Basic Information

Email Address

• Email Address

  kawaguchi.risa.3rkyoto-u.ac.jp

Academic Degree

• 24 Mar. 2017

  東京大学博士（科学）
• 26 Mar. 2014

  東京大学修士（科学）

Academic Resume (Undergraduate School/Majors)

• 東京大学, 理学部生物情報科学科, 卒業

Research History

• From Dec. 2024, To Present

  The University of Tokyo, Graduate School of Pharmaceutical Sciences, Associate Professor
• From Apr. 2023, To Present

  National Institute of Advanced Industrial Science and Technology, Intelligent Bioinformatics Research Team, Artificial Intelligence Research Center (AIRC), Visiting Researcher
• From May 2022, To Present

  Center for iPS Cell Research and Application, Kyoto University, Department of Life Science Frontiers, Junior Associate Professor
• From Apr. 2019, To Mar. 2022

  The National Institute of Advanced Industrial Science and Technology, The Artificial Intelligence Research Center, Collaborative researcher
• From Apr. 2019, To Apr. 2022

  Cold Spring Harbor Laboratory, Postdoc Fellow
• From Apr. 2017, To Mar. 2020

  National Cancer Center Research Institute, Division of Molecular Modification and Cancer Biology, External Research stuff
• From Apr. 2017, To Mar. 2019

  National Institute of Advanced Industrial Science and Technology, Artificial Intelligence Research Center, JSPS postdoctoral research fellow (PD)
• From Apr. 2014, To Mar. 2017

  University of Tokyo, Department of Computational Biology and Medical Sciences, Doctor course, JSPS research fellow (DC1)

ID,URL

• J-Global ID

  201801007866743153

• External link

  https://carushi.github.io/cb_lab/index_en.html

researchmap URL

• https://researchmap.jp/cawatchm

Research

Research Areas

• Life sciences, Molecular biology
• Life sciences, Systems genomics
• Informatics, Biological, health, and medical informatics

Papers

• Preface

  Kawaguchi, R.K.; Iwakiri, J.

  Methods in Molecular Biology, 2023

  
• Erratum: Identification of lysine methylation in the core GTPase domain by GoMADScan (PLoS ONE (2019) 14: 8 (e0219436) DOI: 10.1371/journal.pone.0219436)

  Yoshino, H.; Yin, G.; Kawaguchi, R.; Popov, K.I.; Temple, B.; Sasaki, M.; Kofuji, S.; Wolfe, K.; Kofuji, K.; Okumura, K.; Randhawa, J.; Malhotra, A.; Majd, N.; Ikeda, Y.; Shimada, H.; Kahoud, E.R.; Haviv, S.; Iwase, S.; Asara, J.M.; Campbell, S.L.; Sasaki, A.T.

  PLoS ONE, 2019

  
• A feedback amplifier circuit with Notch and E2A orchestrates T-cell fate and suppresses the innate lymphoid cell lineages during thymic ontogeny.

  Kazuko Miyazaki; Kenta Horie; Hitomi Watanabe; Reiko Hidaka; Rinako Hayashi; Norihito Hayatsu; Kentaro Fujiwara; Rei Kuwata; Takuya Uehata; Yotaro Ochi; Makoto Takenaka; Risa Karakida Kawaguchi; Koichi Ikuta; Osamu Takeuchi; Seishi Ogawa; Katsuto Hozumi; Georg A Holländer; Gen Kondoh; Taishin Akiyama; Masaki Miyazaki

  Genes & development, 04 Feb. 2025

  
• RNAelem: An Algorithm for Discovering Sequence-Structure Motifs in RNA Bound by RNA-Binding Proteins

  Hiroshi Miyake; Risa Karakida Kawaguchi; Hisanori Kiryu

  Bioinformatics Advances, 28 Sep. 2024

  
• The transcriptional legacy of developmental stochasticity

  Sara Ballouz; Risa Karakida Kawaguchi; Maria T. Pena; Stephan Fischer; Megan Crow; Leon French; Frank M. Knight; Linda B. Adams; Jesse Gillis

  Nature Communications, 09 Nov. 2023, Peer-reviewed, Lead author

  
• Comprehensive in virio structure probing analysis of the influenza A virus identifies functional RNA structures involved in viral genome replication

  Naoki Takizawa; Risa Karakida Kawaguchi

  Computational and Structural Biotechnology Journal, Oct. 2023, Peer-reviewed

  Access this paper :

  
• RNA Secondary Structure Alteration Caused by Single Nucleotide Variants

  Risa Karakida Kawaguchi; Hisanori Kiryu

  Methods in Molecular Biology, Jan. 2023, Lead author, Corresponding author

  
• Genome-Wide RNA Secondary Structure Prediction

  Risa Karakida Kawaguchi; Hisanori Kiryu

  Methods in Molecular Biology, Jan. 2023, Lead author, Corresponding author

  
• Learning single-cell chromatin accessibility profiles using meta-analytic marker genes

  Risa Karakida Kawaguchi; Ziqi Tang; Stephan Fischer; Chandana Rajesh; Rohit Tripathy; Peter K Koo; Jesse Gillis

  Briefings in Bioinformatics, 22 Dec. 2022, Peer-reviewed, Lead author

  
• Prevalent and dynamic binding of the cell cycle checkpoint kinase Rad53 to gene promoters

  Yi-Jun Sheu; Risa Karakida Kawaguchi; Jesse Gillis; Bruce Stillman

  eLife, 15 Dec. 2022, Peer-reviewed

  
• Assessing Versatile Machine Learning Models for Glioma Radiogenomic Studies across Hospitals.

  Risa K Kawaguchi; Masamichi Takahashi; Mototaka Miyake; Manabu Kinoshita; Satoshi Takahashi; Koichi Ichimura; Ryuji Hamamoto; Yoshitaka Narita; Jun Sese

  Cancers, 19 Jul. 2021, Peer-reviewed, Lead author

  
• Fine-Tuning Approach for Segmentation of Gliomas in Brain Magnetic Resonance Images with a Machine Learning Method to Normalize Image Differences among Facilities

  Satoshi Takahashi; Masamichi Takahashi; Manabu Kinoshita; Mototaka Miyake; Risa Kawaguchi; Naoki Shinojima; Akitake Mukasa; Kuniaki Saito; Motoo Nagane; Ryohei Otani; Fumi Higuchi; Shota Tanaka; Nobuhiro Hata; Kaoru Tamura; Kensuke Tateishi; Ryo Nishikawa; Hideyuki Arita; Masahiro Nonaka; Takehiro Uda; Junya Fukai; Yoshiko Okita; Naohiro Tsuyuguchi; Yonehiro Kanemura; Kazuma Kobayashi; Jun Sese; Koichi Ichimura; Yoshitaka Narita; Ryuji Hamamoto

  Cancers, 19 Mar. 2021, Peer-reviewed

  
• Intraductal transplantation models of human pancreatic ductal adenocarcinoma reveal progressive transition of molecular subtypes

  Koji Miyabayashi; Lindsey A. Baker; Astrid Deschenes; Benno Traub; Giuseppina Caligiuri; Dennis Plenker; Brinda Alagesan; Pascal Belleau; Siran Li; Jude Kendall; Gun Ho Jang; Risa Karakida Kawaguchi; Tim D.D. Somerville; Herve Tiriac; Chang-Il Hwang; Richard A. Burkhart; Nicholas J. Roberts; Laura D. Wood; Ralph H. Hruban; Jesse Gillis; Alexander Krasnitz; Christopher R. Vakoc; Michael Wigler; Faiyaz Notta; Steven Gallinger; Youngkyu Park; David A. Tuveson

  Cancer Discovery, 23 Jul. 2020, Peer-reviewed

  
• Identification of lysine methylation in the core RAS GTPase domain by GoMADScan

  Hirofumi Yoshino; Guowei Yin; Risa Kawaguchi; Konstantin I. Popov; Brenda Temple; Mika Sasaki; Satoshi Kofuji; Kara Wolfe; Kaori Kofuji; Koichi Okumura; Jaskirat Randhawa; Akshiv Malhotra; Nazanin Majd; Yoshiki Ikeda; Hiroko Shimada; Emily Rose Kahoud; Sasson Haviv; Shigeki Iwase; John M. Asara; Sharon L. Campbell; Atsuo T. Sasaki

  PLOS ONE, Aug. 2019, Peer-reviewed, Lead author

  
• IMP dehydrogenase-2 drives aberrant nucleolar activity and promotes tumorigenesis in glioblastoma.

  Satoshi Kofuji; Akiyoshi Hirayama; Alexander Otto Eberhardt; Risa Kawaguchi; Yuki Sugiura; Oltea Sampetrean; Yoshiki Ikeda; Mikako Warren; Naoya Sakamoto; Shuji Kitahara; Hirofumi Yoshino; Daisuke Yamashita; Kazutaka Sumita; Kara Wolfe; Lisa Lange; Satsuki Ikeda; Hiroko Shimada; Noriaki Minami; Akshiv Malhotra; Shin Morioka; Yuki Ban; Maya Asano; Victoria L Flanary; Annmarie Ramkissoon; Lionel M L Chow; Juri Kiyokawa; Tomoyuki Mashimo; Greg Lucey; Sergey Mareninov; Tatsuya Ozawa; Nobuyuki Onishi; Koichi Okumura; Jumpei Terakawa; Takiko Daikoku; Trisha Wise-Draper; Nazanin Majd; Kaori Kofuji; Mika Sasaki; Masaru Mori; Yonehiro Kanemura; Eric P Smith; Dimitrios Anastasiou; Hiroaki Wakimoto; Eric C Holland; William H Yong; Craig Horbinski; Ichiro Nakano; Ralph J DeBerardinis; Robert M Bachoo; Paul S Mischel; Wataru Yasui; Makoto Suematsu; Hideyuki Saya; Tomoyoshi Soga; Ingrid Grummt; Holger Bierhoff; Atsuo T Sasaki

  Nature cell biology, Aug. 2019, Peer-reviewed

  
• reactIDR: Evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction

  Risa Kawaguchi; Hisanori Kiryu; Junichi Iwakiri; Jun Sese

  BMC Bionifromatics, Mar. 2019, Peer-reviewed, Lead author

  
• Machine-learning approach to predict prognosis from MRI images and genomic features in glioblastoma

  Kawaguchi Risa; Takahashi Masamichi; Miyake Mototaka; Ichimura Koichi; Hamamoto Ryuji; Narita Yoshitaka; Sese Jun

  CANCER SCIENCE, Jan. 2018, Peer-reviewed

  
• グリオブラストーマにおけるMRI画像およびゲノム情報を利用した機械学習手法による予後予測

  河口 理紗; 高橋 雅道; 三宅 基隆; 市村 幸一; 浜本 隆二; 成田 善孝; 瀬々 潤

  日本癌学会総会記事, Sep. 2017, Peer-reviewed

  
• 網羅的構造予測及び再現性を考慮したハイスループット構造解析によるRNA二次構造の全体像の解明

  河口 理紗

  東京大学, Mar. 2017

  
• Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome

  Risa Kawaguchi; Hisanori Kiryu

  BMC BIOINFORMATICS, May 2016, Peer-reviewed, Lead author

  
• Split-alignment of genomes finds orthologies more accurately

  Martin C. Frith; Risa Kawaguchi

  Genome Biology, 21 May 2015, Peer-reviewed

  

Misc.

• Versatile machine-learning approaches for radiogenomics of glioma in different cohorts

  高橋雅道; 河口理紗; 河口理紗; 高橋慧; 三宅基隆; 木下学; 市村幸一; 浜本隆二; 成田善孝; 瀬々潤; 瀬々潤; 瀬々潤

  日本癌学会学術総会抄録集(Web), 2019

  
• GTP METABOLIC SWITCH LEADS TO NUCLEOLAR TRANSFORMATION AND MALIGNANT GROWTH OF GLIOBLASTOMA

  Kofuji Satoshi; Akiyoshi Hirayama; Naoya Sakamoto; Kazutaka Sumita; Hirofumi Yoshino; Mikako Warren; Risa Kawaguchi; Tatsuya Ozawa; Nobuyuki Onishi; Kara Wolfe; Koichi Okumura; Annmarie Ramkissoon; Lionel M. L. Chow; Akshiv Malhotra; Jumpei Terakawa; Takiko Daikoku; Trisha Wise-Draper; Nazanin Majd; Kaori Kofuji; Mika Sasaki; Masaru Mori; Dimitrios Anastasiou; Hiroaki Wakimoto; Holger Bierhoff; Craig M. Horbinski; Wataru Yasui; Hideyuki Saya; Tomoyoshi Soga; Eric Holland; Ingrid Grummt; Paul Mischel; Atsuo Sasaki

  NEURO-ONCOLOGY, Nov. 2017

  
• GTP結合タンパク質PIP4Kβによって制御される,PI(5)Pの標的タンパク質の網羅的探索系の構築

  高橋宏隆; 壽美田一貴; 河口理紗; 河口理紗; 小藤智史; 小藤智史; 笠原亜希子; 井上竜也; 櫻井秀敬; 和田直也; 久保田一石; 佐々木敦朗; 澤崎達也

  日本生化学会大会(Web), 2017

  

Books and Other Publications

• 実験デザインからわかるマルチオミクス研究実践テキスト : 実験・解析・応用まで現場で使えるプログラムコード付き完全ガイド

  大澤, 毅; 島村, 徹平, Contributor, scATAC-Seqによる転写制御解析

  羊土社, Apr. 2025

  Find Kyoto University's collection of books :

  
• Multi-omics: Disease research in data-driven research era

  Risa K. Kawaguchi; Mio Iwasaki, Contributor, 1細胞レベルのマルチオミクス解析のための基盤技術

  羊土社, Sep. 2023

  Find Kyoto University's collection of books :

  
• RNA Structure Prediction, Methods in Molecular Biology

  Risa Karakida Kawaguchi; Junichi Iwakiri, Joint editor

  Humana, New York., Feb. 2023

  Find Kyoto University's collection of books :

  
• 実験医学増刊 Vol.35 No.10 がん代謝 ワールブルグを超えて全容解明に挑む

  河口 理紗, Joint work, 第2章 がん特異的な代謝 7. GTP代謝

  羊土社, Jun. 2017, Not refereed

  

External funds: Kakenhi

• Integrative analysis of the stochasticity of single-cell omics data for predicting pioneerness of transcription factors

  Grant-in-Aid for Early-Career Scientists

  Basic Section 43050:Genome biology-related

  Kyoto University

  河口 理紗

  From 01 Apr. 2023, To 31 Mar. 2027, Granted

  エピゲノム;一細胞解析;機械学習;転写制御;大規模解析

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-23K14165/

Education

Teaching subject(s)

• From 01 Apr. 2024, To 31 Mar. 2025

  Global Frontier in Life Science A

  1018, Spring, Graduate School of Biostudies, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  Global Frontier in Life Science A

  1018, Spring, Graduate School of Biostudies, 2

Participation in PhD Defenses (other than KU)

• MODEC: an unsupervised clustering method integrating omics data for identifying cancer subtypes

  Yanting Zhang, The University of Tokyo, Japan, Sub-chief Examiner

  12 Jan. 2023

Administration

Faculty management (title, position)

• From 01 Oct. 2023, To 31 Mar. 2026

  CiRA研究インターンシップ委員会
• From 01 Apr. 2022, To 31 Mar. 2026

  情報管理委員会

Academic, Social Contribution

Committee Memberships

• From Apr. 2023, To Mar. 2027

  Board of Directors, Study Group Coordinator, Japanese Society for Bioinformatics
• From Sep. 2021, To Sep. 2021

  Program committee, IIBMP2021
• From Apr. 2018, To Mar. 2019

  運営委員, 生命科学系フロンティアミーティング
• From 2014, To 2019

  運営委員, 生命情報科学若手の会
• From Apr. 2017, To Mar. 2018

  代表, 生命情報科学若手の会
• From Apr. 2015, To Mar. 2016

  学生代表, 生命情報科学若手の会
• From 2013, To 2015

  Organizing committee, Asian Young Researchers Conference on Computational and Omics Biology (AYRCOB)

Social Contribution

• Artificial Intelligence to predict epigenome data from genome sequences

  Lecturer

  Information Processing Society of Japan, IPSJ-ONE, To 15 Mar. 2025

  
• Career seminar

  Panelist, Lecturer

  Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo., 大学院入学セミナー, From 04 Apr. 2023

  
• ズレも積もれば発見となる～コンピュータと見つける生物システムの謎～

  Guest, Lecturer

  京都大学iPS細胞研究所, CiRAカフェ, From 28 Jan. 2023

  
• 東京大学理学部 進学選択シンポジウム

  Guest

  From 22 Apr. 2021

  
• Miraibu plus super presentation for SSH students

  Guest

  河合塾みらいぶプラス, 「大学では学問しよう、研究しよう」, From 27 Nov. 2018