H
Hiroki R. Ueda
Researcher at University of Tokyo
Publications - 247
Citations - 21711
Hiroki R. Ueda is an academic researcher from University of Tokyo. The author has contributed to research in topics: Circadian clock & Circadian rhythm. The author has an hindex of 59, co-authored 211 publications receiving 18300 citations. Previous affiliations of Hiroki R. Ueda include Intec, Inc. & Osaka University.
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Journal ArticleDOI
The Transcriptional Landscape of the Mammalian Genome
Piero Carninci,Takeya Kasukawa,Shintaro Katayama,Julian Gough,Martin C. Frith,N. Maeda,Rieko Oyama,Timothy Ravasi,Boris Lenhard,Christine A. Wells,Christine A. Wells,Rimantas Kodzius,Kazuro Shimokawa,Vladimir B. Bajic,Steven E. Brenner,Serge Batalov,Alistair R. R. Forrest,Mihaela Zavolan,Melissa J. Davis,Laurens G. Wilming,Vassilis Aidinis,Jonathan E. Allen,Alberto Ambesi-Impiombato,Rolf Apweiler,Rajith N. Aturaliya,Timothy L. Bailey,Mukesh Bansal,Laura L. Baxter,Kirk W. Beisel,T. Bersano,Hidemasa Bono,Alistair M. Chalk,Kuo Ping Chiu,V. Choudhary,Alan Christoffels,D. R. Clutterbuck,Mark L. Crowe,Emiliano Dalla,Brian P. Dalrymple,Bernard de Bono,G. Della Gatta,Diego di Bernardo,Thomas A. Down,Pär G. Engström,Michela Fagiolini,Geoffrey J. Faulkner,Colin F. Fletcher,T. Fukushima,Masaaki Furuno,Sugiko Futaki,Manuela Gariboldi,P. Georgii-Hemming,Thomas R. Gingeras,Takashi Gojobori,Richard E. Green,Stefano Gustincich,Matthias Harbers,Yoshitaka Hayashi,Takao K. Hensch,Nobutaka Hirokawa,David E. Hill,Lukasz Huminiecki,M. Iacono,Kazuho Ikeo,Atsushi Iwama,T. Ishikawa,M. Jakt,Alexander Kanapin,Masaru Katoh,Yuka Imamura Kawasawa,Janet Kelso,Hiroshi Kitamura,Hiroaki Kitano,George Kollias,S. P. T. Krishnan,Adele Kruger,Sarah K. Kummerfeld,Igor V. Kurochkin,Liana F. Lareau,Dejan Lazarevic,Leonard Lipovich,Jinfeng Liu,Sabino Liuni,Sean McWilliam,M. Madan Babu,Martin Madera,Luigi Marchionni,Hideo Matsuda,Shu-ichi Matsuzawa,Harukata Miki,Flavio Mignone,Sou Miyake,Ken A. Morris,Salim Mottagui-Tabar,Salim Mottagui-Tabar,Nicola Mulder,Naoko Nakano,Hiromitsu Nakauchi,P. Ng,Roland Nilsson,S. Nishiguchi,Seishi Nishikawa,Franco Nori,Osamu Ohara,Yasushi Okazaki,Valerio Orlando,Ken C Pang,William J. Pavan,Giulio Pavesi,Graziano Pesole,Nikolai Petrovsky,Silvano Piazza,Jonathan C. Reed,James F. Reid,Brian Z. Ring,M. Ringwald,Burkhard Rost,Yijun Ruan,Steven L. Salzberg,Albin Sandelin,Claudio Schneider,Christian Schönbach,K. Sekiguchi,Colin A. Semple,Shigeto Seno,Luca Sessa,Y. Sheng,Y. Shibata,Hiroshi Shimada,Kiyo Shimada,D. Silva,B. Sinclair,Silke Sperling,Elia Stupka,Koji Sugiura,Razvan Sultana,Yoichi Takenaka,Kohei Taki,K. Tammoja,Sin Lam Tan,S. Tang,Martin S. Taylor,Jesper Tegnér,Sarah A. Teichmann,Hiroki R. Ueda,Erik van Nimwegen,Roberto Verardo,Chia-Lin Wei,Ken Yagi,H. Yamanishi,E. Zabarovsky,S. Zhu,Andreas Zimmer,Winston Hide,Carol J. Bult,Sean M. Grimmond,Rohan D. Teasdale,Edison T. Liu,Vladimir Brusic,John Quackenbush,Claes Wahlestedt,Claes Wahlestedt,John S. Mattick,David A. Hume,C. Kai,D. Sasaki,Yasuhiro Tomaru,S. Fukuda,Mutsumi Kanamori-Katayama,M. Suzuki,Junken Aoki,Taku Arakawa,J. Iida,Kengo Imamura,Masayoshi Itoh,T. Kato,Hideya Kawaji,N. Kawagashira,Tsugumi Kawashima,M. Kojima,S. Kondo,Hideaki Konno,K. Nakano,Noriko Ninomiya,T. Nishio,M. Okada,Charles Plessy,K. Shibata,Toshiyuki Shiraki,S. Suzuki,Michihira Tagami,Kazunori Waki,Akira Watahiki,Yuko Okamura-Oho,Harukazu Suzuki,Jun Kawai,Yoshihide Hayashizaki,Yoshihide Hayashizaki +197 more
TL;DR: Detailed polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
Journal ArticleDOI
Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma
Brett E. Johnson,Tali Mazor,Chibo Hong,Michael R. Barnes,Koki Aihara,Cory Y. McLean,Shaun D. Fouse,Shogo Yamamoto,Hiroki R. Ueda,Kenji Tatsuno,Saurabh Asthana,Llewellyn E. Jalbert,Sarah J. Nelson,Andrew W. Bollen,W. Clay Gustafson,Elise Charron,William A. Weiss,Ivan Smirnov,Jun S. Song,Adam B. Olshen,Soonmee Cha,Yongjun Zhao,Richard A. Moore,Andrew J. Mungall,Steven J.M. Jones,Martin Hirst,Marco A. Marra,Nobuhito Saito,Hiroyuki Aburatani,Akitake Mukasa,Mitchel S. Berger,Susan M. Chang,Barry S. Taylor,Joseph F. Costello +33 more
TL;DR: Exome sequencing of exomes of 23 initial low-grade gliomas and recurrent tumors resected from the same patients suggests that recurrent tumors are often seeded by cells derived from the initial tumor at a very early stage of their evolution.
Journal ArticleDOI
Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis
Etsuo A. Susaki,Kazuki Tainaka,Kazuki Tainaka,Dimitri Perrin,Fumiaki Kishino,Takehiro Tawara,Tomonobu M. Watanabe,Chihiro Yokoyama,Hirotaka Onoe,Megumi Eguchi,Shun Yamaguchi,Shun Yamaguchi,Takaya Abe,Hiroshi Kiyonari,Yoshihiro Shimizu,Atsushi Miyawaki,Hideo Yokota,Hiroki R. Ueda +17 more
TL;DR: CUBIC enables time-course expression profiling of whole adult brains with single-cell resolution and develops a whole-brain cell-nuclear counterstaining protocol and a computational image analysis pipeline that enable the visualization and quantification of neural activities induced by environmental stimulation.
Journal ArticleDOI
A transcription factor response element for gene expression during circadian night
Hiroki R. Ueda,Wenbin Chen,Akihito Adachi,Hisanori Wakamatsu,Satoko Hayashi,Tomohiro Takasugi,Mamoru Nagano,Ken-ichi Nakahama,Yutaka Suzuki,Sumio Sugano,Masamitsu Iino,Yasufumi Shigeyoshi,Seiichi Hashimoto +12 more
TL;DR: The role of the Rev-ErbA/ROR response element in gene expression during circadian night is demonstrated, which is in phase with Bmal1 and in antiphase to Per2 oscillations.
Journal ArticleDOI
System-level identification of transcriptional circuits underlying mammalian circadian clocks.
Hiroki R. Ueda,Satoko Hayashi,Wenbin Chen,Motoaki Sano,Masayuki Machida,Yasufumi Shigeyoshi,Masamitsu Iino,Seiichi Hashimoto +7 more
TL;DR: The results indicate that circadian transcriptional circuits are governed by two design principles: regulation of E/E′ boxes and RevErbA/ROR binding elements follows a repressor-precedes-activator pattern, resulting in delayed transcriptional activity, whereas regulation of DBP/E4BP4 binding elements following a repression-antiphasic-to-activators mechanism, which generates high-amplitude transcriptionalactivity.