Ueda Hiroki 上田宏生

Researcher Number	70821916
Other IDs
Affiliation (Current)	2026: 東京大学, 先端科学技術研究センター, 特任講師 2026: 千葉大学, 健康疾患オミクスセンター, 特任准教授
Affiliation (based on the past Project Information) *help	2021 – 2025: 東京大学, 先端科学技術研究センター, 特任講師
Review Section/Research Field	Principal Investigator Basic Section 43040:Biophysics-related Except Principal Investigator Basic Section 50020:Tumor diagnostics and therapeutics-related / Broad Section I / Basic Section 53010:Gastroenterology-related / Medium-sized Section 62:Applied informatics and related fields / Basic Section 55010:General surgery and pediatric surgery-related
Keywords	Principal Investigator 深層学習 / ロングリードシーケンサ / RNA修飾 Except Principal Investigator RNA修飾 / シークエンサー / スプライシング / がん / 臓器間ネットワーク / 脂肪細胞 / エピゲノム … More / 肥満 / 網羅的分析 / 網羅的解析 / 肝癌 / mRNA / 翻訳効率 / 配列設計 / RNA修飾塩基 / 質量分析計 / HLA分子 / がん免疫治療 / 遺伝子変異 / ペプチドミクス解析 / オルガノイド / ネオアンチゲン Less

Elucidation of cancer transcriptome dysregulation by full-length RNA modomics
- Principal Investigator
  
  永江玄太
- Project Period (FY)
  2025 – 2028
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 50020:Tumor diagnostics and therapeutics-related
- Research Institution
  The University of Tokyo
Comprehensive Detection and Functional Analysis of Diverse RNA Modifications Using Nanopore Sequencing and Deep LearningPrincipal Investigator
- Principal Investigator
  
  上田宏生
- Project Period (FY)
  2025 – 2027
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 43040:Biophysics-related
- Research Institution
  The University of Tokyo
化学修飾を含むmRNA配列設計の基盤技術
- Principal Investigator
  
  浅井潔
- Project Period (FY)
  2024 – 2027
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Review Section
  
  Medium-sized Section 62:Applied informatics and related fields
- Research Institution
  The University of Tokyo
Elucidation of mRNA dysregulation in hepatocellular carcinoma using a novel mRNA methylome method
- Principal Investigator
  
  Nagae Genta
- Project Period (FY)
  2024
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 53010:Gastroenterology-related
- Research Institution
  The University of Tokyo
A Study on Elucidating Obesity and Lifestyle Diseases through the Epigenome-RNA Modification Axis
- Principal Investigator
  
  酒井寿郎
- Project Period (FY)
  2024 – 2028
- Research Category
  
  Grant-in-Aid for Scientific Research (S)
- Review Section
  
  Broad Section I
- Research Institution
  Tohoku University
Identification of cancer-specific neoantigens in organoid culture
- Principal Investigator
  
  Sasada Tetsuro
- Project Period (FY)
  2021 – 2023
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 55010:General surgery and pediatric surgery-related
- Research Institution
  Kanagawa Cancer Center Research Institute

All 2024 2023 2022 2021 2020

All Journal Article Presentation

[Journal Article] Region‐specific DNA hydroxymethylation along the malignant progression of IDH‐mutant gliomas2024
- Author(s)
  Hana T, Mukasa A, Nomura M, Nagae G, Yamamoto S, Tatsuno K, Ueda H, Fukuda S, Umeda T, Tanaka S, Nejo T, Kitagawa Y, Yamazawa E, Takahashi S, Koike T, Kushihara Y, Takami H, Takayanagi S, Aburatani H, Saito N
- Journal Title
  
  Cancer Science
  
  Volume: 115 Issue: 5 Pages: 1706-1717
- DOI
  10.1111/cas.16127
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23K27713, KAKENHI-PROJECT-24H00065, KAKENHI-PROJECT-23K21431
[Journal Article] iMPAQT reveals that adequate mitohormesis from TFAM overexpression leads to life extension in mice2024
- Author(s)
  Igami Ko、Kittaka Hiroki、Yagi Mikako、Gotoh Kazuhito、Matsushima Yuichi、Ide Tomomi、Ikeda Masataka、Ueda Saori、Nitta Shin-Ichiro、Hayakawa Manami、Nakayama Keiichi I.、Matsumoto Masaki、Kang Dongchon、Uchiumi Takeshi
- Journal Title
  
  Life Science Alliance
  
  Volume: 7 Issue: 7 Pages: e202302498-e202302498
- DOI
  10.26508/lsa.202302498
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-20H05930, KAKENHI-PROJECT-24H00065, KAKENHI-PROJECT-23H00378, KAKENHI-PROJECT-23K24794, KAKENHI-PROJECT-22K19288, KAKENHI-PROJECT-23K23870, KAKENHI-PROJECT-24K21928
[Journal Article] Enhancing Mass spectrometry-based tumor immunopeptide identification: machine learning filter leveraging HLA binding affinity, aliphatic index and retention time deviation2024
- Author(s)
  Wei F, Kouro T, Nakamura Y, Ueda H, Iiizumi S, Hasegawa K, Asahina Y, Kishida T, Morinaga S, Himuro H, Horaguchi S, Tsuji K, Mano Y, Nakamura N, Kawamura T, Sasada T.
- Journal Title
  
  Comput Struct Biotechnol J
  
  Volume: 23 Pages: 859-869
- DOI
  10.1016/j.csbj.2024.01.023
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23K18346, KAKENHI-PROJECT-22K08724, KAKENHI-PROJECT-21H02995
[Journal Article] m6ATM: a deep learning framework for demystifying the m6A epitranscriptome with Nanopore long-read RNA-seq data2024
- Author(s)
  Yu B, Nagae G, Midorikawa Y, Tatsuno K, Dasgupta B, Aburatani H, Ueda H
- Journal Title
  
  Briefings in Bioinformatics
  
  Volume: 25 Issue: 6 Pages: 6-6
- DOI
  10.1093/bib/bbae529
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-24H00065, KAKENHI-PROJECT-23K21431, KAKENHI-PROJECT-21K08807
[Journal Article] Multiancestry genomic and transcriptomic analysis of gastric cancer2023
- Author(s)
  Totoki Y, Saito-Adachi M, Shiraishi Y, Komura D, Nakamura H, Suzuki A, Tatsuno K, Rokutan H, Hama N, Yamamoto S, Ono H, Arai Y, Hosoda F, Katoh H, et al.
- Journal Title
  
  Nature Genetics
  
  Volume: 55 Issue: 4 Pages: 581-594
- DOI
  10.1038/s41588-023-01333-x
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K06937, KAKENHI-PROJECT-22H04990, KAKENHI-PROJECT-19H01031, KAKENHI-PROJECT-20K07378, KAKENHI-PROJECT-21K06882, KAKENHI-PROJECT-20KK0174, KAKENHI-PLANNED-19H05744, KAKENHI-ORGANIZER-22H05021, KAKENHI-PROJECT-23K21431
[Journal Article] direct RNA sequenceとRNA修飾の情報解析2021
- Author(s)
  上田宏生
- Journal Title
  
  実験医学別冊ロングリードWET&DRY解析ガイド
  
  Volume: - Pages: 202-212
- Data Source
  KAKENHI-PROJECT-23K21431
[Journal Article] Genetic and epigenetic basis of hepatoblastoma diversity.2021
- Author(s)
  Nagae G, Yamamoto S, Fujita M, Fujita T, Nonaka A, Umeda T, Fukuda S, Tatsuno K, Maejima K, Hayashi A, Kurihara S, Kojima M, Hishiki T, Watanabe K, Ida K, Yano M, Hiyama Y, Tanaka Y, Inoue T, Ueda H, Nakagawa H, Aburatani H, Hiyama E.
- Journal Title
  
  Nat Commun.
  
  Volume: 12 Issue: 1 Pages: 5423-5423
- DOI
  10.1038/s41467-021-25430-9
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-19H05744, KAKENHI-PROJECT-19H01031, KAKENHI-PROJECT-19H01056, KAKENHI-PROJECT-23K21431
[Journal Article] ナノポアシーケンサーを用いた RNA 修飾の解析2021
- Author(s)
  山崎洋人、上田宏生
- Journal Title
  
  細胞（特集エピトランスクリプトミクス）
  
  Volume: 53(14) Pages: 896-899
- Data Source
  KAKENHI-PROJECT-23K21431
[Journal Article] Base-Resolution Analysis of 5-Hydroxymethylcytidine by Selective Oxidation and Reverse Transcription Arrest2021
- Author(s)
  Koyama, K.; Hayashi, G.; Ueda, H.; Ota, S.; Nagae, G.; Aburatani, H.; Okamoto, A.
- Journal Title
  
  Org. Biomol. Chem.
  
  Volume: 19 Issue: 29 Pages: 6478-6486
- DOI
  10.1039/d1ob00995h
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-18H05504, KAKENHI-PUBLICLY-20H04704, KAKENHI-PROJECT-21K19040, KAKENHI-PROJECT-23K21431, KAKENHI-PUBLICLY-21H00278
[Journal Article] Discovering A-to-I RNA Editing Through Chemical Methodology “ICE-seq”2020
- Author(s)
  Sakurai, M., Okada, S., Ueda, H., and Yang, Y.
- Journal Title
  
  Methods in Molecular Biology
  
  Volume: 2181 Pages: 113-148
- DOI
  10.1007/978-1-0716-0787-9_8
- ISBN
  9781071607862, 9781071607879
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19K16037, KAKENHI-PROJECT-23K21431, KAKENHI-PROJECT-19H03159
[Presentation] ナノポアシーケンサを用いた複数 RNA 修飾の同時検出法の開発2024
- Author(s)
  Hiroki Ueda, Boyi Yu, Keisuke Yamada, Akihide Yoshimi, Genta Nagae, Hiroyuki Aburatani
- Organizer
  第17回日本エピジェネティクス研究会年会
- Data Source
  KAKENHI-PROJECT-24H00065
[Presentation] Exploring aberrant RNA modifications in glioma using direct RNA Nanopore sequencing2024
- Author(s)
  Keisuke Yamada, Boyi Yu,Takanori Fujita, Shunsaku Takayanagi,Hiroki Ueda, Shota Tanaka, Nobuhito Saito, Hiroyuki Aburatani,Genta Nagae
- Organizer
  第83回日本癌学会学術総会
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-24H00065
[Presentation] Demystifying the m6A epitranscriptome: a novel deep neural networkbased method for long-read sequencing data2024
- Author(s)
  Boyi Yu, Genta Nagae, Yutaka Midorikawa, Kenji Tatsuno, Bhaskar Dasgupta, Satoshi Ota, Hiroyuki Aburatani, Hiroki Ueda
- Organizer
  The 29th Annual Meeting of the RNA Society (RNA2024)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-24H00065
[Presentation] Deep learning based end-to-end classification and absolute quantification of E. Coli cellular tRNAs using nanopore sequencing2024
- Author(s)
  Bhaskar Dasgupta, Mai Maeda, Ryo Noguchi , Tsutomu Suzuki, Hiroki Ueda
- Organizer
  The 29th Annual Meeting of the RNA Society (RNA2024)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-24H00065
[Presentation] がんにおけるRNA修飾の網羅的解析2024
- Author(s)
  上田宏生
- Organizer
  がん研究振興財団　令和6年度がん研究シンポジウム
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-24H00065
[Presentation] ナノポアシーケンサと深層学習を用いた m6A RNA 修飾の網羅的な解析2024
- Author(s)
  Yu, B., Nagae, G., Midorikawa, Y., Tatsuno, K., Dasgupta, B., Aburatani, H., & Ueda, H.
- Organizer
  第17回日本エピジェネティクス研究会年会
- Data Source
  KAKENHI-PROJECT-24H00065
[Presentation] Development of a Method for Simultaneous Detection of Multiple RNA Modifications Using Nanopore Sequencing"2024
- Author(s)
  Hiroki Ueda, Bo-yi Yu , Keisuke Yamada, Akihide Yoshimi, Genta Nagae, Hiroyuki Aburatani
- Organizer
  The 29th Annual Meeting of the RNA Society (RNA2024)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-24H00065
[Presentation] Development of a Method for Simultaneous Detection of Multiple RNA Modifications Using Nanopore Sequencing2024
- Author(s)
  Hiroki Ueda, Boyi Yu, Keisuke Yamada, Akihide Yoshimi, Genta Nagae, Hiroyuki Aburatani
- Organizer
  第83回日本癌学会学術総会
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-24H00065
[Presentation] Simultaneous Detection of Multiple RNA Modifications Using Nanopore Sequencing2024
- Author(s)
  Hiroki Ueda, Boyi Yu, Ryo Noguchi, Akihide Yoshimi, Hiroyuki Aburatani, Genta Nagae, Tsutomu Suzuki
- Organizer
  29th tRNA conference
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-24H00065
[Presentation] Exploring the m6A epitranscriptome in cancers: a novel deep neural network-based method for long read analysis2024
- Author(s)
  Boyi Yu, Genta Nagae, Yutaka Midorikawa, Kenji Tatsuno, Bhaskar Dasgupta, Hiroyuki Aburatani, Hiroki Ueda
- Organizer
  第83回日本癌学会学術総会
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-24H00065
[Presentation] Development of a Method for Simultaneous Detection of Multiple RNA Modifications Using Nanopore Sequencing2024
- Author(s)
  Hiroki Ueda ,Bo-Yi Yu ,Keisuke Yamada , Genta Nagae , Hiroyuki Aburatani
- Organizer
  第2回AMED SCARDA「ワクチン開発のための世界トップレベル研究開発拠点の形成事業」合同シンポジウム
- Data Source
  KAKENHI-PROJECT-24H00065
[Presentation] A single molecule detection of tRNA modifications by signal alignment of nanopore sequencing data2024
- Author(s)
  Ryo Noguchi, Qiuyu Wang, Yosei Hanzawa, Mai Maeda, Takayuki Ohira, Bhaskar Dasgupta, Hiroki Ueda, Tsutomu Suzuki
- Organizer
  The 29th Annual Meeting of the RNA Society (RNA2024)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-24H00065
[Presentation] Decoding the epitranscriptome based on the inherent nature of long-read RNA molecules2024
- Author(s)
  Boyi Yu, Genta Nagae, Yutaka Midorikawa, Kenji Tatsuno, Bhaskar Dasgupta, Hiroyuki Aburatani, Hiroki Ueda
- Organizer
  29th tRNA conference
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-24H00065
[Presentation] Establishment of Organoids Derived from Renal Cell Cancer for Immunopeptidome Analysis2023
- Author(s)
  辻嘉代子、中村有子、上田宏生、紅露　拓、魏　菲菲、眞野恭伸、洞口　俊、氷室秀知、星野大輔、川村　猛、笹田哲朗
- Organizer
  第82回日本癌学会学術総会
- Data Source
  KAKENHI-PROJECT-21H02995
[Presentation] HLA-Mascot: Machine Learning-based False Positive Filter in Tumor Immunopeptidomics by Mass Spectrometry2023
- Author(s)
  魏　菲菲，紅露　拓，中村有子，上田宏生，氷室秀知，洞口　俊，辻　嘉代子，眞野恭伸，中村徳弘，川村　猛，笹田哲朗
- Organizer
  第82回日本癌学会学術総会
- Data Source
  KAKENHI-PROJECT-21H02995
[Presentation] Long-read DNA methylation analysis of hepatoblastoma genomes using a nanopore sequencing2022
- Author(s)
  Nagae G, Umeda T, Ueda H, Aburatani H.
- Organizer
  The 81th Japan Cancer Association Annual Meeting
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K21431
[Presentation] 個別化医療のためのネオアンチゲンペプチド同定法2021
- Author(s)
  中村有子、朝比奈佑希、紅露拓、上田宏生、近岡洋子、辰野健二、中村徳弘、油谷浩幸、笹田哲朗、川村猛
- Organizer
  第69回質量分析総合討論会
- Data Source
  KAKENHI-PROJECT-21H02995
[Presentation] Identification of HLA-binding neoepitopes through peptidome analysis with patient-derived xenografts2021
- Author(s)
  Taku Kouro, Takeshi Kawamura, Hiroki Ueda, Hiroyuki Kishi, Hiroyuki Aburatani, Tetsuro Sasada
- Organizer
  第80回日本癌学会学術総会
- Data Source
  KAKENHI-PROJECT-21H02995
[Presentation] ペプチドミクス解析によるネオアンチゲン同定と特異的T細胞樹立による検証2021
- Author(s)
  紅露拓、朝比奈佑希、中村有子、上田宏生、五十嵐友香、東島直子、近岡洋子、辰野健二、岸裕幸、中村徳弘、油谷浩幸、川村猛、笹田哲朗
- Organizer
  第25回日本がん免疫学会
- Data Source
  KAKENHI-PROJECT-21H02995
[Presentation] nanoDoc を用いた RNA 修飾の検出2021
- Author(s)
  Ueda H
- Organizer
  Virtual Nanopore Day
- Data Source
  KAKENHI-PROJECT-23K21431

1. Nagae Genta (10587348)

# of Collaborated Projects: 3 results

# of Collaborated Products: 13 results
2. Sasada Tetsuro (70293967)

# of Collaborated Projects: 1 results

# of Collaborated Products: 6 results
3. 星野大輔 (30571434)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
4. 川村猛 (70306835)

# of Collaborated Projects: 1 results

# of Collaborated Products: 5 results
5. 浅井潔 (30356357)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
6. 佐藤健吾 (20365472)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
7. 阿部洋 (80415067)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
8. 緑川泰 (10292905)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
9. 酒井寿郎 (80323020)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
10. 松村欣宏 (20375257)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
11. 松本雅記 (60380531)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
12. 魏范研 (90555773)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
13. MUKASA Akitake

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
14. 六反啓文

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
15. 岡田俊平

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
16. 油谷浩幸

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
17. 岡本晃充

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Ueda Hiroki 上田 宏生

Research Projects

Research Products

Co-Researchers

Elucidation of cancer transcriptome dysregulation by full-length RNA modomics

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Comprehensive Detection and Functional Analysis of Diverse RNA Modifications Using Nanopore Sequencing and Deep LearningPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

化学修飾を含むmRNA配列設計の基盤技術

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Elucidation of mRNA dysregulation in hepatocellular carcinoma using a novel mRNA methylome method

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

A Study on Elucidating Obesity and Lifestyle Diseases through the Epigenome-RNA Modification Axis

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Identification of cancer-specific neoantigens in organoid culture

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

[Journal Article] Region‐specific DNA hydroxymethylation along the malignant progression of IDH‐mutant gliomas2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] iMPAQT reveals that adequate mitohormesis from TFAM overexpression leads to life extension in mice2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Enhancing Mass spectrometry-based tumor immunopeptide identification: machine learning filter leveraging HLA binding affinity, aliphatic index and retention time deviation2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] m6ATM: a deep learning framework for demystifying the m6A epitranscriptome with Nanopore long-read RNA-seq data2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Multiancestry genomic and transcriptomic analysis of gastric cancer2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] direct RNA sequenceとRNA修飾の情報解析2021

Author(s)

Journal Title

Data Source

[Journal Article] Genetic and epigenetic basis of hepatoblastoma diversity.2021

Author(s)

Journal Title

DOI

Data Source

[Journal Article] ナノポアシーケンサーを用いた RNA 修飾の解析2021

Author(s)

Journal Title

Data Source

[Journal Article] Base-Resolution Analysis of 5-Hydroxymethylcytidine by Selective Oxidation and Reverse Transcription Arrest2021

Author(s)

Ueda Hiroki 上田宏生