理化学研究所ライフサイエンス技術基盤研究センター RIKEN Center for Life Science Technologies

トピックス一覧

  • 研究成果

    CLSTから発表された最新の研究成果をご紹介します。
  • おしらせ

    受賞や協定の締結など、CLSTからのお知らせを掲載します。
  • イベント

    セミナーやシンポジウムなど、各種イベントをご紹介します。

一般の方へ

一人でも多くの方にCLSTの研究を知っていただくために、4つのコンテンツを集めました。
「読む」では研究者のインタビューや講演録などの記事を、「視聴する」では動画をご覧いただけます。「会いに行く」では、実際に研究者と会って話せるイベントをご案内します。「勉強する」は、研究内容をもっと深く知りたい方向けのコンテンツです。
  • 読む
  • 会いに行く
  • 視聴する
  • 勉強する

研究・技術

大容量データ管理技術開発ユニット

縁の下の力持ちではなく新発見を導くデータ管理技術の開発

ユニットリーダー
粕川 雄也   Ph.D.

〒230-0045 神奈川県横浜市鶴見区末広町1-7-22

2_5_kasukawa.png

研究内容

生命科学研究から生み出されるデータは膨大であり、研究者は様々な基礎研究の成果を調査・収集するため逐一論文誌やデータベースを検索することが次第に困難となっています。本ユニットでは、日々生み出される大量の次世代シーケンサーデータなどに対応するため以下の研究開発を行います。(1)大規模ゲノミクスデータセットを適切、効率的にかつ永続性を維持しながら管理するためのシステム要素技術の研究開発、(2)大規模ゲノミクスデータを解析し比較するためのリファレンスデータセットの構築。さらに、これらの研究開発に加えて、ゲノミクス研究をサポートする適切なコンピュータ環境のセットアップを行います。これらの研究開発により、基礎研究における発見を誘発することに加え、応用研究に必要な基礎研究成果や、その付加情報の入手を容易にし、応用研究への橋渡しも支援します。

論文

1

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers.

Kaczkowski B, Tanaka Y, Kawaji H, Sandelin A, Andersson R, Itoh M, Lassmann T, Hayashizaki Y, Carninci P, Forrest AR; FANTOM consortium
Cancer Res., 76(2), 216-226 (2016).
2

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C; FANTOM Consortium, Hume DA, Forrest AR, Sandelin A, Carninci P, Hayashizaki Y.
Science, 347(6225), 1010-1014 (2015).
3

Gateways to the FANTOM5 promoter level mammalian expression atlas

Marina Lizio, Jayson Harshbarger, Hisashi Shimoji, Jessica Severin, Takeya Kasukawa, Serkan Sahin, Imad Abugessaisa, Shiro Fukuda, Fumi Hori, Sachi Ishikawa-Kato, Christopher J Mungall, Erik Arner, J Kenneth Baillie, Nicolas Bertin, Hidemasa Bono, Michiel de Hoon, Alexander D Diehl, Emmanuel Dimont, Tom C Freeman, Kaori Fujieda, Winston Hide, Rajaram Kaliyaperumal, Toshiaki Katayama, Timo Lassmann, Terrence F Meehan, Koro Nishikata, Hiromasa Ono, Michael Rehli, Albin Sandelin, Erik A Schultes, Peter AC ‘t Hoen, Zuotian Tatum, Mark Thompson, Tetsuro Toyoda, Derek W Wright, Carsten O Daub, Masayoshi Itoh, Piero Carninci, Yoshihide Hayashizaki, Alistair RR Forrest,corresponding author Hideya Kawaji,corresponding author and the FANTOM consortium
Genome Biol, 16(1), 22 (2015).
4

A promoter-level mammalian expression atlas

FANTOM Consortium and the RIKEN PMI and CLST (DGT)
Nature, 507(7493), 462-470 (2014).
5

Human blood metabolite timetable indicates internal body time

Kasukawa T, Sugimoto M, Hida A, Minami Y, Mori M, Honma S, Honma K, Mishima K, Soga T, Ueda HR.
Proc Natl Acad Sci USA, 109(37), 15036-15041 (2012).
6

Quantitative expression profile of distinct functional regions in the adult mouse brain.

Kasukawa T, Masumoto KH, Nikaido I, Nagano M, Uno KD, Tsujino K, Hanashima C, Shigeyoshi Y, Ueda HR.
PLoS One, 6(8), e23228 (2011).
7

Measurement of internal body time by blood metabolomics

Minami Y, Kasukawa T, Kakazu Y, Iigo M, Sugimoto M, Ikeda S, Yasui A, van der Horst GT, Soga T, Ueda HR.
Proc Natl Acad Sci USA, 106(24), 9890-9895 (2009).
8

Proof-by-synthesis of the transcriptional logic of mammalian circadian clocks

Ukai-Tadenuma M, Kasukawa T, Ueda HR.
Nat Cell Biol, 10(10), 1154-1163 (2008).
9

Single-cell gene profiling defines differential progenitor subclasses in mammalian neurogenesis.

Kawaguchi A, Ikawa T, Kasukawa T, Ueda HR, Kurimoto K, Saitou M, Matsuzaki F.
Development, 135(18), 3113-3124 (2008).
10

Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.

Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, Engström PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, Bult CJ, Fletcher CF, Forrest AR, Furuno M, Hill D, Itoh M, Kanamori-Katayama M, Katayama S, Katoh M, Kawashima T, Quackenbush J, Ravasi T, Ring BZ, Shibata K, Sugiura K, Takenaka Y, Teasdale RD, Wells CA, Zhu Y, Kai C, Kawai J, Hume DA, Carninci P, Hayashizaki Y.
PLoS Genet, 2(4), e62 (2006).
11

Discrimination of non-protein-coding transcripts from protein-coding mRNA

Frith MC, Bailey TL, Kasukawa T, Mignone F, Kummerfeld SK, Madera M, Sunkara S, Furuno M, Bult CJ, Quackenbush J, Kai C, Kawai J, Carninci P, Hayashizaki Y, Pesole G, Mattick JS.
RNA Biol., 3(1), 40-48 (2006).
12

CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis

Kawaji H, Kasukawa T, Fukuda S, Katayama S, Kai C, Kawai J, Carninci P, Hayashizaki Y.
Nucleic Acids Res, 34, D632-636 (2006).
13

Antisense transcription in the mammalian transcriptome.

Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P, Hayashizaki Y, Wells C, Frith M, Ravasi T, Pang KC, Hallinan J, Mattick J, Hume DA, Lipovich L, Batalov S, Engström PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk AM, Mottagui-Tabar S, Liang Z, Lenhard B, Wahlestedt C; RIKEN Genome Exploration Research Group; Genome Science Group (Genome Network Project Core Group); FANTOM Consortium.
Science, 309(5740), 1564-1566 (2005).
14

The transcriptional landscape of the mammalian genome.

Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schönbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group).
Science, 309(5740), 1564-1566 (2005).
15

Construction of representative transcript and protein sets of human, mouse, and rat as a platform for their transcriptome and proteome analysis.

Kasukawa T, Katayama S, Kawaji H, Suzuki H, Hume DA, Hayashizaki Y.
Genomics, 84(6), 913-921 (2004).
16

Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, Kodzius R, Watahiki A, Nakamura M, Arakawa T, Fukuda S, Sasaki D, Podhajska A, Harbers M, Kawai J, Carninci P, Hayashizaki Y.
Proc Natl Acad Sci USA, 100(26), 15776-15781 (2003).
17

Development and evaluation of an automated annotation pipeline and cDNA annotation system.

Kasukawa T, Furuno M, Nikaido I, Bono H, Hume DA, Bult C, Hill DP, Baldarelli R, Gough J, Kanapin A, Matsuda H, Schriml LM, Hayashizaki Y, Okazaki Y, Quackenbush J.
Genome Res, 13(6B), 1542-1551 (2003).
18

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team
Nature, 420(6915), 563-573 (2002).

>>>すべての論文

メンバー  *:兼務

  • >>>Curriculum vitae