Department of Biosciences and Informatics

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2020

An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data

Jayakumar, V., Ishii, H., Seki, M., Kumita, W., Inoue, T., Hase, S., Sato, K., Okano, H., Sasaki, E. & Sakakibara, Y., 2020 Apr 2, In : BMC Genomics. 21, 243.

Research output: Contribution to journalArticle

Open Access

Avian Influenza Virus Detection by Optimized Peptide Termination on a Boron-Doped Diamond Electrode

Matsubara, T., Ujie, M., Yamamoto, T., Einaga, Y., Daidoji, T., Nakaya, T. & Sato, T., 2020 Feb 28, In : ACS Sensors. 5, 2, p. 431-439 9 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

BRUP-1, an intracellular bilirubin modulator, exerts neuroprotective activity in a cellular Parkinson’s disease model

Kataura, T., Saiki, S., Ishikawa, K. I., Akamatsu, W., Sasazawa, Y., Hattori, N. & Imoto, M., 2020 Jan 1, (Accepted/In press) In : Journal of Neurochemistry.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Cadinane sesquiterpenoids isolated from Santalum album using a screening program for Wnt signal inhibitory activity

Sato, T., Arai, M. A., Yixizhuoma, Hara, Y., Koyano, T., Kowithayakorn, T. & Ishibashi, M., 2020 Mar 1, In : Journal of Natural Medicines. 74, 2, p. 476-481 6 p.

Research output: Contribution to journalArticle

Conformational equilibrium of MinE regulates the allowable concentration ranges of a protein wave for cell division

Kohyama, S., Fujiwara, K., Yoshinaga, N. & Doi, N., 2020 Jun 11, In : Nanoscale. 12, 22, p. 11960-11970 11 p.

Research output: Contribution to journalArticle

Depth Sensor-Based Assessment of Reachable Work Space for Visualizing and Quantifying Paretic Upper Extremity Motor Function in People With Stroke

Okuyama, K., Kawakami, M., Tsuchimoto, S., Ogura, M., Okada, K., Mizuno, K., Ushiba, J. & Liu, M., 2020 May 18, In : Physical Therapy. 100, 5, p. 870-879 10 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Different strategies for tissue scaling in dwarf tailbud embryos revealed by single-cell analysis

Matsumura, K. D., Nakamura, M. J., Koizumi, W. C., Hotta, K. & Oka, K., 2020 Apr 15, In : Developmental Biology. 460, 2, p. 215-223 9 p.

Research output: Contribution to journalArticle

Discovery of “heat shock metabolites” produced by thermotolerant actinomycetes in high-temperature culture

Saito, S., Kato, W., Ikeda, H., Katsuyama, Y., Ohnishi, Y. & Imoto, M., 2020 Apr 1, In : Journal of Antibiotics. 73, 4, p. 203-210 8 p.

Research output: Contribution to journalArticle

Distribution of Macrobiotus shonaicus Stec, Arakawa & Michalczyk, 2018 (Tardigrada: Eutardigrada: Macrobiotidae) in Japan

Sugiura, K., Arakawa, K. & Matsumoto, M., 2020 Apr 23, In : Zootaxa. 4767, 1, p. 56-70 15 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Identification of a master transcription factor and a regulatory mechanism for desiccation tolerance in the anhydrobiotic cell line Pv11

Yamada, T. G., Hiki, Y., Hiroi, N. F., Shagimardanova, E., Gusev, O., Cornette, R., Kikawada, T. & Funahashi, A., 2020, In : PloS one. 15, 3, e0230218.

Research output: Contribution to journalArticle

Open Access

Ikoamide, an Antimalarial Lipopeptide from an Okeania sp. Marine Cyanobacterium

Iwasaki, K., Iwasaki, A., Sumimoto, S., Matsubara, T., Sato, T., Nozaki, T., Saito-Nakano, Y. & Suenaga, K., 2020 Feb 28, In : Journal of Natural Products. 83, 2, p. 481-488 8 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Isolation and evaluation of cardenolides from Lansium domesticum as Notch inhibitors

Tsuchiya, A., Makita, Y., Koyano, T., Kowithayakorn, T., Ishibashi, M. & Arai, M. A., 2020 Sep 1, In : Journal of Natural Medicines. 74, 4, p. 758-766 9 p.

Research output: Contribution to journalArticle

Microfluidic screening system based on boron-doped diamond electrodes and dielectrophoretic sorting for directed evolution of NAD(P)-dependent oxidoreductases

Goto, H., Kanai, Y., Yotsui, A., Shimokihara, S., Shitara, S., Oyobiki, R., Fujiwara, K., Watanabe, T., Einaga, Y., Matsumoto, Y., Miki, N. & Doi, N., 2020 Feb 21, In : Lab on a Chip. 20, 4, p. 852-861 10 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Near-infrared fluorescent probes for imaging of intracellular mg2+ and application to multi-color imaging of mg2+, atp, and mitochondrial membrane potential

Murata, O., Shindo, Y., Ikeda, Y., Iwasawa, N., Citterio, D., Oka, K. & Hiruta, Y., 2020 Jan 7, In : Analytical chemistry. 92, 1, p. 966-974 9 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Near-infrared pH responsive heptamethine cyanine platforms: Modulating the proton acceptor

Kurutos, A., Shindo, Y., Hiruta, Y., Oka, K. & Citterio, D., 2020 Oct, In : Dyes and Pigments. 181, 108611.

Research output: Contribution to journalArticle

Neural differentiation dynamics controlled by multiple feedback loops in a comprehensive molecular interaction network

Iwasaki, T., Takiguchi, R., Hiraiwa, T., Yamada, T. G., Yamazaki, K., Hiroi, N. & Funahashi, A., 2020 Feb 1, In : Processes. 8, 2, 166.

Research output: Contribution to journalArticle

Open Access

Neural properties of fundamental function encoding of sound selectivity in the female avian auditory cortex

Inda, M., Hotta, K. & Oka, K., 2020 Apr 1, In : European Journal of Neuroscience. 51, 8, p. 1770-1783 14 p.

Research output: Contribution to journalArticle

Optical Dissection of Synaptic Plasticity for Early Adaptation in Caenorhabditis elegans

Ashida, K., Shidara, H., Hotta, K. & Oka, K., 2020 Jan 21, In : Neuroscience. 428, p. 112-121 10 p.

Research output: Contribution to journalArticle

Reliability of the thumb localizing test and its validity against quantitative measures with a robotic device in patients with hemiparetic stroke

Otaka, E., Otaka, Y., Kasuga, S., Nishimoto, A., Yamazaki, K., Kawakami, M., Ushiba, J. & Liu, M., 2020 Jul, In : PloS one. 15, 7 July, e0236437.

Research output: Contribution to journalArticle

Open Access

Target protein-oriented isolation of Hes1 dimer inhibitors using protein based methods

Arai, M. A., Morita, K., Kawano, H., Makita, Y., Hashimoto, M., Suganami, A., Tamura, Y., Sadhu, S. K., Ahmed, F. & Ishibashi, M., 2020 Dec 1, In : Scientific reports. 10, 1, 1381.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)
2019

A self-marker-like protein governs hemocyte allorecognition in Halocynthia roretzi

Ema, M., Okada, T., Takahashi, M., Uchiyama, M., Kubo, H., Moriyama, H., Miyakawa, H. & Matsumoto, M., 2019 Dec 16, In : Zoological Letters. 5, 1, 34.

Research output: Contribution to journalArticle

Open Access

Biodegradation of PET: Current Status and Application Aspects

Taniguchi, I., Yoshida, S., Hiraga, K., Miyamoto, K., Kimura, Y. & Oda, K., 2019 Jan 1, In : ACS Catalysis. p. 4089-4105 17 p.

Research output: Contribution to journalArticle

25 Citations (Scopus)

Brain-Machine Interface and Neuro-Rehabilitation

Ushiba, J., 2019 Jul 1, In : Brain and nerve = Shinkei kenkyu no shinpo. 71, 7, p. 793-804 12 p.

Research output: Contribution to journalArticle

CAPZA1 determines the risk of gastric carcinogenesis by inhibiting Helicobacter pylori CagA-degraded autophagy

Tsugawa, H., Mori, H., Matsuzaki, J., Sato, A., Saito, Y., Imoto, M., Suematsu, M. & Suzuki, H., 2019 Feb 1, In : Autophagy. 15, 2, p. 242-258 17 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Cell-sized confinement controls generation and stability of a protein wave for spatiotemporal regulation in cells

Kohyama, S., Yoshinaga, N., Yanagisawa, M., Fujiwara, K. & Doi, N., 2019 Jul, In : eLife. 8, e44591.

Research output: Contribution to journalArticle

Open Access
3 Citations (Scopus)

Chemoenzymatic Cascade Synthesis of Optically Pure Alkanoic Acids by Using Engineered Arylmalonate Decarboxylase Variants

Enoki, J., Mügge, C., Tischler, D., Miyamoto, K. & Kourist, R., 2019 Apr 1, In : Chemistry - A European Journal. 25, 19, p. 5071-5076 6 p.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

Comparison of Sexual Reproductive Behaviors in Two Species of Macrobiotidae (Tardigrada: Eutardigrada)

Sugiura, K., Minato, H., Suzuki, A. C., Arakawa, K., Kunieda, T. & Matsumoto, M., 2019 Jan 1, In : Zoological Science. 36, 2, p. 120-127 8 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Comparison of the transcriptomes of two tardigrades with different hatching coordination

Yoshida, Y., Sugiura, K., Tomita, M., Matsumoto, M. & Arakawa, K., 2019 Dec 9, In : BMC Developmental Biology. 19, 1, 24.

Research output: Contribution to journalArticle

Open Access

Detection of influenza virus by agglutination using nanoparticles conjugated with a sialic acid-mimic peptide

Matsubara, T., Kubo, A. & Sato, T., 2019 Jan 1, (Accepted/In press) In : Polymer Journal.

Research output: Contribution to journalArticle

1 Citation (Scopus)
Open Access
4 Citations (Scopus)

Efficient generation of Knock-in/Knock-out marmoset embryo via CRISPR/Cas9 gene editing

Kumita, W., Sato, K., Suzuki, Y., Kurotaki, Y., Harada, T., Zhou, Y., Kishi, N., Sato, K., Aiba, A., Sakakibara, Y., Feng, G., Okano, H. & Sasaki, E., 2019 Dec 1, In : Scientific reports. 9, 1, 12719.

Research output: Contribution to journalArticle

Open Access
2 Citations (Scopus)

Enzyme kinetics of dUTPase from the planarian Dugesia ryukyuensis

Alam, M. S., Moriyama, H. & Matsumoto, M., 2019 Mar 22, In : BMC Research Notes. 12, 1, 163.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Fast Electrophysiological Mapping of Rat Cortical Motor Representation on a Time Scale of Minutes during Skin Stimulation

Kosugi, A., Castagnola, E., Carli, S., Ricci, D., Fadiga, L., Taoka, M., Iriki, A. & Ushiba, J., 2019 Aug 21, In : Neuroscience. 414, p. 245-254 10 p.

Research output: Contribution to journalArticle

Identification of BMI1 promoter inhibitors from Streptomyces sp. IFM-11958

Yokoyama, Y., Arai, M. A., Hara, Y. & Ishibashi, M., 2019 Jul 1, In : Bioorganic and Medicinal Chemistry. 27, 13, p. 2998-3003 6 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Ktedonoketone and 2’-oxosattabacin, benzenoid metabolites from a thermophilic bacterium Thermosporothrix hazakensis in the phylum Chloroflexi

Igarashi, Y., Yamamoto, K., Ueno, C., Yamada, N., Saito, K., Takahashi, K., Enomoto, M., Kuwahara, S., Oikawa, T., Tashiro, E., Imoto, M., Xiaohanyao, Y., Zhou, T., Harunari, E. & Oku, N., 2019 Sep 1, In : Journal of Antibiotics. 72, 9, p. 653-660 8 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Magnesium is a key player in neuronal maturation and neuropathology

Yamanaka, R., Shindo, Y. & Oka, K., 2019 Jul 2, In : International journal of molecular sciences. 20, 14, 3439.

Research output: Contribution to journalArticle

Open Access
6 Citations (Scopus)
1 Citation (Scopus)

Poly-γ-glutamic acid production of Bacillus subtilis (natto) in the absence of DegQ: A gain-of-function mutation in yabJ gene

Hong, L. T. T., Hachiya, T., Hase, S., Shiwa, Y., Yoshikawa, H., Sakakibara, Y., Nguyen, S. L. T. & Kimura, K., 2019 Jan 1, In : Journal of Bioscience and Bioengineering.

Research output: Contribution to journalArticle

Predicting the future direction of cell movement with convolutional neural networks

Nishimoto, S., Tokuoka, Y., Yamada, T. G., Hiroi, N. F. & Funahashi, A., 2019 Sep 1, In : PloS one. 14, 9, e0221245.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

Preparation of optically pure flurbiprofen via an integrated chemo-enzymatic synthesis pathway

Enoki, J., Linhorst, M., Busch, F., Baraibar, Á. G., Miyamoto, K., Kourist, R. & Mügge, C., 2019 Apr 1, In : Molecular Catalysis. 467, p. 135-142 8 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Regulation of spatiotemporal patterning in artificial cells by a defined protein expression system

Yoshida, A., Kohyama, S., Fujiwara, K., Nishikawa, S. & Doi, N., 2019, In : Chemical Science. 10, 48, p. 11064-11072 9 p.

Research output: Contribution to journalArticle

Open Access
2 Citations (Scopus)

Sensorimotor Connectivity after Motor Exercise with Neurofeedback in Post-Stroke Patients with Hemiplegia

Tsuchimoto, S., Shindo, K., Hotta, F., Hanakawa, T., Liu, M. & Ushiba, J., 2019 Sep 15, In : Neuroscience. 416, p. 109-125 17 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Serotonin modulates behavior-related neural activity of RID interneuron in Caenorhabditis elegans

Mori, H., Ashida, K., Shidara, H., Nikai, T., Hotta, K. & Oka, K., 2019 Dec 1, In : PloS one. 14, 12, e0226044.

Research output: Contribution to journalArticle

Open Access

Stochastic thermodynamic limit on E. coli adaptation by information geometric approach

Ashida, K. & Oka, K., 2019 Jan 15, In : Biochemical and Biophysical Research Communications. 508, 3, p. 690-694 5 p.

Research output: Contribution to journalArticle

Synthesis of Various Glycopolymers Bearing Sialyllactose and the Effect of Their Molecular Mobility on Interaction with the Influenza Virus

Nagao, M., Matsubara, T., Hoshino, Y., Sato, T. & Miura, Y., 2019 Jul 8, In : Biomacromolecules. 20, 7, p. 2763-2769 7 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

The Input-Output Relationship of AIY Interneurons in Caenorhabditis elegans in Noisy Environment

Ashida, K., Hotta, K. & Oka, K., 2019 Sep 27, In : iScience. 19, p. 191-203 13 p.

Research output: Contribution to journalArticle

Open Access
2 Citations (Scopus)

Topological Design of Star Glycopolymers for Controlling the Interaction with the Influenza Virus

Nagao, M., Matsubara, T., Hoshino, Y., Sato, T. & Miura, Y., 2019 Apr 17, In : Bioconjugate Chemistry. 30, 4, p. 1192-1198 7 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Two-stage regression of high-density scalp electroencephalograms visualizes force regulation signaling during muscle contraction

Hayashi, M., Tsuchimoto, S., Mizuguchi, N., Miyatake, M., Kasuga, S. & Ushiba, J., 2019 Aug 21, In : Journal of neural engineering. 16, 5, 056020.

Research output: Contribution to journalArticle

2 Citations (Scopus)