Hiroki Ueda
USERN Advisory Board
Dr. Hiroki R. Ueda was born in Fukuoka, Japan, in 1975. He graduated from the Faculty
of Medicine, the University of Tokyo in 2000, and obtained his Ph.D in 2004 from the
same university. He was appointed as a team leader in RIKEN Center for
Developmental Biology (CDB) from 2003 and promoted to be a project leader at RIKEN
CDB in 2009, and to be a group director at RIKEN Quantitative Biology Center (QBiC) in
2011. He became a professor of Graduate School of Medicine, the University of Tokyo
in 2013. He is currently appointed as a team leader in RIKEN Center for Biosystems
Dynamics Research (BDR), an affiliate professor in Graduate School of Information
Science and Technology and an principle investigator in IRCN (International Research
Center for Neurointelligence) in the University of Tokyo, an invited professor in Osaka
University, and a visiting professor in Tokushima University.
He has an expertise in systems biology and focus on chronobiology by investigating
mammalian circadian clocks and sleep/wake cycles. He determined a basic structure of
a transcriptional circuit of mammalian circadian clocks and identified multiple delayed
negative feedback motifs (Ueda et al, 2002, Ueda et al, 2005, Ukai-Tadenuma et al,
2008, Ukai-Tadenuma 2011). He also focused on long-standing and unsolved questions
in chronobiology and found that a singularity behavior (i.e. temporal stopping of
circadian clocks) is caused by desynchronization of multiple cellular circadian oscillators
(Ukai et al, 2007), and that temperature-insensitive biochemical reactions underlie
temperature compensation of mammalian circadian clocks (Isojima et al, 2009,
Shinohara et al, 2017). He also invented molecular-timetable methods to detect the
circadian time of the body by measuring a snapshot information of circadian clocks
(Ueda et al, 2004, Minami eet al, 2009, Kasukawa et al, 2012, Narumi et al, 2016). For
sleep/wake cycles, he found that Ca2+ and CaMKII-dependent hyperpolarization
pathways underlie sleep homeostasis (Tatsuki et al, 2016, Sunagawa et al, 2016,
Tatsuki et al, 2017, Ode et al, 2017, Shi et al, 2017), and that muscarinic receptors, M1
and M3, as essential genes for REM sleep (Niwa et al, 2018). To accelerate these
studies, he also invented whole-brain and whole-body clearing and imaging methods
called CUBIC (Susaki et al, 2014, Tainaka et al, 2014, Susaki et al, 2015, Susaki et al,
2016, Tainaka et al, 2016, Kubota et al, 2017, Nojima et al, 2017, Murakami et al, 2018,
Tainaka et al, 2018), as well as the next-generation mammalian genetics (Susaki et al,
2017) such as Triple-CRISPR(Sunagawa et al, 2016), ES-mice (Ode et al, 2017, Ukai et
al, 2017) and SSS methods (Sunagawa et al, 2016) for one-step production and
analysis of KO and KI mice without crossing.
He received awards, including Tokyo Techno Forum 21, Gold Medal (Tokyo Techno
Forum 21, 2005), Young Investigator Awards (MEXT, 2006) and IBM Science Award
(IBM, 2009), a Young Investigator Promotion Awards (Japanese Society for
Chronobiology, 2007). He also received Tsukahara Award (Brain Science Foundation,
2012), Japan Innovator Awards (Nikkei Business Publications Inc. 2004),
Yamazaki-Teiichi Prize (Foundation for Promotion of Material Science and Technology
of Japan, 2015), Innovator of the Year (2017) and The Ichimura Prize in Science for
Excellent Achievement (Ichimura Foundation for New Technology, 2018).
Professional Appointments
2013-present: Professor, Graduate School of Medicine and Faculty of Medicine, The
University of Tokyo
2011-present: Laboratory Head, Laboratory for Synthetic Biology, RIKEN
2017-present: Principle Investigator, International Research Center for
Neurointelligence, The University of Tokyo
2016-present: Affiliate Professor, Graduate School of Information Science and
Technology, The University of Tokyo
2011-present: Invited Professor, Graduate School of Frontier Biosciences, Osaka University
2005-present: Visiting Professor, Tokushima University
2012-2013: Visiting Professor, Graduate School of Medicine and Faculty of Medicine,
The University of Tokyo
2010-2013: Visiting Professor, National Institute of Genetics
2009-2013: Invited Professor, Department of Mathematics, Kyoto University
2006-2014: Invited Professor, Department of Biology, Osaka University
2005- 2006: Visiting Professor, Tohoku University
2004-2013: Laboratory Head, Functional Genomics Unit, RIKEN Center for
Developmental Biology
2003-2014: Laboratory Head, Laboratory for Systems Biology, RIKEN Center for
Developmental Biology
2002-2004: Group Leader, Systems Biology Group, NEDO project, Yamanouchi
Pharmaceutical Co., Ltd.
2000-2002: Research Scientist, Yamanouchi Pharmaceutical Co., Ltd.
1999-2000: Technical Staff, Yamanouchi Pharmaceutical Co., Ltd.
1999-2000: Research Assistant, ERATO Kitano Symbiotic Project
1998-1999: Research Assistant, Sony Computer Science Laboratories
Professional Preparation
The University of Tokyo, Faculty of Medicine, M. D., 2000
The University of Tokyo, Graduate School of Medicine, Department of Pharmacology,
Ph. D., 2004
Awards
15 Awards for 13 years, including The Ichimura Prize (2018), Innovator of the Year
(2017), Yamazaki-Teiichi Prize (2015), Tsukahara Nakaakira Memorial Award (2012),
Nagase Award (2011), Changemaker of the year 2011 (2011), JSPS Award (2010), IBM
Science Award (2009), Young Scientist Award (MEXT) (2006), Tokyo Techno-Forum 21
Gold medal (2005), Japan Innovator Award (2004).
Other Activities
Founded Japanese Society of Cell Synthesis Research (2005-)
Scientific Editors for EMBO Journal (2011-), and Genes to Cells (2010-)
Research Supervisor, PREST Control and Design of Cellular Functions (2011-)
Organizer of 10 symposiums over 5 years.
Associate Editor for IEEE Life Sciences Letters (2014-)
Associate Editor for NPJ Systems Biology and Applications (2014-)
Member Science Council of Japan (SCJ) (2014-)
The representative of Young Academy of Japan (2015-2018)
International Advisory Board for Advanced Biosystems (2016-)
iScience, Scientific Advisory Board (2018-)
Professional Societies
Society for Research on Biological Rhythms (SRBR)
Society for Neuroscience (SfN)
European Sleep Research Society (ESRS)
European Biological Rhythms Society (EBRS)
Japanese Society for Cell Synthesis Research
The Molecular Biology Society of Japan
The Japanese Biochemical Society
The Japanese Pharmacological Society
The Japanese Society of Sleep Research
The Biophysical Society of Japan
Japan Society for Marmoset Research
Japanese Society of Anti-aging Medicine
The Japan Neuroscience Society
Most cited publications
The transcriptional landscape of the mammalian genome
P Carninci, T Kasukawa, S Katayama, J Gough, MC Frith, N Maeda, ...
Science 309 (5740), 1559-1563 2005
A transcription factor response element for gene expression during circadian night
HR Ueda, W Chen, A Adachi, H Wakamatsu, S Hayashi, T Takasugi, ...
Nature 418 (6897), 534-539 2002
Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis
EA Susaki, K Tainaka, D Perrin, F Kishino, T Tawara, TM Watanabe, ...
Cell 157 (3), 726-739 2014
System-level identification of transcriptional circuits underlying mammalian circadian clocks
HR Ueda, S Hayashi, W Chen, M Sano, M Machida, Y Shigeyoshi, M Iino, ...
Nature genetics 37 (2), 187-192 2005
Maintenance of selfârenewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b
A Tsumura, T Hayakawa, Y Kumaki, S Takebayashi, M Sakaue, ...
Genes to Cells 11 (7), 805-814 2006
of Medicine, the University of Tokyo in 2000, and obtained his Ph.D in 2004 from the
same university. He was appointed as a team leader in RIKEN Center for
Developmental Biology (CDB) from 2003 and promoted to be a project leader at RIKEN
CDB in 2009, and to be a group director at RIKEN Quantitative Biology Center (QBiC) in
2011. He became a professor of Graduate School of Medicine, the University of Tokyo
in 2013. He is currently appointed as a team leader in RIKEN Center for Biosystems
Dynamics Research (BDR), an affiliate professor in Graduate School of Information
Science and Technology and an principle investigator in IRCN (International Research
Center for Neurointelligence) in the University of Tokyo, an invited professor in Osaka
University, and a visiting professor in Tokushima University.
He has an expertise in systems biology and focus on chronobiology by investigating
mammalian circadian clocks and sleep/wake cycles. He determined a basic structure of
a transcriptional circuit of mammalian circadian clocks and identified multiple delayed
negative feedback motifs (Ueda et al, 2002, Ueda et al, 2005, Ukai-Tadenuma et al,
2008, Ukai-Tadenuma 2011). He also focused on long-standing and unsolved questions
in chronobiology and found that a singularity behavior (i.e. temporal stopping of
circadian clocks) is caused by desynchronization of multiple cellular circadian oscillators
(Ukai et al, 2007), and that temperature-insensitive biochemical reactions underlie
temperature compensation of mammalian circadian clocks (Isojima et al, 2009,
Shinohara et al, 2017). He also invented molecular-timetable methods to detect the
circadian time of the body by measuring a snapshot information of circadian clocks
(Ueda et al, 2004, Minami eet al, 2009, Kasukawa et al, 2012, Narumi et al, 2016). For
sleep/wake cycles, he found that Ca2+ and CaMKII-dependent hyperpolarization
pathways underlie sleep homeostasis (Tatsuki et al, 2016, Sunagawa et al, 2016,
Tatsuki et al, 2017, Ode et al, 2017, Shi et al, 2017), and that muscarinic receptors, M1
and M3, as essential genes for REM sleep (Niwa et al, 2018). To accelerate these
studies, he also invented whole-brain and whole-body clearing and imaging methods
called CUBIC (Susaki et al, 2014, Tainaka et al, 2014, Susaki et al, 2015, Susaki et al,
2016, Tainaka et al, 2016, Kubota et al, 2017, Nojima et al, 2017, Murakami et al, 2018,
Tainaka et al, 2018), as well as the next-generation mammalian genetics (Susaki et al,
2017) such as Triple-CRISPR(Sunagawa et al, 2016), ES-mice (Ode et al, 2017, Ukai et
al, 2017) and SSS methods (Sunagawa et al, 2016) for one-step production and
analysis of KO and KI mice without crossing.
He received awards, including Tokyo Techno Forum 21, Gold Medal (Tokyo Techno
Forum 21, 2005), Young Investigator Awards (MEXT, 2006) and IBM Science Award
(IBM, 2009), a Young Investigator Promotion Awards (Japanese Society for
Chronobiology, 2007). He also received Tsukahara Award (Brain Science Foundation,
2012), Japan Innovator Awards (Nikkei Business Publications Inc. 2004),
Yamazaki-Teiichi Prize (Foundation for Promotion of Material Science and Technology
of Japan, 2015), Innovator of the Year (2017) and The Ichimura Prize in Science for
Excellent Achievement (Ichimura Foundation for New Technology, 2018).
Professional Appointments
2013-present: Professor, Graduate School of Medicine and Faculty of Medicine, The
University of Tokyo
2011-present: Laboratory Head, Laboratory for Synthetic Biology, RIKEN
2017-present: Principle Investigator, International Research Center for
Neurointelligence, The University of Tokyo
2016-present: Affiliate Professor, Graduate School of Information Science and
Technology, The University of Tokyo
2011-present: Invited Professor, Graduate School of Frontier Biosciences, Osaka University
2005-present: Visiting Professor, Tokushima University
2012-2013: Visiting Professor, Graduate School of Medicine and Faculty of Medicine,
The University of Tokyo
2010-2013: Visiting Professor, National Institute of Genetics
2009-2013: Invited Professor, Department of Mathematics, Kyoto University
2006-2014: Invited Professor, Department of Biology, Osaka University
2005- 2006: Visiting Professor, Tohoku University
2004-2013: Laboratory Head, Functional Genomics Unit, RIKEN Center for
Developmental Biology
2003-2014: Laboratory Head, Laboratory for Systems Biology, RIKEN Center for
Developmental Biology
2002-2004: Group Leader, Systems Biology Group, NEDO project, Yamanouchi
Pharmaceutical Co., Ltd.
2000-2002: Research Scientist, Yamanouchi Pharmaceutical Co., Ltd.
1999-2000: Technical Staff, Yamanouchi Pharmaceutical Co., Ltd.
1999-2000: Research Assistant, ERATO Kitano Symbiotic Project
1998-1999: Research Assistant, Sony Computer Science Laboratories
Professional Preparation
The University of Tokyo, Faculty of Medicine, M. D., 2000
The University of Tokyo, Graduate School of Medicine, Department of Pharmacology,
Ph. D., 2004
Awards
15 Awards for 13 years, including The Ichimura Prize (2018), Innovator of the Year
(2017), Yamazaki-Teiichi Prize (2015), Tsukahara Nakaakira Memorial Award (2012),
Nagase Award (2011), Changemaker of the year 2011 (2011), JSPS Award (2010), IBM
Science Award (2009), Young Scientist Award (MEXT) (2006), Tokyo Techno-Forum 21
Gold medal (2005), Japan Innovator Award (2004).
Other Activities
Founded Japanese Society of Cell Synthesis Research (2005-)
Scientific Editors for EMBO Journal (2011-), and Genes to Cells (2010-)
Research Supervisor, PREST Control and Design of Cellular Functions (2011-)
Organizer of 10 symposiums over 5 years.
Associate Editor for IEEE Life Sciences Letters (2014-)
Associate Editor for NPJ Systems Biology and Applications (2014-)
Member Science Council of Japan (SCJ) (2014-)
The representative of Young Academy of Japan (2015-2018)
International Advisory Board for Advanced Biosystems (2016-)
iScience, Scientific Advisory Board (2018-)
Professional Societies
Society for Research on Biological Rhythms (SRBR)
Society for Neuroscience (SfN)
European Sleep Research Society (ESRS)
European Biological Rhythms Society (EBRS)
Japanese Society for Cell Synthesis Research
The Molecular Biology Society of Japan
The Japanese Biochemical Society
The Japanese Pharmacological Society
The Japanese Society of Sleep Research
The Biophysical Society of Japan
Japan Society for Marmoset Research
Japanese Society of Anti-aging Medicine
The Japan Neuroscience Society
Most cited publications
The transcriptional landscape of the mammalian genome
P Carninci, T Kasukawa, S Katayama, J Gough, MC Frith, N Maeda, ...
Science 309 (5740), 1559-1563 2005
A transcription factor response element for gene expression during circadian night
HR Ueda, W Chen, A Adachi, H Wakamatsu, S Hayashi, T Takasugi, ...
Nature 418 (6897), 534-539 2002
Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis
EA Susaki, K Tainaka, D Perrin, F Kishino, T Tawara, TM Watanabe, ...
Cell 157 (3), 726-739 2014
System-level identification of transcriptional circuits underlying mammalian circadian clocks
HR Ueda, S Hayashi, W Chen, M Sano, M Machida, Y Shigeyoshi, M Iino, ...
Nature genetics 37 (2), 187-192 2005
Maintenance of selfârenewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b
A Tsumura, T Hayakawa, Y Kumaki, S Takebayashi, M Sakaue, ...
Genes to Cells 11 (7), 805-814 2006
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