VANDENBON ALEXIS ＶＡＮＤＥＮＢＯＮＡＬＥＸＩＳ

… Alternative Names

Vandenbon Alexis VANDENBON ALEXIS

Alexis Vandenbon

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Researcher Number	60570140
Other IDs
Affiliation (Current)	2025: 京都大学, 医生物学研究所, 准教授
Affiliation (based on the past Project Information) *help	2022 – 2023: 京都大学, 医生物学研究所, 准教授 2021: 京都大学, ウイルス・再生医科学研究所, 准教授 2020: 京都大学, ウイルス・再生医科学研究所, 講師 2016: 大阪大学, 免疫学フロンティア研究センター, 助教 2012 – 2013: 大阪大学, 免疫学フロンティア研究センター, 特任助教 2011: 大阪大学, 免疫学フロンティア研究センター, 特任研究員(常勤)
Review Section/Research Field	Principal Investigator Basic Section 43060:System genome science-related / System genome science Except Principal Investigator Basic Section 43060:System genome science-related / Dermatology
Keywords	Principal Investigator network analysis / RNA-seq / batch effects / database / batch effect correction / data normalization / gene co-expression / gene expression / bioinformatics / 樹状細胞 … More / マクロファージ / 転写因子 / エピジェネティクス / 転写制御 / 配列解析 / バイオインフォマティクス / 自然免疫 … More Except Principal Investigator モチーフ文法 / ゲノム情報解析 / 自然言語モデル / クロマチンループ / 細胞種特異的発現制御 / コファクター / がん抑制遺伝子 / 大規模言語モデル / DNAメチル化 / ハウスキーピング制御領域 / ケモカイン / 接触性皮膚炎 / KikGRマウス / 細胞遊走 / シングルセル解析 / 免疫抑制 / 炎症性皮膚疾患 / 制御性T細胞 Less

Study on the enhancer grammar that specifies cell type-specific gene expression
- Principal Investigator
  
  中井謙太
- Project Period (FY)
  2022 – 2024
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 43060:System genome science-related
- Research Institution
  The University of Tokyo
Comprehensive optimization of cell type-specific gene co-expression networks and construction of a cell type-specific co-expression databasePrincipal Investigator
- Principal Investigator
  
  Vandenbon Alexis
- Project Period (FY)
  2020 – 2022
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 43060:System genome science-related
- Research Institution
  Kyoto University
Establishment of skin inflammation drug to accumulate high-functional regulatory T cells by single-cell gene expression analysis
- Principal Investigator
  
  Ikebuchi Ryoyo
- Project Period (FY)
  2015 – 2016
- Research Category
  
  Grant-in-Aid for Young Scientists (B)
- Research Field
  
  Dermatology
- Research Institution
  Osaka Ohtani University
Comprehensive feature extraction and modeling of promoters controlling the immune responsePrincipal Investigator
- Principal Investigator
  
  VANDENBON ALEXIS
- Project Period (FY)
  2011 – 2012
- Research Category
  
  Grant-in-Aid for Young Scientists (B)
- Research Field
  
  System genome science
- Research Institution
  Osaka University

All 2023 2022 2021 2016 2013 2012

All Journal Article Presentation Book

[Book] Epigenetics in Organ Specific Disorders (ed,: Chandra Boosani, Ritobrata Goswami)2022
- Author(s)
  Kenta Nakai, Alexis Vandenbon
- Total Pages
  666
- Publisher
  Elsevier
- ISBN
  9780128239315
- Data Source
  KAKENHI-PROJECT-22K06189
[Journal Article] Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression2023
- Author(s)
  Loza Martin、Vandenbon Alexis、Nakai Kenta
- Journal Title
  
  Nucleic Acids Research
  
  Volume: 52 Issue: 3 Pages: 1107-1119
- DOI
  10.1093/nar/gkad1164
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K06189, KAKENHI-PROJECT-22K21301
[Journal Article] Murine breast cancers disorganize the liver transcriptome in a zonated manner2023
- Author(s)
  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
- Journal Title
  
  Communications Biology
  
  Volume: 6(1) Issue: 1 Pages: 97-97
- DOI
  10.1038/s42003-023-04479-w
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22H04925, KAKENHI-PROJECT-20H03451, KAKENHI-PROJECT-20K06609
[Journal Article] Evaluation of critical data processing steps for reliable prediction of gene co-expression from large collections of RNA-seq data2022
- Author(s)
  Vandenbon Alexis
- Journal Title
  
  PLOS ONE
  
  Volume: 17 Issue: 1 Pages: e0263344-e0263344
- DOI
  10.1371/journal.pone.0263344
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K06609
[Journal Article] A universal differential expression prediction tool for single-cell and spatial genomics data2022
- Author(s)
  Vandenbon Alexis、Diez Diego
- Journal Title
  
  bioRxiv
  
  Volume: -
- DOI
  10.1101/2022.11.13.516355
- Open Access
- Data Source
  KAKENHI-PROJECT-20K06609
[Journal Article] Guidance for RNA-seq co-expression estimates: the importance of data normalization, batch effects, and correlation measures2021
- Author(s)
  Vandenbon Alexis
- Journal Title
  
  bioRxiv
  
  Volume: -
- DOI
  10.1101/2021.03.11.435043
- Open Access
- Data Source
  KAKENHI-PROJECT-20K06609
[Journal Article] A rare subset of skin-tropic regulatory T cells expressing Il10/Gzmb inhibits the cutaneous immune response.2016
- Author(s)
  Ikebuchi R, Teraguchi S, Vandenbon A, Honda T, Shand FH, Nakanishi Y, Watanabe T, Tomura M.
- Journal Title
  
  Sci Rep. 6: 35002, doi:
  
  Volume: 6 Issue: 1 Pages: 35002-35002
- DOI
  10.1038/srep35002
- NAID
  120006223629
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-24111007, KAKENHI-PLANNED-24111009, KAKENHI-PROJECT-15F15113, KAKENHI-PROJECT-15K19687
[Journal Article] A Parzen window-based approach for the detection of locally enriched transcription factor binding sites2013
- Author(s)
  Vandenbon A, Kumagai Y, Teraguchi S, Amada KM, Akira S, Standley DM
- Journal Title
  
  BMC Bioinformatics
  
  Volume: Vol.14 Issue: 1 Pages: 26-26
- DOI
  10.1186/1471-2105-14-26
- Data Source
  KAKENHI-PROJECT-23710234
[Journal Article] A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription2012
- Author(s)
  Vandenbon A, Kumagai Y, Akira S, Standley DM
- Journal Title
  
  BMC Genomics
  
  Volume: Vol.13 Suppl 7 Issue: Suppl 7 Pages: S11-S11
- DOI
  10.1186/1471-2164-13-s7-s11
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23710234
[Presentation] Human Housekeeping Cis-Reulatory Elements and their involvement in tumor suppression2023
- Author(s)
  Martin Loza, Alexis Vandenbon and Kenta Nakai
- Organizer
  Indian Conference on Bioinformatics 2023 - Inbix'23
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K06189
[Presentation] Characterization of housekeeping regulatory elements in the human genome2023
- Author(s)
  Loza, M., Vandenbon, A., & Nakai, K.
- Organizer
  The Biology of Genomes(CSHL)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K06189
[Presentation] Unveiling the existence of housekeeping cis-regulatory elements: epigenetic characterization and implications in cancer development2023
- Author(s)
  Loza, M., Vandenbon, A., & Nakai, K.
- Organizer
  The 22nd International Conference on Bioinformatics (InCoB2023)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K06189
[Presentation] Evaluation of critical data processing steps for reliable prediction of gene co-expression from large collections of RNA-seq data2022
- Author(s)
  Alexis Vandenbon
- Organizer
  第１１回生命医薬情報学連合大会
- Data Source
  KAKENHI-PROJECT-20K06609
[Presentation] Single-cell Gene & Protein Expression Analysis Revealed Unique Functional Subsets of Regulatory T Cells2016
- Author(s)
  Ryoyo IKEBUCHI, Shunsuke TERAGUCHI, Alexis VANDENBON, Yasutaka NAKANISHI, Taiki MORIYA, Hiromi OKUYAMA, Yutaka KUSUMOTO, Tetsuya HONDA, Michio TOMURA
- Organizer
  International Conference on Single Cell Research 2016
- Place of Presentation
  Tokyo, Japan
- Year and Date
  2016-11-16
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15K19687
[Presentation] Sets of principal transcription factors define properties and dynamics of enhancers following LPS stimulation2013
- Author(s)
  Vandenbon A.
- Organizer
  EMBO Workshop Complex Systems in Immunology
- Place of Presentation
  Biopolis (Singapore)
- Data Source
  KAKENHI-PROJECT-23710234
[Presentation] Properties and dynamics of enhancers are defined by small sets of principal regulators2013
- Author(s)
  Alexis Vandenbon
- Organizer
  次世代シークエンサ現場の会　第３回研究会 (NGS現場の会)
- Place of Presentation
  神戸国際会議場、神戸
- Data Source
  KAKENHI-PROJECT-23710234
[Presentation] Towards Comprehensive Understanding of the Dynamic Control of the Immune Response on the Transcriptional and Epigenetic Level2013
- Author(s)
  Vandenbon A.
- Organizer
  The 24th CDB Meeting : Genomics and Epigenomics with Deep Sequencing
- Place of Presentation
  RIKEN CDB, Kobe (Japan)
- Data Source
  KAKENHI-PROJECT-23710234
[Presentation] Properties and dynamics of enhancers are defined by small sets of principal regulators2013
- Author(s)
  Vandenbon A.
- Organizer
  次世代シークエンサ現場の会第3回研究会 (NGS現場の会)
- Place of Presentation
  Kobe International Conference Center, Kobe, (Japan)
- Data Source
  KAKENHI-PROJECT-23710234
[Presentation] Towards Comprehensive Understanding of the Dynamic Control of the Immune Response on the Transcriptional and Epigenetic Level2013
- Author(s)
  Alexis Vandenbon
- Organizer
  The 24th CDB Meeting: Genomic and Epigenomics with Deep Sequencing
- Place of Presentation
  RIKEN CDB、神戸
- Data Source
  KAKENHI-PROJECT-23710234
[Presentation] Sets of principal transcription factors define properties and dynamics of enhancers following LPS stimulation2013
- Author(s)
  Alexis Vandenbon
- Organizer
  EMBO Workshop Complex Systems in Immunology
- Place of Presentation
  Biopolis, Singapore
- Data Source
  KAKENHI-PROJECT-23710234
[Presentation] A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription2012
- Author(s)
  Alexis Vandenbon
- Organizer
  11th International Conference on Bioinformatics (InCoB2012)
- Place of Presentation
  Centara Grand at Central Plaza Ladprao (Bangkok, Thailand)
- Data Source
  KAKENHI-PROJECT-23710234
[Presentation] Sequence analysis of promoter and enhancer regions in mouse macrophages2012
- Author(s)
  Vandenbon A.
- Organizer
  次世代シークエンサ現場の会第2回研究会(NGS現場の会)
- Place of Presentation
  Hotel Hankyu Expo Park, Osaka (Japan)
- Data Source
  KAKENHI-PROJECT-23710234
[Presentation] Sequence analysis of mouse macrophage promoter and enhancer regions reveals several subclasses of enhancers2012
- Author(s)
  Vandenbon A.
- Organizer
  ICSB (the 13th International Conference of Systems Biology)
- Place of Presentation
  University of Toronto, Toronto (Canada)
- Data Source
  KAKENHI-PROJECT-23710234
[Presentation] Sequence Analysis Reveals Several Subtypes of Macrophage Enhancers2012
- Author(s)
  Vandenbon A.
- Organizer
  TCUID2012
- Place of Presentation
  Osaka University, Osaka (Japan)
- Data Source
  KAKENHI-PROJECT-23710234
[Presentation] Predicting combinatorial regulation of transcription from motif co-occurrence2012
- Author(s)
  Vandenbon A.
- Organizer
  InCoB2012 (11th International Conference on Bioinformatics)
- Place of Presentation
  Centara Grand at Central Plaza Ladprao, Bangkok (Thailand)
- Data Source
  KAKENHI-PROJECT-23710234
[Presentation] A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription2012
- Author(s)
  Vandenbon A.
- Organizer
  11th International Conference on Bioinformatics (InCoB2012)
- Place of Presentation
  Centara Grand at Central Plaza Ladprao, Bangkok (Thailand)
- Year and Date
  2012-10-05
- Data Source
  KAKENHI-PROJECT-23710234

1. Ikebuchi Ryoyo (00747529)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
2. TOMURA Michio (30314321)

# of Collaborated Projects: 1 results

# of Collaborated Products: 2 results
3. KUSUMOTO Yutaka (40252689)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
4. MORIYA Taiki (30759759)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
5. TERAGUCHI Shunsuke (00467276)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
6. NAKAYAMA Takashi (60319663)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
7. MATSUO Kazuhiko (70615921)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
8. 中井謙太 (60217643)

# of Collaborated Projects: 1 results

# of Collaborated Products: 5 results
9. ITOH Takehiko

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
10. 鈴木穣

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
11. 中村保一

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

VANDENBON ALEXIS ＶＡＮＤＥＮＢＯＮ ＡＬＥＸＩＳ

Vandenbon Alexis VANDENBON ALEXIS

Alexis Vandenbon

Research Projects

Research Products

Co-Researchers

Study on the enhancer grammar that specifies cell type-specific gene expression

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Comprehensive optimization of cell type-specific gene co-expression networks and construction of a cell type-specific co-expression databasePrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Establishment of skin inflammation drug to accumulate high-functional regulatory T cells by single-cell gene expression analysis

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

Comprehensive feature extraction and modeling of promoters controlling the immune responsePrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

[Book] Epigenetics in Organ Specific Disorders (ed,: Chandra Boosani, Ritobrata Goswami)2022

Author(s)

Total Pages

Publisher

ISBN

Data Source

[Journal Article] Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Murine breast cancers disorganize the liver transcriptome in a zonated manner2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Evaluation of critical data processing steps for reliable prediction of gene co-expression from large collections of RNA-seq data2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] A universal differential expression prediction tool for single-cell and spatial genomics data2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Guidance for RNA-seq co-expression estimates: the importance of data normalization, batch effects, and correlation measures2021

Author(s)

Journal Title

DOI

Data Source

[Journal Article] A rare subset of skin-tropic regulatory T cells expressing Il10/Gzmb inhibits the cutaneous immune response.2016

Author(s)

Journal Title

DOI

NAID

Data Source

[Journal Article] A Parzen window-based approach for the detection of locally enriched transcription factor binding sites2013

Author(s)

Journal Title

DOI

Data Source

[Journal Article] A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription2012

Author(s)

Journal Title

DOI

Data Source

[Presentation] Human Housekeeping Cis-Reulatory Elements and their involvement in tumor suppression2023

Author(s)

Organizer

VANDENBON ALEXIS ＶＡＮＤＥＮＢＯＮＡＬＥＸＩＳ