Miyamoto Y, Takimoto N, Kusakabe T, Nakai K.

DNA Res. 2008 Feb 29;15(1):3-11. doi: 10.1093/dnares/dsm034. Epub 2008 Feb 7.

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