Biographical Sketch
Hiroki R. Ueda
Dr. Hiroki R. Ueda was born in Fukuoka, Japan, in 1975. He graduated from the Facultyof Medicine, the University of Tokyo in 2000, and obtained his Ph.D in 2004 from thesame 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 Tokyoin 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 ResearchCenter 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 ofa 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 ofcircadian 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 thecircadian 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 thesestudies, 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 etal, 2017) and SSS methods (Sunagawa et al, 2016) for one-step production andanalysis 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 Technologyof 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
ResearchCenterfor
Neurointelligence, The University of Tokyo

2016-present: Affiliate Professor, Graduate School of Information Science andTechnology, 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
Awards15 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 JapanThe 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

Publication (Original Paper)
Sumiyama K, Matsumoto N, Garçon-Yoshida J, Ukai H, Ueda HR, Tanaka Y.
Easy and efficient production of completely embryonic-stem-cell-derived mice using a
micro-aggregation device. PLoS One. 2018 Sep 19;13(9):e0203056.
Yoshida K, Shi S, Ukai-Tadenuma M, Fujishima H, Ohno RI, Ueda HR. Leak potassiumchannels regulate sleep duration.Proc Natl Acad Sci U S A. 2018 Sep 17.
Niwa Y, Kanda GN, Yamada RG, Shi S, Sunagawa GA, Ukai-Tadenuma M, Fujishima H,
Matsumoto N, Masumoto K, Nagano M, Kasukawa T, Galloway J, Perrin D, Shigeyoshi
Y, Ukai H, Kiyonari H, Sumiyama K, Ueda HR. Muscarinic Acetylcholine Receptors
Chrm1 and Chrm3 Are Essential for REM Sleep. Cell Rep. 2018 Aug 28;24:
2231–2247.
Tainaka K, Murakami TC, Susaki EA, Shimizu C, Saito R, Takahashi K, Hayashi-Takagi
A, Sekiya H, Arima Y, Nojima S, Ikemura M, Ushiku T, Shimizu Y, Murakami M, Tanaka
KF, Iino M, Kasai H, Sasaoka T, Kobayashi K, Miyazono K, Morii E, Isa T, Fukayama M,
Kakita A, Ueda HR. Chemical Landscape for Tissue Clearing Based on Hydrophilic
Reagents. Cell Rep. 2018 Aug 21;24: 2196–2210.
Murakami TC, Mano T, Saikawa S, Horiguchi SA, Shigeta D, Baba K, Sekiya H,
Shimizu Y, Tanaka KF, Kiyonari H, Iino M, Mochizuki H, Tainaka K, Ueda HR. A
three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion
microscopy and tissue clearing. Nat Neurosci. 2018 Apr;21(4):625-637.
Udagawa T, Harita Y, Miura K, Mitsui J, Ode KL, Morishita S, Urae S, Kanda S, Kajiho Y,
Tsurumi H, Ueda HR, Tsuji S, Saito A, Oka A. Amnionless-mediated glycosylation is
crucial for cell surface targeting of cubilin in renal and intestinal cells. Sci Rep. 2018
Feb 5;8(1):2351.
Yamamoto J, Imai J, Izumi T, Takahashi H, Kawana Y, Takahashi K, Kodama S,
Kaneko K, Gao J, Uno K, Sawada S, Asano T, Kalinichenko VV, Susaki EA, Kanzaki M,
Ueda HR, Ishigaki Y, Yamada T, Katagiri H. Neuronal signals regulate obesity induced
β-cell proliferation by FoxM1 dependent mechanism. Nat Commun. 2017 Dec
5;8(1):1930.
Hughes ME et al, Guidelines for Genome-Scale Analysis of Biological Rhythms. J Biol
Rhythms. 2017 Oct;32(5):380-393.

Ukai H, Kiyonari H, Ueda HR. Production of knock-in mice in a single generation fromembryonic stem cells. Nat Protoc. 2017 Nov;12(12):2513-30.
Shinohara Y, Koyama YM, Ukai-Tadenuma M, Hirokawa T, Fujishima H, Umehara T,
Tainaka K, Ueda HR. Temperature-Sensitive Substrate and Product Binding Underlie
Temperature-Compensated Phosphorylation in the Clock. Molecular Cell. 2017
Sep7;67(5): 783-798
Nojima S, Susaki EA, Yoshida K, Takemoto H, Tsujimura N, Iijima S, Takachi K,
Nakahara Y, Tahara S, Ohshima K, Kurashige M, Hori Y, Wada N, Ikeda J, Kumanogoh
A, Morii E, Ueda HR. CUBIC pathology: three-dimensional imaging for pathologicaldiagnosis. Scientific Reports. 2017 Aug 24; 9269
Kubota SI, Takahashi K, Nishida J, Morishita Y, Ehata S, Tainaka K, Miyazono K, Ueda
HR. Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution. Cell Rep.
2017 Jul 5;20(1):236-250.
Sugai SS, Ode KL, Ueda HR. A Design Principle for an Autonomous Post-translational
Pattern Formation. Cell Rep. 2017 Apr 25;19(4):863-874.
Hosoya M, Fujioka M, Sone T, Okamoto S, Akamatsu W, Ukai H, Ueda HR, Ogawa K,
Matsunaga T, Okano H. Cochlear Cell Modeling Using Disease-Specific iPSCs Unveilsa Degenerative Phenotype and Suggests Treatments for Congenital Progressive
Hearing Loss. Cell Rep. 2017 Jan 3;18(1):68-81.
Ode KL, Ukai H, Susaki EA, Narumi R, Matsumoto K, Hara J, Koide N, Abe T,
Kanemaki MT, Kiyonari H, Ueda HR. Knockout-Rescue Embryonic Stem Cell-Derived
Mouse Reveals Circadian-Period Control by Quality and Quantity of CRY1. Mol Cell.
2017 Jan 5;65(1):176-190.
Narumi R, Shimizu Y, Ukai-Tadenuma M, Ode KL, Kanda GN, Shinohara Y, Sato A,
Matsumoto K, Ueda HR. Mass spectrometry-based absolute quantification reveals
rhythmic variation of mouse circadian clock proteins. Proc Natl Acad Sci U S A. 2016
Jun 14;113(24):E3461-7.
Okamoto M, Miyata T, Konno D, Ueda HR, Kasukawa T, Hashimoto M, Matsuzaki F,
Kawaguchi A. Cell-cycle-independent transitions in temporal identity of mammalianneural progenitor cells. Nat Commun. 2016 Apr 20;7:11349.
Tatsuki F, Sunagawa GA, Shi S, Susaki EA, Yukinaga H, Perrin D, Sumiyama K,
Ukai-Tadenuma M, Fujishima H, Ohno R, Tone D, Ode KL, Matsumoto K, Ueda HR.
Involvement of Ca(2+)-Dependent Hyperpolarization in Sleep Duration in Mammals.
Neuron. 2016 Apr 6;90(1):70-85.
Sunagawa GA, Sumiyama K, Ukai-Tadenuma M, Perrin D, Fujishima H, Ukai H,
Nishimura O, Shi S, Ohno R, Narumi R, Shimizu Y, Tone D, Ode KL, Kuraku S, Ueda
HR. Mammalian Reverse Genetics without Crossing Reveals Nr3a as a Short-Sleeper
Gene. Cell Rep. 2016 Jan 26;14(3):662-77.

Susaki EA, Tainaka K, Perrin D, Yukinaga H, Kuno A, Ueda HR. Advanced CUBIC
protocols for whole-brain and whole-body clearing and imaging. Nat Protoc. 2015
Nov;10(11):1709-27.
Tainaka K, Kubota SI, Suyama TQ, Susaki EA, Perrin D, Ukai-Tadenuma M, Ukai H,
Ueda HR. Whole-body imaging with single-cell resolution by tissue decolorization. Cell.
2014 Nov 6;159(4):911-24.
Jolley CC, Ukai-Tadenuma M, Perrin D, Ueda HR. A mammalian circadian clock model
incorporating daytime expression elements. Biophys J. 2014 Sep 16;107(6):1462-73.
Susaki EA, Tainaka K, Perrin D, Kishino F, Tawara T, Watanabe TM, Yokoyama C,
Onoe H, Eguchi M, Yamaguchi S, Abe T, Kiyonari H, Shimizu Y, Miyawaki A, Yokota H,
Ueda HR. Whole-brain imaging with single-cell resolution using chemical cocktails andcomputational analysis. Cell. 2014 Apr 24;157(3):726-39.
Ikeda S, Tainaka K, Matsumoto K, Shinohara Y, Ode KL, Susaki EA, Ueda HR.
Non-enzymatic DNA cleavage reaction induced by 5-ethynyluracil in methylamineaqueous solution and application to DNA concatenation. PLoS One. 2014 Mar
19;9(3):e92369.
Adachi K, Nikaido I, Ohta H, Ohtsuka S, Ura H, Kadota M, Wakayama T, Ueda HR,
Niwa H. Context-dependent wiring of Sox2 regulatory networks for self-renewal ofembryonic and trophoblast stem cells. Mol Cell. 2013 Nov 7;52(3):380-92.
Honda KK, Kawamoto T, Ueda HR, Nakashima A, Ueshima T, Yamada RG, Nishimura
M, Oda R, Nakamura S, Kojima T, Noshiro M, Fujimoto K, Hashimoto S, Kato Y.
Different circadian expression of major matrix-related genes in various types ofcartilage: modulation by light-dark conditions. J Biochem. 2013 Oct;154(4):373-81.
Tsujino K, Narumi R, Masumoto KH, Susaki EA, Shinohara Y, Abe T, Iigo M, Wada A,
Nagano M, Shigeyoshi Y, Ueda HR. Establishment of TSH β real-time monitoring
system in mammalian photoperiodism. Genes Cells. 2013 Jul;18(7):575-88.
Sunagawa GA, Séi H, Shimba S, Urade Y, Ueda HR. FASTER: an unsupervised fully
automated sleep staging method for mice. Genes Cells. 2013 Jun;18(6):502-18.
Sasagawa Y, Nikaido I, Hayashi T, Danno H, Uno KD, Imai T, Ueda HR. Quartz-Seq: ahighly reproducible and sensitive single-cell RNA sequencing method, reveals
non-genetic gene-expression heterogeneity. Genome Biol. 2013 Apr 17;14(4):R31.
Freeman GM Jr, Nakajima M, Ueda HR, Herzog ED. Picrotoxin dramatically speeds the
mammalian circadian clock independent of Cys-loop receptors. J Neurophysiol. 2013
Jul;110(1):103-8.
Yoshimoto N, Kida A, Jie X, Kurokawa M, Iijima M, Niimi T, Maturana AD, Nikaido I,
Ueda HR, Tatematsu K, Tanizawa K, Kondo A, Fujii I, Kuroda S. An automated system
for high-throughput single cell-based breeding. Sci Rep. 2013;3:1191.
Jolley CC, Ode KL, Ueda HR. A design principle for a posttranslational biochemical
oscillator. Cell Rep. 2012 Oct 25;2(4):938-50.

Okamura-Oho Y, Shimokawa K, Takemoto S, Hirakiyama A, Nakamura S, Tsujimura Y,
Nishimura M, Kasukawa T, Masumoto KH, Nikaido I, Shigeyoshi Y, Ueda HR, Song G,
Gee J, Himeno R, Yokota H. Transcriptome tomography for brain analysis in the
web-accessible anatomical space. PLoS One. 2012;7(9):e45373.
Kasukawa T, Sugimoto M, Hida A, Minami Y, Mori M, Honma S, Honma K, Mishima K,
Soga T, Ueda HR. Human blood metabolite timetable indicates internal body time. Proc
Natl Acad Sci U S A. 2012 Sep 11;109(37):15036-41.
Khan SK, Xu H, Ukai-Tadenuma M, Burton B, Wang Y, Ueda HR, Liu AC. Identificationof a novel cryptochrome differentiating domain required for feedback repression incircadian clock function. J Biol Chem. 2012 Jul 27;287(31):25917-26.
Koyama YM, Kobayashi TJ, Ueda HR. Perturbation analyses of intermolecularinteractions. Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Aug;84(2 Pt 2):026704.
Kasukawa T, Masumoto KH, Nikaido I, Nagano M, Uno KD, Tsujino K, Hanashima C,
Shigeyoshi Y, Ueda HR. Quantitative expression profile of distinct functional regions in
the adult mouse brain. PLoS One. 2011;6(8):e23228.
Ukai-Tadenuma M, Yamada RG, Xu H, Ripperger JA, Liu AC, Ueda HR. Delay infeedback repression by cryptochrome 1 is required for circadian clock function. Cell.
2011 Jan 21;144(2):268-81.
Masumoto KH, Ukai-Tadenuma M, Kasukawa T, Nagano M, Uno KD, Tsujino K,
Horikawa K, Shigeyoshi Y, Ueda HR. Acute induction of Eya3 by late-night lightstimulation triggers TSHβ expression in photoperiodism. Curr Biol. 2010 Dec
21;20(24):2199-206.
Harumoto T, Ito M, Shimada Y, Kobayashi TJ, Ueda HR, Lu B, Uemura T. Atypicalcadherins Dachsous and Fat control dynamics of noncentrosomal microtubules inplanar cell polarity. Dev Cell. 2010 Sep 14;19(3):389-401.
Alev C, Wu Y, Kasukawa T, Jakt LM, Ueda HR, Sheng G. Transcriptomic landscape of
the primitive streak. Development. 2010 Sep 1;137(17):2863-74.
Isojima Y, Nakajima M, Ukai H, Fujishima H, Yamada RG, Masumoto KH, Kiuchi R,
Ishida M, Ukai-Tadenuma M, Minami Y, Kito R, Nakao K, Kishimoto W, Yoo SH,
Shimomura K, Takao T, Takano A, Kojima T, Nagai K, Sakaki Y, Takahashi JS, Ueda
HR. CKIepsilon/delta-dependent phosphorylation is a temperature-insensitive,
period-determining process in the mammalian circadian clock. Proc Natl Acad Sci U S
A. 2009 Sep 15;106(37):15744-9.
Minami Y, Kasukawa T, Kakazu Y, Iigo M, Sugimoto M, Ikeda S, Yasui A, van der Horst
GT, Soga T, Ueda HR. Measurement of internal body time by blood metabolomics.
Proc Natl Acad Sci U S A. 2009 Jun 16;106(24):9890-5.
Drengstig T, Ueda HR, Ruoff P. Predicting perfect adaptation motifs in reaction kinetic
networks. J Phys Chem B. 2008 Dec 25;112(51):16752-8. Izumikawa M, Ukai H, Takagi
M, Ueda HR, Shin-Ya K. JBIR-26, a novel natural compound from Streptomyces sp.

AK-AH76, regulates
Dec;61(12):756-8.

mammalian

circadianclock.

J

Antibiot(Tokyo).

2008

Watanabe T, Suzuki T, Ishikawa A, Yokota Y, Ueda HR, Yamada RG, Tei H, Imai S,
Tomida S, Kobayashi J, Naito E, Yasuo S, Nakao N, Namikawa T, Yoshimura T,
Ebihara S. Genetic and molecular analysis of wild-derived arrhythmic mice. PLoS One.
2009;4(1):e4301.
Koyama YM, Kobayashi TJ, Tomoda S, Ueda HR. Perturbational formulation ofprincipal component analysis in molecular dynamics simulation. Phys Rev E Stat
Nonlin Soft Matter Phys. 2008 Oct;78(4 Pt 2):046702.
Kumaki Y, Ukai-Tadenuma M, Uno KD, Nishio J, Masumoto KH, Nagano M, Komori T,
Shigeyoshi Y, Hogenesch JB, Ueda HR. Analysis and synthesis of high-amplitude
Cis-elements in the mammalian circadian clock. Proc Natl Acad Sci U S A. 2008 Sep
30;105(39):14946-51.
Ukai-Tadenuma M, Kasukawa T, Ueda HR. Proof-by-synthesis of the transcriptional
logic of mammalian circadian clocks. Nat Cell Biol. 2008 Oct;10(10):1154-63.
Kawaguchi A, Ikawa T, Kasukawa T, Ueda HR, Kurimoto K, Saitou M, Matsuzaki F.
Single-cell gene profiling defines differential progenitor subclasses in mammalian
neurogenesis. Development. 2008 Sep;135(18):3113-24.
Nakao N, Ono H, Yamamura T, Anraku T, Takagi T, Higashi K, Yasuo S, Katou Y,
Kageyama S, Uno Y, Kasukawa T, Iigo M, Sharp PJ, Iwasawa A, Suzuki Y, Sugano S,
Niimi T, Mizutani M, Namikawa T, Ebihara S, Ueda HR, Yoshimura T. Thyrotrophin in
the pars tuberalis triggers photoperiodic response. Nature. 2008 Mar
20;452(7185):317-22.
Kiyohara YB, Nishii K, Ukai-Tadenuma M, Ueda HR, Uchiyama Y, Yagita K. Detectionof a circadian enhancer in the mDbp promoter using prokaryotic transposon
vector-based strategy. Nucleic Acids Res. 2008 Mar;36(4):e23.
Ukai H, Kobayashi TJ, Nagano M, Masumoto KH, Sujino M, Kondo T, Yagita K,
Shigeyoshi Y, Ueda HR. Melanopsin-dependent photo-perturbation reveals
desynchronization underlying the singularity of mammalian circadian clocks. Nat Cell
Biol. 2007 Nov;9(11):1327-34.
Matsumoto A, Ukai-Tadenuma M, Yamada RG, Houl J, Uno KD, Kasukawa T,
Dauwalder B, Itoh TQ, Takahashi K, Ueda R, Hardin PE, Tanimura T, Ueda HR. A
functional genomics strategy reveals clockwork orange as a transcriptional regulator in
the Drosophila circadian clock. Genes Dev. 2007 Jul 1;21(13):1687-700.
Yamada R, Ueda HR. Microarrays: statistical methods for circadian rhythms. Methods
Mol Biol. 2007;362:245-64.
Uno K, Ueda HR. Microarrays: quality control and hybridization protocol. Methods Mol
Biol. 2007;362:225-43.
Ueda HR. Systems biology flowering in the plant clock field. Mol Syst Biol. 2006;2:60.

Tsumura A, Hayakawa T, Kumaki Y, Takebayashi S, Sakaue M, Matsuoka C,
Shimotohno K, Ishikawa F, Li E, Ueda HR, Nakayama J, Okano M. Maintenance ofself-renewal ability of mouse embryonic stem cells in the absence of DNA
methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Genes Cells. 2006 Jul;11(7):805-14.
Kiyohara YB, Tagao S, Tamanini F, Morita A, Sugisawa Y, Yasuda M, Yamanaka I,
Ueda HR, van der Horst GT, Kondo T, Yagita K. The BMAL1 C terminus regulates thecircadian transcription feedback loop. Proc Natl Acad Sci U S A. 2006 Jun
27;103(26):10074-9.
Kurimoto K, Yabuta Y, Ohinata Y, Ono Y, Uno KD, Yamada RG, Ueda HR, Saitou M. An
improved single-cell cDNA amplification method for efficient high-density
oligonucleotide microarray analysis. Nucleic Acids Res. 2006 Mar 17;34(5):e42.
Sato TK, Yamada RG, Ukai H, Baggs JE, Miraglia LJ, Kobayashi TJ, Welsh DK, Kay SA,
Ueda HR, Hogenesch JB. Feedback repression is required for mammalian circadianclock function. Nat Genet. 2006 Mar;38(3):312-9.
Carninci P et al, The transcriptional landscape of the mammalian genome. Science.
2005 Sep 2;309(5740):1559-63.
Ueda HR, Hayashi S, Chen W, Sano M, Machida M, Shigeyoshi Y, Iino M, Hashimoto S.
System-level identification of transcriptional circuits underlying mammalian circadianclocks. Nat Genet. 2005 Feb;37(2):187-92.
Ueda HR, Chen W, Minami Y, Honma S, Honma K, Iino M, Hashimoto S.
Molecular-timetable methods for detection of body time and rhythm disorders fromsingle-time-point genome-wide expression profiles. Proc Natl Acad Sci U S A. 2004
Aug 3;101(31):11227-32.
Ueda HR, Hayashi S, Matsuyama S, Yomo T, Hashimoto S, Kay SA, Hogenesch JB,
Iino M. Universality and flexibility in gene expression from bacteria to human. Proc Natl
Acad Sci U S A. 2004 Mar 16;101(11):3765-9.
Miyatake T, Matsumoto A, Matsuyama T, Ueda HR, Toyosato T, Tanimura T. The
period gene and allochronic reproductive isolation in Bactrocera cucurbitae. Proc Biol
Sci. 2002 Dec 7;269(1508):2467-72.
Ueda HR, Chen W, Adachi A, Wakamatsu H, Hayashi S, Takasugi T, Nagano M,
Nakahama K, Suzuki Y, Sugano S, Iino M, Shigeyoshi Y, Hashimoto S. A transcription
factor response element for gene expression during circadian night. Nature. 2002 Aug
1;418(6897):534-9.
Ueda HR, Hirose K, Iino M. Intercellular coupling mechanism for synchronized andnoise-resistant circadian oscillators. J Theor Biol. 2002 Jun 21;216(4):501-12. PubMed
PMID: 12151263.
Ueda HR, Matsumoto A, Kawamura M, Iino M, Tanimura T, Hashimoto S.
Genome-wide transcriptional orchestration of circadian rhythms in Drosophila. J Biol
Chem. 2002 Apr 19;277(16):14048-52.

Ueda HR, Hagiwara M, Kitano H. Robust oscillations within the interlocked feedback
model of Drosophila circadian rhythm. J Theor Biol. 2001 Jun 21;210(4):401-6.

Publication (Review)
Shi S, Ueda HR. Ca(2+) -Dependent Hyperpolarization Pathways in Sleep Homeostasis
and Mental Disorders. Bioessays. 2018 Jan;40(1).
Ode KL, Ueda HR. Design Principles of Phosphorylation-Dependent Timekeeping inEukaryotic Circadian Clocks. Cold Spring Harb Perspect Biol. 2017 Oct 16. pii:
a028357.
Susaki EA, Ukai H, Ueda HR. Next-generation mammalian genetics toward
organism-level systems biology. NPJ Syst Biol Appl. 2017 Jun 5;3:15.
Ode KL, Katsumata T, Tone D, Ueda HR. Fast and slow Ca2+-dependent
hyperpolarization mechanisms connect membrane potential and sleep homeostasis.
Curr Opin Neurobiol. 2017 May 30;44:212-221.
Yamada RG, Ueda HR. Compass in the data ocean: Toward chronotherapy. Proc Natl
Acad Sci U S A. 2017 May 9. pii: 201705326.
Tatsuki F, Ode KL, Ueda HR. Ca(2+)-dependent hyperpolarization hypothesis for
mammalian sleep. Neurosci Res. 2017 Apr 19. pii: S0168-0102(17)30112-8.
Millius A, Ueda HR. Systems Biology-Derived Discoveries of Intrinsic Clocks. Front
Neurol. 2017 Feb 6;8:25.
Tainaka K, Kuno A, Kubota SI, Murakami T, Ueda HR. Chemical Principles in Tissue
Clearing and Staining Protocols for Whole-Body Cell Profiling. Annu Rev Cell Dev Biol.
2016 Oct 6;32:713-741.
Susaki EA, Ueda HR. Whole-body and Whole-Organ Clearing and Imaging Techniqueswith Single-Cell Resolution: Toward Organism-Level Systems Biology in Mammals. Cell
Chem Biol. 2016 Jan 21;23(1):137-57.
Ode KL, Ueda HR. Seeing the forest and trees: whole-body and whole-brain imaging forcircadian biology. Diabetes Obes Metab. 2015 Sep;17 Suppl 1:47-54.
Minami Y, Ode KL, Ueda HR. Mammalian circadian clock: the roles of transcriptional
repression and delay. Handb Exp Pharmacol. 2013;(217):359-77.
Hogenesch JB, Ueda HR. Understanding systems-level properties: timely stories fromthe study of clocks. Nat Rev Genet. 2011 Jun;12(6):407-16.
Susaki EA, Stelling J, Ueda HR. Challenges in synthetically designing mammalian
circadian clocks. Curr Opin Biotechnol. 2010 Aug;21(4):556-65.

Ukai H, Ueda HR. Systems biology of mammalian circadian clocks. Annu Rev Physiol.
2010;72:579-603.
Ueda HR. Systems biology of mammalian circadian clocks. Cold Spring Harb Symp
Quant Biol. 2007;72:365-80.