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Publications

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2016
"Knockout-Rescue Embryonic Stem Cell-Derived Mouse Reveals Circadian-Period Control by Quality and Quantity of CRY1"
Koji L. Ode, Hideki Ukai, Etsuo A. Susaki, Ryohei Narumi, Katsuhiko Matsumoto, Junko Hara, Naoshi Koide, Takaya Abe, Masato T. Kanemaki, Hiroshi Kiyonari, Hiroki R. Ueda
Molecular Cell in press [PDF]  
Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins.
Ryohei Narumi, Yoshihiro Shimizu, Maki Ukai-Tadenuma, Koji L. Ode, Genki N. Kanda, Yuta Shinohara, Aya Sato, Katsuhiko Matsumoto, and Hiroki R. Ueda
PNAS 113(24):E3461-7 [PDF]  
Involvement of Ca2+-Dependent Hyperpolarization in Sleep Duration in Mammals
Fumiya Tatsuki, Genshiro A. Sunagawa, Shoi Shi, Etsuo A. Susaki, Hiroko Yukinaga, Dimitri Perrin, Kenta Sumiyama, Maki Ukai-Tadenuma, Hiroshi Fujishima, Rei-ichiro Ohno, Daisuke Tone, Koji L. Ode, Katsuhiko Matsumoto, Hiroki R. Ueda
Neuron 90: 1-16 [PDF]  
Whole-body and Whole-Organ Clearing and Imaging Techniques with Single-Cell Resolution: Toward Organism-Level Systems Biology in Mammals.
Etsuo A. Susaki, Hiroki R. Ueda
Cell Chemical Biology 23(1):137-57 [PDF]  
Mammalian Reverse Genetics without Crossing Reveals Nr3a as a Short-Sleeper Gene.
Genshiro A. Sunagawa, Kenta Sumiyama, Maki Ukai-Tadenuma, Dimitri Perrin, Hiroshi Fujishima, Hideki Ukai, Osamu Nishimura, Shoi Shi, Rei-ichiro Ohno, Ryohei Narumi, Yoshihiro Shimizu, Daisuke Tone, Koji L. Ode, Shigehiro Kuraku and Hiroki R. Ueda
Cell Reports 14(3):662-77 [PDF]   [Supplemental1 pdf file] [Supplemental2 xlsx file] [Supplemental3 xlsx file] [Supplemental4 pdf file]
2015
Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging.
Etsuo A Susaki, Kazuki Tainaka, Dimitri Perrin, Hiroko Yukinaga, Akihiro Kuno, Hiroki R Ueda
Nature protocols 10(11):1709-27(2015) [PDF] [Supplemental movie]
2014
Whole-Body Imaging with Single-Cell Resolution by Tissue Decolorization
Kazuki Tainaka, Shimpei I. Kubota, Takeru Q. Suyama, Etsuo A. Susaki, Dimitri Perrin, Maki Ukai-Tadenuma, Hideki Ukai, Hiroki R. Ueda.
Cell 159(6):911-24(2014) [PDF] [Supplemetal Table] [Supplemental Information]
[Movie-1] [Movie-2] [Movie-3] [Movie-4] [Movie-5] [Movie-6]
A Mammalian Circadian Clock Model Incorporating Daytime Expression Elements
Craig C. Jolley, Maki Ukai-Tadenuma, Dimitri Perrin, Hiroki R. Ueda
Biophysical Journal 107(6):1462-1473 [PDF] [Supporting Information]
Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis.
Etsuo A. Susaki, Kazuki Tainaka, Dimitri Perrin, Fumiaki Kishino, Takehiro Tawara, Tomonobu M. Watanabe,Chihiro Yokoyama, Hirotaka Onoe, Megumi Eguchi, Shun Yamaguchi, Takaya Abe, Hiroshi Kiyonari, Yoshihiro Shimizu, Atsushi Miyawaki, Hideo Yokota and Hiroki R. Ueda.
Cell 157(3):726-39(2014) [PDF] [Supplemental Table] [Supplemental Information]
[Movie-1] [Movie-2] [Movie-3] [Movie-4] [Movie-5] [Movie-6] [Movie-7]
Non-Enzymatic DNA Cleavage Reaction Induced by 5-Ethynyluracil in Methylamine Aqueous Solution and Application to DNA Concatenation
Shuji Ikeda, Kazuki Tainaka, Katsuhiko Matsumoto, Yuta Shinohara, Koji L. Ode, Etsuo A. Susaki, Hiroki R Ueda
PLOS ONE 9(3)e92369 [PDF] [Supporting Information]
2013
Establishment of TSH β real-time monitoring system in mammalian photoperiodism.
Tsujino K, Narumi R, Masumoto KH, Susaki EA, Shinohara Y, Abe T, Iigo M, Wada A, Nagano M, Shigeyoshi Y, Ueda HR.
Genes Cells 18(7) (2013) [PDF]
FASTER: an unsupervised fully automated sleep staging method for mice.
Sunagawa GA, Sei H, Shimba S, Urade Y, Ueda HR.
Genes Cells 18(6) (2013) [PDF]
Quartz-Seq: a highly reproducible and sensitive single-cell RNA-Seq reveals non-genetic gene expression heterogeneity.
Sasagawa Y, Nikaido I, Hayashi T, Danno H, Uno KD, Imai T, Ueda HR.
Genome Biology 14(4):R31 (2013) [PDF]
An automated system for high-throughput single cell-based breeding
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.
Scientific Reports 3(1191) (2013) [PDF]
2012
A design principle for a posttranslational biochemical oscillator
Jolley CC, Ode KL, Ueda HR.
Cell Reports 2012 Oct 25;2(4):938-50 (2012) [PDF]
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.
PNAS 109(37):15036-41 (2012) [PDF]
Identification of a novel cryptochrome differentiating domain required for feedback repression in circadian clock function
Khan SK, Xu H, Ukai-Tadenuma M, Burton B, Wang Y, Ueda HR, Liu AC.
The Journal of Biological Chemistry 287(31):25917-26 (2012) [PDF]
2011
Quantitative expression profile of distinct functional regions in the adult mouse brain
Takeya Kasukawa, Koh-hei Masumoto, Itoshi Nikaido, Mamoru Nagano, Kenichiro D. Uno, Kaori Tsujino, Carina Hanashima, Yasufumi Shigeyoshi, Hiroki R. Ueda.
PLoS ONE 6(8), e23228 (2011) [PDF]
Perturbation analyses of intermolecular interactions
Yohei M. Koyama, Tetsuya J. Kobayashi, and Hiroki R. Ueda.
Physical Review E 84, 026704 (2011) [PDF]
Understanding systems-level properties: timely stories from the study of clocks
Hogenesch JB, Ueda HR.
Nature Reviews Genetics Jun;12(6):407-16 (2011). Epub 2011 May 10. [PDF]
Delay in feedback repression by cryptochrome 1 is required for circadian clock function.
Ukai-Tadenuma M, Yamada RG, Xu H, Ripperger JA, Liu AC, Ueda HR.
Cell 144(2):268-81 (2011) [PDF]
2010
Acute induction of Eya3 by late-night light stimulation triggers TSHβ expression in photoperiodism.
Masumoto KH, Ukai-Tadenuma M, Kasukawa T, Nagano M, Uno KD, Tsujino K, Horikawa K, Shigeyoshi Y, Ueda HR.
Current Biology 20(24):2199-206. (2010) [PDF] [Supporting Information 1] [Supporting Information 2]
Challenges in synthetically designing mammalian circadian clocks.
Susaki EA, Stelling J, Ueda HR.
Current Opinion in Biotechnology 21:1-10. (2010) [PDF]
Transcriptomic landscape of the primitive streak
Alev C, Wu Y, Kasukawa T, Jakt LM, Ueda HR, Sheng G
Development Sep;137(17):2863-74. (2010) [PDF]
Systems Biology of Mammalian Circadian Clocks
Ukai H, and Ueda HR.
Annual Review of Physiology 72: 579-603 (2010) [PDF]
2009
CKIε/δ-dependent phosphorylation is a temperature-insensitive, period-determining process in the mammalian circadian clock
Isojima Y, Nakajima M, Ukai H, Fujishima H, Yamada RG, Masumoto K, Kiuchia 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, and Ueda, HR
PNAS 106(37):15744-15749. (2009) [PDF]
[Supporting Information] [Table S3] [Table S4] [Dataset ST1] [Dataset ST2]
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.
PNAS Jun 16; 106(24):9890-5. (2009) [PDF] [Supporting Information] [Supporting data]
Genetic and molecular analysis of wild-derived arrhythmic mice
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.
PLoS ONE 4(1): e4301. doi:10.1371/journal.pone.0004301 (2009) [PDF]
2008
Predicting Perfect Adaptation Motifs in Reaction Kinetic Networks
Tormod Drengstig, Hiroki R. Ueda, and Peter Ruoff
The Journal of Physical Chemistry B 112 (51), 16752-16758 (2008) [PDF]
Perturbational formulation of principal component analysis in molecular dynamics simulation
Yohei M. Koyama, Tetsuya J. Kobayashi, Shuji Tomoda, and Hiroki R. Ueda
Physical Review E 78, 046702 (2008) [PDF]
Proof-by-Synthesis of the Transcriptional Logic of Mammalian Circadian Clocks
*Maki Ukai-Tadenuma, *Takeya Kasukawa and Hiroki R. Ueda
Nature Cell Biology (2008) [PDF] [Supplementary]
Analysis and Synthesis of High-amplitude Cis-elements in the Mammalian Circadian Clock
Yuichi Kumaki, Maki Ukai-Tadenuma, Ken-ichiro D. Uno, Junko Nishio, Koh-hei Masumoto, Mamoru Nagano, Takashi Komori, Yasufumi Shigeyoshi, John B. Hogenesch, and Hiroki R. Ueda
PNAS vol.105 no.39 14946-14951 (2008) [PDF] [Supplement: Appendix] [Supplement: Supporting Information]
Detection of a circadian enhancer in the mDbp promoter using prokaryotic 5 transposon vector-based strategy
Yota B. Kiyohara, Keigo Nishii, Maki Ukai-Tadenuma, Hiroki R. Ueda*, Yasuo Uchiyama and Kazuhiro Yagita,
Nucleic Acids Research 36(4): e23 (2008) [PDF] [Supplementary]
Thyrotrophin in the pars tuberalis triggers photoperiodic response.
Nobuhiro Nakao, Hiroko Ono, Takashi Yamamura, Tsubasa Anraku, Tsuyoshi Takagi, Kumiko Higashi, Shinobu Yasuo, Yasuhiro Katou, Saburo Kageyama, Yumiko Uno, Takeya Kasukawa, Masayuki Iigo, Peter J. Sharp, Atsushi Iwasawa, Yutaka Suzuki, Sumio Sugano, Teruyuki Niimi, Makoto Mizutani, Takao Namikawa, Shizufumi Ebihara, Hiroki R. Ueda, and Takashi Yoshimura
Nature 452, 317-322 (20 March 2008) [PDF] [Supplementary]
2007
Systems Biology of Mammalian Circadian Clocks
Ueda HR
Cold Spring Harbor Symposia on Quantitative Biology (DEC 2007) [PDF]
Melanopsin-dependent photo-perturbation reveals desynchronization underlying the singularity of mammalian circadian clocks.
*Ukai H, *Kobayashi TJ, Nagano M, Masumoto K, Sujino M, Kondo T, Yagita K, Shigeyoshi Y and Ueda HR
Nature Cell Biology 9(11):1327-34. (NOV 2007) [PDF] [Supplementary]
* These authors contribeted equally to this work.
A functional genomics strategy reveals clockwork orange as a transcriptional regulator in the Drosophila circadian clock.
*Matsumoto A, *Ukai-Tadenuma M, *Yamada R, Houl J, Uno K, Kasukawa T, Dauwalder B, Itoh T, Takahashi K, Ueda R,Hardin P, Tanimura T and Ueda HR
Genes & Development 21(13):1687-700. (JUL 2007). [PDF] [Supplementary]
* These authors contribeted equally to this work.
Microarrays: Statistical Methods for Circadian Rhythms.
Yamada R and Ueda HR
Circadian Rhythms: Methods And Protocols (Methods in Molecular Biology (Clifton, N.J. ), V.362.) Humana Press 245-264, (2007). [PDF]
Microarrays: Quality Control and Hybridization Protocol.
Uno K and Ueda HR
Circadian Rhythms: Methods And Protocols (Methods in Molecular Biology (Clifton, N.J. ), V.362.) Humana Press 225-243, (2007). [PDF]
2006
Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b.
Tsumura A, Hayakawa T, Kumaki Y, Takebayashi S, Sakaue M, Matsuoka C, Shimotohno K, Ishikawa F, Li E, Ueda HR, Nakayama J, Okano M
Genes to Cells 11 (7):805-814. JUL (JUL 2006). [PDF] [Supplementary]
The BMAL1 C terminus regulates the circadian transcription feedback loop.
Kiyohara YB, Tagao S, Tamanini, Morita A, Sugisawa Y, Yasuda M, Yamanaka I, Ueda HR, van der Horst GTJ, Kondo T, Yagita K
Proc Natl Aacad Sci USA 103 (26):10074-10079. (JUN 27 2006). [PDF] [Supplementary]
An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis .
Kurimoto K, Yabuta Y, Ohinata Y, Ono Y, Uno KD, Yamada RG, Ueda HR, Saitou M
Nucleic Acids Research 34 (5):Art. No. e42 (2006). [PDF] [Supplementary]
Feedback repression is required for mammalian circadian clock function.
*Sato TK, *Yamada RG, *Ukai H, Baggs JE, Miraglia LJ, Kobayashi TJ, Welsh DK, Kay SA, **Ueda HR, **Hogenesch JB
Nature Genetics 38 (3):312-319. (MAR 2006) [PDF] [Supplementary]
* These authors contribeted equally to this work. **corresponding authors.
Systems biology flowering in the plant clock field.
Ueda HR Molecular Systems Biology 2:Art. No. 60 (2006). [PDF]
2005
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 ARR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato X, 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 SPT, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Babu MM, 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, Schonbach C, Sekiguchi K, Semple CAM, 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
Science 309 (5740):1559-1563. (SEP 2 2005). [PDF] [Supplementary]
System-level identification of transcriptional circuits underlying mammalian circadian clocks.
Ueda H R, Hayashi S, Chen W, Sano M, Machida M, Shigeyoshi Y, Iino M and Hashimoto S
Nature Genetics (2005) [PDF]
2004
Molecular-timetable methods for detection of body time and rhythm disorders from single-time-point genome-wide expression profiles.
Ueda H R, Chen W, Minami Y, Honma S, Honma K, Iino M and Hashimoto S
PNAS 101(31) 11227-11232 (2004). [PDF] [Supplementary]
Universality and flexibility in gene expression from bacteria to human.
Ueda H R, Hayashi S, Matsuyama S, Yomo T, Hashimoto S, Kay S A, Hogesesch J B and Iino M
PNAS 101(11) 3765-3769 (2004). [PDF] [Supplementary]
2002
A transcription factor response element for gene expression during circadian night.
Ueda H R, Chen W, Adachi A, Wakamatsu H, Hayashi S, Takasugi T, Nagano M, Nakahama K, Suzuki Y, Sugano S, Iino M, Shigeyoshi Y and Hashimoto S
Nature 418:534-9(2002). [PDF] [Supplementary]
Genome-wide transcriptional orchestration of circadian rhythms in Drosophila.
Ueda H R, Matsumoto A, Kawamura M Iino M, Tanimura T and Hashimoto S
J Biol Chem 277:14048-52(2002). [PDF] [Supplementary]
Intercellular coupling mechanism for synchronized and noise-resistant circadian oscillators.
Ueda H R, Hirose K, Iino M
J Theor Biol 216:501-12(2002). [PDF]
2001
Robust oscillations within the interlocked feedback model of Drosophila circadian rhythm.
Ueda H R, Hagiwara M, Kitano H
J Theor Biol 210:401-6(2001). [PDF]
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