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| 2023 |
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Circadian ribosome profiling reveals a role for the Period2 upstream open reading frame in sleep.
Millius A, Yamada RG, Fujishima H, Maeda K, Standley DM, Sumiyama K, Perrin D, Ueda HR.
Proc Natl Acad Sci U S A. 2023 Oct 3;120(40):e2214636120
[PDF]
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Elucidation of the mechanism of amyloid A and transthyretin formation using mass spectrometry-based absolute quantification.
Shintani-Domoto Y, Ode KL, Nomura S, Abe H, Ueda HR, Sakatani T, Ohashi R.
Virchows Arch. 2023 Feb 22;17:1124333.
[PDF]
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A growing understanding of the role of muscarinic receptors in the molecular pathology and treatment of schizophrenia.
Dean B, Bakker G, Ueda HR, Tobin AB, Brown A, Kanaan RAA.
Neurosci. 2023 Feb 22;17:1124333.
[PDF]
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CCPG1 recognizes endoplasmic reticulum luminal proteins for selective ER-phagy.
Ishii S, Chino H, Ode KL, Kurikawa Y, Ueda HR, Matsuura A, Mizushima N, Itakura
Mol Biol Cell. 2023 Apr 1;34(4):ar29.
[PDF]
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The role of calcium and CaMKII in sleep.
Wang Y, Minami Y, Ode KL, Ueda HR.
Front Syst Neurosci. 2022 Dec 22;16:1059421.
[PDF]
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| 2022 |
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Distinct phosphorylation states of mammalian CaMKIIβ control the induction and maintenance of sleep
Tone D, Ode KL, Zhang Q, Fujishima H, Yamada RG, Nagashima Y, Matsumoto K, Wen Z, Yoshida SY, Mitani TT, Arisato Y, Ohno RI, Ukai-Tadenuma M, Yoshida Garçon J, Kaneko M, Shi S, Ukai H, Miyamichi K, Okada T, Sumiyama K, Kiyonari H, Ueda HR.
PLOS Biol. 20, e3001813 (2022)
[PDF]
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Ubiquitination of phosphatidylethanolamine in organellar membranes
Sakamaki JI, Ode KL, Kurikawa Y, Ueda HR, Yamamoto H, Mizushima N.
Mol. Cell 82, 19, 3677-3692.e11 (2022)
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An analysis modality for vascular structures combining tissue-clearing technology and topological data analysis
Takahashi K, Abe K, Kubota SI, Fukatsu N, Morishita Y, Yoshimatsu Y, Hirakawa S, Kubota Y, Watabe T, Ehata S, Ueda HR, Shimamura T, Miyazono K.
Nat. Commun. 13, 5239 (2022)
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A Novel Three-Dimensional Imaging System Based on Polysaccharide Staining for Accurate Histopathologic Diagnosis of Inflammatory Bowel Diseases
Nojima S, Ishida S, Terayama K, Matsumoto K, Matsui T, Tahara S, Ohshima K, Kiyokawa H, Kido K, Ukon K, Yoshida SY, Mitani TT, Doki Y, Mizushima T, Okuno Y, Susaki EA, Ueda HR, Morii E.
Cell. Mol. Gastroenterol. Hepatol. 14, 905-924 (2022)
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A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues
Glaser AK, Bishop KW, Barner LA, Susaki EA, Kubota SI, Gao G, Serafin RB, Balaram P, Turschak E, Nicovich PR, Lai H, Lucas LAG, Yi Y, Nichols EK, Huang H, Reder NP, Wilson JJ, Sivakumar R, Shamskhou E, Stoltzfus CR, Wei X, Hempton AK, Pende M, Murawala P, Dodt HU, Imaizumi T, Shendure J, Beliveau BJ, Gerner MY, Xin L, Zhao H, True LD, Reid RC, Chandrashekar J, Ueda HR, Svoboda K, Liu JTC.
Nat. Methods. 19, 613-619 (2022)
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Phosphorylation by casein kinase 2 enhances the interaction between ER-phagy receptor TEX264 and ATG8 proteins
Chino H., Yamasaki A., Ode K.L., Ueda H.R., Noda N.N., Mizushima N.,
EMBO Rep. 23:e54801 (2022)
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The 103,200-arm acceleration dataset in the UK Biobank revealed a landscape of human sleep phenotypes
Katori M., Shi S., Ode K.L., Tomita Y., Ueda H.R.,
Proc. Natl. Acad. Sci. U.S.A. 119, e2116729119 (2022)
[PDF]
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A design principle of spindle oscillations in mammalian sleep
Yamada T., Shi S., Ueda H.R.,
iScience 25, 103873 (2022)
[PDF]
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High-throughput Genetically Modified Animal Experiments Achieved by Next-generation Mammalian
Minami Y., Yuan Y., Ueda H.R.,
J. Biol. Rhythms 37, 135-151 (2022)
[PDF]
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A jerk-based algorithm ACCEL for the accurate classification of sleep–wake states from arm acceleration
Ode K.L., Shi S., Katori M., Mitsui K., Takanashi S., Oguchi R., Aoki D., Ueda H.R.,
iScience 25, 103727 (2022)
[PDF]
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Fluorescence tissue microscopy
Sacconi L., Ueda H.R., Pagès S., Silvestri L.
Prog. Biophys. Mol. Biol. 168, 1-2 (2022)
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The circadian clock ticks in organoids
Yamada R.G., Ueda H.R.,
EMBO J. 41, e110157 (2022)
[PDF]
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| 2021 |
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TISSUE CLEARING.
Richardson D.S., Guan W., Matsumoto K., Pan C., Chung K., Ertürk A., Ueda H.R., Lichtman J.W.
Nat. Rev. Methods Primers 1, 84 (2021)
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Towards organism-level systems biology by next-generation genetics and whole-organ cell profiling.
Minami Y., Yuan Y., Ueda H.R.
Biophys. Rev. 13, 1113-1126 (2021)
[PDF]
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Mechanical load regulates bone growth via periosteal Osteocrin.
Miyazaki T., Tainaka K., Harada I., Sato S., Sawada Y., Minamino N., Takeda S., Ueda H.R., Yasoda A., Mochizuki N.
Cell Rep. 1, 109380 (2021)
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CUBIC-Cloud provides an integrative computational framework toward community-driven whole-mouse-brain mapping
Mano T., Murata K., Kon K., Shimizu C., Ono H., Shi S., Yamada R.G., Miyamichi K., Susaki E.A., Touhara K., Ueda H.R.
Cell Rep. Methods 1, 100038 (2021)
[PDF]
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Visualization of the cancer cell cycle by tissue-clearing technology using the Fucci reporter system
Takahashi K., Tanabe R., Ehata S., Kubota S.I., Morishita Y., Ueda H.R., Miyazono K.
Cancer Sci. 112(9):3796-3809 (2021)
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NEK9 regulates primary cilia formation by acting as a selective autophagy adaptor for MYH9/myosin IIA
Yamamoto Y., Chino H., Tsukamoto S., Ode K.L., Ueda H.R., Mizushima N.
Nat. Commun. 12, 3292 (2021)
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Activation of Sympathetic Signaling in Macrophages Blocks Systemic Inflammation and Protects against Renal Ischemia-Reperfusion Injury
Hasegawa S., Inoue T., Nakamura Y., Fukaya D., Uni R., Wu C.H., Fujii R., Peerapanyasut W., Taguchi A., Kohro T., Yamada S., Katagiri M., Ko T., Nomura S., Nakanishi Ozeki A., Susaki E.A., Ueda H.R., Akimitsu N., Wada Y., Komuro I., Nangaku M., Inagi R.
J. Am. Soc. Nephrol. 32, 1599-1615 (2021)
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Whole-organ analysis of TGF-β-mediated remodelling of the tumour microenvironment by tissue clearing
Kubota S.I., Takahashi K., Mano T., Matsumoto K., Katsumata T., Shi S., Tainaka K., Ueda H.R., Ehata S., Miyazono K.
Commun. Biol. 4, 294 (2021)
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Malignant subclone drives metastasis of genetically and phenotypically heterogenous cell clusters through fibrotic niche generation
Kok S.Y., Oshima H., Takahashi K., Nakayama M., Murakami K., Ueda H.R., Miyazono K., Oshima M.
Nat. Commun. 12, 863 (2021)
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A design principle for posttranslational chaotic oscillators
Yamagichi H.Q., Ode K.L., Ueda H.R.
iScience 1, 101946 (2021)
[PDF]
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| 2020 |
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Reflections on the past two decades of neuroscience
Danielle S. Bassett, Kathleen E. Cullen, Simon B. Eickhoff, Martha J. Farah, Yukiko Goda, Patrick Haggard, Hailan Hu, Yasmin L. Hurd, Sheena A. Josselyn, Baljit S. Khakh, Jürgen A. Knoblich, Panayiota Poirazi, Russell A. Poldrack, Marco Prinz, Pieter R. Roelfsema, Tara L. Spires-Jones, Mriganka Sur & Hiroki R. Ueda
Nature Reviews Neuroscience Volume 21, 2 Sep 2020, Pages 524-534
[PDF]
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Whole-Brain Profiling of Cells and Circuits in Mammals by Tissue Clearing and Light-Sheet Microscopy
Hiroki R.Ueda, Hans-Ulrich Dodt, Pavel Osten, Michael N.Economo, Jayaram Chandrashekar, Philipp J.Keller
Neuron Volume 106, Issue 3, 6 May 2020, Pages 369-387
[PDF]
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Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues
Etsuo A. Susaki, Chika Shimizu, Akihiro Kuno, Kazuki Tainaka, Xiang Li, Kengo Nishi, Ken Morishima, Hiroaki Ono, Koji L. Ode, Yuki Saeki, Kazunari Miyamichi, Kaoru Isa, Chihiro Yokoyama, Hiroki Kitaura, Masako Ikemura, Tetsuo Ushiku, Yoshihiro Shimizu, Takashi Saito, Takaomi C. Saido, Masashi Fukayama, Hirotaka Onoe, Kazushige Touhara, Tadashi Isa, Akiyoshi Kakita, Mitsuhiro Shibayama & Hiroki R. Ueda
Nature Communications Volume 11, Article number: 1982 (2020)
[PDF]
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Visualization and molecular characterization of whole-brain vascular networks with capillary resolution.
Takeyuki Miyawaki, Shota Morikawa, Etsuo A. Susaki, Ai Nakashima, Haruki Takeuchi, Shun Yamaguchi, Hiroki R. Ueda & Yuji Ikegaya
Nature Communications Volume 11, Article number: 1104 (2020)
[PDF]
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The oral hypoxia-inducible factor prolyl hydroxylase inhibitor enarodustat counteracts alterations in renal energy metabolism in the early stages of diabetic kidney disease.
Sho Hasegawa, Tetsuhiro Tanaka, Tomoyuki Saito, Kenji Fukui, Takeshi Wakashima, Etsuo A.Susaki, Hiroki R.Ueda, Masaomi Nangaku
Kidney International Volume 97, Issue 5, May 2020, Pages 934-950
[PDF]
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Molecular Mechanisms of REM Sleep
Rikuhiro G. Yamada, Hiroki R. Ueda
Frontiers in Neuroscience January 2020, Volume 13, Article 1402
[PDF]
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Tissue clearing and its applications in neuroscience
Hiroki R. Ueda, Ali Ertürk, Kwanghun Chung, Viviana Gradinaru, Alain Chédotal, Pavel Tomancak and Philipp J. Keller
Nature Review Neuroscience doi:10.1038/s41583-019-0250-1 (2020)
[PDF]
[Supplemental xlsx file]
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| 2019 |
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Advanced CUBIC tissue clearing for whole-organ cell profiling
Katsuhiko Matsumoto, Tomoki T. Mitani, Shuhei A. Horiguchi, Junichi Kaneshiro, Tatsuya C. Murakami, Tomoyuki Mano, Hiroshi Fujishima, Ayumu Konno, Tomonobu M. Watanabe, Hirokazu Hirai & Hiroki R. Ueda
nature protocols 14, 3506-3537
[PDF]
[Supplemental1 pdf file]
[Supplemental2 mov file]
[Supplemental3 mov file]
[Supplemental4 mov file]
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A period without PER: understanding 24-h rhythms without classic transcription and translation feedback loops
Millius A., Ode K.L., Ueda H.R.
F1000Res. 8, 499
[PDF]
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Comprehensive three-dimensional analysis (CUBIC-kidney) visualizes abnormal renal sympathetic nerves after ischemia/reperfusion injury
Hasegawa S., Susaki E.A., Tanaka T., Komaba H., Wada T., Fukagawa M., Ueda H.R., Nangaku M.
Kidny Int. Advanced online publication
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Next-generation human genetics for organism-level systems biology
Ukai H., Sumiyama K., Ueda H.R.
Curr. Opin. Biotechnol. 58, 137-145
[PDF]
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| 2018 |
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Muscarinic Acetylcholine Receptors Chrm1 and Chrm3 Are Essential for REM Sleep
Niwa Y., Kanda G.N., Yamada R.G., Shi S., Sunagawa G.A., 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 H.R.
Cell Reports VOLUME 24, ISSUE 9, P2231-2247.E7 (2018)
[PDF]
[additional analysis]
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Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents
Tainaka K., Murakami T.C., Susaki E.A., Shimizu C., Saito R., Takahashi K., Hayashi-Takagi A., Sekiya H., Arima Y., Nojima S., Ikemura M., Ushiku T., Shimizu Y., Murakami M., Tanaka K.F., Iino M., Kasai H., Sasaoka T., Kobayashi K., Miyazono K., Morii E., Isa T., Fukayama M., Kakita A., Ueda H.R.
Cell Reports VOLUME 24, ISSUE 8, P2196-2210.E9 (2018)
[PDF]
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A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing
Murakami T.C., Mano T., Saikawa S., Horiguchi S.A., Shigeta D., Baba K.,Sekiya H., Shimizu Y., Tanaka K.F., Kiyonari H., Iino M., Mochizuki H.,Tainaka K., Ueda H.R.
Nature Neuroscience 21, 625-637 (2018)
[PDF]
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Amnionless-mediated glycosylation is crucial for cell surface targeting of cubilin in renal and intestinal cells
Udagawa T., Harita Y., Miura K., Mitsui J., Ode K.L., Morishita S., Urae S.,Kanda S., Kajiho Y., Tsurumi H., Ueda H.R., Tsuji S., Saito A. Oka A.
Scientific reports 8, 2351 (2018)
[PDF]
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Ca2+-Dependent Hyperpolarization Pathways in Sleep Homeostasis and Mental Disorders
Shi S., Ueda H.R.
BioEssays Jan;40(1) 2018
[PDF]
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| 2017 |
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Production of knock-in mice in a single generation from embryonic stem cells
Ukai H, Kiyonari H, Ueda HR.
Nature protocols 12(12):2513-2530 (2017)
[PDF]
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Temperature-Sensitive Substrate and Product Binding Underlie Temperature-Compensated Phosphorylation in the Clock
Shinohara Y, Koyama YM, Ukai-Tadenuma M, Hirokawa T, Kikuchi M, Yamada RG, Ukai H, Fujishima H, Umehara T, Tainaka K, Ueda HR.
Mol. Cell 67, 783-798 (2017)
[PDF]
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CUBIC pathology: three-dimensional imaging for pathological diagnosis
Nojima S., Susaki E.A., Yoshida K., Takemoto H., Tsujimura N., Iijima S., Takachi K., Nakahara Y., Tahara S., Ohshima K., Kurashige M., Hori Y., Wada N., Ikeda J.I., Kumanogoh A., Morii E., Ueda H.R.
Sci. Rep. 7, 9269 (2017)
[PDF]
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Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution
Kubota S.I., Takahashi K., Nishida J., Morishita Y., Ehata S., Tainaka K., Miyazono K., Ueda H.R.
Cell Rep. 20, 236-250 (2017)
[PDF]
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Next-generation mammalian genetics toward organism-level systems biology
Susaki E.A., Ukai H., Ueda H.R.
npj. Syst. Biol. Appl. 3, article number 15 (2017)
[PDF]
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Fast and slow Ca2+-dependent hyperpolarization mechanisms connect membrane potential and sleep homeostasis
Ode K.L., Katsumata T., Tone D., Ueda H.R.
Curr. Opin. Neurobiol. 44, 212-221 (2017)
[PDF]
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Compass in the data ocean: Toward chronotherapy.
Yamada R.G. and Ueda H.R.
PNAS 114(20),5069-5071 (2017)
[PDF]
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A Design Principle for an Autonomous Post-translational Pattern Formation
Sugai S.S., Ode K.L., Ueda H.R.
Cell Rep. 19, 863-874 (2017)
[PDF]
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Systems biology-derived discoveries of intrinsic clocks
Millius A., Ueda H.R.
Front. Neurol. 8:25 (2017)
[PDF]
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Ca2+-dependent hyperpolarization hypothesis for mammalian sleep
Tatsuki F., Ode K.L., Ueda H.R.
Neurosci. Res. 118, 48-55 (2017)
[PDF]
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Knockout-Rescue Embryonic Stem Cell-Derived Mouse Reveals Circadian-Period Control by Quality and Quantity of CRY1
Ode K.L., Ukai H., Susaki E.A., Narumi R., Matsumoto K., Hara J., Koide N., Abe T., Kanemaki M.T., Kiyonari H., Ueda H.R.
Mol. Cell 65, 176-190 (2017)
[PDF]
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| 2016 |
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"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 45(1):176-190
[PDF]
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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]
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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]
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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]
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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]
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| 2015 |
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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]
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| 2014 |
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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]
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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]
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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]
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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]
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| 2013 |
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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]
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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]
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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]
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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]
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| 2012 |
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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]
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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]
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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]
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| 2011 |
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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]
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Perturbation analyses of intermolecular interactions
Yohei M. Koyama, Tetsuya J. Kobayashi, and Hiroki R. Ueda.
Physical Review E 84, 026704 (2011)
[PDF]
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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]
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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]
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| 2010 |
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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]
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Challenges in synthetically designing mammalian circadian clocks.
Susaki EA, Stelling J, Ueda HR.
Current Opinion in Biotechnology 21:1-10. (2010)
[PDF]
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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]
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Systems Biology of Mammalian Circadian Clocks
Ukai H, and Ueda HR.
Annual Review of Physiology 72: 579-603 (2010)
[PDF]
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| 2009 |
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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]
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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]
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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]
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| 2008 |
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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]
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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]
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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]
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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]
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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]
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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]
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| 2007 |
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Systems Biology of Mammalian Circadian Clocks
Ueda HR
Cold Spring Harbor Symposia on Quantitative Biology (DEC 2007)
[PDF]
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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.
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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.
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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]
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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]
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| 2006 |
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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]
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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]
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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]
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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.
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Systems biology flowering in the plant clock field.
Ueda HR
Molecular Systems Biology 2:Art. No. 60 (2006).
[PDF]
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| 2005 |
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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]
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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]
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| 2004 |
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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]
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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]
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| 2002 |
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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]
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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]
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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]
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