Takeya Kasukawa

Takeya Kasukawa

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Takeya Kasukawa

Publications by authors named "Takeya Kasukawa"

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The Number of Transcription Factors at an Enhancer Determines Switch-like Gene Expression.

Cell Rep 2020 Jun;31(9):107724

Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan; RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2020.107724DOI Listing
June 2020

Mesenchymal-epithelial transition regulates initiation of pluripotency exit before gastrulation.

Development 2020 Feb 3;147(3). Epub 2020 Feb 3.

International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto 860-0811, Japan

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http://dx.doi.org/10.1242/dev.184960DOI Listing
February 2020

refTSS: A Reference Data Set for Human and Mouse Transcription Start Sites.

J Mol Biol 2019 06 8;431(13):2407-2422. Epub 2019 May 8.

RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-Cho, Tsurumi-Ku, Yokohama, Kanagawa 230-0045, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2019.04.045DOI Listing
June 2019

Muscarinic Acetylcholine Receptors Chrm1 and Chrm3 Are Essential for REM Sleep.

Cell Rep 2018 08;24(9):2231-2247.e7

Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.07.082DOI Listing
August 2018

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

Methods Mol Biol 2017 ;1611:199-217

Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1007/978-1-4939-7015-5_15DOI Listing
February 2018

Genome Annotation.

Methods Mol Biol 2017 ;1525:107-121

Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1007/978-1-4939-6622-6_5DOI Listing
January 2018

SCPortalen: human and mouse single-cell centric database.

Nucleic Acids Res 2018 01;46(D1):D781-D787

Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1093/nar/gkx949DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753281PMC
January 2018

FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki.

Database (Oxford) 2016 9;2016. Epub 2016 Jul 9.

Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Kanagawa 230-0045, Japan RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan Preventive Medicine and Applied Genomics Unit, RIKEN Advanced Center for Computing and Communication, Kanagawa 230-0045, Japan

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http://dx.doi.org/10.1093/database/baw105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940433PMC
November 2017

Self-patterning of rostral-caudal neuroectoderm requires dual role of Fgf signaling for localized Wnt antagonism.

Nat Commun 2017 11 7;8(1):1339. Epub 2017 Nov 7.

Laboratory for Organogenesis and Neurogenesis, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.

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http://dx.doi.org/10.1038/s41467-017-01105-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5673904PMC
November 2017

FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies.

Sci Data 2017 08 29;4:170107. Epub 2017 Aug 29.

RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1038/sdata.2017.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5574367PMC
August 2017

FANTOM5 CAGE profiles of human and mouse samples.

Authors:
Shuhei Noguchi Takahiro Arakawa Shiro Fukuda Masaaki Furuno Akira Hasegawa Fumi Hori Sachi Ishikawa-Kato Kaoru Kaida Ai Kaiho Mutsumi Kanamori-Katayama Tsugumi Kawashima Miki Kojima Atsutaka Kubosaki Ri-Ichiroh Manabe Mitsuyoshi Murata Sayaka Nagao-Sato Kenichi Nakazato Noriko Ninomiya Hiromi Nishiyori-Sueki Shohei Noma Eri Saijyo Akiko Saka Mizuho Sakai Christophe Simon Naoko Suzuki Michihira Tagami Shoko Watanabe Shigehiro Yoshida Peter Arner Richard A Axton Magda Babina J Kenneth Baillie Timothy C Barnett Anthony G Beckhouse Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher Ailsa J Carlisle Hans C Clevers Carrie A Davis Michael Detmar Taeko Dohi Albert S B Edge Matthias Edinger Anna Ehrlund Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Afsaneh Eslami Michela Fagiolini Lynsey Fairbairn Mary C Farach-Carson Geoffrey J Faulkner Carmelo Ferrai Malcolm E Fisher Lesley M Forrester Rie Fujita Jun-Ichi Furusawa Teunis B Geijtenbeek Thomas Gingeras Daniel Goldowitz Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Yuki Hasegawa Meenhard Herlyn Peter Heutink Kelly J Hitchens David A Hume Tomokatsu Ikawa Yuri Ishizu Chieko Kai Hiroshi Kawamoto Yuki I Kawamura Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura Sarah Klein S Peter Klinken Alan J Knox Soichi Kojima Haruhiko Koseki Shigeo Koyasu Weonju Lee Andreas Lennartsson Alan Mackay-Sim Niklas Mejhert Yosuke Mizuno Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Kelly J Morris Hozumi Motohashi Christine L Mummery Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Tadasuke Nozaki Soichi Ogishima Naganari Ohkura Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Robert Passier Margaret Patrikakis Ana Pombo Swati Pradhan-Bhatt Xian-Yang Qin Michael Rehli Patrizia Rizzu Sugata Roy Antti Sajantila Shimon Sakaguchi Hiroki Sato Hironori Satoh Suzana Savvi Alka Saxena Christian Schmidl Claudio Schneider Gundula G Schulze-Tanzil Anita Schwegmann Guojun Sheng Jay W Shin Daisuke Sugiyama Takaaki Sugiyama Kim M Summers Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Andru Tomoiu Hiroo Toyoda Marc van de Wetering Linda M van den Berg Roberto Verardo Dipti Vijayan Christine A Wells Louise N Winteringham Ernst Wolvetang Yoko Yamaguchi Masayuki Yamamoto Chiyo Yanagi-Mizuochi Misako Yoneda Yohei Yonekura Peter G Zhang Silvia Zucchelli Imad Abugessaisa Erik Arner Jayson Harshbarger Atsushi Kondo Timo Lassmann Marina Lizio Serkan Sahin Thierry Sengstag Jessica Severin Hisashi Shimoji Masanori Suzuki Harukazu Suzuki Jun Kawai Naoto Kondo Masayoshi Itoh Carsten O Daub Takeya Kasukawa Hideya Kawaji Piero Carninci Alistair R R Forrest Yoshihide Hayashizaki

Sci Data 2017 08 29;4:170112. Epub 2017 Aug 29.

RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1038/sdata.2017.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5574368PMC
August 2017

The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types.

Sci Data 2017 08 29;4:170113. Epub 2017 Aug 29.

RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan.

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http://dx.doi.org/10.1038/sdata.2017.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5574373PMC
August 2017

Establishment of Functional Genomics Pipeline in Mouse Epiblast-Like Tissue by Combining Transcriptomic Analysis and Gene Knockdown/Knockin/Knockout, Using RNA Interference and CRISPR/Cas9.

Hum Gene Ther 2016 06 28;27(6):436-50. Epub 2016 Apr 28.

4 Laboratory for Organogenesis and Neurogenesis, RIKEN Center for Developmental Biology , Hyogo, Japan .

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http://dx.doi.org/10.1089/hum.2015.148DOI Listing
June 2016

Cell-cycle-independent transitions in temporal identity of mammalian neural progenitor cells.

Nat Commun 2016 Apr 20;7:11349. Epub 2016 Apr 20.

Department of Anatomy and Cell Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya, Aichi 466-8550, Japan.

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http://dx.doi.org/10.1038/ncomms11349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4842982PMC
April 2016

EpiFactors: a comprehensive database of human epigenetic factors and complexes.

Database (Oxford) 2015 7;2015:bav067. Epub 2015 Jul 7.

Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7489 Trondheim, Norway,

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http://dx.doi.org/10.1093/database/bav067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4494013PMC
March 2016

STAP cells are derived from ES cells.

Nature 2015 Sep;525(7570):E4-5

Cell Asymmetry, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.

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http://dx.doi.org/10.1038/nature15366DOI Listing
September 2015

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

Authors:
Erik Arner Carsten O Daub Kristoffer Vitting-Seerup Robin Andersson Berit Lilje Finn Drabløs Andreas Lennartsson Michelle Rönnerblad Olga Hrydziuszko Morana Vitezic Tom C Freeman Ahmad M N Alhendi Peter Arner Richard Axton J Kenneth Baillie Anthony Beckhouse Beatrice Bodega James Briggs Frank Brombacher Margaret Davis Michael Detmar Anna Ehrlund Mitsuhiro Endoh Afsaneh Eslami Michela Fagiolini Lynsey Fairbairn Geoffrey J Faulkner Carmelo Ferrai Malcolm E Fisher Lesley Forrester Daniel Goldowitz Reto Guler Thomas Ha Mitsuko Hara Meenhard Herlyn Tomokatsu Ikawa Chieko Kai Hiroshi Kawamoto Levon M Khachigian S Peter Klinken Soichi Kojima Haruhiko Koseki Sarah Klein Niklas Mejhert Ken Miyaguchi Yosuke Mizuno Mitsuru Morimoto Kelly J Morris Christine Mummery Yutaka Nakachi Soichi Ogishima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry Ovchinnikov Robert Passier Margaret Patrikakis Ana Pombo Xian-Yang Qin Sugata Roy Hiroki Sato Suzana Savvi Alka Saxena Anita Schwegmann Daisuke Sugiyama Rolf Swoboda Hiroshi Tanaka Andru Tomoiu Louise N Winteringham Ernst Wolvetang Chiyo Yanagi-Mizuochi Misako Yoneda Susan Zabierowski Peter Zhang Imad Abugessaisa Nicolas Bertin Alexander D Diehl Shiro Fukuda Masaaki Furuno Jayson Harshbarger Akira Hasegawa Fumi Hori Sachi Ishikawa-Kato Yuri Ishizu Masayoshi Itoh Tsugumi Kawashima Miki Kojima Naoto Kondo Marina Lizio Terrence F Meehan Christopher J Mungall Mitsuyoshi Murata Hiromi Nishiyori-Sueki Serkan Sahin Sayaka Nagao-Sato Jessica Severin Michiel J L de Hoon Jun Kawai Takeya Kasukawa Timo Lassmann Harukazu Suzuki Hideya Kawaji Kim M Summers Christine Wells David A Hume Alistair R R Forrest Albin Sandelin Piero Carninci Yoshihide Hayashizaki

Science 2015 Feb 12;347(6225):1010-4. Epub 2015 Feb 12.

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http://dx.doi.org/10.1126/science.1259418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681433PMC
February 2015

A promoter-level mammalian expression atlas.

Authors:
Alistair R R Forrest Hideya Kawaji Michael Rehli J Kenneth Baillie Michiel J L de Hoon Vanja Haberle Timo Lassmann Ivan V Kulakovskiy Marina Lizio Masayoshi Itoh Robin Andersson Christopher J Mungall Terrence F Meehan Sebastian Schmeier Nicolas Bertin Mette Jørgensen Emmanuel Dimont Erik Arner Christian Schmidl Ulf Schaefer Yulia A Medvedeva Charles Plessy Morana Vitezic Jessica Severin Colin A Semple Yuri Ishizu Robert S Young Margherita Francescatto Intikhab Alam Davide Albanese Gabriel M Altschuler Takahiro Arakawa John A C Archer Peter Arner Magda Babina Sarah Rennie Piotr J Balwierz Anthony G Beckhouse Swati Pradhan-Bhatt Judith A Blake Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher A Maxwell Burroughs Andrea Califano Carlo V Cannistraci Daniel Carbajo Yun Chen Marco Chierici Yari Ciani Hans C Clevers Emiliano Dalla Carrie A Davis Michael Detmar Alexander D Diehl Taeko Dohi Finn Drabløs Albert S B Edge Matthias Edinger Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Michela Fagiolini Lynsey Fairbairn Hai Fang Mary C Farach-Carson Geoffrey J Faulkner Alexander V Favorov Malcolm E Fisher Martin C Frith Rie Fujita Shiro Fukuda Cesare Furlanello Masaaki Furino Jun-ichi Furusawa Teunis B Geijtenbeek Andrew P Gibson Thomas Gingeras Daniel Goldowitz Julian Gough Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Matthias Harbers Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Takehiro Hashimoto Meenhard Herlyn Kelly J Hitchens Shannan J Ho Sui Oliver M Hofmann Ilka Hoof Furni Hori Lukasz Huminiecki Kei Iida Tomokatsu Ikawa Boris R Jankovic Hui Jia Anagha Joshi Giuseppe Jurman Bogumil Kaczkowski Chieko Kai Kaoru Kaida Ai Kaiho Kazuhiro Kajiyama Mutsumi Kanamori-Katayama Artem S Kasianov Takeya Kasukawa Shintaro Katayama Sachi Kato Shuji Kawaguchi Hiroshi Kawamoto Yuki I Kawamura Tsugumi Kawashima Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura S Peter Klinken Alan J Knox Miki Kojima Soichi Kojima Naoto Kondo Haruhiko Koseki Shigeo Koyasu Sarah Krampitz Atsutaka Kubosaki Andrew T Kwon Jeroen F J Laros Weonju Lee Andreas Lennartsson Kang Li Berit Lilje Leonard Lipovich Alan Mackay-Sim Ri-ichiroh Manabe Jessica C Mar Benoit Marchand Anthony Mathelier Niklas Mejhert Alison Meynert Yosuke Mizuno David A de Lima Morais Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Efthymios Motakis Hozumi Motohashi Christine L Mummery Mitsuyoshi Murata Sayaka Nagao-Sato Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Kenichi Nakazato Erik van Nimwegen Noriko Ninomiya Hiromi Nishiyori Shohei Noma Shohei Noma Tadasuke Noazaki Soichi Ogishima Naganari Ohkura Hiroko Ohimiya Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Arnab Pain Robert Passier Margaret Patrikakis Helena Persson Silvano Piazza James G D Prendergast Owen J L Rackham Jordan A Ramilowski Mamoon Rashid Timothy Ravasi Patrizia Rizzu Marco Roncador Sugata Roy Morten B Rye Eri Saijyo Antti Sajantila Akiko Saka Shimon Sakaguchi Mizuho Sakai Hiroki Sato Suzana Savvi Alka Saxena Claudio Schneider Erik A Schultes Gundula G Schulze-Tanzil Anita Schwegmann Thierry Sengstag Guojun Sheng Hisashi Shimoji Yishai Shimoni Jay W Shin Christophe Simon Daisuke Sugiyama Takaai Sugiyama Masanori Suzuki Naoko Suzuki Rolf K Swoboda Peter A C 't Hoen Michihira Tagami Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Zuotian Tatum Mark Thompson Hiroo Toyodo Tetsuro Toyoda Elvind Valen Marc van de Wetering Linda M van den Berg Roberto Verado Dipti Vijayan Ilya E Vorontsov Wyeth W Wasserman Shoko Watanabe Christine A Wells Louise N Winteringham Ernst Wolvetang Emily J Wood Yoko Yamaguchi Masayuki Yamamoto Misako Yoneda Yohei Yonekura Shigehiro Yoshida Susan E Zabierowski Peter G Zhang Xiaobei Zhao Silvia Zucchelli Kim M Summers Harukazu Suzuki Carsten O Daub Jun Kawai Peter Heutink Winston Hide Tom C Freeman Boris Lenhard Vladimir B Bajic Martin S Taylor Vsevolod J Makeev Albin Sandelin David A Hume Piero Carninci Yoshihide Hayashizaki

Nature 2014 Mar;507(7493):462-70

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http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014

Human blood metabolite timetable indicates internal body time.

Proc Natl Acad Sci U S A 2012 Sep 27;109(37):15036-41. Epub 2012 Aug 27.

Functional Genomics Unit, RIKEN Center for Developmental Biology, Chuo-ku, Kobe, Hyogo 650-0047, Japan.

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http://dx.doi.org/10.1073/pnas.1207768109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443163PMC
September 2012

Acute induction of Eya3 by late-night light stimulation triggers TSHβ expression in photoperiodism.

Curr Biol 2010 Dec 2;20(24):2199-206. Epub 2010 Dec 2.

Laboratory for Systems Biology, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.

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http://dx.doi.org/10.1016/j.cub.2010.11.038DOI Listing
December 2010

Transcriptomic landscape of the primitive streak.

Development 2010 Sep 28;137(17):2863-74. Epub 2010 Jul 28.

Laboratory for Early Embryogenesis, RIKEN Center for Developmental Biology, Kobe, Hyogo, Japan.

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http://dx.doi.org/10.1242/dev.053462DOI Listing
September 2010

[Physical simulation of the transcriptional network of mammalian circadian clocks].

Tanpakushitsu Kakusan Koso 2009 Dec;54(15):1958-64

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December 2009

Measurement of internal body time by blood metabolomics.

Proc Natl Acad Sci U S A 2009 Jun 1;106(24):9890-5. Epub 2009 Jun 1.

Laboratory for Systems Biology, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.

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http://dx.doi.org/10.1073/pnas.0900617106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689311PMC
June 2009

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

Nat Cell Biol 2008 Oct 21;10(10):1154-63. Epub 2008 Sep 21.

Laboratory for Systems Biology, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.

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http://dx.doi.org/10.1038/ncb1775DOI Listing
October 2008

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

Development 2008 Sep;135(18):3113-24

Laboratory for Cell Asymmetry, Center for Developmental Biology, RIKEN Kobe Institute, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.

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http://dx.doi.org/10.1242/dev.022616DOI Listing
September 2008

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

RNA Biol 2006 Jan-Mar;3(1):40-8. Epub 2006 Apr 3.

Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Kanagawa, Japan.

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http://dx.doi.org/10.4161/rna.3.1.2789DOI Listing
September 2007

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

Nucleic Acids Res 2006 Jan;34(Database issue):D632-6

NTT Software Corporation, Teisan Kannai Building 209, Yamashita-cho Naka-ku, Yokohama, Kanagawa, 231-8551, Japan.

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http://dx.doi.org/10.1093/nar/gkj034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347397PMC
January 2006

MaXML: mouse annotation XML.

In Silico Biol 2004 26;4(1):7-15. Epub 2003 Dec 26.

Network Service Solution Business Group, Content Sharing Service Business Unit, NTT Software Corporation, Yokohama, Kanagawa, Japan.

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December 2004

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

Genomics 2004 Dec;84(6):913-21

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1016/j.ygeno.2004.08.011DOI Listing
December 2004

[RTPS].

Authors:
Takeya Kasukawa

Tanpakushitsu Kakusan Koso 2004 Dec;49(17 Suppl):2871-6

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December 2004

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

Authors:
Tadashi Imanishi Takeshi Itoh Yutaka Suzuki Claire O'Donovan Satoshi Fukuchi Kanako O Koyanagi Roberto A Barrero Takuro Tamura Yumi Yamaguchi-Kabata Motohiko Tanino Kei Yura Satoru Miyazaki Kazuho Ikeo Keiichi Homma Arek Kasprzyk Tetsuo Nishikawa Mika Hirakawa Jean Thierry-Mieg Danielle Thierry-Mieg Jennifer Ashurst Libin Jia Mitsuteru Nakao Michael A Thomas Nicola Mulder Youla Karavidopoulou Lihua Jin Sangsoo Kim Tomohiro Yasuda Boris Lenhard Eric Eveno Yoshiyuki Suzuki Chisato Yamasaki Jun-ichi Takeda Craig Gough Phillip Hilton Yasuyuki Fujii Hiroaki Sakai Susumu Tanaka Clara Amid Matthew Bellgard Maria de Fatima Bonaldo Hidemasa Bono Susan K Bromberg Anthony J Brookes Elspeth Bruford Piero Carninci Claude Chelala Christine Couillault Sandro J de Souza Marie-Anne Debily Marie-Dominique Devignes Inna Dubchak Toshinori Endo Anne Estreicher Eduardo Eyras Kaoru Fukami-Kobayashi Gopal R Gopinath Esther Graudens Yoonsoo Hahn Michael Han Ze-Guang Han Kousuke Hanada Hideki Hanaoka Erimi Harada Katsuyuki Hashimoto Ursula Hinz Momoki Hirai Teruyoshi Hishiki Ian Hopkinson Sandrine Imbeaud Hidetoshi Inoko Alexander Kanapin Yayoi Kaneko Takeya Kasukawa Janet Kelso Paul Kersey Reiko Kikuno Kouichi Kimura Bernhard Korn Vladimir Kuryshev Izabela Makalowska Takashi Makino Shuhei Mano Regine Mariage-Samson Jun Mashima Hideo Matsuda Hans-Werner Mewes Shinsei Minoshima Keiichi Nagai Hideki Nagasaki Naoki Nagata Rajni Nigam Osamu Ogasawara Osamu Ohara Masafumi Ohtsubo Norihiro Okada Toshihisa Okido Satoshi Oota Motonori Ota Toshio Ota Tetsuji Otsuki Dominique Piatier-Tonneau Annemarie Poustka Shuang-Xi Ren Naruya Saitou Katsunaga Sakai Shigetaka Sakamoto Ryuichi Sakate Ingo Schupp Florence Servant Stephen Sherry Rie Shiba Nobuyoshi Shimizu Mary Shimoyama Andrew J Simpson Bento Soares Charles Steward Makiko Suwa Mami Suzuki Aiko Takahashi Gen Tamiya Hiroshi Tanaka Todd Taylor Joseph D Terwilliger Per Unneberg Vamsi Veeramachaneni Shinya Watanabe Laurens Wilming Norikazu Yasuda Hyang-Sook Yoo Marvin Stodolsky Wojciech Makalowski Mitiko Go Kenta Nakai Toshihisa Takagi Minoru Kanehisa Yoshiyuki Sakaki John Quackenbush Yasushi Okazaki Yoshihide Hayashizaki Winston Hide Ranajit Chakraborty Ken Nishikawa Hideaki Sugawara Yoshio Tateno Zhu Chen Michio Oishi Peter Tonellato Rolf Apweiler Kousaku Okubo Lukas Wagner Stefan Wiemann Robert L Strausberg Takao Isogai Charles Auffray Nobuo Nomura Takashi Gojobori Sumio Sugano

PLoS Biol 2004 Jun 20;2(6):e162. Epub 2004 Apr 20.

Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.

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http://dx.doi.org/10.1371/journal.pbio.0020162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC393292PMC
June 2004

FREP: a database of functional repeats in mouse cDNAs.

Nucleic Acids Res 2004 Jan;32(Database issue):D471-5

Biomedical Knowledge Discovery Team, Bioinformatics Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1093/nar/gkh123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308857PMC
January 2004

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

Proc Natl Acad Sci U S A 2003 Dec 8;100(26):15776-81. Epub 2003 Dec 8.

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1073/pnas.2136655100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC307644PMC
December 2003

Comprehensive analysis of the mouse metabolome based on the transcriptome.

Genome Res 2003 Jun;13(6B):1345-9

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1101/gr.974603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403659PMC
June 2003

CDS annotation in full-length cDNA sequence.

Genome Res 2003 Jun;13(6B):1478-87

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1101/gr.1060303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403693PMC
June 2003

Inferring higher functional information for RIKEN mouse full-length cDNA clones with FACTS.

Genome Res 2003 Jun;13(6B):1520-33

Biomedical Knowledge Discovery Team, Bioinformatics Group, RIKEN Genomic Sciences Center (GSC), Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1101/gr.1019903DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403704PMC
June 2003

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

Genome Res 2003 Jun;13(6B):1542-51

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1101/gr.992803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403710PMC
June 2003

[FANTOM-DB: database of functional annotation of RIKEN mouse cDNA clones].

Seikagaku 2003 Feb;75(2):149-52

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045.

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February 2003

FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones.

Nucleic Acids Res 2002 Jan;30(1):116-8

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99137PMC
http://dx.doi.org/10.1093/nar/30.1.116DOI Listing
January 2002

READ: RIKEN Expression Array Database.

Nucleic Acids Res 2002 Jan;30(1):211-3

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99103PMC
http://dx.doi.org/10.1093/nar/30.1.211DOI Listing
January 2002