Publications

Last update: 2026 March 19  ·  *: corresponding author  ·  †: equal contribution

• 50.
  Yasuda K., Aoki J., Tanaka K., Shichinohe S., Ono C., Vandenbon A., Ohara D., Muramoto Y., Li S., Motooka D., Watanabe H., Hirota K., Kondoh G., Noda T., Standley D.M., Ikehara Y., Okada S., Watanabe T., Matsuura Y. and Takeuchi O., Regnase-1-mediated regulation of neutrophils modulates SARS-CoV-2 pneumonia, PLoS Pathogens, 22(2):e1013969, 2026. link to article
• 49.
  Honcharuk V., Zainab A., Horimoto Y., Takemoto K., Diez D., Kawaoka S. and Vandenbon A.*, DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of tissues and tissue microenvironments, Nucleic Acids Res., 54(D1): D1017–D1030, 2026. link to article

• 48.
  Prabhune N., Du Y., Zainab A., Ebihara S., Takeoka S., Kawaoka S. and Vandenbon A.*, Mining Spatial Transcriptomics Datasets using DeepSpaceDB, Journal of Visualized Experiments, 2025(223) e68892, 2025. link to article
• 47.
  Vandenbon A.* and Takemoto K., DeepSpaceDB―空間トランスクリプトーム公開データの直感的かつ高速な探索, 実験医学増刊, 43(20), 2025. link to article
• 46.
  Vandenbon A.* and Takemoto K., DeepSpaceDB：空間トランスクリプトミクスデータの探索的解析, 実験医学, 43(6), 2025. link to article

• 45.
  Maeshima Y., Kataoka T.R., Vandenbon A., Hirata M., Takeuchi Y., Suzuki Y., Fukui Y., Kawashima M., Takada M., Ibi Y., Haga H., Morita S., Toi M., Kawaoka S. and Kawaguchi K., Intra-patient spatial comparison of non-metastatic and metastatic lymph nodes reveals a reduction in CD169+ macrophages within metastatic breast cancers, EBioMedicine, 107:105271, 2024. link to article
• 44.
  Loza M., Vandenbon A. and Nakai K., Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression, Nucleic Acids Research, gkad1164, 2024. link to article
• 43.
  Uehata T., Yamada S., Ori D., Vandenbon A., Giladi A., Jelinski A., Murakawa Y., Watanabe H., Takeuchi K., Toratani K., Mino T., Kiryu H., Standley D.M., Tsujimura T., Ikawa T., Kondoh G., Landthaler M., Kawamoto H., Rodewald H.R., Amit I., Yamamoto R., Miyazaki M. and Takeuchi O., Regulation of lymphoid-myeloid lineage bias through regnase-1/3-mediated control of Nfkbiz, Blood, 143(3):243-257, 2024. link to article

• 42.
  Abe S., Asahi T., Hara T., Cui G., Shimba A., Tani-Ichi S., Yamada K., Miyazaki K., Miyachi H., Kitano S., Nakamura N., Kikuta J., Vandenbon A., Miyazaki M., Yamada R., Ohteki T., Ishii M., Sexl V., Nagasawa T. and Ikuta K., Hematopoietic cell-derived IL-15 supports NK cell development in scattered and clustered localization within the bone marrow, Cell Reports, 42(9):113127, 2023. link to article
• 41.
  Vandenbon A.*† and Diez D.*, A universal differential expression prediction tool for single-cell and spatial genomics data, Scientific Reports, 13(1), 2023. link to article
• 40.
  Vandenbon A.*†, Mizuno R.*, Konishi R.*, Onishi M.*, Musuda K., Kobayashi Y., Kawamoto H., Suzuki A., He C., Nakamura Y., Kawaguchi K., Toi M., Shimizu M., Tanaka Y., Suzuki Y.† and Kawaoka S.†, Murine breast cancers disorganize the liver transcriptome in a zonated manner, Communications Biology, 6(1):97, 2023. link to article
• 39.
  Nakai K. and Vandenbon A., Chapter: Higher-order chromatin structure and gene regulation, in Epigenetics in Organ Specific Disorders, Volume 34. Editors: Boosani C. and Goswami R., Elsevier, 2023.

• 38.
  Yoshinaga M., Han K., Morgens D.W., Horii T., Kobayashi R., Tsuruyama T., Hia F., Yasukura S., Kajiya A., Cai T., Cruz P.H.C., Vandenbon A., Suzuki Y., Kawahara Y., Hatada I., Bassik M.C., Takeuchi O., The N6-methyladenosine methyltransferase METTL16 enables erythropoiesis through safeguarding genome integrity, Nature Communications, 13(1):6435, 2022. link to article
• 37.
  Yaku A., Inagaki T., Asano R., Okazawa M., Mori H., Sato A., Hia F., Masaki T., Manabe Y., Ishibashi T., Vandenbon A., Nakatsuka Y., Akaki K., Yoshinaga M., Uehata T., Mino T., Morita S., Ishibashi-Ueda H., Morinobu A., Tsujimura T., Ogo T., Nakaoka Y. and Takeuchi O., Regnase-1 Prevents Pulmonary Arterial Hypertension via mRNA Degradation of IL-6 and PDGF in Alveolar Macrophages, Circulation, 146(13), 2022. link to article
• 36.
  Ohgushi M., Taniyama N., Vandenbon A. and Eiraku M., Delamination of trophoblast-like syncytia from the amniotic ectodermal analogue in human primed embryonic stem cell-based differentiation model, Cell Reports, 39(12):110973, 2022. link to article
• 35.
  Tse K.M., Vandenbon A., Cui X., Mino T., Uehata T., Yasuda K., Sato A., Tsujimura T., Hia F., Yoshinaga M., Kinoshita M., Okuno T. and Takeuchi O., Manipulation of Regnase-1 expression with stem-loop-targeting antisense oligonucleotides alleviates inflammatory diseases, Science Translational Medicine, Vol 14, Issue 644, 2022. link to article
• 34.
  Chong Y.K., Tartey S., Yoshikawa Y., Imami K., Li S., Yoshinaga M., Hirabayashi A., Liu G., Vandenbon A., Hia F., Uehata T., Mino T., Suzuki Y., Noda T., Ferrandon D., Standley D.M., Ishihama Y. and Takeuchi O., The Cyclin J-CDK complex regulates innate immune responses by controlling macrophage metabolism, Science Signaling, Vol 15, Issue 729, 2022. link to article
• 33.
  Vandenbon A.*, Evaluation of critical data processing steps for reliable prediction of gene co-expression from large collections of RNA-seq data, PLoS ONE, 17(1):e0263344, 2022. link to article

• 32.
  Nakatsuka Y., Yaku A., Handa T., Vandenbon A., Hikichi Y., Motomura Y., Sato A., Yoshinaga M., Tanizawa K., Watanabe K., Hirai T., Chin K., Suzuki Y., Uehata T., Mino T., Tsujimura T., Moro K., Takeuchi O., Profibrotic function of pulmonary group 2 innate lymphoid cells is controlled by Regnase-1, Eur Respir J, 57:2000018, 2021. link to article

• 31.
  Vandenbon A.* and Diez D., A clustering-independent method for finding differentially expressed genes in single-cell transcriptome data, Nature Communications, 11(1):4318, 2020. link to article · GitHub · CRAN
• 30.
  Maruyama K., Kidoya H., Takemura N., Sugisawa E., Takeuchi O., Kondo T., Eid M.M.A., Tanaka H., Martino M.M., Takakura N., Takayama Y., Akira S., Vandenbon A., Kumagai Y., Zinc Finger Protein St18 Protects against Septic Death by Inhibiting VEGF-A from Macrophages, Cell Reports, 32:107906, 2020. link to article

• 29.
  Hia F., Yang S.F., Shichino Y., Yoshinaga M., Murakawa Y., Vandenbon A., Fukao A., Fujiwara T., Landthaler M., Natsume T., Adachi S., Iwasaki S., Takeuchi O., Codon bias confers stability to human mRNAs, EMBO Rep, e48220, 2019. link to article

• 28.
  Vandenbon A.*†, Kumagai Y.†, Lin M., Suzuki Y., Nakai K.*, Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation, Genome Biology, 19:138, 2018. link to article
• 27.
  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., and Takeuchi O., Pulmonary Regnase-1 orchestrates the interplay of epithelium and adaptive immune systems to protect against pneumonia, Mucosal Immunol, 11(4):1203-1218, 2018. link to article

• 26.
  López Y., Vandenbon A., Nose A., and Nakai K., Modeling the cis-regulatory modules of genes expressed in developmental stages of Drosophila melanogaster, PeerJ, 5:e3389, 2017.
• 25.
  Yoshinaga M., Nakatsuka Y., Vandenbon A., Ori D., Uehata T., Tsujimura T., Suzuki Y., Mino T., and Takeuchi O., Regnase-1 maintains iron homeostasis via the degradation of transferrin receptor 1 and prolyl hydroxylase domain-containing protein 3 mRNAs, Cell Reports, 19:1614-1630, 2017.
• 24.
  Matsushima H., Kumagai Y., Vandenbon A., Kataoka H., Kadena M., Fukamachi H., Arimoto T., Morisaki H., Fujiwara N., Okahashi N., and Kuwata H., Microarray analysis of macrophage response to infection with Streptococcus oralis reveals the immunosuppressive effect of hydrogen peroxide, Biochem Biophys Res Commun, 485(2):461-467, 2017.
• 23.
  Kadena M., Kumagai Y., Vandenbon A., Matsushima H., Fukamachi H., Maruta N., Kataoka H., Arimoto T., Morisaki H., Funatsu T., and Kuwata H., Microarray and gene co-expression analysis reveals that melatonin attenuates immune responses and modulates actin rearrangement in macrophages, Biochem Biophys Res Commun, 485(2):414-420, 2017.
• 22.
  Nosirov B., Billaud J., Vandenbon A., Diez D., Wijaya E., Ishii K., Teraguchi S., and Standley D.M., Mapping circulating serum miRNAs to their immune-related target mRNAs, Adv Appl Bioinform Chem, 10:1-9, 2017.
• 21.
  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., and Sakaguchi S., Guidance of regulatory T cell development by Satb1-dependent super-enhancer establishment, Nat Immunol, 18(2):173-183, 2017.

• 20.
  Kumagai Y., Vandenbon A., Teraguchi S., Akira S., and Suzuki Y., 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, BMC Genomics, 17(Suppl 13):1032, 2016.
• 19.
  Ikebuchi R., Teraguchi S., Vandenbon A., Honda T., Shand F.H.W., Nakanishi Y., Watanabe T., and Tomura M., A rare subset of skin-tropic regulatory T cells expressing Il10/Gzmb inhibits the cutaneous immune response, Sci Rep, 6:35002, 2016.
• 18.
  Vandenbon A.*, Dinh V.H., Mikami N., Kitagawa Y., Teraguchi S., Ohkura N., and Sakaguchi S.*, Immuno-Navigator, a batch-corrected co-expression database, reveals cell type-specific gene networks in the immune system, Proc Natl Acad Sci USA, 113(17):E2393-402, 2016. link to article

• 17.
  Mino T., Murakawa Y., Fukao A., Vandenbon A., Wessels H.H., Ori D., Uehata T., Tartey S., Akira S., Suzuki Y., Vinuesa C.G., Ohler U., Standley D.M., Landthaler M., Fujiwara T., and Takeuchi O., Regnase-1 and Roquin regulate a common element in inflammatory mRNAs by spatiotemporally distinct mechanisms, Cell, 161(5):1058-73, 2015.
• 16.
  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 D.M., Kurosaki T., Coban C., Aoshi T., Kuroda E. and Ishii K., Hydroxypropyl-β-cyclodextrin spikes local inflammation that induce Th2 and Tfh responses to the coadministered antigen, J Immunol, 194(6):2673-82, 2015.

• 15.
  Vandenbon A.*, Teraguchi S., Suzuki Y., Takeuchi O. and Standley D.M.*, Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation, BMC Genomics, 15 Suppl 10:S4, 2014. link to article
• 14.
  López Y., Vandenbon A. and Nakai K., A Set of Structural Features Defines the cis-Regulatory Modules of Antenna-Expressed Genes in Drosophila melanogaster, PLoS ONE, 9(8):e104342, 2014.
• 13.
  Tartey S., Matsushita K., Vandenbon A., Ori D., Imamura T., Mino T., Standley D.M., Hoffmann J.A., Reichhart J.M., Akira S., Takeuchi O., Akirin2 is critical for inducing inflammatory genes by bridging IκB-ζ and the SWI/SNF complex, EMBO J, 33(20):2332-48, 2014.
• 12.
  Morikawa H., Ohkura N., Vandenbon A., Itoh M., Nagao-Sato S., Kawaji H., Lassmann T., Carninci P., Hayashizaki Y., Forrest A.R.R., Standley D.M., Date H., Sakaguchi S., and the FANTOM Consortium, Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation, Proc Natl Acad Sci USA, 111(14):5289-94, 2014.

• 11.
  Uehata T., Iwasaki H., Vandenbon A., Matsushita K., Hernandez-Cuellar E., Kuniyoshi K., Satoh T., Mino T., Suzuki Y., Standley D.M., Tsujimura T., Rakugi H., Isaka Y., Takeuchi O., Akira S., Malt1-induced cleavage of Regnase-1 in CD4+ helper T cells regulates immune activation, Cell, 153(5):1036-49, 2013.
• 10.
  Vandenbon A.*, Kumagai Y., Teraguchi S., Amada K.M., Akira S., Standley D.M.*, A Parzen window-based approach for the detection of locally enriched transcription factor binding sites, BMC Bioinformatics, 14:26, 2013. link to article

• 9.
  Maruyama K., Fukasaka M., Vandenbon A., Saitoh T., Kawasaki T., Kondo T., Yokoyama K.K., Kidoya H., Takakura N., Standley D., Takeuchi O., Akira S., The transcription factor Jdp2 controls bone homeostasis and antibacterial immunity by regulating osteoclast and neutrophil differentiation, Immunity, 37(6):1024-36, 2012.
• 8.
  Vandenbon A.*†, Kumagai Y.†, Akira S., Standley D.M.*, A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription, BMC Genomics, 13 Suppl 7:S11, 2012. link to article
• 7.
  Vandenbon A.†, Teraguchi S.†, Akira S., Takeda K., Standley D.M., Systems biology approaches to toll-like receptor signaling, Wiley Interdiscip Rev Syst Biol Med, 4(5):497-507, 2012.

• 6.
  Teraguchi S., Kumagai Y., Vandenbon A., Akira S., Standley D.M., Stochastic binary modeling of cells in continuous time as an alternative to biochemical reaction equations, Phys Rev E, 84(6 Pt 1):062903, 2011.

• 5.
  Miyake T., Satoh T., Kato H., Matsushita K., Kumagai Y., Vandenbon A., Tani T., Muta T., Akira S., Takeuchi O., IκBζ is essential for natural killer cell activation in response to IL-12 and IL-18, Proc Natl Acad Sci USA, 107(41):17680-5, 2010.
• 4.
  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 D.M., Nakanishi K., Nakai K., Akira S., The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection, Nat Immunol, 11(10):936-44, 2010.
• 3.
  Vandenbon A. and Nakai K., Modeling tissue-specific structural patterns in human and mouse promoters, Nucleic Acids Res., 38(1):17-25, 2010. link to article

• 2.
  Vandenbon A. and Nakai K., Using simple rules on presence and positioning of motifs for promoter structure modeling and tissue specific expression prediction, Genome Inform, 21:188-99, 2008.
• 1.
  Vandenbon A., Miyamoto Y., Takimoto N., Kusakabe T., Nakai K., Markov chain-based promoter structure modeling for tissue-specific expression pattern prediction, DNA Res, 15(1):3-11, 2008.