Kentaro Shimizu

Profile Information

Affiliation: Professor, Faculty of Science Department of Mathematics, Physics and Computer Science, Japan Women's University
: Graduate School of Agricultural and Life Sciences, The University of Tokyo

Degree: Master of Science(The University of Tokyo)
Doctor of Science(The University of Tokyo)

J-GLOBAL ID: 200901005695595964
researchmap Member ID: 1000017440

External link: http://www.bi.a.u-tokyo.ac.jp/~shimizu/

Research Interests

Research Areas

Research History

Apr, 2024 - Present

Graduate School of Agricultural and Life Sciences, The University of Tokyo
Apr, 2023 - Present

Faculty of Science Department of Mathematics, Physics and Computer Science, Japan Women's University
Dec, 1998 - Mar, 2023

Graduate School of Agricultural and Life Sciences, The University of Tokyo
1996 - 1998

Graduate School of Agricultural and Life Sciences, The University of Tokyo
1992 - 1996

電気通信大学情報工学科助教授
1996

- 東京大学大学院理学系研究科兼担
1991 - 1992

電気通信大学情報工学科講師
1986 - 1991

Faculty of Science, The University of Tokyo
1985 - 1986

東京大学大型計算機センター助手

Education

- 1985

The University of Tokyo
- 1985

Graduate School, Division of Science, The University of Tokyo
- 1980

Faculty of Science, The University of Tokyo
- 1980

Faculty of Science, The University of Tokyo

Papers

125

QM/MM Study of the Catalytic Mechanism and Substrate Specificity of the Aromatic Substrate C-Methyltransferase Fur6

Fan Zhao, Yoshitaka Moriwaki, Tomohiro Noguchi, Kentaro Shimizu, Tomohisa Kuzuyama, Tohru Terada

Biochemistry, Feb 29, 2024
Comprehensive computational analysis of the SRK–SP11 molecular interaction underlying self-incompatibility in Brassicaceae using improved structure prediction for cysteine-rich proteins

Tomoki Sawa, Yoshitaka Moriwaki, Hanting Jiang, Kohji Murase, Seiji Takayama, Kentaro Shimizu, Tohru Terada

bioRxiv, Jun 21, 2023
Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides

Kano Hasegawa, Yoshitaka Moriwaki, Tohru Terada, Cao Wei, Kentaro Shimizu

Journal of Bioinformatics and Computational Biology, 20(06), Dec, 2022
Prediction of protein mononucleotide binding sites using AlphaFold2 and machine learning

Shohei Yamaguchi, Haruka Nakashima, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu

Computational Biology and Chemistry, 107744-107744, Jul, 2022
Mutagenesis Analysis of GMN Motif in Arabidopsis thaliana Mg2+ Transporter MRS2-1

Xiaoyu Yang, Natsuko I Kobayashi, Yoshiki Hayashi, Koichi Ito, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu, Motoyuki Hattori, Ren Iwata, Hisashi Suzuki …

Bioscience, Biotechnology, and Biochemistry, May 7, 2022
Structural and Molecular Basis of the Catalytic Mechanism of Geranyl Pyrophosphate C6‐Methyltransferase: Creation of an Unprecedented Farnesyl Pyrophosphate C6‐Methyltransferase

Hayama Tsutsumi, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu, Kazuo Shin‐ya, Yohei Katsuyama, Yasuo Ohnishi

Angewandte Chemie International Edition, 61(1), Jan 3, 2022
Differential expression analysis using a model-based gene clustering algorithm for RNA-seq data

Takayuki Osabe, Kentaro Shimizu, Koji Kadota

BMC Bioinformatics, 22(1) 511, Oct, 2021 Peer-reviewed
Prediction and analysis of antifreeze proteins

Ryosuke Miyata, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu

Heliyon, 7(9) e07953-e07953, Sep, 2021
EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation

Keisuke Yanagisawa, Yoshitaka Moriwaki, Tohru Terada, Kentaro Shimizu

Journal of Chemical Information and Modeling, Jun 1, 2021
Mechanism of self/nonself-discrimination in Brassica self-incompatibility

Kohji Murase, Yoshitaka Moriwaki, Tomoyuki Mori, Xiao Liu, Chiho Masaka, Yoshinobu Takada, Ryoko Maesaki, Masaki Mishima, Sota Fujii, Yoshinori Hirano …

Nature Communications, 11(1), Dec, 2020
Commentary: A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines

Koji Kadota, Kentaro Shimizu

Frontiers in Genetics, 11, Sep 4, 2020
Development of a deep learning-based method to identify "good" regions of a cryo-electron microscopy grid.

Yuichi Yokoyama, Tohru Terada, Kentaro Shimizu, Kouki Nishikawa, Daisuke Kozai, Atsuhiro Shimada, Akira Mizoguchi, Yoshinori Fujiyoshi, Kazutoshi Tani

Biophysical reviews, 12(2) 349-354, Mar 11, 2020 Peer-reviewed
NRBP1-Containing CRL2/CRL4A Regulates Amyloid β Production by Targeting BRI2 and BRI3 for Degradation

Takashi Yasukawa, Aya Tsutsui, Chieri Tomomori-Sato, Shigeo Sato, Anita Saraf, Michael P. Washburn, Laurence Florens, Tohru Terada, Kentaro Shimizu, Ronald C. Conaway …

Cell Reports, 30(10) 3478-3491, Mar, 2020 Peer-reviewed
Structural analysis of β-L-arabinobiose-binding protein in the metabolic pathway of hydroxyproline-rich glycoproteins in Bifidobacterium longum

Masayuki Miyake, Tohru Terada, Michiko Shimokawa, Naohisa Sugimoto, Takatoshi Arakawa, Kentaro Shimizu, Kiyohiko Igarashi, Kiyotaka Fujita, Shinya Fushinobu

FEBS Journal, 2020 Peer-reviewed
Coarse-grained molecular dynamics simulation of protein conformational change coupled to ligand binding

Tatsuki Negami, Kentaro Shimizu, Tohru Terada

Chemical Physics Letters, 742 137144, Jan, 2020 Peer-reviewed
Functional characterisation of two ferric-ion coordination modes of TtFbpA, the periplasmic subunit of an ABC-type iron transporter from Thermus thermophilus HB8

Peng Lu, Yoshitaka Moriwaki, Mimin Zhang, Yukie Katayama, Yi Lu, Ken Okamoto, Tohru Terada, Kentaro Shimizu, Mengyao Wang, Takehiro Kamiya …

Metallomics, 11(12) 2078-2088, Dec, 2019 Peer-reviewed
Understanding the Molecular Mechanism Underlying the High Catalytic Activity of p-Hydroxybenzoate Hydroxylase Mutants for Producing Gallic Acid

Yoshitaka Moriwaki, Mirai Yato, Tohru Terada, Seiji Saito, Noriyuki Nukui, Takumi Iwasaki, Tatsunari Nishi, Yuko Kawaguchi, Ken Okamoto, Takatoshi Arakawa …

Biochemistry, 58(45) 4543-4558, Nov, 2019 Peer-reviewed
Dissecting the Stereocontrolled Conversion of Short-Lived Sulfenic Acid by Lachrymatory Factor Synthase

Takatoshi Arakawa, Yuta Sato, Masayuki Yamada, Jumpei Takabe, Yoshitaka Moriwaki, Noriya Masamura, Masahiro Kato, Morihiro Aoyagi, Takahiro Kamoi, Tohru Terada …

ACS Catalysis, 9, Nov, 2019 Peer-reviewed
Prediction of protein–metal ion-binding sites using sequence homology and machine-learning methods

Zihan Tian, Cao Wei, Yutaka Moriwaki, Tohru Terada, Shugo Nakamura, Kazuya Sumikoshi, Fang Chun, Kentaro Shimizu

Advanced Bioinformatics & Chemistry, 1(1) 025-036, Sep, 2019 Peer-reviewed
Accurate Classification of Differential Expression Patterns in a Bayesian Framework With Robust Normalization for Multi-Group RNA-Seq Count Data.

Osabe T, Shimizu K, Kadota K

Bioinform Biol Insights, 13 1177932219860817, Jul, 2019 Peer-reviewed

Misc.

217

次世代シーケンサーデータの解析手法：第15回RNA-seq解析(その3)

寺田朋子, 清水謙多郎, 門田幸二

日本乳酸菌学会誌, 31(1) 25-34, 2020
次世代シーケンサーデータの解析手法：第14回RNA-seq 解析（その2）

寺田朋子, 清水謙多郎, 門田幸二

日本乳酸菌学会誌, 30(2) 153-161, Nov, 2019 Invited
Methods for analyzing next-generation sequencing data XIII. RNA-seq analysis (Part 1)

Terada, T, Sakamoto, M, Shimizu, K, Kadota, K

Japanese Journal of Lactic Acid Bacteria, 30(1) 38-45, Mar, 2019 Invited
次世代シーケンサーデータの解析手法：第12回Galaxy：ヒストリーとワークフロー

寺田朋子, 大田達郎, 清水謙多郎, 門田幸二

29(2) 79-88, Jul, 2018 Invited
Methods for analyzing next-generation sequencing data: XI. Galaxy -an integrated data analysis environment

Tazro Ohta, Tomoko Terada, Kentaro Shimizu, Koji Kadota

28(3) 167-175, Nov, 2017 Invited
Methods for analyzing next-generation sequencing data(8)Genome annotation, visualization, and registration to DDBJ

谷澤靖洋, 真島淳, 藤澤貴智, 李慶範, 中村保一, 清水謙多郎, 門田幸二

日本乳酸菌学会誌 = Japanese journal of lactic acid bacteria, 28(1) 3-11, 2017
Methods for analyzing next-generation sequencing data X. Registration to DDBJ through Mass Submission System

谷澤靖洋, 藤澤貴智, 真島淳, 李慶範, 遠野雅徳, 坂本光央, 大熊盛也, 中村保一, 清水謙多郎, 門田幸二

日本乳酸菌学会誌 = Japanese journal of lactic acid bacteria, 28(2) 94-100, 2017
タンパク質の溶解度と配列・構造特徴との網羅的相関解析

中村周吾, 丹羽達也, 清水謙多郎, 田口英樹, 上田卓也

日本蛋白質科学会年会プログラム・要旨集, 16th 28, May 19, 2016
Insight into a Rapid Heme Transfer Reaction between Near Transporter Domains of Staphylococcus Aureus: A Theoretical Study using QM/MM and MD Simulations

Yoshitaka Moriwaki, Tohru Terada, Kouhei Tsumoto, Kentaro Shimizu

BIOPHYSICAL JOURNAL, 110(3) 381A-381A, Feb, 2016
A Multiscale Approach To Understanding Protein Ligand Binding Process

Tohru Terada, Tatsuki Negami, Kentaro Shimizu

BIOPHYSICAL JOURNAL, 110(3) 642A-642A, Feb, 2016
Methods for analyzing next-generation sequencing data VIII. Post-assembly analysis

Tanizawa Yasuhiro, Kaminuma Eli, Nakamura Yasukazu, Tohno Masanori, Terada Tomoko, Shimizu Kentaro, Kadota Koji

Japanese Journal of Lactic Acid Bacteria, 27(3) 187-195, 2016
Methods for analyzing next-generation sequencing data VII. long-read assembly

Tanizawa Yasuhiro, Kaminuma Eli, Nakamura Yasukazu, Tohno Masanori, Osaki Ken, Shimizu Kentaro, Kadota Koji

Japanese Journal of Lactic Acid Bacteria, 27(2) 101-110, 2016
Methods for analyzing next-generation sequencing dataVI. genome assembly

Tanizawa Yasuhiro, Kaminuma Eli, Nakamura Yasukazu, Shimizu Kentaro, Kadota Koji

Japanese Journal of Lactic Acid Bacteria, 27(1) 41-52, 2016
Methods for analyzing next-generation sequencing data V. assembly, mapping, and quality control

Sun Jianqiang, Shimizu Kentaro, Kadota Koji

Japanese Journal of Lactic Acid Bacteria, 26(3) 193-201, Nov, 2015 Invited
Methods for analyzing next-generation sequencing data IV. FASTQ quality control and program installation

26(2) 124-132, Jun, 2015 Invited
機械学習を用いたタンパク質機能予測における配列特徴の抽出法の検討

植木快, 中村周吾, 角越和也, 清水謙多郎

日本蛋白質科学会年会プログラム・要旨集, 15th 69, May 26, 2015
Methods for analyzing next-generation sequencing data III. From setting a Linux environment to manipulating Lactobacillus RNA-seq data

Sun Jianqiang, Miura Aya, Shimizu Kentaro, Kadota Koji

Japanese Journal of Lactic Acid Bacteria, 26(1) 32-41, Mar, 2015 Invited
次世代シーケンサーデータの解析手法：第2回GUI環境からコマンドライン環境へ

孫建強, 湯敏, 西岡輔, 清水謙多郎, 門田幸二

日本乳酸菌学会誌, 25(3) 166-174, Nov, 2014 Invited
Methods for analyzing next-generation sequencing data I. Introduction

Kadota Koji, Sun Jianqiang, Tang Min, Nishioka Tasuku, Shimizu Kentaro

Nyusankin Kenkyu Shudan Kaishi, 25(2) 87-94, Jul, 2014 Invited
位置特異的スコアリングマトリックスとサポートベクターマシーンを用いた脂質結合タンパク予測手法の開発

植木快, 番野雅城, 中村周吾, 清水謙多郎

日本蛋白質科学会年会プログラム・要旨集, 14th 128, May 26, 2014

Books and Other Publications

大人のための「情報」教科書（共著）

数研出版, 2003
高校教科書「情報C」（共著）

数研出版, 2003
高校教科書「情報B」（共著）

数研出版, 2003
高校教科書「情報A」（共著）

数研出版, 2003
分子動力学シミュレーションの並列計算

化学フロンティア, 東京化学同人, 2002
エンサイクロペディア情報処理

情報処理学会編集, オーム社, 2002
Parallel computing in molecular simulation

Fronteer of Chemistry, Tokyo Kagaku Dozin Co. Ltd., 2002
マイクロアレイ技術を用いた発現データベース構築とデータマイニング, 大規模ゲノム解析技術とポストシーケンス時代の遺伝子機能解析

中山書店, 2001
エンサイクロベディア情報処理2000-2001

オーム社(情報処理学会), 2000
情報処理ハンドブック(一部執筆)

オーム社, 1995
詳細OSハンドブック(一部執筆)

ソフトサーチセンター, 1994
オペレーティングシステム

岩波書店, 1992
Operating Systems

1992
分散オペレーティングシステム

共立出版, 1991
Distributed Operating Systems

1991

Professional Memberships

Works

Research Projects

Docking prediction and design of peptides by molecluar simulation and deep learning

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Japan Society for the Promotion of Science, Apr, 2021 - Mar, 2024
ゲノムジャンク領域にコードされる機能ペプチドの制御機構の情報学的推定と実験的検証

科学研究費助成事業, 基盤研究(C), 日本学術振興会, Apr, 2021 - Mar, 2024

福吉修一, 伊藤素行, 清水謙多郎
非コード領域・タンパク構造情報を含むオミクス統合解析に基づく精密医療の実現

科学研究費助成事業, 基盤研究(B), 日本学術振興会, Apr, 2021 - Mar, 2024

高橋広夫, 伊藤素行, 佐々木博己, 清水謙多郎
Prediction and analysis of intrinsically disordered regions in membrane proteins

Grants-in-Aid for Scientific Research, Grant-in-Aid for JSPS Fellows, Japan Society for the Promotion of Science, Oct, 2017 - Mar, 2020
Development of protein-carbohydrate binding prediction systems and databases

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science, Apr, 2011 - Mar, 2015

SHIMIZU Kentaro, TERADA Tohru, SUMIKOSHI Kazuya
Database Development and Functional Analysis of Protein Disorder Regions

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Japan Society for the Promotion of Science, 2008 - 2010

SHIMIZU Kentaro
タンパク質相互作用のネットワーク予測から原子レベルの結合予測までの統合的研究

科学研究費助成事業, 特定領域研究, 日本学術振興会, 2008 - 2010

清水謙太郎, 中村周吾, 角越和也
高精度のドッキング機能を有するタンパク質間相互作用予測システムの開発

科学研究費助成事業, 特定領域研究, 日本学術振興会, 2006 - 2007

清水謙多郎, 中村周吾, 寺田透, 角越和也
Development of methods for high-resolution protein structure modeling and for model structure assessment

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Japan Society for the Promotion of Science, 2005 - 2007

SHIMIZU Kentaro, NAKAMURA Shugo, TERADA Tohru
高精度のドッキング機能を有するタンパク質間相互作用予測システムの開発

科学研究費助成事業, 特定領域研究, 日本学術振興会, 2005 - 2005

清水謙多郎, 中村周吾, 寺田透
大規模分散データの真に透過で効率的な共有を実現する分散共有配列システムの開発

科学研究費助成事業, 特定領域研究, 日本学術振興会, 2004 - 2005

清水謙多郎, 中村周吾, 寺田透
ホモロジーモデリングとアビニシオ法の統合による高精度タンパク質構造予測手法の開発

科学研究費助成事業, 特定領域研究, 日本学術振興会, 2004 - 2004

清水謙多郎, 中村周吾, 寺田透
大規模分散データの効率的な共有を実現する並列コンピューティング環境の開発

科学研究費助成事業, 特定領域研究, 日本学術振興会, 2003 - 2003

清水謙多郎, 中村周吾
ホモロジーモデリングとアビニシオ法の統合による高精度タンパク質構造予測手法の開発

科学研究費助成事業, 特定領域研究, 日本学術振興会, 2003 - 2003

清水謙多郎, 寺田透, 中村周吾
Development of a Parallel Programming Environment based on Distributed Shared Arrays with Application-Specific Resource Management

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Japan Society for the Promotion of Science, 2001 - 2003

SHIMIZU Kentaro
大規模分散データの効率的な共有を実現する並列コンピューティング環境の開発

科学研究費助成事業, 特定領域研究, 日本学術振興会, 2002 - 2002

清水謙多郎, 中村周吾
大規模分散データの効率的な共有を実現する並列コンピューティング環境の開発

科学研究費助成事業, 特定領域研究(C), 日本学術振興会, 2001 - 2001

清水謙多郎, 中村周吾
Development of a Parallel Programming Environment with Dynamic Resource Management Facilities

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science, 1999 - 2001

SHIMIZU Kentaro, NAKAURA Shugo
Efficient Processor Allocation Policies for Massively Parallel Systems

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Japan Society for the Promotion of Science, 1998 - 2000

SHIMIZU Kentaro, NAKAMURA Shugo
大規模並列処理技術を用いたタンパク質の構造解析システムの開発

ＪＳＴ計算科学技術活用型特定研究開発推進事業（ＡＣＴ－ＪＳＴ）, 1999 - 1999

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