Publication
Research articles
Upcoming
Kawaguchi RK†, et al. (in prep)
..., Kawaguchi RK, et al. (submitted)
..., Kawaguchi RK, et al. (submitted)
..., Kawaguchi RK, et al. (in prep)
2023
”Ballouz S†, Kawaguchi RK†, Pena MT, Fischer S, Crow M, French L, Knight FM, Adams LB, Gillis J*. "The transcriptional legacy of developmental stochasticity."
Nature Communications, 14:7226 (2023)
bioRxiv 2019.12.11.873265 (DOI: https://doi.org/10.1101/2019.12.11.873265)
Takizawa N*, Kawaguchi RK. "Comprehensive in virio structure probing analysis of the influenza A virus identifies functional RNA structures involved in viral genome replication.”
Computational and Structural Biotechnology Journal, 21:5259-72, (2023)
bioRxiv 2020.03.05.975870 (DOI: https://doi.org/10.1101/2020.03.05.975870)
Kawaguchi RK and Kiryu H. "Genome-Wide RNA Secondary Structure Prediction"
RNA Structure Prediction, Methods in Molecular Biology 2586. (Protocol review)
Kawaguchi RK and Kiryu H. "RNA Secondary Structure Alteration Caused by Single Nucleotide Variants"
RNA Structure Prediction, Methods in Molecular Biology 2586. (Protocol review)
2022
Kawaguchi RK, Tang Z, Fischer S, Rajesh C, Tripathy R, Koo PK, Gillis J. "Learning single-cell chromatin accessibility profiles using meta-analytic marker genes"
Briefings in Bioinformatics 1:bbac541.
bioRxiv 2021.04.01.438068 (DOI: https://doi.org/10.1101/2021.04.01.438068)
Sheu Y, Kawaguchi RK, Gillis J, Stillman B. "Prevalent and Dynamic Binding of the Cell Cycle Checkpoint Kinase Rad53 to Gene Promoters"
eLife 11:e84320 (DOI: doi.org/10.7554/eLife.84320)
bioRxiv 2021.05.23.445333 (DOI: https://doi.org/10.1101/2021.05.23.445333)
2021
Kawaguchi RK †, Takahashi M*,†, Miyake M, Kinoshita M, Takahashi S, Ichimura K, Hamamoto R, Narita Y, Sese J. "Assessing Versatile Machine Learning Models for Glioma Radiogenomic Studies across Hospitals"
Cancers (Basel). 2021, 13(14), 3611
DOI: 10.3390/cancers13143611. PMID: 34298824.
Takahashi S, Takahashi M, Kinoshita M, Miyake M, Kawaguchi R, Shinojima N, Mukasa A, Saito K, Nagane M, Otani R, Higuchi F, Tanaka S, Hata N, Tamura K, Tateishi K, Nishikawa R, Arita H, Nonaka M, Uda T, Fukai J, Okita Y, Tsuyuguchi N, Kanemura Y, Kobayashi K, Sese J, Ichimura K, Narita Y, Hamamoto R. "Fine-Tuning Approach for Segmentation of Gliomas in Brain Magnetic Resonance Images with a Machine Learning Method to Normalize Image Differences among Facilities"
Cancers (Basel). 2021 Mar 19;13(6):1415
DOI: 10.3390/cancers13061415. PMID: 33808802.
2020
Miyabayashi K, Baker L, Deschênes A, Traub B, Caligiuri G, Plenker D, Alagesan B, Belleau P, Li S, Kendall J, Jang G, Kawaguchi RK, Somerville T, Tiriac H, Hwang C, Burkhart R, Roberts N, Wood L, Hruban R, Gillis J, Krasnitz A, Vakoc C, Wigler M, Notta F, Gallinger S, Park Y, and Tuveson D. "Intraductal transplantation models of human pancreatic ductal adenocarcinoma reveal progressive transition of molecular subtypes"
Cancer Discov 10(10):1566-89 (2020)
DOI: 10.1158/2159-8290.CD-20-0133
Takizawa N, Higashi K, Kawaguchi RK, Gotoh Y, Suzuki Y, Hayashi T, and Kurokawa K. "A functional RNA structure in the influenza A virus ribonucleoprotein complex for segment bundling"
2019
Kawaguchi R, Kiryu H, Iwakiri J and Sese J. "reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction"
BMC Bioinformatics 20 (Suppl 3) :130 (2019). ー Selected for APBC '19 proceedings
Kofuji S, Hirayama A, Eberhardt AO, Kawaguchi R, et al. "IMP dehydrogenase-2 drives aberrant nucleolar activity and promotes tumorigenesis in glioblastoma".
Nature Cell Biology, 21:1003–1014 (2019)
PDF link: https://rdcu.be/bMHNW
News ecancer science daily
Yoshino H†, Yin G†, Kawaguchi R†, Popov K, Temple B, Sasaki M, Kofuji S, Wolfe K, Kofuji K, Okumura K, Randhawa J, Malhotra A, Majd N, Ikeda Y, Shimada H, Kahoud ER, Haviv S, Iwase S, Asara JM, Campbell SL, and Sasaki AT. "Identification of lysine methylation in the core RAS GTPase domain by GoMADScan" .
PLOS ONE, 14(8): e0219436 (2019)
† equal contribution
2016
Kawaguchi R and Kiryu H. "Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome. "
BMC Bioinformatics 17:203 (2016).
For its complete DP explanation, please see my doctoral thesis (some literal errors were also fixed).
2015
Frith MC and Kawaguchi R. "Split-alignment of genomes finds orthologies more accurately."
Genome biology 16:106 (2015).
Invited talk and Seminar
2024: Tsukuba Bioinformatics lab セミナー （Jan 29th @ Tsukuba）
「Beyond Nature and Nurture: Does Stochastic Noise Change the Cellular Epigenetic Landscape?」(生まれと育ちを超えて：確率的ノイズは細胞のエピジェネティックランドスケープを変化させるか？)
2023: NGS EXPO 2023 (Nov. 15th @ Osaka International Convention Center for iPS Cell Research and Application)
"一細胞レベルのゆらぎにより細胞集団の“個性”が生み出されるメカニズムに迫る" 河口 理紗
2023: 生命情報科学若手の会 第15回年会
"マルチオミクス情報からたどる細胞間の確率的ゆらぎが生み出す四つ子の”個性" 河口 理紗
2023: LINK-J セミナー 異分野融合による「次世代」iPS細胞研究～京都大学iPS細胞研究所（CiRA）の挑戦～ (Jan. 17th @ Nihonbashi Life Science Building)
"一細胞エピゲノム解析のメタ統合解析による細胞分化メカニズムの解明" 河口 理紗
2022: 定量生物学の会チュートリアル (Dec. 7th online)
"離散的配列情報と高次元生命情報をつなぐ統計と機械学習" 河口 理紗
2018: 国立がん研究センター研究所 市村研究室セミナー（Dec. 11th @ National Cancer Center）
"機械学習を利用したMRI画像によるグリオーマ患者のゲノム・エピゲノム情報予測" 河口 理紗
2018: 筑波大学バイオインフォマティクスセミナー第1回 (Nov. 22th @ Tsukuba Univ)
"井の中のバイオインフォ解析にならないために" 河口 理紗
2018: 生命の機能とかたち 連携セミナーシリーズ第4回 (Mar. 8th @ Tsukuba Univ)
"生命データの洪水のあと - 時系列マルチオミクス解析で迫るがん代謝" 河口 理紗
2017: International GTP symposium (Jun. 1-2 @ Cincinnati, OH, USA)
"Multi-omics analyses to reveal the mechanism of GTP sensor" Risa Kawaguchi
2016: Riken Bioinformatics Seminar (Jul. 20 @ Wako, Riken)
"RNA二次構造予測から見る転写領域の配列的制約" 河口 理紗
Talk
2024: 未踏探索における個性と集団の役割（Feb. 22 @ Kyoto, Japan）
"確率的細胞運命の運河化と可塑性―一卵性四つ子のアルマジロの多様性"
2024: iPSアカデミアジャパン成果報告会（Feb. 9 @ Kyoto, Japan）
"iPS細胞の分化過程における転写因子のパイオニアネス変化予測"
2023: Commemorative Symposium for the 39th International Prize for Biology (Dec. 16-17 @ Yokohama, Japan)
"Deciphering epigenetic landscapes for variations in gene regulatory networks in mammals" Risa Kawaguchi
2023: 2nd GTP hackathon (Dec. 9-11 @ Yamanashi, Japan)
"一細胞レベルのゆらぎにより細胞集団の“個性”が生み出されるメカニズムに迫る" 河口 理紗
2023: The 46th Annual Meeting of Molecular Biology Society of Japan 2023 (Dec. 6-8 @ Kobe, Japan)
"Analyzing comprehensive single-cell transcriptome data to estimate the activity of GTP sensor regulatory network in a cell-type specific manner" Risa K. Kawaguchi
2023: CiRA 2023 International Symposium (Nov. 29-30 @ Kyoto, Japan)
"Prediction of epigenetic regulatory variation at single-cell level and its applications for stem cell biology" Risa K. Kawaguchi.
2023: 第12回生命医薬情報学連合大会 (Sep. 7-9 @ Kashiwa, Japan)
"Nine-banded armadillo transcriptome and chromatin accessibility at single-cell reveal persistent identity signatures in concordance with cell population biases" Risa K. Kawaguchi†, Sara Ballouz†, Maria T. Pena, Frank M. Knight, Linda B. Adams, Jesse Gillis.
2023: RNAインフォマティクス道場2023 (Aug. 22 @ Kobe, Japan)
2023: 28th International Conference on Statistical Physics (STATPHYS28) satellite meeting “Statistical Physics and Information-Processing in Living Systems” (Aug. 3-5th @ Tokyo, Japan)
"Nine-banded armadillo transcriptome analysis reveals the persistent identity signatures derived from stochastic variability" Risa Kawaguchi
2023: The 5th Annual Meeting of the Japanese Association for Medical Artificial Intelligence. (Jun. 17-18th @ Tokyo, Japan)
"一細胞エピゲノム解析のメタ統合解析による細胞分化メカニズムの解明" 河口 理紗
2022: GTP hackathon (Dec. 10 @ Tsuruoka, Japan)
"データサイエンティストが紐解く老化と発達の切っても切れない関係" 河口 理紗
2022: The 45th Annual Meeting of the Molecular Biology Society of Japan 2022 GTPと疾患治療 (Dec. 2nd @ Makuhari, Japan)
"Elucidating GTP sensor regulatory network that reconciles the imbalance of metabolism and its association with human phenotypic traits" Risa K. Kawaguchi.
2022: The 45th Annual Meeting of the Molecular Biology Society of Japan 2022 オミクスを重ねた解析から我々は何を知ることができるのか？ (Nov. 30th @ Makuhari, Japan)
"Armadillo single-cell transcriptome and chromatin accessibility reveal the persistent identity signatures derived from developmental perturbation" Kawaguchi RK, Ballouz S, Pena MT, Knight FM, Adams LB, Gillis J.
2022: 幹細胞の培養法・培養工学のためのコンソーシアム第6回シンポジウム (Nov. 19th @ Osaka, Japan)
"情報生命科学による幹細胞研究の新展開" 河口 理紗
2022: The 22nd Annual Meeting of the RNA society of Japan (Jul. 20-23 @ Kyoto, Japan)
"Nine-banded armadillo transcriptome and chromatin accessibility exhibit variability in identity at cellular resolution" Risa K. Kawaguchi
2021: The 44th Annual Meeting of the Molecular Biology Society of Japan 2021 (Dec. 2-4 @ Japan)
"Multi-omics approach to reveal the landscape of GTP sensor regulatory network that reconciles the imbalance of metabolism" (organizer) Risa K. Kawaguchi
2021: The 94th Annual Meeting of the Japanese Biochemical Society (Nov. 3-5 @ Japan)
"Exploiting marker genes for robust classification and characterization of single-cell chromatin accessibility" Risa K. Kawaguchi
2020: The 43rd Annual Meeting of the Molecular Biology Society of Japan 2020 (Dec. 2-4 @ Japan)
"Multi-omics approach to reveal the regulatory mechanism between GTP metabolism and tumorigenesis" Risa K. Kawaguchi
2020: Genome Informatics 2020 (Sep. 14-16 @ Hinxton, UK - virtual)
"Assessment of Chromatin Accessibility Cell-type Annotation Using a Reference Mouse Cortex Atlas" Risa K. Kawaguchi
2020: Informatics In Biology, Medicine and Pharmacology (IIBMP) 2020 (Sep. 1-3rd @ Japan - virtual)
"共発現ネットワークを利用したマウスの脳組織一細胞ATAC-seq解析の網羅的比較" Risa K. Kawaguchi
2019: The 17th Asia Pacific Bioinformatics Conference (Jan. 14-16 @ Wuhan, China)
"reactIDR: Evaluation of the statistical reproducibility of high-throughput structural analyses for a robust RNA reactivity classification" Risa Kawaguchi*, Hisanori Kiryu, Junichi Iwakiri and Jun Sese
accepted ratio=0.34 (51/150)
2018: The 41st Annual Meeting of the Molecular Biology Society of Japan (Nov. 28-30 @ Yokohama, Japan)
"Evolution and function of GTP sensing system" workshop (organizer)
"When, how, and why a GTP sensor has emerged" Risa Kawaguchi
"神経膠腫の初回術前 MRI 画像に対する網羅的画像特徴を用いた遺伝子情報予測" Risa Kawaguchi
2017: The 76th Annual Meeting of the Japanese Cancer Association (Sep. 28-30 @ Yokohama, Japan)
"Machine-learning approach to predict prognosis from MRI images and genomic features in glioblastoma" Risa Kawaguchi
2017: Japanese association of the younger researchers of bioinformatics, 9th meeting. (Oct. 6-8 @ Aichi, Japan)
"reactIDR: 再現性を考慮したハイスループットRNA構造解析のための統計的アプローチ" 河口 理紗
2017: Consortium of Biological Sciences 2017 (Dec. 6-9 @ Kobe, Japan)
"Multidisciplinary Approach Reveals Novel Function of GTP Energy and Strategy to Cure Human Diseases" workshop
"Time-course multiomics analysis to reveal a hidden connection between GTP metabolism and tumorigenesis" Risa Kawaguchi
2016: Informatics in Biology, Medicine, and Pharmacology, Highlight track (Sep. 29 - Oct. 1)
"Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome" Risa Kawaguchi
2015: Computational Analysis of RNA Structure and Function (Jul. 19-31 @ Benasque, Spain)
"ParasoR: Genome-wide computational analysis of local RNA secondary structure" Risa Kawaguchi
2015: RNA research meeting (Aug. 19-22 @ Hokkaido, Japan)
"タフでグローバルなRNA二次構造解析に向けて" 河口 理紗
2014: Japanese association of the younger researchers of bioinformatics, 7th meeting. (Sep. @ Yamagata, Japan)
"ゲノムワイド局所的二次構造解析によるイントロン領域の塩基対の安定化傾向" 河口 理紗
2014: RNA research meeting (Aug. 25-29 @ Hokkaido, Japan)
"Genome-wide analysis of a landscape of RNA secondary structure" Risa Kawaguchi
2014: Japanese association of the younger researchers of bioinformatics, 6th meeting. (Oct. 29-30 @ Kobe, Japan)
"ゲノムワイドRNA二次構造解析による転写領域の二次構造的性質" 河口 理紗
2013: 7th Asian Young Researchers Conference on Computational and Omics Biology (AYRCOB) (Sep. 9-10 @ Tokyo, Japan)
"An algorithm for evolutionary analysis about the influence of single nucleotide variants on RNA secondary structure landscape" Risa Kawaguchi
2013: RiboClub2013 (Sep. 23-25 @ Quebec, Canada)
"A comprehensive analysis of RNA secondary structure with deletion, insertion and mutation" Risa Kawaguchi
Poster
2023: 第12回生命医薬情報学連合大会 (Sep. 7-9 @ Kashiwa, Japan)
"Nine-banded armadillo transcriptome and chromatin accessibility at single-cell reveal persistent identity signatures in concordance with cell population biases" Risa K. Kawaguchi†, Sara Ballouz†, Maria T. Pena, Frank M. Knight, Linda B. Adams, Jesse Gillis.
2023: 28th International Conference on Statistical Physics (STATPHYS28) satellite meeting “Statistical Physics and Information-Processing in Living Systems” (Aug. 3-5th @ Tokyo, Japan)
"Nine-banded armadillo transcriptome analysis reveals the persistent identity signatures derived from stochastic variability" Risa Kawaguchi
2023: The 31st Annual Intelligent Systems For Molecular Biology and the 22nd Annual European Conference on Computational Biology (ISMBECCB 2023) (Jul 23-27 @ Lyon, France)
" Large-scale integration analysis of epigenetic data for inferring the binding modes of reprogramming transcription factors" Risa Kawaguchi
2023: The 24th Annual meeting of RNA Society of Japan (Jul 5-7@ Okinawa, Japan)
"Large-scale integration analysis of epigenetic data for inferring the context-dependent stochastic binding of reprogramming transcription factors " Risa K Kawaguchi.
2021: Single cell analysis, CSHL meeting series (Nov. 10-12 @ CSHL, NY, USA)
"Exploiting marker genes for robust classification and characterization of single-cell chromatin accessibility" Risa K. Kawaguchi, Ziqi Tang, Stephan Fischer, Chandana Rajesh, Rohit Tripathy, Peter K. Koo, and Jesse Gillis
2021: Probabilistic modeling in Genomics 2021, CSHL meeting series (Apr. 14-16 @ CSHL, NY, USA)
"Assessment of chromatin accessibility cell-type annotation using a reference mouse cortex atlas" Risa K. Kawaguchi, Ziqi Tang, Stephan Fischer, Rohit Tripathy, Peter K. Koo, and Jesse Gillis
2020: Biology of Genomes 2020, CSHL meeting series (May. 5-8th @ CSHL, NY, USA)
"Supervised single-cell chromatin accessibility analysis to establish cell-type annotation for mouse cortex scATAC-seq data with a massive reference atlas" Risa K. Kawaguchi, Stephan Fischer, Jesse Gillis
2019: Informatics In Biology, Medicine and Pharmacology (IIBMP) 2019 (Sep. 9-11th @ Tokyo Institute of Technology, Tokyo, Japan )
"The challenge of detecting chromatin co-accessible structures in mouse brain" Risa K. Kawaguchi, Stephan Fischer, Jesse Gillis
2018: Life Science Frontier Meeting 2018 (Oct. 5-7th @ National Institute of Genetics, Sizuoka, Japan)
"マルチオミクスデータにおけるエンリッチメント解析の傾向と対策" 河口理紗, Jesse Gillis
2018: Informatics In Biology, Medicine and Pharmacology (IIBMP) 2018 (Sep. 19-21 @ Yamagata, Japan)
"機械学習を利用したMRI画像によるグリオーマ患者のゲノム・エピゲノム情報予測" 河口理紗, 高橋雅道, 三宅基隆, 木下学, 市村幸一, 浜本隆二, 成田善孝, 瀬々潤
2018: CSHL meeting series "Mechanisms & Models of Cancer" (Aug. 14-18 @ NY, USA)
"Multi-omics approach to reveal the regulatory mechanism between GTP metabolism and tumorigenesis" Risa Kawaguchi et al.
2017: ISMB/ECCB 2017 (Jul. 21-25 @ Prague, Czech)
"reactIDR: Statistical approach to robust RNA reactivity classification based on reproducible high-throughput structure analyses" Risa Kawaguchi and Hisanori Kiryu.
2017: NGS genba meeting (May. 22-24 @ Sendai, Japan)
"再現性を考慮したハイスループット構造解析によるRNA二次構造予測のための統計的アプローチ" Risa Kawaguchi and Hisanori Kiryu.
2016: Japanese association of the bioinformatics young researchers committee, 8th meeting Lightning talk (Oct. 12-14 @ Hokkaido, Japan)
"IDRを利用したハイスループット構造解析におけるスコアリング手法の開発" 河口理紗, 木立尚孝
2015: The 17th Annual meeting of RNA Society of Japan (Jul @ Hokkaido, Japan)
"ゲノムワイド局所的二次構造解析により明らかになったイントロン領域における塩基対の安定化傾向" 河口理紗, 木立尚孝
2015: NGS genba meeting (Jul. @ Ibaraki, Japan)
"ゲノムワイド局所RNA二次構造予測による転写領域の構造的性質の解析" 河口理紗, 木立尚孝
2014: The 37th Annual Meeting of the Molecular Biology Society of Japan (Nov. @ Yokohama, Japan)
"Genome-wide prediction and characterization of RNA secondary structure landscape" 河口理紗, 木立尚孝
2014: The 16th Annual meeting of RNA Society of Japan (Jul @ Hokkaido, Japan)
"ゲノムワイドRNA二次構造予測による二次構造ランドスケープの特性の解明" 河口理紗, 木立尚孝
Awards
2018 Poster award, Informatics In Biology, Medicine and Pharmacology (IIBMP) 2018.
2017 Dean's Awards and Excellent Research Awards, Department of Computational Biology and Medical Science, the University of Tokyo.
2016 Young Scientist Superior Oral Presentation Awards. the University of Tokyo.
2014 Dean's Awards for AYRCOB committee. the University of Tokyo.
Grants/Fellowship
2023 iPS Academia Japan, Inc. Research grant
2021 Overseas postdoctoral fellowship, Uehara memorial foundation.
2017- 2019 JSPS's Research Fellowships for Young Postdoctoral Researchers
2014-2017 JSPS's Research Fellowships for Young Scientists
2015 新学術領域研究「ノンコーディングRNAネオタクソノミ」Travel fellowship