巨人の肩に.
Bioorthogonal chemical labeling of endogenous neurotransmitter receptors in living mouse brains.
Nonaka H, Sakamoto S, Shiraiwa K, Ishikawa M, Tamura T, Okuno K, Kondo T, Kiyonaka S, Susaki EA, Shimizu C, Ueda HR, Kakegawa W, Arai I, Yuzaki M, Hamachi I.
Proc. Natl. Acad. Sci. U.S.A. 121, e2313887121 (2023)
[Link]
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. 120, e2214636120 (2023)
[PDF]
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. 120, e2214636120 (2023)
[Link]
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.
Front. Cell Neurosci. 17, 1124333 (2023)
[Link]
CCPG1 recognizes ER luminal proteins for selective ER-phagy.
Ishii S, Chino H, Ode KL, Kurikawa Y, Ueda HR, Matsuura A, Mizushima N, Itakura E.
Mol. Biol. Cell 34, ar29 (2023)
[Link]
The role of calcium and CaMKII in sleep
Wang Y, Minami Y, Ode KL, Ueda HR.
Front. Syst. Neurosci. 16, 1059421 (2022)
[PDF]
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]
Ubiquitination of phosphatidylethanolamine in organellar membranes
Sakamaki JI, Ode KL, Kurikawa Y, Ueda HR, Yamamoto H, Mizushima N.
Mol. Cell 82, 3677-3692 (2022)
[Link]
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)
[Link]
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)
[Link]
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)
[Link]
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. e54801 online ahead of print
[Link]
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]
A design principle of spindle oscillations in mammalian sleep.
Yamada T., Shi S., Ueda H.R.
iScience 25, 103873 (2022)
[PDF]
High-throughput Genetically Modified Animal Experiments Achieved by Next-generation Mammalian Genetics.
Minami Y., Yuan Y., Ueda H.R.
J. Biol. Rhythms 37, 135-151 (2022)
[PDF]
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]
Fluorescence tissue microscopy
Sacconi L., Ueda H.R., Pagès S., Silvestri L.
Prog. Biophys. Mol. Biol. 41, e110157 (2022)
[Link]
The circadian clock ticks in organoids
Yamada R.G., Ueda H.R.
EMBO J. 41, e110157 (2022)
[Link]
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)
[Link]
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]
Mechanical load regulates bone growth via periosteal Osteocrin.
Watanabe-Takano H., Ochi H., Chiba A., Matsuo A., Kanai Y., Fukuhara S., Ito N., Sako K., 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)
[Link]
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 36, 100038 (2021)
[PDF]
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. DOI: 10.1111/cas.15034 online ahead of print
[Link]
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)
[Link]
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)
[Link]
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)
[Link]
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)
[Link]
A design principle for posttranslational chaotic oscillators
Yamaguchi H.Q., Ode K.L., Ueda H.R.
iScience 24, 101946 (2021)
[PDF]
Protocol for Imaging and Analysis of Mouse Tumor Models with CUBIC Tissue Clearing
Takahashi K, Kubota S.I., Ehata S., Ueda H.R., Miyazono K.
STAR Protoc. 1, 100191 (2020)
[Link]
Generation of gene-corrected iPSCs line (KEIUi001-A) from a PARK8 patient iPSCs with familial Parkinson's disease carrying the I2020T mutation in LRRK2.
Ohta E., Sone T., Ukai H., Hisamatsu T., Kitagawa T., Ishikawa M., Nagai M., Ueda H.R., Obata F., Okano H.
Stem Cell Res. 49, 102073 (2020)
[Link]
Phosphorylation Hypothesis of Sleep
Ode K.L., Ueda H.R.
Front. Psychol. 11, 575328 (2020)
[PDF]
Rapid and easy-to-use ES cell manipulation device with a small groove near culturing wells.
Funano S.I., Tone D., Ukai H., Ueda H.R., Tanaka Y.
BMC Res. Notes. 13, 453 (2020)
[Link]
Generation of a p16 Reporter Mouse and Its Use to Characterize and Target p16high Cells In Vivo
Omori S., Wang T., Johmura Y., Kanai T., Nakano Y., Kido T., Susaki E.A., Nakajima T., Shichino S., Ueha S., Ozawa M, Yokote K., Kumamoto S., Nishiyama A., Sakamoto T., Yamaguchi K., Hatakeyama S., Shimizu E., Katayama K., Yamada Y., Yamazaki S., Iwasaki K., Miyoshi C., Funato H., Yanagisawa M., Ueno H., Imoto S., Furukawa Y., Yoshida N., Matsushima K., Ueda H.R., Miyajima A., Nakanishi M.
Cell Metab. 32, 814-828 (2020)
[Link]
Reflections on the past two decades of neuroscience
Bassett D.S., Cullen K.E., Eickhoff S.B., Farah M.J., Goda Y., Haggard P., Hu H., Hurd Y.L., Josselyn S.A., Khakh B.S., Knoblich J.A., Poirazi P., Poldrack R.A., Prinz M., Roelfsema P.R., Spires-Jones T.L., Sur M., Ueda H.R.
Nat. Rev. Neurosci. 21, 524-534 (2020)
[PDF]
Mass Spectrometry-Based Absolute Quantification of Amyloid Proteins in Pathology Tissue Specimens: Merits and Limitations
Ogawa M., Shintani-Domoto Y., Nagashima Y., Ode K.L., Sato A., Shimizu Y., Ohashi K., Roehrl M.H.A., Ushiku T., Ueda H.R., Fukayama M.
PLOS ONE 15, e0235143 (2020)
[Link]
The cellular model of albumin endocytosis uncovers link between membrane and nuclear proteins
Urae S., Harita Y., Udagawa T., Ode K.L., Nagahama M., Kajiho Y., Kanda S., Saito A., Ueda H.R., Nangaku M., Oka A.
J. Cell Sci. 133, jcs242859 (2020)
[Link]
Whole-Brain Profiling of Cells and Circuits in Mammals by Tissue Clearing and Light-Sheet Microscopy
Ueda H.R., Dodt H., Osten P., Economo M.N., Chandrashekar J., Keller P.J.
Neuron 106, 369-387 (2020)
[PDF]
Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues
Susaki E.A., Shimizu C., Kuno A., Tainaka K., Li X., Nishi K., Morishima K., Ono H., Ode K.L., Saeki Y., Miyamichi K., Isa K., Yokoyama C., Kitaura H., Ikemura M., Ushiku T., Shimizu Y., Saito T., Saido T.C., Fukayama M., Onoe H., Touhara K., Isa T., Kakita A., Shibayama M., Ueda H.R.
Nat. Commun. 11, 1982 (2020)
[PDF]
The oral hypoxia-inducible factor prolyl hydroxylase inhibitor enarodustat counteracts alterations in renal energy metabolism in the early stages of diabetic kidney disease
Hasegawa S., Tanaka T., Saito T., Fukui K., Wakashima T., Susaki E.A., Ueda H.R., Nangaku M.
Kidney Int. 97, 934-950 (2020)
[Link]
Visualization and molecular characterization of whole-brain vascular networks with capillary resolution
Miyawaki T., Morikawa S., Susaki E.A., Nakashima A., Takeuchi H., Yamaguchi S., Ueda H.R., Ikegaya Y.
Nat. Commun. 11, 1104 (2020)
[Link]
Molecular Mechanisms of REM Sleep
Yamada R.G., Ueda H.R.
Front. Neurosci. 13, 1402 (2020)
[PDF]
Tissue clearing and its applications in neuroscience
Ueda H.R., Ertürk A., Chung K., Gradinaru V., Chédotal A., Tomancak P., Keller P.J.
Nat. Rev. Neurosci. doi:10.1038/s41583-019-0250-1 (2020)
[PDF] [Sup table]
Advanced CUBIC tissue clearing for whole-organ cell profiling
Matsumoto K., Mitani T.T., Horiguchi S.A., Kaneshiro J., Murakami T.C., Mano T., Fujishima H., Konno A., Watanabe T.M., Hirai H., Ueda H.R.
Nat. Protoc. 14, 3506-3537 (2019)
[PDF]
Novel 3D analysis using optical tissue clearing documents the evolution of murine rapidly progressive glomerulonephritis
Puelles V.G., Fleck D., Ortz L., Papadouri S., Strieder T., Böhner A.M.C., van der Wolde J.W., Vogt M., Saritas T., Kuppe C., Fuss A., Menzel S., Klinkhammer B.M., Müller-Newen G., Heymann F., Decker L., Braun F., Kretz O., Moeller M.J.
Kidny Int. 96, 505-516 (2019)
[Link]
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 (2019)
[PDF]
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. 96, 129-138 (2019)
[Link]
Next-generation human genetics for organism-level systems biology
Ukai H., Sumiyama K., Ueda H.R.
Curr. Opin. Biotechnol. 58, 137-145 (2019)
[PDF]
Whole-Brain Analysis of Cells and Circuits by Tissue Clearing and Light-Sheet Microscopy
Mano T., Albanese A., Dodt H.U., Erturk A., Gradinaru V., Treweek J.B., Miyawaki A., Chung K., Ueda H.R.
J. Neurosci. 38, 9330-9337 (2018)
[PDF]
Leak potassium channels regulate sleep duration
Yoshida K., Shi S., Ukai-Tadenuma M., Fujishima H., Ohno R., Ueda H.R.
Proc. Natl. Acad. Sci. USA 115, E9459-E9468 (2018)
[PDF]
Lost in clocks: non‐canonical circadian oscillation discovered in Drosophila cells
Ode K.L., Ueda H.R.
Mol. Syst. Biol. 14, e8567 (2018)
[PDF]
Easy and efficient production of completely embryonic-stem-cell-derived mice using a micro-aggregation device
Sumiyama K., Matsumoto N., Garçon-Yoshida J., Ukai H., Ueda H.R., Tanaka Y.
PLoS One 13, e0203056 (2018)
[Link]
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 Rep. 24, 2231-2247 (2018)
[PDF] [追加解析データ]
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 Rep. 24, 2196-2210 (2018)
[PDF]
Design Principles of Phosphorylation-Dependent Timekeeping in Eukaryotic Circadian Clocks
Ode K.L., Ueda H.R.
Cold Spring Harb. Perspect. Biol. 10, a028357 (2018)
[PDF]
Cell-free synthesis of stable isotope-labeled internal standards for targeted quantitative proteomics
Narumi R. Masuda K. Tomonaga T. Adachi J., Ueda H.R., Shimizu Y.
Synth. Syst. Biotechnol. 3, 97-104 (2018)
[Link]
Comparison of the 3-D patterns of the parasympathetic nervous system in the lung at late developmental stages between mouse and chicken
Watanabe T. Nakamura R. Takasea Y. Susaki E.A., Ueda H.R., Tadokoro R., Takahash Y.
Dev. Biol. 444 Suppl 1, S325-S336 (2018)
[Link]
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.
Nat. Neurosci. 21, 625-637 (2018)
[PDF]
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.
Sci. Rep. 8, 2351 (2018)
[PDF]
Ca2+-Dependent Hyperpolarization Pathways in Sleep Homeostasis and Mental Disorders
Shi S., Ueda H.R.
BioEssays 40, 1700105 (2018)
[PDF]
Neuronal signals regulate obesity induced β-cell proliferation by FoxM1 dependent mechanism
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 V.V., Susaki E.A., Kanzaki M., Ueda H.R., Ishigaki Y., Yamada T., Katagiri H.
Nat. Commun. 8, 1930 (2017)
[PDF]
Production of knock-in mice in a single generation from embryonic stem cells
Ukai H., Kiyonari H., Ueda H.R.
Nat. Protoc. 12, 2513-2530 (2017)
[PDF]
Temperature-Sensitive Substrate and Product Binding Underlie Temperature-Compensated Phosphorylation in the Clock
Shinohara Y., Koyama Y.M., Ukai-Tadenuma M., Hirokawa T., Kikuchi M., Yamada R.G., Ukai H., Fujishima H., Umehara T., Tainaka K., Ueda H.R.
Mol. Cell 67, 783-798 (2017)
[PDF]
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]
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]
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]
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]
Compass in the data ocean: Toward chronotherapy.
Yamada R.G., Ueda H.R.
Proc. Natl. Acad. Sci. USA 114, 5069-5071 (2017)
[PDF]
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]
Systems biology-derived discoveries of intrinsic clocks
Millius A., Ueda H.R.
Front. Neurol. 8:25 (2017)
[PDF]
Ca2+-dependent Hyperpolarization Hypothesis for Mammalian Sleep
Tatsuki F., Ode K.L., Ueda H.R.
Neurosci. Res. 118, 48-55 (2017)
[PDF]
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]
Chemical principles in tissue clearing and staining protocols for whole-body cell profiling
Tainaka K., Kuno A., Kubota S.I., Murakami T., Ueda H.R.
Annu. Rev. Cell Dev. Biol 32, 713-741 (2016)
[PDF]
Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins
Narumi R., Shimizu Y., Ukai-Tadenuma M., Ode K.L., Kanda G.N., Shinohara Y., Sato A., Matsumoto K., Ueda H.R.
Proc. Natl. Acad. Sci. USA 133, E3461-E3467 (2016)
[PDF]
Involvement of Ca2+-dependent hyperpolarization in sleep duration in mammals
Tatsuki F., Sunagawa G.A., Shi S., Susaki E.A., Yukinaga H., Perrin D., Sumiyama K., Ukai-Tadenuma M., Fujishima H., Ohno R., Tone D., Ode K.L., Matsumoto K., Ueda H.R.
Neuron 90, 70-85 (2016)
[PDF]
Whole-body and whole-organ clearing and imaging techniques with single-cell resolution: toward organism-level systems biology in mammals
Susaki E.A., Ueda H.R.
Cell Chem. Biol. 23, 137-157 (2016)
[PDF]
Mammalian reverse genetics without crossing reveals Nr3a as a short-sleeper gene
Sunagawa G.A., Sumiyama K. Ukai-Tadenuma M., Perrin D., Fujishima H., Ukai H., Nishimura O., Shi S., Ohno R., Narumi R., Shimizu Y., Tone D., Ode K.L., Kuraku S., Ueda H.R.
Cell Rep. 14, 662-677 (2016)
[PDF]
Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging
Susaki E.A, Tainaka K., Perrin D., Yukinaga H., Kuno A., Ueda H.R.
Nat. Protoc. 10, 1709-1727 (2015)
[PDF]
Seeing the forest and trees: whole-body and whole-brain imaging for circadian biology
Ode K.L., Ueda H.R.
Diabetes Obes. Metab. 17 Suupl 1, 47-54 (2015)
[PDF]
Whole-body imaging with single-cell resolution by tissue-decolorization
Tainaka K., Kubota S.I., Suyama T.Q., Susaki E.A., Perrin D., Ukai-Tadenuma M., Ukai H., Ueda H.R.
Cell 159, 911-924 (2014)
[PDF]
Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis
Susaki E.A., Tainaka K., Perrin D., Kishino F., Tawara T., Watanabe T.M., Yokoyama C., Onoe H., Eguchi M., Yamaguchi S., Abe T., Kiyonari H., Shimizu Y., Miyawaki A., Yokota H., Ueda H.R.
Cell 157, 726-739 (2014)
[PDF]
Non-enzymatic DNA cleavage reaction induced by 5-ethynyluracil in methylamine aqueous solution and application to DNA concatenation
Ikeda S., Tainaka K., Matsumoto K., Shinohara Y., Ode K.L., Susaki E.A., Ueda H.R.
PLoS One 9, e92369 (2014)
[PDF]
Context-dependent wiring of sox2 regulatory networks for self-renewal of embryonic and trophoblast stem cells
Adachi K., Nikaido I., Ohta H., Ohtsuka S., Ura H., Kadota M., Wakayama T., Ueda H.R., Niwa H.
Mol. Cell 52, 380-392 (2013)
[PDF]
Establishment of TSHβ real-time monitoring system in mammalian photoperiodism
Tsujino K., Narumi R., Masumoto K.H., Susaki E.A., Shinohara Y., Abe T., Iigo M., Wada A., Nagano M., Shigeyoshi Y., Ueda H.R.
Genes Cells 18, 575-588 (2013)
[PDF]
FASTER: an unsupervised fully automated sleep staging method for mice
Sunagawa G.A., Sei H., Shimba S., Urade Y., Ueda H.R.
Genes Cells 18, 502-518 (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 K.D., Imai T., Ueda H.R.
Genome Biol. 14, R31 (2013)
[PDF]
Mammalian circadian clock: the roles of transcriptional repression and delay
Minami Y., Ode K.L., Ueda H.R.
Handb. Exp. Pharmacol. 217, 359-377 (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 A.D., Nikaido I., Ueda H.R., Tatematsu K., Tanizawa K., Kondo A., Fujii I., Kuroda S.
Sci. Rep. 3, 1191 (2013)
[PDF]
A design principle for a posttranslational biochemical oscillator
Jolley C.C., Ode K.L., Ueda H.R.
Cell Rep. 2, 938-950 (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 H.R.
Proc. Natl. Acad. Sci. USA 109, 15036-15041 (2012)
[PDF]
Identification of a novel cryptochrome differentiating domain required for feedback repression in circadian clock function
Khan S.K., Xu H., Ukai-Tadenuma M., Burton B., Wang Y., Ueda H.R., Liu A.C.
J. Biol. Chem. 287, 25917-25926 (2012)
[PDF]
Quantitative expression profile of distinct functional regions in the adult mouse brain
Kasukawa T., Masumoto K., Nikaido I., Nagano M., Uno K.D., Tsujino K., Hanashima C., Shigeyoshi Y., Ueda H.R.
PLoS ONE 6, e23228 (2011)
[PDF]
Perturbation analyses of intermolecular interactions
Koyama Y.M., Kobayashi T.J., Ueda H.R.
Phys. Rev. E 84, 026704 (2011)
[PDF]
Understanding systems-level properties: timely stories from the study of clocks
Hogenesch J.B., Ueda H.R.
Nat. Rev. Genet. 12, 407-416 (2011)
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Delay in feedback repression by cryptochrome 1 is required for circadian clock function
Ukai-Tadenuma M., Yamada R.G., Xu H., Ripperger J.A., Liu A.C., Ueda H.R.
Cell 144, 268-281 (2011)
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Acute induction of Eya3 by late-night light stimulation triggers TSHβ expression in photoperiodism
Masumoto K.H., Ukai-Tadenuma M., Kasukawa T., Nagano M., Uno K.D., Tsujino K., Horikawa K., Shigeyoshi Y., Ueda H.R.
Curr. Biol. 20, 2199-2206 (2010)
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Challenges in synthetically designing mammalian circadian clocks
Susaki E.A., Stelling J., Ueda H.R.
Curr. Opin. Biotechnol. 21, 556-565 (2010)
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Transcriptomic landscape of the primitive streak
Alev C., Wu Y., Kasukawa T., Jakt L.M., Ueda H.R., Sheng G.
Development 137, 2863-2874 (2010)
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Systems biology of mammalian circadian clocks
Ukai H. Ueda H.R.
Ann. Rev. Physiol. 72, 579-603 (2010)
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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 R.G., Masumoto K., Kiuchia R., Ishida M., Ukai-Tadenuma M., Minami Y., Kito R., Nakao K., Kishimoto W., Yoo S.H., Shimomura K., Takao T., Takano A., Kojima T., Nagai K., Sakaki Y., Takahashi J.S., and Ueda H.R.
Proc. Natl. Acad. Sci. USA 106, 15744-15749 (2009)
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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 G.T., Soga T., Ueda H.R.
Proc. Natl. Acad. Sci. USA 106, 9890-9895 (2009)
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Genetic and molecular analysis of wild-derived arrhythmic mice
Watanabe T., Suzuki T., Ishikawa A., Yokota Y., Ueda H.R., Yamada R.G., Tei H., Imai S., Tomida S., Kobayashi J., Naito E., Yasuo S., Nakao N., Namikawa T., Yoshimura T., Ebihara S.
PLoS ONE 4, e4301 (2009)
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Predicting perfect adaptation motifs in reaction kinetic networks
Drengstig T., Ueda H.R., Ruoff P.
J. Phys. Chem. B 112, 16752-16758 (2008)
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Perturbational formulation of principal component analysis in molecular dynamics simulation
Koyama Y.M., Kobayashi T.J., Tomoda S., Ueda H.R.
Phys. Rev. E 78, 046702 (2008)
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Proof-by-synthesis of the transcriptional logic of mammalian circadian clocks
Ukai-Tadenuma M., Kasukawa T, Ueda H.R.
Nat. Cell Biol. 78, 1154-1163 (2008)
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Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock
Kumaki Y., Ukai-Tadenuma M., Uno K.D., Nishio J., Masumoto K., Nagano M., Komori T., Shigeyoshi Y., Hogenesch J.B., Ueda H.R.
Proc. Natl. Acad. Sci. USA 105, 14946-14951 (2008)
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Detection of a circadian enhancer in the mDbp promoter using prokaryotic 5 transposon vector-based strategy
Kiyohara Y.B., Nishii K., Ukai-Tadenuma M., Ueda H.R., Uchiyama Y., Yagita K.
Nucleic Acids Res. 36, e23 (2008)
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Thyrotrophin in the pars tuberalis triggers photoperiodic response
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 P.J., Iwasawa A., Suzuki Y., Sugano S., Niimi T., Mizutani M., Namikawa T., Ebihara S., Ueda H.R., Yoshimura T.
Nature 452, 317-322 (2008)
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Systems biology of mammalian circadian clocks
Ueda H.R.
Cold Spring Harb. Symp. Quant. Biol. 72, 365-380 (2007)
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Melanopsin-dependent photo-perturbation reveals desynchronization underlying the singularity of mammalian circadian clocks
Ukai H., Kobayashi T.J., Nagano M., Masumoto K., Sujino M., Kondo T., Yagita K., Shigeyoshi Y., Ueda H.R.
Nat. Cell. Biol. 9, 1327-1334 (2007)
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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.G, Houl J., Uno K.D., Kasukawa T., Dauwalder B., Itoh T., Takahashi K., Ueda R., Hardin P., Tanimura T., Ueda H.R.
Genes. Dev. 21, 1687-1700 (2007)
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Microarrays: statistical methods for circadian rhythms
Yamada R., Ueda H.R.
Methods Mol. Biol. 362, 254-264 (2007)
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Microarrays: quality control and hybridization protocol
Uno K., Ueda H.R.
Methods Mol. Biol. 362, 225-243 (2007)
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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 H.R., Nakayama J., Okano M.
Genes Cells 11, 805-814 (2006)
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The BMAL1 C terminus regulates the circadian transcription feedback loop
Kiyohara Y.B., Tagao S., Tamanini F., Morita A., Sugisawa Y., Yasuda M., Yamanaka I., Ueda H.R., van der Horst G.T., Kondo T., Yagita K.
Proc. Natl. Acad. Sci. USA 103, 10074-10079 (2006)
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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 K.D., Yamada R.G., Ueda H.R., Saitou M.
Nucleic Acids Res. 34, e42 (2006)
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Feedback repression is required for mammalian circadian clock function
Sato T.K., Yamada R.G., Ukai H., Baggs J.E., Miraglia L.J., Kobayashi T.J., Welsh D.K., Kay S.A., Ueda H.R., Hogenesch J.B.
Nat. Genet. 38, 312-319 (2006)
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Systems biology flowering in the plant clock field
Ueda H.R.
Mol. Sys. Biol. 2, 60 (2006)
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The transcriptional landscape of the mammalian genome
Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R.R., Zavolan M., Davis M.J., Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato X., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., 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 S.P.T., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Babu M.M., 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 K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schonbach C., Sekiguchi K., Semple C.A.M., 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 S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., 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, 1559-1563 (2005)
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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., Hashimoto S.
Nat. Genet. 37, 187-192 (2005)
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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., Hashimoto S.
Proc. Natl. Acad. Sci. USA 101, 11227-11232 (2004)
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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., Hogenesch J.B., Iino M.
Proc. Natl. Acad. Sci. USA 101, 3765-3769 (2004)
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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., Hashimoto S.
Nature 418, 534-539 (2002)
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Genome-wide transcriptional orchestration of circadian rhythms in Drosophila
Ueda H.R., Matsumoto A., Kawamura M., Iino M., Tanimura T., Hashimoto S.
J. Biol. Chem. 227, 14048-14052 (2002)
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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, 501-512 (2002)
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Robust oscillations within the interlocked feedback model of Drosophila circadian rhythm
Ueda H.R., Hagiwara M., Kitano H.
J. Theor. Biol. 210, 401-406 (2001)
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