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Items: 1 to 50 of 97

1.

Lost in clocks: non-canonical circadian oscillation discovered in Drosophila cells.

Ode KL, Ueda HR.

Mol Syst Biol. 2018 Sep 24;14(9):e8567. doi: 10.15252/msb.20188567. No abstract available.

2.

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 HR, Tanaka Y.

PLoS One. 2018 Sep 19;13(9):e0203056. doi: 10.1371/journal.pone.0203056. eCollection 2018.

3.

Leak potassium channels regulate sleep duration.

Yoshida K, Shi S, Ukai-Tadenuma M, Fujishima H, Ohno RI, Ueda HR.

Proc Natl Acad Sci U S A. 2018 Oct 2;115(40):E9459-E9468. doi: 10.1073/pnas.1806486115. Epub 2018 Sep 17.

PMID:
30224462
4.

Muscarinic Acetylcholine Receptors Chrm1 and Chrm3 Are Essential for REM Sleep.

Niwa Y, Kanda GN, Yamada RG, Shi S, Sunagawa GA, Ukai-Tadenuma M, Fujishima H, Matsumoto N, Masumoto KH, Nagano M, Kasukawa T, Galloway J, Perrin D, Shigeyoshi Y, Ukai H, Kiyonari H, Sumiyama K, Ueda HR.

Cell Rep. 2018 Aug 28;24(9):2231-2247.e7. doi: 10.1016/j.celrep.2018.07.082.

5.

Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents.

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.

Cell Rep. 2018 Aug 21;24(8):2196-2210.e9. doi: 10.1016/j.celrep.2018.07.056.

6.

Cell-free synthesis of stable isotope-labeled internal standards for targeted quantitative proteomics.

Narumi R, Masuda K, Tomonaga T, Adachi J, Ueda HR, Shimizu Y.

Synth Syst Biotechnol. 2018 Feb 21;3(2):97-104. doi: 10.1016/j.synbio.2018.02.004. eCollection 2018 Jun. Review.

7.

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, Takase Y, Susaki EA, Ueda HR, Tadokoro R, Takahashi Y.

Dev Biol. 2018 May 21. pii: S0012-1606(18)30096-4. doi: 10.1016/j.ydbio.2018.05.014. [Epub ahead of print]

PMID:
29792856
8.

A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing.

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.

Nat Neurosci. 2018 Apr;21(4):625-637. doi: 10.1038/s41593-018-0109-1. Epub 2018 Mar 5.

PMID:
29507408
9.

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 KL, Morishita S, Urae S, Kanda S, Kajiho Y, Tsurumi H, Ueda HR, Tsuji S, Saito A, Oka A.

Sci Rep. 2018 Feb 5;8(1):2351. doi: 10.1038/s41598-018-20731-4.

10.

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 VV, Susaki EA, Kanzaki M, Ueda HR, Ishigaki Y, Yamada T, Katagiri H.

Nat Commun. 2017 Dec 5;8(1):1930. doi: 10.1038/s41467-017-01869-7.

11.

Ca2+ -Dependent Hyperpolarization Pathways in Sleep Homeostasis and Mental Disorders.

Shi S, Ueda HR.

Bioessays. 2018 Jan;40(1). doi: 10.1002/bies.201700105. Epub 2017 Dec 4. Review.

PMID:
29205420
12.

Production of knock-in mice in a single generation from embryonic stem cells.

Ukai H, Kiyonari H, Ueda HR.

Nat Protoc. 2017 Dec;12(12):2513-2530. doi: 10.1038/nprot.2017.110. Epub 2017 Nov 16.

PMID:
29189772
13.

Guidelines for Genome-Scale Analysis of Biological Rhythms.

Hughes ME, Abruzzi KC, Allada R, Anafi R, Arpat AB, Asher G, Baldi P, de Bekker C, Bell-Pedersen D, Blau J, Brown S, Ceriani MF, Chen Z, Chiu JC, Cox J, Crowell AM, DeBruyne JP, Dijk DJ, DiTacchio L, Doyle FJ, Duffield GE, Dunlap JC, Eckel-Mahan K, Esser KA, FitzGerald GA, Forger DB, Francey LJ, Fu YH, Gachon F, Gatfield D, de Goede P, Golden SS, Green C, Harer J, Harmer S, Haspel J, Hastings MH, Herzel H, Herzog ED, Hoffmann C, Hong C, Hughey JJ, Hurley JM, de la Iglesia HO, Johnson C, Kay SA, Koike N, Kornacker K, Kramer A, Lamia K, Leise T, Lewis SA, Li J, Li X, Liu AC, Loros JJ, Martino TA, Menet JS, Merrow M, Millar AJ, Mockler T, Naef F, Nagoshi E, Nitabach MN, Olmedo M, Nusinow DA, Ptáček LJ, Rand D, Reddy AB, Robles MS, Roenneberg T, Rosbash M, Ruben MD, Rund SSC, Sancar A, Sassone-Corsi P, Sehgal A, Sherrill-Mix S, Skene DJ, Storch KF, Takahashi JS, Ueda HR, Wang H, Weitz C, Westermark PO, Wijnen H, Xu Y, Wu G, Yoo SH, Young M, Zhang EE, Zielinski T, Hogenesch JB.

J Biol Rhythms. 2017 Oct;32(5):380-393. doi: 10.1177/0748730417728663. Epub 2017 Nov 3.

14.

Design Principles of Phosphorylation-Dependent Timekeeping in Eukaryotic Circadian Clocks.

Ode KL, Ueda HR.

Cold Spring Harb Perspect Biol. 2018 Aug 1;10(8). pii: a028357. doi: 10.1101/cshperspect.a028357. Review.

PMID:
29038116
15.

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. 2017 Sep 7;67(5):783-798.e20. doi: 10.1016/j.molcel.2017.08.009.

16.

CUBIC pathology: three-dimensional imaging for pathological diagnosis.

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 JI, Kumanogoh A, Morii E, Ueda HR.

Sci Rep. 2017 Aug 24;7(1):9269. doi: 10.1038/s41598-017-09117-0.

17.

Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution.

Kubota SI, Takahashi K, Nishida J, Morishita Y, Ehata S, Tainaka K, Miyazono K, Ueda HR.

Cell Rep. 2017 Jul 5;20(1):236-250. doi: 10.1016/j.celrep.2017.06.010.

18.

Next-generation mammalian genetics toward organism-level systems biology.

Susaki EA, Ukai H, Ueda HR.

NPJ Syst Biol Appl. 2017 Jun 5;3:15. doi: 10.1038/s41540-017-0015-2. eCollection 2017. Review.

19.

Fast and slow Ca2+-dependent hyperpolarization mechanisms connect membrane potential and sleep homeostasis.

Ode KL, Katsumata T, Tone D, Ueda HR.

Curr Opin Neurobiol. 2017 Jun;44:212-221. doi: 10.1016/j.conb.2017.05.007. Epub 2017 May 30. Review.

PMID:
28575719
20.

A Design Principle for an Autonomous Post-translational Pattern Formation.

Sugai SS, Ode KL, Ueda HR.

Cell Rep. 2017 May 16;19(7):1494. doi: 10.1016/j.celrep.2017.05.017. No abstract available.

21.

Compass in the data ocean: Toward chronotherapy.

Yamada RG, Ueda HR.

Proc Natl Acad Sci U S A. 2017 May 16;114(20):5069-5071. doi: 10.1073/pnas.1705326114. Epub 2017 May 9. No abstract available.

22.

A Design Principle for an Autonomous Post-translational Pattern Formation.

Sugai SS, Ode KL, Ueda HR.

Cell Rep. 2017 Apr 25;19(4):863-874. doi: 10.1016/j.celrep.2017.03.081. Erratum in: Cell Rep. 2017 May 16;19(7):1494.

23.

Ca2+-dependent hyperpolarization hypothesis for mammalian sleep.

Tatsuki F, Ode KL, Ueda HR.

Neurosci Res. 2017 May;118:48-55. doi: 10.1016/j.neures.2017.03.012. Epub 2017 Apr 20. Review.

PMID:
28433628
24.

[Molecular Mechanisms of Circadian Rhythm and Sleep Homeostasis].

Kon K, Ode KL, Ueda HR.

Brain Nerve. 2017 Mar;69(3):257-264. doi: 10.11477/mf.1416200735. Review. Japanese.

PMID:
28270635
25.

Systems Biology-Derived Discoveries of Intrinsic Clocks.

Millius A, Ueda HR.

Front Neurol. 2017 Feb 6;8:25. doi: 10.3389/fneur.2017.00025. eCollection 2017. Review.

26.

Erratum to: Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity.

Sasagawa Y, Nikaido I, Hayashi T, Danno H, Uno KD, Imai T, Ueda HR.

Genome Biol. 2017 Jan 18;18(1):9. doi: 10.1186/s13059-017-1154-x. No abstract available.

27.

Cochlear Cell Modeling Using Disease-Specific iPSCs Unveils a Degenerative Phenotype and Suggests Treatments for Congenital Progressive Hearing Loss.

Hosoya M, Fujioka M, Sone T, Okamoto S, Akamatsu W, Ukai H, Ueda HR, Ogawa K, Matsunaga T, Okano H.

Cell Rep. 2017 Jan 3;18(1):68-81. doi: 10.1016/j.celrep.2016.12.020.

28.

Knockout-Rescue Embryonic Stem Cell-Derived Mouse Reveals Circadian-Period Control by Quality and Quantity of CRY1.

Ode KL, Ukai H, Susaki EA, Narumi R, Matsumoto K, Hara J, Koide N, Abe T, Kanemaki MT, Kiyonari H, Ueda HR.

Mol Cell. 2017 Jan 5;65(1):176-190. doi: 10.1016/j.molcel.2016.11.022. Epub 2016 Dec 22.

29.

Chemical Principles in Tissue Clearing and Staining Protocols for Whole-Body Cell Profiling.

Tainaka K, Kuno A, Kubota SI, Murakami T, Ueda HR.

Annu Rev Cell Dev Biol. 2016 Oct 6;32:713-741. Epub 2016 Jun 8. Review.

PMID:
27298088
30.

Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins.

Narumi R, Shimizu Y, Ukai-Tadenuma M, Ode KL, Kanda GN, Shinohara Y, Sato A, Matsumoto K, Ueda HR.

Proc Natl Acad Sci U S A. 2016 Jun 14;113(24):E3461-7. doi: 10.1073/pnas.1603799113. Epub 2016 May 31.

31.

Cell-cycle-independent transitions in temporal identity of mammalian neural progenitor cells.

Okamoto M, Miyata T, Konno D, Ueda HR, Kasukawa T, Hashimoto M, Matsuzaki F, Kawaguchi A.

Nat Commun. 2016 Apr 20;7:11349. doi: 10.1038/ncomms11349.

32.

Involvement of Ca(2+)-Dependent Hyperpolarization in Sleep Duration in Mammals.

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.

Neuron. 2016 Apr 6;90(1):70-85. doi: 10.1016/j.neuron.2016.02.032. Epub 2016 Mar 17.

33.

Whole-body and Whole-Organ Clearing and Imaging Techniques with Single-Cell Resolution: Toward Organism-Level Systems Biology in Mammals.

Susaki EA, Ueda HR.

Cell Chem Biol. 2016 Jan 21;23(1):137-157. doi: 10.1016/j.chembiol.2015.11.009. Review.

34.

Mammalian Reverse Genetics without Crossing Reveals Nr3a as a Short-Sleeper Gene.

Sunagawa GA, Sumiyama K, Ukai-Tadenuma M, Perrin D, Fujishima H, Ukai H, Nishimura O, Shi S, Ohno RI, Narumi R, Shimizu Y, Tone D, Ode KL, Kuraku S, Ueda HR.

Cell Rep. 2016 Jan 26;14(3):662-677. doi: 10.1016/j.celrep.2015.12.052. Epub 2016 Jan 7.

35.

Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging.

Susaki EA, Tainaka K, Perrin D, Yukinaga H, Kuno A, Ueda HR.

Nat Protoc. 2015 Nov;10(11):1709-27. doi: 10.1038/nprot.2015.085. Epub 2015 Oct 8.

PMID:
26448360
36.

Seeing the forest and trees: whole-body and whole-brain imaging for circadian biology.

Ode KL, Ueda HR.

Diabetes Obes Metab. 2015 Sep;17 Suppl 1:47-54. doi: 10.1111/dom.12511. Review.

PMID:
26332968
37.

Whole-body imaging with single-cell resolution by tissue decolorization.

Tainaka K, Kubota SI, Suyama TQ, Susaki EA, Perrin D, Ukai-Tadenuma M, Ukai H, Ueda HR.

Cell. 2014 Nov 6;159(4):911-24. doi: 10.1016/j.cell.2014.10.034.

38.

A mammalian circadian clock model incorporating daytime expression elements.

Jolley CC, Ukai-Tadenuma M, Perrin D, Ueda HR.

Biophys J. 2014 Sep 16;107(6):1462-73. doi: 10.1016/j.bpj.2014.07.022.

39.

[Multilayered control of the Mammalian circadian system].

Ode KL, Ueda HR.

Brain Nerve. 2014 Jun;66(6):681-9. Review. Japanese.

PMID:
24899350
40.

Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis.

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.

Cell. 2014 Apr 24;157(3):726-39. doi: 10.1016/j.cell.2014.03.042. Epub 2014 Apr 17.

41.

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 KL, Susaki EA, Ueda HR.

PLoS One. 2014 Mar 19;9(3):e92369. doi: 10.1371/journal.pone.0092369. eCollection 2014.

42.

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 HR, Niwa H.

Mol Cell. 2013 Nov 7;52(3):380-92. doi: 10.1016/j.molcel.2013.09.002. Epub 2013 Oct 10.

43.

Different circadian expression of major matrix-related genes in various types of cartilage: modulation by light-dark conditions.

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.

J Biochem. 2013 Oct;154(4):373-81. doi: 10.1093/jb/mvt068. Epub 2013 Aug 11.

PMID:
23940085
44.

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. 2013 Jul;18(7):575-88. doi: 10.1111/gtc.12063. Epub 2013 Jun 12.

45.

FASTER: an unsupervised fully automated sleep staging method for mice.

Sunagawa GA, Séi H, Shimba S, Urade Y, Ueda HR.

Genes Cells. 2013 Jun;18(6):502-18. doi: 10.1111/gtc.12053. Epub 2013 Apr 28.

46.

Mammalian circadian clock: the roles of transcriptional repression and delay.

Minami Y, Ode KL, Ueda HR.

Handb Exp Pharmacol. 2013;(217):359-77. doi: 10.1007/978-3-642-25950-0_15. Review.

PMID:
23604487
47.

Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity.

Sasagawa Y, Nikaido I, Hayashi T, Danno H, Uno KD, Imai T, Ueda HR.

Genome Biol. 2013 Apr 17;14(4):R31. doi: 10.1186/gb-2013-14-4-r31. Erratum in: Genome Biol. 2017 Jan 18;18(1):9.

48.

Picrotoxin dramatically speeds the mammalian circadian clock independent of Cys-loop receptors.

Freeman GM Jr, Nakajima M, Ueda HR, Herzog ED.

J Neurophysiol. 2013 Jul;110(1):103-8. doi: 10.1152/jn.00220.2013. Epub 2013 Apr 10.

49.

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.

Sci Rep. 2013;3:1191. doi: 10.1038/srep01191. Epub 2013 Feb 1.

50.

A design principle for a posttranslational biochemical oscillator.

Jolley CC, Ode KL, Ueda HR.

Cell Rep. 2012 Oct 25;2(4):938-50. doi: 10.1016/j.celrep.2012.09.006. Epub 2012 Oct 19.

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