Ueda Hiroki 上田宏生

Researcher Number	70821916
Other IDs
Affiliation (Current)	2025: 東京大学, 先端科学技術研究センター, 特任講師
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 53010:Gastroenterology-related / Medium-sized Section 62:Applied informatics and related fields / Broad Section I / Basic Section 55010:General surgery and pediatric surgery-related
Keywords	Except Principal Investigator RNA修飾 / 網羅的解析 / 網羅的分析 / 肝癌 / 翻訳効率 / 配列設計 / RNA修飾塩基 / 臓器間ネットワーク / 脂肪細胞 / エピゲノム … More / 肥満 / 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

ナノポアシーケンサと深層学習を用いた多種RNA修飾の網羅的検出および機能解析Principal 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
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
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
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
Elucidation of mRNA dysregulation in hepatocellular carcinoma using a novel mRNA methylome method
- Principal Investigator
  
  永江玄太
- Project Period (FY)
  2021 – 2024
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 53010:Gastroenterology-related
- Research Institution
  The University of Tokyo

All 2024 2023 2022 2021 2020

All Journal Article Presentation

[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] 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] 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] 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] 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
[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] 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] 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. 永江玄太 (10587348)

# of Collaborated Projects: 2 results

# of Collaborated Products: 1 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. 酒井寿郎 (80323020)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
6. 魏范研 (90555773)

# of Collaborated Projects: 1 results

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

# of Collaborated Projects: 1 results

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

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
9. 浅井潔 (30356357)

# of Collaborated Projects: 1 results

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

# of Collaborated Projects: 1 results

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

# of Collaborated Projects: 1 results

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

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
13. 油谷浩幸

# 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. 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

ナノポアシーケンサと深層学習を用いた多種RNA修飾の網羅的検出および機能解析Principal Investigator

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

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

Identification of cancer-specific neoantigens in organoid culture

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

[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] Multiancestry genomic and transcriptomic analysis of gastric cancer2023

Author(s)

Journal Title

DOI

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] direct RNA sequenceとRNA修飾の情報解析2021

Author(s)

Journal Title

Data Source

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

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Discovering A-to-I RNA Editing Through Chemical Methodology “ICE-seq”2020

Author(s)

Journal Title

DOI

ISBN

Data Source

[Presentation] HLA-Mascot: Machine Learning-based False Positive Filter in Tumor Immunopeptidomics by Mass Spectrometry2023

Author(s)

Organizer

Data Source

[Presentation] Establishment of Organoids Derived from Renal Cell Cancer for Immunopeptidome Analysis2023

Author(s)

Organizer

Data Source

[Presentation] Long-read DNA methylation analysis of hepatoblastoma genomes using a nanopore sequencing2022

Author(s)

Organizer

Data Source

Ueda Hiroki 上田宏生