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Publicationfrom the Systems Pharmacology

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  • CUBIC-Atlas
  • Triple CRISPR
  • CUBIC resource
  • Brain stars
  • 2020

    Phosphorylation Hypothesis of Sleep
    Ode K.L., Ueda H.R.
    Front. Psychol. online ahead of print

    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. online ahead of print

    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)

    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)

    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)

    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)

    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)

    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)

    Molecular Mechanisms of REM Sleep
    Yamada R.G., Ueda H.R.
    Front. Neurosci. 13, 1402 (2020)

    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)

    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)

    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)

    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)

    Next-generation human genetics for organism-level systems biology
    Ukai H., Sumiyama K., Ueda H.R.
    Curr. Opin. Biotechnol. 58, 137-145 (2019)


    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)

    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)

    Lost in clocks: non‐canonical circadian oscillation discovered in Drosophila cells
    Ode K.L., Ueda H.R.
    Mol. Syst. Biol. 14, e8567 (2018)

    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)

    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)

    Design Principles of Phosphorylation-Dependent Timekeeping in Eukaryotic Circadian Clocks
    Ode K.L., Ueda H.R.
    Cold Spring Harb. Perspect. Biol. 10, a028357 (2018)

    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)

    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)

    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)

    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)

    Ca2+-Dependent Hyperpolarization Pathways in Sleep Homeostasis and Mental Disorders
    Shi S., Ueda H.R.
    BioEssays 40, 1700105 (2018)


    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)

    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)

    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)

    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)

    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)

    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)

    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)

    Compass in the data ocean: Toward chronotherapy.
    Yamada R.G., Ueda H.R.
    Proc. Natl. Acad. Sci. USA 114, 5069-5071 (2017)

    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)

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

    Ca2+-dependent Hyperpolarization Hypothesis for Mammalian Sleep
    Tatsuki F., Ode K.L., Ueda H.R.
    Neurosci. Res. 118, 48-55 (2017)

    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)


    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)

    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)

    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)

    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)

    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)


    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)

    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)


    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)

    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)

    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)


    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)

    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)

    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)

    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)

    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)

    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)


    A design principle for a posttranslational biochemical oscillator
    Jolley C.C., Ode K.L., Ueda H.R.
    Cell Rep. 2, 938-950 (2012)

    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)

    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)


    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)

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

    Understanding systems-level properties: timely stories from the study of clocks
    Hogenesch J.B., Ueda H.R.
    Nat. Rev. Genet. 12, 407-416 (2011)

    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)


    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)

    Challenges in synthetically designing mammalian circadian clocks
    Susaki E.A., Stelling J., Ueda H.R.
    Curr. Opin. Biotechnol. 21, 556-565 (2010)

    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)

    Systems biology of mammalian circadian clocks
    Ukai H. Ueda H.R.
    Ann. Rev. Physiol. 72, 579-603 (2010)


    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)

    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)

    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)


    Predicting perfect adaptation motifs in reaction kinetic networks
    Drengstig T., Ueda H.R., Ruoff P.
    J. Phys. Chem. B 112, 16752-16758 (2008)

    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)

    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)

    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)

    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)

    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)


    Systems biology of mammalian circadian clocks
    Ueda H.R.
    Cold Spring Harb. Symp. Quant. Biol. 72, 365-380 (2007)

    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)

    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)

    Microarrays: statistical methods for circadian rhythms
    Yamada R., Ueda H.R.
    Methods Mol. Biol. 362, 254-264 (2007)

    Microarrays: quality control and hybridization protocol
    Uno K., Ueda H.R.
    Methods Mol. Biol. 362, 225-243 (2007)


    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)

    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)

    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)

    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)

    Systems biology flowering in the plant clock field
    Ueda H.R.
    Mol. Sys. Biol. 2, 60 (2006)


    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)

    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)


    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)

    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)


    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)

    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)

    Intercellular coupling mechanism for synchronized and noise-resistant circadian oscillators
    Ueda H.R., Hirose K., Iino M.
    J. Theor. Biol. 216, 501-512 (2002)


    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)