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  • Triple CRISPR
  • CUBIC resource
  • Brain stars
  • 2017

    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)
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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)
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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)
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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)
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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)
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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)
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    Systems biology-derived discoveries of intrinsic clocks
    Millius A., Ueda H.R.
    Front. Neurol. 8:25 (2017)
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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)
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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)
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    2016

    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)
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    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)
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    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)
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    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)
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    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)
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    2015

    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)
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    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)
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    2014

    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)
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    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)
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    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)
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    2013

    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)
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    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)
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    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)
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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 K.D., Imai T., Ueda H.R.
    Genome Biol. 14, R31 (2013)
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    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)
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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 A.D., Nikaido I., Ueda H.R., Tatematsu K., Tanizawa K., Kondo A., Fujii I., Kuroda S.
    Sci. Rep. 3, 1191 (2013)
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    2012

    A design principle for a posttranslational biochemical oscillator
    Jolley C.C., Ode K.L., Ueda H.R.
    Cell Rep. 2, 938-950 (2012)
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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 H.R.
    Proc. Natl. Acad. Sci. USA 109, 15036-15041 (2012)
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    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)
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    2011

    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)
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    Perturbation analyses of intermolecular interactions
    Koyama Y.M., Kobayashi T.J., Ueda H.R.
    Phys. Rev. E 84, 026704 (2011)
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    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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    2010

    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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    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 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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    2008

    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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    2007

    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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    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 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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    2005

    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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    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., 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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    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., 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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    2001

    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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