Basic Information

Affiliated programs (koza)

• Graduate School of Biostudies, 高次生命科学専攻 生体動態制御学, 准教授

Faculty

• 国際高等教育院

Academic Degree

• Ｍ．Ｓ．(Katholieke HogeschoolBrugge-Oostende)
• Ｍ．Ｓ．(Ghent University)
• 博士（生命科学）(東京大学)

Research History

• From Aug. 2017, To Mar. 2022

  Kyoto University, Lecturer
• From Aug. 2012, To Jul. 2017

  The University of Osaka, Specially Appointed Assistant Professor
• From Oct. 2009, To Jul. 2012

  Osaka University, Specially Appointed Researcher
• From Apr. 2022, To Present

  Kyoto University, Associate Professor

ID,URL

• ORCID ID

  0000-0003-2180-5732

• J-Global ID

  201601007061521273

• External link

  https://genomics.virus.kyoto-u.ac.jp/

Website(s) (URL(s))

• https://genomics.virus.kyoto-u.ac.jp/alexisvdb/

researchmap URL

• https://researchmap.jp/alexisvdb

Research

Research Topics, Overview of the research

• Research Topics

  Bioinformatics analysis of single-cell and spatial genomics data. Prediction of regulatory mechanisms of gene expression at the epigenetic, transcriptional, and post-transcriptional level.

• Overview of the research

  Biological data is often high-dimensional, and therefore difficult to process, visualize, and analyze. The goal of my research is the discovery of new insights in biological data using bioinformatics approaches. Recent projects include the analysis of single-cell and spatial transcriptomics data, and the development of bioinformatics methods for conducting such analyses.

Research Interests

• spatial transcriptomics
• single-cell transcriptomics
• bioinformatics

Research Areas

• Life sciences, Genomics
• Life sciences, Systems genomics

Papers

• Intra-patient spatial comparison of non-metastatic and metastatic lymph nodes reveals the reduction of CD169+ macrophages by metastatic breast cancers.

  Yurina Maeshima; Tatsuki R Kataoka; Alexis Vandenbon; Masahiro Hirata; Yasuhide Takeuchi; Yutaka Suzuki; Yukiko Fukui; Masahiro Kawashima; Masahiro Takada; Yumiko Ibi; Hironori Haga; Satoshi Morita; Masakazu Toi; Shinpei Kawaoka; Kosuke Kawaguchi

  EBioMedicine, Sep. 2024

  Access this paper :

  
• Selective elimination of CD169⁺ macrophages in lymph nodes invaded by breast cancers

  Alexis Vandenbon

  BioRxiv, 2023

  
• Guidance for RNA-seq co-expression estimates: the importance of data normalization, batch effects, and correlation measures

  Alexis Vandenbon

  BioRxiv, 2021

  
• Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression.

  Martin Loza; Alexis Vandenbon; Kenta Nakai

  Nucleic acids research, 09 Feb. 2024

  
• Hematopoietic cell-derived IL-15 supports NK cell development in scattered and clustered localization within the bone marrow.

  Shinya Abe; Takuma Asahi; Takahiro Hara; Guangwei Cui; Akihiro Shimba; Shizue Tani-Ichi; Kohei Yamada; Kazuko Miyazaki; Hitoshi Miyachi; Satsuki Kitano; Naotoshi Nakamura; Junichi Kikuta; Alexis Vandenbon; Masaki Miyazaki; Ryo Yamada; Toshiaki Ohteki; Masaru Ishii; Veronika Sexl; Takashi Nagasawa; Koichi Ikuta

  Cell reports, 26 Sep. 2023

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• A universal tool for predicting differentially active features in single-cell and spatial genomics data.

  Alexis Vandenbon; Diego Diez

  Scientific reports, 22 Jul. 2023, Lead author, Corresponding author

  Access this paper :

  
• Regulation of lymphoid-myeloid lineage bias through Regnase-1/3-mediated control of Nfkbiz.

  Takuya Uehata; Shinnosuke Yamada; Daisuke Ori; Alexis Vandenbon; Amir Giladi; Adam Jelinski; Yasuhiro Murakawa; Hitomi Watanabe; Kazuhiro Takeuchi; Kazunori Toratani; Takashi Mino; Hisanori Kiryu; Daron M Standley; Tohru Tsujimura; Tomokatsu Ikawa; Gen Kondoh; Markus Landthaler; Hiroshi Kawamoto; Hans-Reimer Rodewald; Ido Amit; Ryo Yamamoto; Masaki Miyazaki; Osamu Takeuchi

  Blood, 03 Nov. 2023

  
• Murine breast cancers disorganize the liver transcriptome in a zonated manner.

  Alexis Vandenbon; Rin Mizuno; Riyo Konishi; Masaya Onishi; Kyoko Masuda; Yuka Kobayashi; Hiroshi Kawamoto; Ayako Suzuki; Chenfeng He; Yuki Nakamura; Kosuke Kawaguchi; Masakazu Toi; Masahito Shimizu; Yasuhito Tanaka; Yutaka Suzuki; Shinpei Kawaoka

  Communications biology, 24 Jan. 2023, Peer-reviewed, Lead author, Corresponding author

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• The N6-methyladenosine methyltransferase METTL16 enables erythropoiesis through safeguarding genome integrity.

  Masanori Yoshinaga; Kyuho Han; David W Morgens; Takuro Horii; Ryosuke Kobayashi; Tatsuaki Tsuruyama; Fabian Hia; Shota Yasukura; Asako Kajiya; Ting Cai; Pedro H C Cruz; Alexis Vandenbon; Yutaka Suzuki; Yukio Kawahara; Izuho Hatada; Michael C Bassik; Osamu Takeuchi

  Nature communications, 28 Oct. 2022

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• Regnase-1 Prevents Pulmonary Arterial Hypertension Through mRNA Degradation of Interleukin-6 and Platelet-Derived Growth Factor in Alveolar Macrophages.

  Ai Yaku; Tadakatsu Inagaki; Ryotaro Asano; Makoto Okazawa; Hiroyoshi Mori; Ayuko Sato; Fabian Hia; Takeshi Masaki; Yusuke Manabe; Tomohiko Ishibashi; Alexis Vandenbon; Yoshinari Nakatsuka; Kotaro Akaki; Masanori Yoshinaga; Takuya Uehata; Takashi Mino; Satoshi Morita; Hatsue Ishibashi-Ueda; Akio Morinobu; Tohru Tsujimura; Takeshi Ogo; Yoshikazu Nakaoka; Osamu Takeuchi

  Circulation, 23 Aug. 2022

  
• Delamination of trophoblast-like syncytia from the amniotic ectodermal analogue in human primed embryonic stem cell-based differentiation model.

  Masatoshi Ohgushi; Nobuko Taniyama; Alexis Vandenbon; Mototsugu Eiraku

  Cell reports, 21 Jun. 2022

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• Evaluation of critical data processing steps for reliable prediction of gene co-expression from large collections of RNA-seq data.

  Alexis Vandenbon

  PloS one, 2022, Lead author, Last author, Corresponding author

  
• Enhancement of Regnase-1 expression with stem loop-targeting antisense oligonucleotides alleviates inflammatory diseases.

  Ka Man Tse; Alexis Vandenbon; Xiaotong Cui; Takashi Mino; Takuya Uehata; Keiko Yasuda; Ayuko Sato; Tohru Tsujimura; Fabian Hia; Masanori Yoshinaga; Makoto Kinoshita; Tatsusada Okuno; Osamu Takeuchi

  Science translational medicine, 11 May 2022

  
• Cyclin J-CDK complexes limit innate immune responses by reducing proinflammatory changes in macrophage metabolism.

  Yee Kien Chong; Sarang Tartey; Yuki Yoshikawa; Koshi Imami; Songling Li; Masanori Yoshinaga; Ai Hirabayashi; Guohao Liu; Alexis Vandenbon; Fabian Hia; Takuya Uehata; Takashi Mino; Yutaka Suzuki; Takeshi Noda; Dominique Ferrandon; Daron M Standley; Yasushi Ishihama; Osamu Takeuchi

  Science signaling, 12 Apr. 2022

  
• Profibrotic function of pulmonary group 2 innate lymphoid cells is controlled by regnase-1.

  Yoshinari Nakatsuka; Ai Yaku; Tomohiro Handa; Alexis Vandenbon; Yuki Hikichi; Yasutaka Motomura; Ayuko Sato; Masanori Yoshinaga; Kiminobu Tanizawa; Kizuku Watanabe; Toyohiro Hirai; Kazuo Chin; Yutaka Suzuki; Takuya Uehata; Takashi Mino; Tohru Tsujimura; Kazuyo Moro; Osamu Takeuchi

  The European respiratory journal, Mar. 2021, Peer-reviewed

  
• A clustering-independent method for finding differentially expressed genes in single-cell transcriptome data.

  Alexis Vandenbon; Diego Diez

  Nature communications, 28 Aug. 2020, Peer-reviewed, Lead author, Corresponding author

  
• Zinc Finger Protein St18 Protects against Septic Death by Inhibiting VEGF-A from Macrophages.

  Kenta Maruyama; Hiroyasu Kidoya; Naoki Takemura; Erika Sugisawa; Osamu Takeuchi; Takeshi Kondo; Mohammed Mansour Abbas Eid; Hiroki Tanaka; Mikaël M Martino; Nobuyuki Takakura; Yasunori Takayama; Shizuo Akira; Alexis Vandenbon; Yutaro Kumagai

  Cell reports, 14 Jul. 2020, Peer-reviewed

  
• Codon bias confers stability to human mRNAs.

  Fabian Hia; Sheng Fan Yang; Yuichi Shichino; Masanori Yoshinaga; Yasuhiro Murakawa; Alexis Vandenbon; Akira Fukao; Toshinobu Fujiwara; Markus Landthaler; Tohru Natsume; Shungo Adachi; Shintaro Iwasaki; Osamu Takeuchi

  EMBO reports, 05 Nov. 2019, Peer-reviewed

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

  Alexis Vandenbon; Yutaro Kumagai; Mengjie Lin; Yutaka Suzuki; Kenta Nakai

  Genome biology, 19 Sep. 2018, Peer-reviewed, Lead author, Corresponding author

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

  Yoshinari Nakatsuka; Alexis Vandenbon; Takashi Mino; Masanori Yoshinaga; Takuya Uehata; Xiaotong Cui; Ayuko Sato; Tohru Tsujimura; Yutaka Suzuki; Atsuyasu Sato; Tomohiro Handa; Kazuo Chin; Teiji Sawa; Toyohiro Hirai; Osamu Takeuchi

  Mucosal immunology, Jul. 2018, Peer-reviewed

  
• Guidance of regulatory T cell development by Satb1-dependent super-enhancer establishment (vol 18, pg 173, 2017)

  Yohko Kitagawa; Naganari Ohkura; Yujiro Kidani; Alexis Vandenbon; Keiji Hirota; Ryoji Kawakami; Keiko Yasuda; Daisuke Motooka; Shota Nakamura; Motonari Kondo; Ichiro Taniuchi; Terumi Kohwi-Shigematsu; Shimon Sakaguchi

  NATURE IMMUNOLOGY, Nov. 2017, Peer-reviewed

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

  Masanori Yoshinaga; Yoshinari Nakatsuka; Alexis Vandenbon; Daisuke Ori; Takuya Uehata; Tohru Tsujimura; Yutaka Suzuki; Takashi Mino; Osamu Takeuchi

  CELL REPORTS, May 2017, Peer-reviewed

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

  Yosvany Lopez; Alexis Vandenbon; Akinao Nose; Kenta Nakai

  PEERJ, May 2017, Peer-reviewed

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

  Hitomi Matsushima; Yutaro Kumagai; Alexis Vandenbon; Hideo Kataoka; Miki Kadena; Haruka Fukamachi; Takafumi Arimoto; Hirobumi Morisaki; Nagatoshi Fujiwara; Nobuo Okahashi; Hirotaka Kuwata

  BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, Apr. 2017, Peer-reviewed

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

  Miki Kadena; Yutaro Kumagai; Alexis Vandenbon; Hitomi Matsushima; Haruka Fukamachi; Noboru Maruta; Hideo Kataoka; Takafumi Arimoto; Hirobumi Morisaki; Takahiro Funatsu; Hirotaka Kuwata

  BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, Apr. 2017, Peer-reviewed

  
• 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

  Nature immunology, Mar. 2017, Peer-reviewed

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

  Yohko Kitagawa; Naganari Ohkura; Yujiro Kidani; Alexis Vandenbon; Keiji Hirota; Ryoji Kawakami; Keiko Yasuda; Daisuke Motooka; Shota Nakamura; Motonari Kondo; Ichiro Taniuchi; Terumi Kohwi-Shigematsu; Shimon Sakaguchi

  NATURE IMMUNOLOGY, Feb. 2017, Peer-reviewed

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

  Bakhtiyor Nosirov; Joël Billaud; Alexis Vandenbon; Diego Diez; Edward Wijaya; Ken J Ishii; Shunsuke Teraguchi; Daron M Standley

  Advances and applications in bioinformatics and chemistry : AABC, 2017, Peer-reviewed

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• 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

  Yutaro Kumagai; Alexis Vandenbon; Shunsuke Teraguchi; Shizuo Akira; Yutaka Suzuki

  BMC GENOMICS, Dec. 2016, Peer-reviewed

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

  Ryoyo Ikebuchi; Shunsuke Teraguchi; Alexis Vandenbon; Tetsuya Honda; Francis H. W. Shand; Yasutaka Nakanishi; Takeshi Watanabe; Michio Tomura

  SCIENTIFIC REPORTS, Oct. 2016, Peer-reviewed

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

  Alexis Vandenbon; Viet H. Dinh; Norihisa Mikami; Yohko Kitagawa; Shunsuke Teraguchi; Naganari Ohkura; Shimon Sakaguchi

  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Apr. 2016, Peer-reviewed, Lead author, Corresponding author

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

  Takashi Mino; Yasuhiro Murakawa; Akira Fukao; Alexis Vandenbon; Hans-Hermann Wessels; Daisuke Ori; Takuya Uehata; Sarang Tartey; Shizuo Akira; Yutaka Suzuki; Carola G. Vinuesa; Uwe Ohler; Daron M. Standley; Markus Landthaler; Toshinobu Fujiwara; Osamu Takeuchi

  CELL, May 2015, Peer-reviewed

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• Hydroxypropyl-beta-Cyclodextrin Spikes Local Inflammation That Induces Th2 Cell and T Follicular Helper Cell Responses to the Coadministered Antigen

  Motoyasu Onishi; Koji Ozasa; Kouji Kobiyama; Keiichi Ohata; Mitsutaka Kitano; Keiichi Taniguchi; Tomoyuki Homma; Masanori Kobayashi; Akihiko Sato; Yuko Katakai; Yasuhiro Yasutomi; Edward Wijaya; Yoshinobu Igarashi; Noriyuki Nakatsu; Wataru Ise; Takeshi Inoue; Hiroshi Yamada; Alexis Vandenbon; Daron M. Standley; Tomohiro Kurosaki; Cevayir Coban; Taiki Aoshi; Etsushi Kuroda; Ken J. Ishii

  JOURNAL OF IMMUNOLOGY, Mar. 2015, Peer-reviewed

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

  Alexis Vandenbon; Shunsuke Teraguchi; Osamu Takeuchi; Yutaka Suzuki; Daron M. Standley

  BMC GENOMICS, Dec. 2014, Peer-reviewed, Lead author, Corresponding author

  
• Akirin2 is critical for inducing inflammatory genes by bridging I kappa B-zeta and the SWI/SNF complex

  Sarang Tartey; Kazufumi Matsushita; Alexis Vandenbon; Daisuke Ori; Tomoko Imamura; Takashi Mino; Daron M. Standley; Jules A. Hoffmann; Jean-Marc Reichhart; Shizuo Akira; Osamu Takeuchi

  EMBO JOURNAL, Oct. 2014, Peer-reviewed

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• A Set of Structural Features Defines the Cis-Regulatory Modules of Antenna-Expressed Genes in Drosophila melanogaster

  Yosvany Lopez; Alexis Vandenbon; Kenta Nakai

  PLOS ONE, Aug. 2014, Peer-reviewed

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

  Hiromasa Morikawa; Naganari Ohkura; Alexis Vandenbon; Masayoshi Itoh; Sayaka Nagao-Sato; Hideya Kawaji; Timo Lassmann; Piero Carninci; Yoshihide Hayashizaki; Alistair R. R. Forrest; Daron M. Standley; Hiroshi Date; Shimon Sakaguchi

  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Apr. 2014, Peer-reviewed

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

  Takuya Uehata; Hidenori Iwasaki; Alexis Vandenbon; Kazufumi Matsushita; Eduardo Hernandez-Cuellar; Kanako Kuniyoshi; Takashi Satoh; Takashi Mino; Yutaka Suzuki; Daron M Standley; Tohru Tsujimura; Hiromi Rakugi; Yoshitaka Isaka; Osamu Takeuchi; Shizuo Akira

  Cell, 23 May 2013, Peer-reviewed

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

  Alexis Vandenbon; Yutaro Kumagai; Shunsuke Teraguchi; Karlou Mar Amada; Shizuo Akira; Daron M. Standley

  BMC BIOINFORMATICS, Jan. 2013, Peer-reviewed, Lead author, Corresponding author

  
• The Transcription Factor Jdp2 Controls Bone Homeostasis and Antibacterial Immunity by Regulating Osteoclast and Neutrophil Differentiation

  Kenta Maruyama; Masahiro Fukasaka; Alexis Vandenbon; Tatsuya Saitoh; Takumi Kawasaki; Takeshi Kondo; Kazunari K. Yokoyama; Hiroyasu Kidoya; Nobuyuki Takakura; Daron Standley; Osamu Takeuchi; Shizuo Akira

  IMMUNITY, Dec. 2012, Peer-reviewed

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

  Alexis Vandenbon; Yutaro Kumagai; Shizuo Akira; Daron M. Standley

  BMC GENOMICS, Dec. 2012, Peer-reviewed, Lead author, Corresponding author

  
• Systems biology approaches to toll-like receptor signaling

  Alexis Vandenbon; Shunsuke Teraguchi; Shizuo Akira; Kiyoshi Takeda; Daron M. Standley

  WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE, Sep. 2012, Peer-reviewed, Lead author

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

  Shunsuke Teraguchi; Yutaro Kumagai; Alexis Vandenbon; Shizuo Akira; Daron M. Standley

  PHYSICAL REVIEW E, Dec. 2011, Peer-reviewed

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

  Takashi Satoh; Osamu Takeuchi; Alexis Vandenbon; Koubun Yasuda; Yoshiaki Tanaka; Yutaro Kumagai; Tohru Miyake; Kazufumi Matsushita; Toshihiko Okazaki; Tatsuya Saitoh; Kiri Honma; Toshifumi Matsuyama; Katsuyuki Yui; Tohru Tsujimura; Daron M. Standley; Kenji Nakanishi; Kenta Nakai; Shizuo Akira

  NATURE IMMUNOLOGY, Oct. 2010, Peer-reviewed

  
• I kappa B zeta is essential for natural killer cell activation in response to IL-12 and IL-18

  Tohru Miyake; Takashi Satoh; Hiroki Kato; Kazufumi Matsushita; Yutaro Kumagai; Alexis Vandenbon; Tohru Tani; Tatsushi Muta; Shizuo Akira; Osamu Takeuchi

  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Oct. 2010, Peer-reviewed

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

  Alexis Vandenbon; Kenta Nakai

  NUCLEIC ACIDS RESEARCH, Jan. 2010, Peer-reviewed, Lead author

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

  Alexis Vandenbon; Yuki Miyamoto; Noriko Takimoto; Takehiro Kusakabe; Kenta Nakai

  DNA RESEARCH, Feb. 2008, Peer-reviewed, Lead author

  
• USING SIMPLE RULES ON PRESENCE AND POSITIONING OF MOTIFS FOR PROMOTER STRUCTURE MODELING AND TISSUE-SPECIFIC EXPRESSION PREDICTION

  Alexis Vandenbon; Kenta Nakai

  GENOME INFORMATICS 2008, VOL 21, 2008, Peer-reviewed, Lead author

  

Misc.

• DeepSpaceDB：空間トランスクリプトミクスデータの探索的解析

  Alexis Vandenbon; 竹本経緯子

  実験医学, Apr. 2025, Lead author, Corresponding author

  

Presentations

• DeepSpaceDB: an Interactive Database for Spatial Transcriptomics Data

  Alexis Vandenbon

  30th East Asia Joint Symposium, 29 Oct. 2024

  
• DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of tissues and tissue microenvironments

  Alexis Vandenbon

  Asia & Pacific Bioinformatics Joint Conference 2024, 23 Oct. 2024

  
• DeepSpaceDB: a spatial transcriptomics atlas that allows interactive in-depth analysis of tissues and tissue microenvironments

  Alexis Vandenbon

  NGS EXPO 2024, 04 Sep. 2024

  
• SingleCellHaystack: A universal tool for predicting differentially active features in single-cell and spatial genomics data

  Alexis Vandenbon

  MBSJ2023, 01 Dec. 2023

  
• SingleCellHaystack: A universal differential expression prediction tool for single-cell and spatial genomics data

  Alexis Vandenbon

  GIW ISCB-Asia, 19 Nov. 2023

  
• Spatial transcriptomics analysis reveals how murine breast cancers disorganize the liver transcriptome in a zonated manner

  Alexis Vandenbon

  NGS Expo 2023, 15 Nov. 2023

  
• SingleCellHaystack: A universal differential expression prediction tool for single-cell and spatial genomics data

  Alexis Vandenbon

  Informatics in Biology, Medicine and Pharmacology 2023, 07 Sep. 2023

  
• Exploratory analysis of various single-cell and spatial transcriptomics data types

  Alexis Vandenbon

  Institute for Quantitative Biosciences student seminar, the University of Tokyo, 29 Sep. 2022, Invited

  
• singleCellHaystack: A clustering-independent method for finding differentially expressed genes in single-cell transcriptome data

  Alexis Vandenbon

  Tsukuba Bioinformatics Assembly, 21 Oct. 2021, Invited

  
• singleCellHaystack: A clustering-independent method for predicting differentially expressed genes in single cell transcriptome data

  Alexis Vandenbon

  1st International Symposium of CCII -Bioinformatics and its application to cancer and other diseases, 15 Jan. 2021

  
• singleCellHaystack: A clustering-independent method for predicting differentially expressed genes in single cell transcriptome data

  Alexis Vandenbon

  Human Cell Atlas Asia Meeting 2020, 22 Oct. 2020

  
• Prediction of regulatory mechanisms of gene expression at the epigenetic, transcriptional and post-transcriptional level

  Alexis Vandenbon

  IIBMP2019, 10 Sep. 2019, Invited

  
• singleCellHaystack, A clustering-independent method for predicting differentially expressed genes in single cell transcriptome data

  Alexis Vandenbon

  IIBMP2019, 10 Sep. 2019

  
• Navigating gene co-expression data in the immune system and finding interesting genes in single-cell haystacks

  Alexis Vandenbon

  08 Mar. 2019, Invited

  
• Reconstructing biological networks using large-scale gene expression data

  Alexis Vandenbon

  Biological Information Symposium, 21 Feb. 2017

  
• Waves of chromatin remodeling in mouse dendritic cells in response to lipopolysaccharide stimulation

  Alexis Vandenbon

  The 54th Annual Meeting of the Biophysical Society of Japan, 24 Nov. 2016, Invited

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

  Alexis Vandenbon

  IIBMP2016, 30 Sep. 2016

  
• Analysing cell type-specific gene networks using Immuno-Navigator

  Alexis Vandenbon

  InCoB2016, 21 Sep. 2016

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

  Alexis Vandenbon

  GIW ISCB-ASIA 2014, 17 Dec. 2014

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

  Alexis Vandenbon

  InCoB2012, 05 Oct. 2012

  
• Modeling the structures of promoters of virus-induced genes

  Alexis Vandenbon

  Bioinformatics in Immunology workshop, 06 Nov. 2009

  
• Towards a More Complex Grammar for Promoter Architecture Models

  Alexis Vandenbon

  JSBi 2008, 16 Dec. 2008

  
• Using Simple Rules on Presence and Positioning of Motifs for Promoter Structure Modeling and Tissue-specific Expression Prediction

  Alexis Vandenbon

  GIW 2008, 03 Dec. 2008

  
• Markov Chain-based Promoter Structure Modeling

  Alexis Vandenbon

  ISMB/ECCB 2007, 25 Jul. 2007

  

Books and Other Publications

• Epigenetics in organ specific disorders

  Boosani, Chandra; Goswami, Ritobrata, Joint work, Chapter 2 - Higher-order chromatin structure and gene regulation

  Academic Press, 2023

  Find Kyoto University's collection of books :

  

Awards

• 10 Sep. 2019

  Japanese Society for Bioinformatics, Oxford Journals - Japanese Society for Bioinformatics Prize

External funds: Kakenhi

• Comprehensive optimization of cell type-specific gene co-expression networks and construction of a cell type-specific co-expression database

  Grant-in-Aid for Scientific Research (C)

  Basic Section 43060:System genome science-related

  Kyoto University

  Alexis Vandenbon

  From 01 Apr. 2020, To 31 Mar. 2023, Project Closed

  bioinformatics;gene expression;gene co-expression;data normalization;batch effect correction;database;batch effects;RNA-seq;network analysis

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20K06609/
• Establishment of skin inflammation drug to accumulate high-functional regulatory T cells by single-cell gene expression analysis

  Grant-in-Aid for Young Scientists (B)

  Osaka Ohtani University

  Ryoyo Ikebuchi

  From 01 Apr. 2015, To 31 Mar. 2017, Project Closed

  制御性T細胞;炎症性皮膚疾患;免疫抑制;シングルセル解析;細胞遊走;KikGRマウス;接触性皮膚炎;ケモカイン

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-15K19687/
• Comprehensive feature extraction and modeling of promoters controlling the immune response

  Grant-in-Aid for Young Scientists (B)

  Osaka University

  ALEXIS VANDENBON

  From 01 Apr. 2011, To 31 Mar. 2013, Project Closed

  自然免疫;バイオインフォマティクス;配列解析;転写制御;エピジェネティクス;転写因子;マクロファージ;樹状細胞

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-23710234/
• Study on the enhancer grammar that specifies cell type-specific gene expression

  Grant-in-Aid for Scientific Research (C)

  Basic Section 43060:System genome science-related

  The University of Tokyo

  中井 謙太

  From 01 Apr. 2022, To 31 Mar. 2025, Granted

  ハウスキーピング制御領域;DNAメチル化;大規模言語モデル;がん抑制遺伝子;コファクター;細胞種特異的発現制御;クロマチンループ;自然言語モデル;ゲノム情報解析;モチーフ文法

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-22K06189/

Education

Teaching subject(s)

• From 01 Apr. 2025, To 31 Mar. 2026

  ILAS Seminar-E2

  Z002, Spring, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2025, To 31 Mar. 2026

  Interdisciplinary Sciences-E2

  Y102, Fall, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2025, To 31 Mar. 2026

  Basic Data Analysis-E2

  N809, Spring, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2025, To 31 Mar. 2026

  Introductory Statistics-E2

  N804, Fall, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2025, To 31 Mar. 2026

  Life Science: From Basics to Applications, from Molecular Biology to Systems Biology

  1026, Spring, Graduate School of Biostudies, 1
• From 01 Apr. 2025, To 31 Mar. 2026

  Experimental Course and Seminar D

  2009, Fall, Graduate School of Biostudies, 5
• From 01 Apr. 2025, To 31 Mar. 2026

  Experimental Course and Seminar C

  2008, Spring, Graduate School of Biostudies, 5
• From 01 Apr. 2025, To 31 Mar. 2026

  Experimental Course and Seminar C

  2008, Fall, Graduate School of Biostudies, 5
• From 01 Apr. 2025, To 31 Mar. 2026

  Experimental Course and Seminar D

  2009, Spring, Graduate School of Biostudies, 5
• From 01 Apr. 2025, To 31 Mar. 2026

  Experimental Course and Seminar A

  2006, Fall, Graduate School of Biostudies, 5
• From 01 Apr. 2025, To 31 Mar. 2026

  Experimental Course and Seminar B

  2007, Spring, Graduate School of Biostudies, 5
• From 01 Apr. 2025, To 31 Mar. 2026

  Experimental Course and Seminar B

  2007, Fall, Graduate School of Biostudies, 5
• From 01 Apr. 2025, To 31 Mar. 2026

  Experimental Course and Seminar A

  2006, Spring, Graduate School of Biostudies, 5
• From 01 Apr. 2025, To 31 Mar. 2026

  Advanced Experiments in Systemic Life Sciences

  5013, Fall, Graduate School of Biostudies, 4
• From 01 Apr. 2025, To 31 Mar. 2026

  Advanced Experiments in Systemic Life Sciences

  5013, Spring, Graduate School of Biostudies, 4
• From 01 Apr. 2024, To 31 Mar. 2025

  ILAS Seminar-E2

  Z002, Spring, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Interdisciplinary Sciences-E2

  Y102, Fall, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Basic Data Analysis-E2

  N809, Spring, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Introductory Statistics-E2

  N804, Fall, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Life Science: From Basics to Applications, from Molecular Biology to Systems Biology

  1026, Spring, Graduate School of Biostudies, 1
• From 01 Apr. 2024, To 31 Mar. 2025

  Experimental Course and Seminar A

  2006, Fall, Graduate School of Biostudies, 5
• From 01 Apr. 2024, To 31 Mar. 2025

  Advanced Experiments in Systemic Life Sciences

  5013, Spring, Graduate School of Biostudies, 4
• From 01 Apr. 2024, To 31 Mar. 2025

  Advanced Experiments in Systemic Life Sciences

  5013, Fall, Graduate School of Biostudies, 4
• From 01 Apr. 2024, To 31 Mar. 2025

  Experimental Course and Seminar D

  2009, Spring, Graduate School of Biostudies, 5
• From 01 Apr. 2024, To 31 Mar. 2025

  Experimental Course and Seminar B

  2007, Spring, Graduate School of Biostudies, 5
• From 01 Apr. 2024, To 31 Mar. 2025

  Experimental Course and Seminar B

  2007, Fall, Graduate School of Biostudies, 5
• From 01 Apr. 2024, To 31 Mar. 2025

  Experimental Course and Seminar A

  2006, Spring, Graduate School of Biostudies, 5
• From 01 Apr. 2024, To 31 Mar. 2025

  Experimental Course and Seminar D

  2009, Fall, Graduate School of Biostudies, 5
• From 01 Apr. 2024, To 31 Mar. 2025

  Experimental Course and Seminar C

  2008, Spring, Graduate School of Biostudies, 5
• From 01 Apr. 2024, To 31 Mar. 2025

  Experimental Course and Seminar C

  2008, Fall, Graduate School of Biostudies, 5
• From 01 Apr. 2023, To 31 Mar. 2024

  ILAS Seminar-E2

  Z002, Spring, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  ILAS Seminar-E2

  Z002, Fall, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  Basic Data Analysis-E2

  N809, Spring, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  Introductory Statistics-E2

  N804, Fall, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  Life Science: From Basics to Applications, from Molecular Biology to Systems Biology

  1026, Spring, Graduate School of Biostudies, 1
• From 01 Apr. 2023, To 31 Mar. 2024

  Experimental Course and Seminar D

  2009, Fall, Graduate School of Biostudies, 5
• From 01 Apr. 2023, To 31 Mar. 2024

  Experimental Course and Seminar C

  2008, Spring, Graduate School of Biostudies, 5
• From 01 Apr. 2023, To 31 Mar. 2024

  Experimental Course and Seminar C

  2008, Fall, Graduate School of Biostudies, 5
• From 01 Apr. 2023, To 31 Mar. 2024

  Experimental Course and Seminar D

  2009, Spring, Graduate School of Biostudies, 5
• From 01 Apr. 2023, To 31 Mar. 2024

  Experimental Course and Seminar B

  2007, Spring, Graduate School of Biostudies, 5
• From 01 Apr. 2023, To 31 Mar. 2024

  Experimental Course and Seminar B

  2007, Fall, Graduate School of Biostudies, 5
• From 01 Apr. 2023, To 31 Mar. 2024

  Experimental Course and Seminar A

  2006, Spring, Graduate School of Biostudies, 5
• From 01 Apr. 2023, To 31 Mar. 2024

  Experimental Course and Seminar A

  2006, Fall, Graduate School of Biostudies, 5
• From 01 Apr. 2023, To 31 Mar. 2024

  Advanced Experiments in Systemic Life Sciences

  5013, Fall, Graduate School of Biostudies, 4
• From 01 Apr. 2023, To 31 Mar. 2024

  Advanced Experiments in Systemic Life Sciences

  5013, Spring, Graduate School of Biostudies, 4
• From 01 Apr. 2022, To 31 Mar. 2023

  ILAS Seminar-E2

  Z002, Spring, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Introductory Statistics-E2

  N804, Fall, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  ILAS Seminar-E2

  Z002, Fall, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Basic Data Analysis-E2

  N809, Spring, Institute for Liberal Arts and Sciences, 2
• From Apr. 2018, To Mar. 2019

  Basic Data Analysis-E2

  Spring, 全学共通科目
• From Apr. 2018, To Mar. 2019

  ILAS Seminar-E2

  Spring, 全学共通科目
• From Apr. 2018, To Mar. 2019

  ILAS Seminar-E2

  Fall, 全学共通科目
• From Apr. 2018, To Mar. 2019

  Introductory Statistics-E2

  Fall, 全学共通科目
• From Apr. 2019, To Mar. 2020

  Basic Data Analysis-E2

  Spring, 全学共通科目
• From Apr. 2019, To Mar. 2020

  ILAS Seminar-E2

  Spring, 全学共通科目
• From Apr. 2019, To Mar. 2020

  ILAS Seminar-E2

  Fall, 全学共通科目
• From Apr. 2019, To Mar. 2020

  Introductory Statistics-E2

  Fall, 全学共通科目
• From Apr. 2020, To Mar. 2021

  Basic Data Analysis-E2

  Spring, 全学共通科目
• From Apr. 2020, To Mar. 2021

  ILAS Seminar-E2 :Introductory Bioinformatics

  Fall, 全学共通科目
• From Apr. 2020, To Mar. 2021

  ILAS Seminar-E2 :Programming for data analysis

  Spring, 全学共通科目
• From Apr. 2020, To Mar. 2021

  Introductory Statistics-E2

  Fall, 全学共通科目
• From Apr. 2021, To Mar. 2022

  Basic Data Analysis-E2

  Spring, 全学共通科目
• From Apr. 2021, To Mar. 2022

  ILAS Seminar-E2 :Introductory Bioinformatics

  Fall, 全学共通科目
• From Apr. 2021, To Mar. 2022

  ILAS Seminar-E2 :Programming for data analysis

  Spring, 全学共通科目
• From Apr. 2021, To Mar. 2022

  Introductory Statistics-E2

  Fall, 全学共通科目

Administration

Faculty management (title, position)

• From 01 Apr. 2022

  情報セキュリティ委員会　委員