Takeya Kasukawa

Profile Information

Affiliation: RIKEN
: Institute for Protein Research, Osaka University
: Visiting Professor, Graduate School of Medical Life Science, Yokohama City University

Degree: Ph.D (informatics)(Mar, 2005, Osaka University)

J-GLOBAL ID: 201301049355449068
researchmap Member ID: B000234429

Research Interests

Research Areas

Research History

Apr, 2022 - Present

Visiting Professor, Graduate School of Medical Life Science, Yokohama City University
Oct, 2019 - Present

Team Leader, RIKEN Center for Integrative Medical Sciences, RIKEN
Oct, 2018 - Present

Visiting Professor, Institute for Protein Research, Osaka University
Apr, 2018 - Sep, 2019

Unit Leader, RIKEN Center for Integrative Medical Sciences, RIKEN
Apr, 2013 - Mar, 2018

Unit Leader, Center for Life Science Technology, RIKEN
Apr, 2005 - Mar, 2013

Research Scientist, Center for Developmental Biology, RIKEN
Apr, 2000 - Mar, 2005

NTT Software Corporation
Apr, 1998 - Mar, 2000

Assistant professor, Graduate School of Engineering, Osaka University

Papers

Annotation of nuclear lncRNAs based on chromatin interactions

Saumya Agrawal, Andrey Buyan, Jessica Severin, Masaru Koido, Tanvir Alam, Imad Abugessaisa, Howard Y. Chang, Josée Dostie, Masayoshi Itoh, Juha Kere …

PLOS ONE, 19(5) e0295971-e0295971, May 6, 2024
OVCH1 Antisense RNA 1 is differentially expressed between non-frail and frail old adults.

Imad Abugessaisa, Ri-Ichiroh Manabe, Tsugumi Kawashima, Michihira Tagami, Chitose Takahashi, Yasushi Okazaki, Stefania Bandinelli, Takeya Kasukawa, Luigi Ferrucci

GeroScience, 46(2) 2063-2081, Apr, 2024
ROR2 expression predicts human induced pluripotent stem cell differentiation into neural stem/progenitor cells and GABAergic neurons.

Takuya Kuroda, Satoshi Yasuda, Satoko Matsuyama, Takumi Miura, Rumi Sawada, Akifumi Matsuyama, Yumiko Yamamoto, Masaki Suimye Morioka, Hideya Kawaji, Takeya Kasukawa …

Scientific reports, 14(1) 690-690, Jan 6, 2024
A single-cell atlas of transcribedcis-regulatory elements in the human genome

Jonathan Moody, Tsukasa Kouno, Miki Kojima, Ikuko Koya, Julio Leon, Akari Suzuki, Akira Hasegawa, Taishin Akiyama, Nobuko Akiyama, Masayuki Amagai …

Nov 14, 2023
Single-Cell RNA-Seq Reveals LRRC75A-Expressing Cell Population Involved in VEGF Secretion of Multipotent Mesenchymal Stromal/Stem Cells Under Ischemia

Takumi Miura, Tsukasa Kouno, Megumi Takano, Takuya Kuroda, Yumiko Yamamoto, Shinji Kusakawa, Masaki Suimye Morioka, Tohru Sugawara, Takamasa Hirai, Satoshi Yasuda …

Stem Cells Translational Medicine, 12(6) 379-390, Jun 1, 2023
Computational approach to evaluate scRNA-seq data quality and gene body coverage with SkewC.

Imad Abugessaisa, Akira Hasegawa, Shintaro Katayama, Juha Kere, Takeya Kasukawa

STAR protocols, 4(1) 102038-102038, Mar 17, 2023
Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types

Chi Wai Yip, Chung-Chau Hon, Kayoko Yasuzawa, Divya M. Sivaraman, Jordan A. Ramilowski, Youtaro Shibayama, Saumya Agrawal, Anika V. Prabhu, Callum Parr, Jessica Severin …

Cell Reports, 41(13) 111893-111893, Dec, 2022
Systematic Functional Annotation Workflow for Insects.

Hidemasa Bono, Takuma Sakamoto, Takeya Kasukawa, Hiroko Tabunoki

Insects, 13(7), Jun 27, 2022
SkewC: Identifying cells with skewed gene body coverage in single-cell RNA sequencing data.

Imad Abugessaisa, Akira Hasegawa, Shuhei Noguchi, Melissa Cardon, Kazuhide Watanabe, Masataka Takahashi, Harukazu Suzuki, Shintaro Katayama, Juha Kere, Takeya Kasukawa

iScience, 25(2) 103777-103777, Feb 18, 2022
Prediction of transcription factors associated with DNA demethylation during human cellular development.

Yurina Miyajima, Shuhei Noguchi, Yuki Tanaka, Jing-Ru Li, Hajime Nishimura, Mami Kishima, Joanne Lim, Erina Furuhata, Takahiro Suzuki, Takeya Kasukawa …

Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology, Feb 10, 2022
Inducing human retinal pigment epithelium-like cells from somatic tissue.

Ivo Ngundu Woogeng, Bogumil Kaczkowski, Imad Abugessaisa, Haiming Hu, Akihiro Tachibana, Yoshiki Sahara, Chung-Chau Hon, Akira Hasegawa, Noriko Sakai, Mitsuhiro Nishida …

Stem cell reports, 17(2) 289-306, Feb 8, 2022
Author Correction: RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions (Nature Communications, (2020), 11, 1, (1018), 10.1038/s41467-020-14337-6)

Alessandro Bonetti, Federico Agostini, Ana Maria Suzuki, Kosuke Hashimoto, Giovanni Pascarella, Juliette Gimenez, Leonie Roos, Alex J. Nash, Marco Ghilotti, Christopher J. F. Cameron …

Nature Communications, 12(1), Dec 1, 2021
IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells.

Minami Ando, Shigeyuki Magi, Masahide Seki, Yutaka Suzuki, Takeya Kasukawa, Diane Lefaudeux, Alexander Hoffmann, Mariko Okada

NPJ systems biology and applications, 7(1) 42-42, Dec 1, 2021
The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background

Luca Ducoli, Saumya Agrawal, Chung-Chau Hon, Jordan A. Ramilowski, Eliane Sibler, Michihira Tagami, Masayoshi Itoh, Naoto Kondo, Imad Abugessaisa, Akira Hasegawa …

BMC Genomic Data, 22(1), Dec, 2021
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli, Jordan A. Ramilowski, Jessica Severin, Yoshihide Hayashizaki, Masayoshi Itoh, Michihira Tagami, Mitsuyoshi Murata …

Nature Communications, 12(1), Dec, 2021
Automatic identification of small molecules that promote cell conversion and reprogramming.

Francesco Napolitano, Trisevgeni Rapakoulia, Patrizia Annunziata, Akira Hasegawa, Melissa Cardon, Sara Napolitano, Lorenzo Vaccaro, Antonella Iuliano, Luca Giorgio Wanderlingh, Takeya Kasukawa …

Stem cell reports, Apr 10, 2021
Functional annotation of human long noncoding RNAs using chromatin conformation data

Saumya Agrawal, Tanvir Alam, Masaru Koido, Ivan V. Kulakovskiy, Jessica Severin, Imad Abugessaisa, Andrey Buyan, Josee Dostie, Masayoshi Itoh, Naoto Kondo …

Jan 14, 2021
FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs.

Imad Abugessaisa, Jordan A Ramilowski, Marina Lizio, Jesicca Severin, Akira Hasegawa, Jayson Harshbarger, Atsushi Kondo, Shuhei Noguchi, Chi Wai Yip, Jasmine Li Ching Ooi …

Nucleic acids research, 49(D1) D892-D898, Jan 8, 2021
Single-cell transcriptomics, scRNA-Seq and C1 CAGE discovered distinct phases of pluripotency during naïve-to-primed conversion in mice

Michael Böttcher, Yuhki Tada, Jonathan Moody, Masayo Kondo, Hiroki Ura, Imad Abugessaisa, Takeya Kasukawa, Chung-Chau Hon, Koji Nagao, Piero Carninci …

Sep 25, 2020
Recounting the FANTOM CAGE-Associated Transcriptome.

Eddie Luidy Imada, Diego Fernando Sanchez, Leonardo Collado-Torres, Christopher Wilks, Tejasvi Matam, Wikum Dinalankara, Aleksey Stupnikov, Francisco Lobo-Pereira, Chi-Wai Yip, Kayoko Yasuzawa …

Genome research, 30(7) 1073-1081, Jul, 2020

Misc.

The FANTOM5 Computation Ecosystem: Genomic Information Hub for Promoters and Active Enhancers.

Abugessaisa I, Noguchi S, Carninci P, Kasukawa T

Methods in molecular biology (Clifton, N.J.), 1611 199-217, 2017 Peer-reviewed
FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells

T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin …

HUMAN GENOMICS, 10, May, 2016
睡眠基礎研究の萌芽的シンポジウムヒト血液代謝産物を用いた2時点の血液サンプルによる体内時刻測定法

粕川雄也, 杉本昌弘, 肥田昌子, 南陽一, 森雅代, 本間さと, 本間研一, 三島和夫, 曽我朋義, 上田泰己

日本睡眠学会定期学術集会プログラム・抄録集, 38回 111-111, Jun, 2013
ヒト血液代謝産物を用いた分子時刻表法による簡便なヒト体内時計の同定方法

粕川雄也, 杉本昌弘, 肥田昌子, 南陽一, 森雅代, 本間さと, 本間研一, 三島和夫, 曽我朋義, 上田泰己

日本分子生物学会年会プログラム・要旨集(Web), 35th WEB ONLY 2W1I-8, 2012
Physical simulation of the transcriptional network of mammalian circadian clocks

Protein, nucleic acid and enzyme, 54(15) 1958-1964, Dec, 2009
メタボローム解析による体内時刻の診断 (特集時間と病気--生体時計から時間医学へ)

南陽一, 粕川雄也, 上田泰己

メディカルバイオ, 6(6) 21-26, Nov, 2009
メタボロームによる哺乳類の体内時間の測定

南陽一, 粕川雄也, 上田泰己

生化学, 82回 ROMBUNNO.3S13A-5-5, Sep 25, 2009
メタボローム解析に基づく体内時刻診断法の開発

南陽一, 粕川雄也, 嘉数勇二, 飯郷雅之, 杉本正弘, 池田五月, 曽我朋義, 上田泰己

Program & Abstracts. 6th Congress of Asian Sleep Research Society, 34th Annual Meeting of Japanese Society of Sleep Research, 16th Annual Meeting of Japanese Society for Chronobiology Joint Congress 2009, 259, 2009
脊椎動物の季節繁殖のシステム生物学

小野ひろ子, 中尾暢宏, 山村崇, 安楽翼, 東久美子, 安尾しのぶ, 加藤泰弘, 影山三朗, 宇野有美子, 粕川雄也 …

日本畜産学会大会講演要旨, 109th 5, Mar 27, 2008
Detection of internal body time based on blood metabolome analysis using CE-TOFMS

Minami Yoichi, Kasukawa Takeya, Ikeda Satsuki, Satoh Sachie, Kakazu Yuji, Masayuki Iigo, Soga Tomoyoshi, Ueda Hiroki

Proceedings of Annual Meeting of the Physiological Society of Japan, 2008 87-87, 2008
Genome-wide analysis of mammalian promoter architecture and evolution (vol 38, pg 626, 2006)

Piero Carninci, Albin Sandelin, Boris Lenhard, Shintaro Katayama, Kazuro Shimokawa, Jasmina Ponjavic, Colin A. M. Semple, Martin S. Taylor, Paer G. Engstroem, Martin C. Frith …

NATURE GENETICS, 39(9) 1174-1174, Sep, 2007
ネットワーク科学最前線--世界の"つながり"を知る科学と思考(7)遺伝子発現ダイナミクスの統計則

小林徹也, 粕川雄也, 上田泰己

数理科学, 45(4) 70-77, Apr, 2007
再構成による哺乳類概日時計の転写ネットワークの理解

鵜飼(蓼沼)磨貴, 粕川雄也, 上田泰己

生化学, 1P-0933, 2007
脊椎動物の光周性の機能ゲノム的解析II:光周性制御遺伝子の機能解析

小野ひろ子, 中尾暢宏, 山村崇, 安楽翼, 粕川雄也, 飯郷雅之, 岩澤淳, 鈴木穣, 菅野純夫, 海老原史樹文 …

生化学, 1P-0930, 2007
鳥類の光周性分子機構の解明

中尾暢宏, 小野ひろ子, 山村崇, 安楽翼, 東久美子, 安尾しのぶ, 加藤泰弘, 影山三朗, 宇野有美子, 粕川雄也 …

Annual Meeting of Japanese Avian Endocrinology, 32nd 51-52, 2007
脊椎動物の光周性の機能ゲノム的解析I:ゲノムスケールの発現解析

中尾暢宏, 小野ひろ子, 東久美子, 安尾しのぶ, 加藤泰弘, 影山三朗, 宇野有美子, 粕川雄也, 飯郷雅之, SHARP Peter J …

生化学, 1P-0929, 2007
Response [2]

Piero Carninci, Julian Gough, Takeya Kasukawa, Yoshihide Hayashizaki

Science, 311(5768) 1709-1711, Mar 24, 2006
RTPS (ゲノムネットワーク) -- (横断的解析方法とデータゲノムネットワークのインフォマティクス)

粕川雄也

蛋白質核酸酵素, 49(17) 2871-2876, Dec, 2004
FANTOM-DB: database of functional annotation of RIKEN mouse cDNA clones

H Bono, T Kasukawa, M Furuno, Y Hayashizaki, Y Okazaki

SEIKAGAKU, 75(2) 149-152, Feb, 2003
発生研究のためのEST発現データベース構築機能予測から機能注釈へ FANTOM(Functional Annotation of Mouse)の経験から

坊農秀雅, 粕川雄也, 古野正朗, 林崎良英, 岡崎康司

日本発生生物学会大会講演要旨集, 35回 67-67, May, 2002

Books and Other Publications

時間薬理学による最新の治療戦略

大戸茂弘

医薬ジャーナル社, Apr, 2013 (ISBN: 4753226042)
体内時計の科学と産業応用 (バイオテクノロジーシリーズ)

柴田重信

シーエムシー出版, May, 2011 (ISBN: 4781303404)
改訂第2版バイオデータベースとウェブツールの手とり足とり活用法 ― 遺伝子の配列・機能解析、タンパク質解析、プロテオミクス、文献検索、検索エンジン…etc.真に役立つサイトを使い倒す！

中村保一, 石川淳, 礒合敦, 平川美夏, 坊農秀雅

羊土社, Oct 1, 2007 (ISBN: 4758108110)
RとBioconductorを用いたバイオインフォマティクス

R. ジェントルマン, V.J. カリー, W. フーバー, R.A. イリザリー, S. ドュドイト, 荒川和晴, 粕川雄也, 川路英哉, 河野信, 神田将和, 鈴木治夫, 田中伸也, 中尾光輝, 長嶋剛史, 二階堂愛, 宮本真理 (Role: Joint translator) (Original Author(s): R.ジェントルマン)

シュプリンガー・ジャパン株式会社, Jul 9, 2007 (ISBN: 4431734643)
バイオインフォマティクスゲノム配列から機能解析へ第2版

マウントデービッド W, 岡崎康司, 坊農秀雅

メディカル・サイエンス・インターナショナル, Dec 15, 2005 (ISBN: 4895924262)
ゲノム情報はこう活かせ!―比較ゲノム学を遺伝子・タンパク質の機能解析や疾患遺伝子探索に活用する方法がわかる

岡崎康司, 坊農秀雅

羊土社, Aug, 2005 (ISBN: 4897064856)
バイオインフォマティクスゲノム配列から機能解析へ

岡崎康司, 坊農秀雅, David W. Mount

メディカル・サイエンス・インターナショナル, May 25, 2002 (ISBN: 489592307X)

Presentations

Updating a data warehouse with low traffic cost

KASUKAWA TAKEYA, NAKANISHI MICHIO, HASHIMOTO AKIHIRO

IPSJ SIG Notes, Jan 21, 1997

Professional Memberships

Research Projects

A multi-omics study on multiple system atrophy patients with family history

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science, Apr, 2022 - Mar, 2025
転写ユニティー機構を構築する多因子間相互作用の時空間的かつ定量的解明

科学研究費助成事業, 学術変革領域研究(B), 日本学術振興会, Aug, 2021 - Mar, 2024

二村圭祐, 粕川雄也
Development of data analysis platform technology for data-driven genomic breeding

Grants-in-Aid for Scientific Research, Grant-in-Aid for Challenging Research (Exploratory), Japan Society for the Promotion of Science, Jul, 2021 - Mar, 2023

Industrial Property Rights

特開2010-261764 哺乳類の体内時刻の新規なインジケーター、及びその利用

上田泰己, 南陽一, 粕川雄也, 曽我朋義, 嘉数勇二

Profile Information

Research Interests

Research Areas

Research History

Papers

Misc.

Books and Other Publications

Presentations

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Research Projects

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