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Publications

2024

  • Kumagai, Y.
    BootCellNet, a resampling-based procedure, promotes unsupervised identification of cell populations via robust inference of gene regulatory networks.
    PLOS COMPUT BIOL. 2024 Sep 30;20(9):e1012480. doi: 10.1371/journal.pcbi.1012480
  • Wadhwa, R; Wang, J; Shefrin, S; Zhang, H; Sundar, D; Kaul, SC.
    Molecular Insights into the Anticancer Activity of Withaferin-A: The Inhibition of Survivin Signaling.
    CANCERS (Basel). 2024 Sep 5;16(17):3090. doi: 10.3390/cancers16173090
  • Morikawa, K; Nagasaki, A; Sun, L; Kawase, E; Ebihara, T; Shirayoshi, Y.
    Optogenetic control of early embryos labeling using photoactivatable Cre recombinase 3.0.
    FEBS OPEN BIO. 2024 Sep 2. doi: 10.1002/2211-5463.13862
  • Koshiguchi, M; Yonezawa, N; Hatano, Y; Suenaga, H; Yamagata, K; Kobayashi, S.
    A system to analyze the initiation of random X-chromosome inactivation using time-lapse imaging of single cells.
    SCI REP. 2024 Sep 2;14(1):20327. doi: 10.1038/s41598-024-71105-y
  • Kurosu, J; Sakamaki, T; Kanai, K; Morishita, K; Sumaru, K; Tsutsumi, J.
    Spatiotemporal dynamics of microscopic biological barrier visualized by electric-double-layer modulation imaging.
    BIOSENS BIOELECTRON. 2024 Aug 30;266:116721. doi: 10.1016/j.bios.2024.116721
  • Inuzuka, N; Shobayashi, Y; Tateshima, S; Sato, Y; Ohba, Y; Ishihara, K; Teramura, Y.
    Stable and Thin-Polymer-Based Modification of Neurovascular Stents with 2-Methacryloyloxyethyl Phosphorylcholine Polymer for Antithrombogenicity.
    BIOENGINEERING (Basel). 2024 Aug 15;11(8):833. doi: 10.3390/bioengineering11080833
  • Hayashi, Y; Tajiri, K; Ozawa, T; Angata, K; Sato, T; Togayachi, A; Nagashima, I; Shimizu, H; Murayama, A; Muraishi, N; Narimatsu, H; Yasuda, I.
    Impact of preS1 Evaluation in the Management of Chronic Hepatitis B Virus Infection.
    MEDICINA (Kaunas). 2024 Aug 16;60(8):1334. doi: 10.3390/medicina60081334
  • Tokuoka, SM; Hamano, F; Kobayashi, A; Adachi, S; Andou, T; Natsume, T; Oda, Y.
    Plasma proteomics and lipidomics facilitate elucidation of the link between Alzheimers disease development and vessel wall fragility.
    SCI REP. 2024 Aug 27;14(1):19901. doi: 10.1038/s41598-024-71097-9
  • Sato, Y; Baba, T; Uchida, T; Chung, UI; Teramura, Y.
    Cell membrane fusion induced by surface modification with cell-penetrating peptide–lipid conjugates that facilitates close contact between distinct membranes.
    Mater. Adv. 2024 May 11. doi: 10.1039/D4MA00193A
  • Satoh, T; Yagi-Utsumi, M; Ishii, N; Mizushima, T; Yagi, H; Kato, R; Tateno, H; Matsuo, I; Kato, K; Suzuki, T; Yoshida, Y.
    Structural basis of sugar recognition by SCFFBS2 ubiquitin ligase involved in NGLY1 deficiency.
    FEBS LETTERS. 2024 Aug 22. doi: 10.1002/1873-3468.15003
  • Shi, Y; He, H; Zhang, H; Yuan, T; Zhang, Z; DeSilva, R; Ishida, Y; Terao, K; Kaul, SC; Wadhwa, R.
    Cyclodextrin-assisted Aqueous Extract of Cinnamon for Cancer and Stress Management.
    CURR TOP MED CHEM. 2024 Aug 20. doi: 10.2174/0115680266309291240808114508
  • Nagai-Okatani, C; Tominaga, D; Tomioka, A; Sakaue, H; Goda, N; Ko, S; Kuno, A; Kaji, H.
    GRable version 1.0: A software tool for site-specific glycoform analysis with improved MS1-based glycopeptide detection with parallel clustering and confidence evaluation with MS2 information.
    MOL CELL PROTEOMICS. 2024 Aug 22:100833. doi: 10.1016/j.mcpro.2024.100833
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  • Páez-Watson, T; Tomás-Martínez, S; de, Wit R; Keisham, S; Tateno, H; van, Loosdrecht MCM; Lin, Y.
    Sweet Secrets: Exploring Novel Glycans and Glycoconjugates in the Extracellular Polymeric Substances of “Candidatus Accumulibacter”.
    ACS ES T WATER. 2024 Jul 12;4(8):3391-3399. doi: 10.1021/acsestwater.4c00247
  • Tomita, T; Nakajima, Y; Ohmiya, Y; Miyazaki, K.
    Novel three-dimensional live skin-like in vitro composite for bioluminescence reporter gene assay.
    FEBS JOURNAL. 024 Aug 15. doi: 10.1111/febs.17246
  • Sato, Y; Zhang, WX; Baba, T; Chung, UI; Teramura, Y.
    Extracellular vesicle-liposome hybrids via membrane fusion using cell-penetrating peptide-conjugated lipids.
    REGENERATIVE THERAPY. 2024 Jul 29. doi: 10.1016/j.reth.2024.07.006
  • Xu, Z; Zhang, H; Tian, J; Ku, X; Wei, R; Hou, J; Zhang, C; Yang, F; Zou, X; Li, Y; Kaji, H; Tao, SC; Kuno, A; Yan, W; Da, LT; Zhang, Y.
    O-glycosylation of SARS-CoV-2 spike protein by host O-glycosyltransferase strengthens its trimeric structure.
    ACTA BIOCHIM BIOPHYS SIN (Shanghai). 2024 Jul 26. doi: 10.3724/abbs.2024127
  • Ma, ST; Yoda, H; Dang, T; Yang, JQ; Ando, I; Sato, Y; Teramura, Y; Tabata, H; Matsui, H.
    Light Polarization Effects of Chemical Sensing in the Mid-Infrared Region Using ZnO: Ga-Based Plasmonic Surface Lattice Resonances.
    JOURNAL OF PHYSICAL CHEMISTRY C. July 15, 2024. doi: 10.1021/acs.jpcc.4c02354
  • Kano, R; Kusano, T; Takeda, R; Shirakawa, H; Poole, DC; Kano, Y; Hoshino, D.
    Eccentric contraction increases hydrogen peroxide levels and alters gene expression through Nox2 in skeletal muscle of male mice.
    J APPL PHYSIOL (1985). 2024 Jul 25. doi: 10.1152/japplphysiol.00335.2024
  • Yamasaki, K; Tsuzuki, S; Tateno, H.
    Stabilization of the Protein Structure by the Many-Body Cooperative Effect in the NH/π Hydrogen-bonding Tryptophan Triad.
    J PHYS CHEM B. 2024 Jul 17. doi: 10.1021/acs.jpcb.4c02391
  • Arai, J; Hayakawa, Y; Tateno, H; Fujiwara, H; Kasuga, M; Fujishiro, M.
    The role of gastric mucins and mucin-related glycans in gastric cancers.
    CANCER SCI. 2024 Jul 19. doi: 10.1111/cas.16282
  • Fuseya, S; Ono, A; Ootani, H; Mizukado, S; Obayashi, T; Tanaka, N; Shimazaki, H; Kajiyama, K; Ashitomi, M; Yasuda, S; Miyabe, T; Nakamura, K; Segawa, O; Sawakami, K; Kuno, A.
    Rapid Glyco-Qualitative Assessment of Recombinant Proteins Using a Fully Automated System.
    J VIS EXP. 2024 Jun 28;(208). doi: 10.3791/66571
  • Akagi, Y; Norimoto, A; Kawamura, T; Kida, YS.
    Label-Free Assessment of Neuronal Activity Using Raman Micro-Spectroscopy.
    MOLECULES. 2024 Jul 3;29(13):3174. doi: 10.3390/molecules29133174
  • Inuzuka, N; Shobayashi, Y; Tateshima, S; Sato, Y; Ohba, Y; Ekdahl, KN; Nilsson, B; Teramura, Y.
    Stent coating containing a charged silane coupling agent that regulates protein adsorption to confer antithrombotic and cell-adhesion properties.
    SCI REP. 2024 Jul 10;14(1):15178. doi: 10.1038/s41598-024-65832-5
  • Shu, Y; Otake, M; Seta, Y; Hori, K; Kuramochi, A; Ohba, Y; Teramura, Y.
    Activation of cellular antioxidative stress and migration activities by purified components from immortalized stem cells from human exfoliated deciduous teeth.
    SCI REP. 2024 Jul 3;14(1):15340. doi: 10.1038/s41598-024-66213-8
  • Wadhwa, R; Yang, S; Meidinna, HN; Sari, AN; Bhargava, P;Kaul, SC.
    Mixtures of Three Mortaparibs with Enhanced Anticancer, Anti-Migration, and Antistress Activities: Molecular Characterization in p53-Null Cancer Cells.
    Cancers (Basel). 2024 Jun 17;16(12):2239. doi: 10.3390/cancers16122239
  • Wadhwa, R; Hegde, M; Zhang, HY; Kaul, A; Wang, J; Ishida, Y; Terao, K; Kunnumakkara, AB; Kaul, SC.
    Antistress and Antiaging Potentials of Alpha-Lipoic Acid: Insights from Cell Culture-Based Experiments.
    APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY. 2024 Jun 28. doi: 10.1007/s12010-024-04994-4
  • Wang, ZG; Yang, ZH; Shishido, M; Daoudi, K; Hidaka, M; Tateno, H; Futai, E; Ogawa, T.
    Microcystis viridis NIES-102 Cyanobacteria Lectin (MVL) Interacts with SARS-CoV-2 Spike Protein Receptor Binding Domains (RBDs) via Protein-Protein Interaction.
    INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. 2024 Jun 18;25(12):6696. doi: 10.3390/ijms25126696
  • Fujii, Y; Kamata, K; Gerdol, M; Hasan, I; Rajia, S; Kawsar, SMA; Padma, S; Chatterjee, BP; Ohkawa, M; Ishiwata, R; Yoshimoto, S; Yamada, M; Matsuzaki, N; Yamamoto, K; Niimi, Y; Miyanishi, N; Konno, M; Pallavicini, A; Kawasaki, T; Ogawa, Y; Ozeki, Y; Fujita, H.
    Multifunctional Cell Regulation Activities of the Mussel Lectin SeviL: Induction of Macrophage Polarization toward the M1 Functional Phenotype.
    MARINE DRUGS. 2024 Jun 11;22(6):269. doi: 10.3390/md22060269
  • Hayashi, T; Sadaki, S; Tsuji, R; Okada, R; Fuseya, S; Kanai, M; Nakamura, A; Okamura, Y; Muratani, M; Wenchao, G; Sugasawa, T; Mizuno, S; Warabi, E; Kudo, T; Takahashi, S; Fujita, R.
    Dual-specificity phosphatases 13 and 27 as key switches in muscle stem cell transition from proliferation to differentiation.
    STEM CELLS. 2024 Jul 8:sxae045. doi: 10.1093/stmcls/sxae045
  • Shimada, N; Kameyama, A; Watanabe, M; Sahara, T; Matsuzawa, T.
    Identification and characterization of xyloglucan-degradation related α-1,2-l-fucosidase in Aspergillus oryzae.
    J BIOSCI BIOENG. 2024 Jun 12:S1389-1723(24)00159-2. doi: 10.1016/j.jbiosc.2024.05.011
  • Watanabe, A; Koyano, F; Imai, K; Hizukuri, Y; Ogiwara, S; Ito, T; Miyamoto, J; Shibuya, C; Kimura, M; Toriumi, K; Motono, C; Arai, M; Tanaka, K; Akiyama, Y; Yamano, K; Matsuda, N.
    The origin of esterase activity of Parkinsons disease causative factor DJ-1 implied by evolutionary trace analysis of its prokaryotic homolog HchA.
    J BIOL CHEM. 2024 Jun 13:107476. doi: 10.1016/j.jbc.2024.107476
  • Tomita, T; Wadhwa, R; Onishi, Y.
    Natural Compounds that Modulate Circadian Rhythms.
    CURR TOP MED CHEM. 2024 May 30. doi: 10.2174/0115680266300569240514101800
  • Kato, A; Iwasaki, R; Takeshima, K; Maruzuru, Y; Koyanagi, N; Natsume, T; Kusano, H; Adachi, S; Kawano, S; Kawaguchi, Y.
    Identification of a novel neurovirulence factor encoded by the cryptic orphan gene UL31.6 of herpes simplex virus 1.
    J VIROL. 2024 May 31:e0074724. doi: 10.1128/jvi.00747-24
  • Yamaguchi, Y; Ishii, K; Koizumi, S; Sakaue, H; Maruno, T; Fukuhara, M; Shibuya, R; Tsunaka, Y; Matsushita, A; Bandoh, K; Torisu, T; Murata-Kishimoto, C; Tomioka, A; Mizukado, S; Kaji, H; Kashiwakura, Y; Ohmori, T; Kuno, A;; Uchiyama, S.
    Glycosylation of recombinant adeno-associated virus serotype 6.
    MOL THER METHODS CLIN DEV. 2024 Apr 25;32(2):101256. doi: 10.1016/j.omtm.2024.101256
  • Nishimura, T; Kudo, K; Izumikawa, M; Kozone, I; Hashimoto, J; Kagaya, N; Suenaga, H; Takeuchi, K; Shin-Ya, K.
    Isolation and Structure Elucidation of JBIR-157, a Skeletally Novel Aromatic Polyketide Produced by the Heterologous Expression of a Cryptic Gene Cluster.
    CHEM PHARM BULL (Tokyo). 2024;72(5):475-479. doi: 10.1248/cpb.c24-00144
  • Song, X; Nihashi, Y; Imai, Y; Mori, N; Kagaya, N; Suenaga, H; Shin-Ya, K; Yamamoto, M; Setoyama, D; Kunisaki Y; Kida, YS .
    Collagen Lattice Model, Populated with Heterogeneous Cancer-Associated Fibroblasts, Facilitates Advanced Reconstruction of Pancreatic Cancer Microenvironment.
    INT J MOL SCI. 2024 Mar 27;25(7):3740. doi: 10.3390/ijms25073740
  • Nie, H; Saini, P; Miyamoto, T; Liao, L; Zielinski, RJ; Liu, H; Zhou, W; Wang, C; Murphy, B; Towers, M; Yang, T; Qi, Y; Kannan, T; Kossenkov, A; Tateno, H; Claiborne, DT; Zhang, N; Abdel-Mohsen, M; Zhang, R.
    Targeting branched N-glycans and fucosylation sensitizes ovarian tumors to immune checkpoint blockade.
    NAT COMMUN. 2024 Apr 2;15(1):2853. doi: 10.1038/s41467-024-47069-y
  • Arai, J; Hayakawa, Y; Tateno, H; Murakami, K; Hayashi, T; Hata, M; Matsushita, Y; Kinoshita, H; Abe, S; Kurokawa, K; Oya, Y; Tsuboi, M; Ihara, S; Niikura, R; Suzuki, N; Iwata, Y; Shiokawa, T; Shiomi, C; Uekura, C; Yamamoto, K; Fujiwara, H; Kawamura, S; Nakagawa, H; Mizuno, S; Kudo, T; Takahashi, S; Ushiku, T; Hirata, Y; Fujii, C; Nakayama, J; Shibata, S; Woods, S; Worthley, DL; Hatakeyama, M; Wang, TC; Fujishiro, M.
    Impaired glycosylation of gastric mucins drives gastric tumorigenesis and serves as a novel therapeutic target.
    GASTROENTEROLOGY. 2024 Apr 5:S0016-5085(24)00363-9. doi: 10.1053/j.gastro.2024.03.037
  • Hiono, T; Sakaue, H; Tomioka, A; Kaji, H; Sasaki, M; Orba, Y; Sawa, H; Kuno, A.
    Combinatorial Approach with Mass Spectrometry and Lectin Microarray Dissected Site-Specific Glycostem and Glycoleaf Features of the Virion-Derived Spike Protein of Ancestral and γ Variant SARS-CoV-2 Strains.
    J PROTEOME RES. 2024 Mar 27. doi: 10.1021/acs.jproteome.3c00874
  • Miura, I; Shams, F; Ohki, J; Tagami, M; Fujita, H; Kuwana, C; Nanba, C; Matsuo, T Ogata, M; Mawaribuchi, S; Shimizu, N; Ezaz, T.
    Multiple Transitions between Y Chromosome and Autosome in Tagos Brown Frog Species Complex.
    GENES (Basel). 2024 Feb 26;15(3):300. doi: 10.3390/genes15030300
  • Hagihara, H; Shoji, H; Hattori, S; Sala, G; Takamiya, Y; Tanaka, M; Ihara, M; Shibutani, M; Hatada, I; Hori, K;... Oishi, K; ... Miyakawa, T.
    Large-scale animal model study uncovers altered brain pH and lactate levels as a transdiagnostic endophenotype of neuropsychiatric disorders involving cognitive impairment.
    Elife. 2024 Mar 26:12:RP89376. doi: 10.7554/eLife.89376
  • Nakahashi, H; Oda, T; Shimomura, O; Akashi, Y; Takahashi, K; Miyazaki, Y; Furuta, T; Kuroda, Y; Louphrasitthiphol, P; Mathis, BJ; Tateno, H.
    Aberrant Glycosylation in Pancreatic Ductal Adenocarcinoma 3D Organoids Is Mediated by KRAS Mutations.
    J ONCOL. 2024 Mar 18;2024:1529449. doi: 10.1155/2024/1529449

2023

  • Ohkura, N; Morimoto-Kamata ,R; Kamikubo, Y; Takahashi, Y; Oishi, K.
    Hypofibrinolytic phenotype in Tsumura Suzuki Obese Diabetes (TSOD) mice unrelated to hyperglycemia.
    Drug Discov Ther. 2023 Nov 18;17(5):346-350. doi: 10.5582/ddt.2023.01064
  • Ohkura, N; Morimoto-Kamata, R; Oishi, K; Higo-Yamamoto, S; Fujinami, A; Inoue, KI; Ohta, M.
    Supplementation with Ashitaba (Angelica keiskei) yellow stem exudate prevents aging-induced thrombotic tendencies and systemic inflammation without affecting body weight gain in mice.
    J Med Food. 2023 Nov;26(11):843-848. doi: 10.1089/jmf.2023.K.0140
  • Oishi, K; Yajima, Y; Yoshida, Y; Hagihara, H; Miyakawa, T; Higo-Yamamoto, S; Toyoda, A.
    Metabolic profiles of saliva in male mouse models of chronic sleep disorders induced by psychophysiological stress.
    Sci Rep. 2023;13(1):11156. doi: 10.1038/s41598-023-38289-1
  • Kanie, S; Wu, C; Kihira, K; Yasuno, R; Mitani, Y; Ohmiya, Y.
    Bioluminescence of (R)-Cypridina Luciferin with Cypridina Luciferase.
    INT J MOL SCI. 2024 Feb 26;25(5):2699. doi: 10.3390/ijms25052699
  • Sakata, S; Li, J; Yasuno, Y; Shinada, T; Shin-ya, K;Katsuyama, Y; Ohnishi, Y.
    Identification of the cirratiomycin biosynthesis gene cluster in Streptomyces cirratus: elucidation of the biosynthetic pathways for 2,3-diaminobutyric acid and hydroxymethylserine.
    CHEMISTRY. 2024 Mar 8:e202400271. doi: 10.1002/chem.202400271
  • Zheng, Y; Morita, N; Takagi, H; Shiozaki-Sato, Y; Ishikawa, J; Shin-ya, K;Takahashi, S.
    Alanyl-tRNA Synthetase-like Enzyme-Catalyzed Aminoacylation in Nucleoside Sulfamate Ascamycin Biosynthesis.
    ACS CATALYSIS. 2024 FEB 20. doi: 10.1021/acscatal.3c05667
  • Kudo, K; Nishimura, T; Izumikawa, M; Kozone, I; Hashimoto, J; Fujie, M; Suenaga, H; Ikeda, H; Satoh, N; Shin-Ya, K.
    Capability of a large bacterial artificial chromosome clone harboring multiple biosynthetic gene clusters for the production of diverse compounds.
    J ANTIBIOT (Tokyo). 2024 Mar 4. doi: 10.1038/s41429-024-00711-9
  • Miyashita, S; Ogura, T; Matsuura, S; Fukuda, E.
    Particle Size Measurement and Detection of Bound Proteins of Non-Porous/Mesoporous Silica Microspheres by Single-Particle Inductively Coupled Plasma Mass Spectrometry.
    MOLECULES. 2024 Feb 6. 29(5):1086. doi: 10.3390/molecules29051086
  • Phuyathip, W; Putthisen, S; Panawan O, Ma-In P; Teeravirote, K; Sintusen, P; Udomkitkosol, S; Detarya, M; Luang. S; Mahalapbutr, P; Sato, T; Kuno, A; Chuangchaiya, S; Silsirivanit, A.
    Role of Wisteria floribunda agglutinin binding glycans in carcinogenesis and metastasis of cholangiocarcinoma.
    HISTOCHEM CELL BIOL. 2024 Feb 23. doi: 10.1007/s00418-024-02270-4
  • Qayyum, MZ; Imashimizu, M; Leanca, M; Vishwakarma, RK; Riaz-Bradley, A; Yuzenkova, Y; Murakami, KS.
    Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase.
    PROC NATL ACAD SCI U S A. 2024 Feb 20;121(8):e2311480121. doi: 10.1073/pnas.2311480121
  • Nagashima, I; Shimizu, H.
    Preparation of Mucin Glycopeptides by Organic Synthesis.
    METHODS MOL BIOL. 2024;2763:187-199. doi: 10.1007/978-1-0716-3670-1_16
  • Matsuda, A; Boottanun, P; Koizumi, S; Nagai, M; Kuno, A.
    Differential Glycoform Analysis of MUC1 Derived from Biological Specimens Using an Antibody-Overlay Lectin Microarray.
    METHODS MOL BIOL. 2024;2763:223-236. doi: 10.1007/978-1-0716-3670-1_19
  • Higo, J; Bekker, GJ; Kamiya, N; Fukuda, I; Fukunishi, Y;.
    Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics.
    BIOPHYS PHYSICOBIOL. 2023 Dec 13;20(4):e200047. doi: 10.2142/biophysico.bppb-v20.0047
  • Sun, L; Morikawa, K; Sogo, Y; Sugiura, Y.
    MHY1485 potentiates immunogenic cell death induction and anti-cancer immunity following irradiation.
    J RADIAT RES. 2024 Feb 8:rrad107. doi: 10.1093/jrr/rrad107
  • Dong, W; Kameyama, A.
    Succinylation-Alcian Blue Staining of Mucins on Polyvinylidene Difluoride Membrane.
    METHODS MOL BIOL. 2024;2763:111-117. doi: 10.1007/978-1-0716-3670-1_9
  • Kameyama, A.
    Eliminative Oximation of O-Glycans from Mucins.
    METHODS MOL BIOL. 2024;2763:151-158. doi: 10.1007/978-1-0716-3670-1_13
  • Kameyama, A.
    Supported Molecular Matrix Electrophoresis.
    METHODS MOL BIOL. 2024;2763:79-97. doi: 10.1007/978-1-0716-3670-1_7
  • Sugiura, T; Kameyama, A.
    Preparation of Soluble Mucin Solutions from the Salivary Glands.
    METHODS MOL BIOL. 2024;2763:45-50. doi: 10.1007/978-1-0716-3670-1_3
  • Hasegawa, T; Nakagawara, A; Takagi, T; Shimoaka, T; Shioya, N; Sonoyama, M.
    Phonon modes controlled by primary chemical structure of partially fluorinated dimyristoylphosphatidylcholine (DMPC) revealed by multiple-angle incidence resolution spectrometry (MAIRS).
    J CHEM PHYS. 2024 Feb 14;160(6):064704. doi: 10.1063/5.0190441
  • Niibori-Nambu, A; Yamasaki, Y; Kobayashi, D; Angata, K; Kuno, A; Panawan, O; Silsilivanit, A; Narimatsu, H; Araki, N.
    Chondroitin sulfate modification of CSPG4 regulates the maintenance and differentiation of glioma initiating cells via integrin-associated signaling.
    J BIOL CHEM. 2024 Feb 1:105706. doi: 10.1016/j.jbc.2024.105706
  • Bekker, GJ; Fukunishi, Y; Higo, J; Kamiya, N.
    Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations.
    ACS OMEGA. 2024 Jan 10;9(3):3412-3422. doi: 10.1021/acsomega.3c06826 eCollection
  • Sato, T; Oishi, K.
    Time-restricted feeding has a limited effect on hepatic lipid accumulation, inflammation and fibrosis in a choline-deficient high-fat diet-induced murine NASH model.
    PLOS ONE. 2024 Jan 29;19(1):e0296950. doi: 10.1371/journal.pone.0296950
  • Kumar, V; Sari, AN; Gupta, D; Ishida, Y; Terao, K; Kaul, SC; Vrati, S; Sundar, D; Wadhwa, R.
    Anti-COVID-19 Potential of Withaferin-A and Caffeic Acid Phenethyl Ester.
    CURR TOP MED CHEM. 2024 Jan 24. doi: 10.2174/0115680266280720231221100004
  • Chen, LM; Keisham, S; Tateno, H; van, Ede J; Pronk, M; van, Loosdrecht MCM; Lin, Y.
    Alterations of Glycan Composition in Aerobic Granular Sludge during the Adaptation to Seawater Conditions.
    ACS ES T WATER. 2023 Dec 27;4(1):279-286. doi: 10.1021/acsestwater.3c00625
  • Kishimoto, T; Nishimura, K; Morishita, K; Fukuda, A; Miyamae, Y; Kumagai, Y; Sumaru, K; Nakanishi, M; Hisatake, K; Sano, M.
    An engineered ligand-responsive Csy4 endoribonuclease controls transgene expression from Sendai virus vectors.
    J BIOL ENG. 2024 Jan 16;18(1):9. doi: 10.1186/s13036-024-00404-9
  • Hashimoto, T; Suenaga, H; Amagai, K; Hashimoto, J; Kozone, I; Takahashi, S; Shin-Ya, K.
    In Vitro Module Editing Of NRPS Enables Production Of Highly Potent Gq-Signaling Inhibitor FR900359 Derived From Unculturable Plant Symbiont.
    ANGEW CHEM INT ED ENGL. 2024 Jan 18:e202317805. doi: 10.1002/anie.202317805
  • Germany, EM; Thewasano, N; Imai, K; Maruno, Y; Bamert, RS; Stubenrauch, CJ; Dunstan, RA; Ding, Y; Nakajima, Y; Lai, X; Webb, CT; Hidaka, K; Tan, KS; Shen, H; Lithgow, T; Shiota, T.
    Dual recognition of multiple signals in bacterial outer membrane proteins enhances assembly and maintains membrane integrity.
    ELIFE. 2024 Jan 16;12:RP90274. doi: 10.7554/eLife.90274
  • Shimizu, R; Murai, K; Tanaka, K; Sato, Y; Takeda, N; Nakasyo, S; Shirasaki, T; Kawaguchi, K; Shimakami, T; Nio, K; Nakaya, Y; Kagiwada, H Horimoto, K; Mizokami, M; Kaneko, S; Murata, K; Yamashita, T; Honda, M.
    Nucleos(t)ide analogs for hepatitis B virus infection differentially regulate the growth factor signaling in hepatocytes.
    HEPATOL COMMUN. 2024 Jan 5;8(1):e0351. doi: 10.1097/HC9.0000000000000351
  • Zhang, Y; Yang, W; Kumagai, YLoza, M; Zhang, W; Park, SJ; Nakai, K.
    Multi-omics computational analysis unveils the involvement of AP-1 and CTCF in hysteresis of chromatin states during macrophage polarization.
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    Droplet-Based Glycan and RNA Sequencing for Profiling the Distinct Cellular Glyco-States in Single Cells.
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    Molecular insights to the anti-COVID-19 potential of α-, β- and γ-cyclodextrins.
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    A cutoff-based method with charge-distribution-data driven pair potentials for efficiently estimating electrostatic interactions in molecular systems.
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    Atg15 is a vacuolar phospholipase that disintegrates organelle membranes.
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    Thermodynamic study on hydrated bilayers of ether-linked phosphatidylcholines with terminal perfluorobutyl group.
    BIOCHIM BIOPHYS ACTA BIOMEMBR. 2023 Dec 13:184261. doi: 10.1016/j.bbamem.2023.184261
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    Circadian and sleep phenotypes in a mouse model of Alzheimers disease characterized by intracellular accumulation of amyloid β oligomers.
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    Antistress activity of some phytochemicals: screening, identification, validation, and potential applications.
    ANNALS OF NUTRITION AND METABOLISM. 2023;79 (suppl 1) 1087-1087; AUG. doi: 10.1159/000530786
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    Involvement of transcription repressor Bach1 in function of intestinal goblet cells.
    ANNALS OF NUTRITION AND METABOLISM. 2023;79 (suppl 1) 1170-1170; AUG. doi: 10.1159/000530786
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    Functional engineering of human iPSC-derived parasympathetic neurons enhances responsiveness to gastrointestinal hormones.
    FEBS OPEN BIO. 2023 Nov 27. doi: 10.1002/2211-5463.13741
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    Non-destructive and efficient method for obtaining miRNA information in cells by artificial extracellular vesicles.
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    Regulation of the innate immune system by fragmented heparin-conjugated lipids on lipid bilayered membranes in vitro.
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    Efficient genome editing by controlled release of Cas9 ribonucleoprotein in plant cytosol using polymer-modified microneedle array.
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    Nanoendoscopy-AFM for Visualizing Intracellular Nanostructures of Living Cells.
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    MBTD1 preserves adult hematopoietic stem cell pool size and function.
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    Target-Specific O-linked N-acetylglucosamine Modification with a Dual-Specificity Aptamer Reveals Functions of O-GlcNAcylation in beta-catenin.
    TRENDS IN GLYCOSCIENCE AND GLYCOTECHNOLOGY. May 25, 2023; Volume 35(2023) Issue 205. doi: 10.4052/tigg.2309.6E
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    An improved evanescent fluorescence scanner suitable for high-resolution glycome mapping of formalin-fixed paraffin-embedded tissue sections.
    ANALYTICAL AND BIOANALYTICAL CHEMISTRY. 2023 JUL 3. doi: 10.1007/s00216-023-04824-2
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    Identification of compounds that preferentially suppress the growth of T-cell acute lymphoblastic leukemia-derived cells.
    CANCER SCI. 2023 Jul 31. doi: 10.1111/cas.15918
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    Decoding Metabolic Symbiosis between Pancreatic Cancer Cells and Cancer-Associated Fibroblasts Using Cultured Tumor Microenvironment.
    INT J MOL SCI. 2023 Jul 3;24(13):11015. doi: 10.3390/ijms241311015
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    Near-infrared radiation causes sebaceous gland enlargement along with an ROS-dependent augmentation of epidermal growth factor receptor expression in hamsters.
    EXPERIMENTAL DERMATOLOGY. 2023 JUL 4. doi: 10.1111/exd.14878
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    Reduction in disialyl-T antigen levels in mice deficient for both St6galnac3 and St6galnac4 results in blood filling of lymph nodes.
    SCI REP. 2023 Jun 29;13(1):10582. doi: 10.1038/s41598-023-37363-y
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    Sialylation shapes mucus architecture inhibiting bacterial invasion in the colon.
    MUCOSAL IMMUNOL. 2023 Jun 27:S1933-0219(23)00049-1. doi: 10.1016/j.mucimm.2023.06.004
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    Mechanisms of mechanical overload-induced skeletal muscle hypertrophy: current understanding and future directions.
    PHYSIOL REV. 2023 Jun 29. doi: 10.1152/physrev.00039.2022
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    Evolution of genetic architecture and gene regulation in biphenyl/PCB-degrading bacteria.
    FRONTIERS IN MICROBIOLOGY. 2023 Jun 7;14:1168246. doi: 10.3389/fmicb.2023.1168246
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    Construction of a spheroid array culture system on a suspended permeable hydrogel membrane scaffold for improving the expression of a liver-specific drug-metabolizing enzyme of HepG2 cells.
    BIOMATER SCI. 2023 Jun 22. doi: 10.1039/d3bm00071k
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    RNA Modification Related Diseases and Sensing Methods.
    APPLIED SCIENCES-BASEL. 2023 13(11) 6376. doi: 10.3390/app13116376
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    A ketogenic diet containing medium-chain triglycerides reduces REM sleep duration without significant influence on mouse circadian phenotypes.
    FOOD RESEARCH INTERNATIONAL. 2023 Jul;169:112852. doi: 10.1016/j.foodres.2023.112852
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    Lectin Blotting of Cell Lysates.
    CURR PROTOC. 2023 May;3(5):e790. doi: 10.1002/cpz1.790
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    Deciphering the Molecular Mechanisms of Autonomic Nervous System Neuron Induction through Integrative Bioinformatics Analysis.
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    Sudachitin and Nobiletin Stimulate Lipolysis via Activation of the cAMP/PKA/HSL Pathway in 3T3-L1 Adipocytes.
    FOODS. 2023 May 10;12(10):1947. doi: 10.3390/foods12101947
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    Novel positron emission tomography imaging targeting cell surface glycans for pancreatic cancer: (18) F-labeled rBC2LCN lectin.
    CANCER SCI. 2023 May 19. doi: 10.1111/cas.15846
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    Carrier Protein Mediated Formation of the Dihydropyridazinone Ring in Actinopyridazinone Biosynthesis.
    ANGEW CHEM INT ED ENGL. 2023 May 17:e202305155. doi: 10.1002/anie.202305155
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    Cucurbitacin-B inhibits cancer cell migration by targeting mortalin and HDM2: computational and in vitro experimental evidence.
    J BIOMOL STRUCT DYN. 2023 May 2:1-10. doi: 10.1080/07391102.2023.2206914
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    Phototunable Cell Killing by Photochromic Diarylethene of Thiazoyl and Thienyl Derivatives.
    JOURNAL OF MEDICINAL CHEMISTRY. 2023, 66 (8) 5937-5949. doi: 10.1021/acs.jmedchem.3c00164
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    A multiomics atlas of brown adipose tissue development over time.
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    Three-way Cell-based Screening of Antistress Compounds: Identification, Validation, and Relevance to Old-age Related Pathologies.
    J GERONTOL A BIOL SCI MED SCI. 2023 Apr 15:glad103. doi: 10.1093/gerona/glad103
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    Expression and localisation of MUC1 modified with sialylated core-2 O-glycans in mucoepidermoid carcinoma.
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    3,4-Dihydroxybenzalacetone Inhibits the Propagation of Hydrogen Peroxide-Induced Oxidative Effect via Secretory Components from SH-SY5Y Cells.
    BIOL PHARM BULL. 2023;46(4):599-607. doi: 10.1248/bpb.b22-00727

2022

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    Automated cell isolation from photodegradable hydrogel based on fluorescence image analysis.
    BIOTECHNOL BIOENG. 2023 Mar 15. doi: 10.1002/bit.28375
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    Liquid chromatography-mass spectrometry analyses of polyprenyl phosphates in Escherichia coli cells in which genes for isoprenoid synthesis are amplified.
    J BIOSCI BIOENG. 2023 Mar 1:S1389-1723(23)00047-6. doi: 10.1016/j.jbiosc.2023.02.003
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    Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches.
    FRONT MOL BIOSCI. 2023 Feb 6;10:1110567. doi: 10.3389/fmolb.2023.1110567
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    Parallel Evolution of Sex-Linked Genes across XX/XY and ZZ/ZW Sex Chromosome Systems in the Frog Glandirana rugosa.
    GENES (Basel). 2023 Jan 18;14(2):257. doi: 10.3390/genes14020257
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    Biomimetic polyelectrolyte coating of stem cells suppresses thrombotic activation and enhances its survival and function.
    BIOMATER ADV. 2023 Feb 8;147:213331. doi: 10.1016/j.bioadv.2023.213331
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    Canonical Wnt signaling activation by chimeric antigen receptors for efficient cardiac differentiation from mouse embryonic stem cells.
    INFLAMM REGEN. 2023 Feb 10;43(1):11. doi: 10.1186/s41232-023-00258-6
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    Computational and experimental evidence of the anti-COVID-19 potential of honeybee propolis ingredients, caffeic acid phenethyl ester and artepillin c.
    PHYTOTHER RES. 2023 Feb 9. doi: 10.1002/ptr.7717
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    Size distributions of cellulose nanocrystals in dispersions using the centrifugal sedimentation method.
    INT J BIOL MACROMOL. 2023 Feb 2:123520. doi: 10.1016/j.ijbiomac.2023.123520
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    rBC2LCN-reactive SERPINA3 is a glycobiomarker candidate for pancreatic ductal adenocarcinoma.
    GLYCOBIOLOGY. 2023 Feb 2:cwad009. doi: 10.1093/glycob/cwad009
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    Significance of anti-transcobalamin receptor antibodies in cutaneous arteritis revealed by proteome-wide autoantibody screening.
    J AUTOIMMUN. 2023 Jan 30;135:102995. doi: 10.1016/j.jaut.2023.102995
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    Spatiotemporal changes of tissue glycans depending on localization in cardiac aging.
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    Surface modulation of extracellular vesicles with cell-penetrating peptide-conjugated lipids for improvement of intracellular delivery to endothelial cells.
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    Selection of the methylotrophic yeast Ogataea minuta as a high-producing host for heterologous protein expression.
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    Designed fabrication of active tumor targeting covalent organic framework nanotherapeutics via a simple post-synthetic strategy.
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    Aging is associated with impaired postprandial response of skeletal muscle protein synthesis to high-intensity muscle contraction in mice.
    J GERONTOL A BIOL SCI MED SCI. 2023 Jan 12:glad014. doi: 10.1093/gerona/glad014
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    Evolutionary features of ligands and their receptors via protein-protein interactions and essentiality in primates.
    GENES CELLS. 2023 Jan 9. doi: 10.1111/gtc.13006
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    Acyltransferase Domain Exchange between Two Independent Type I Polyketide Synthases in the Same Producer Strain of Macrolide Antibiotics.
    CHEMBIOCHEM. 2023 Jan 5. doi: 10.1002/cbic.202200670
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    A multipoint guidance mechanism for β-barrel folding on the SAM complex.
    NAT STRUCT MOL BIOL. 2023 Jan 5. doi: 10.1038/s41594-022-00897-2
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    Gravity-driven microfluidic device placed on a slow-tilting table enables constant unidirectional perfusion culture of human induced pluripotent stem cells.
    J BIOSCI BIOENG. 2022 Dec 29:S1389-1723(22)00346-2. doi: 10.1016/j.jbiosc.2022.11.007
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    C-shaped dipper: A novel useful auxiliary tool for preparation of specimen grids for transmission electron microscopy.
    MICROSC RES TECH. 2022 Dec 29. doi: 10.1002/jemt.24283
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    Elucidation of ubiquitin-conjugating enzymes that interact with RBR-type ubiquitin ligases using a liquid-liquid phase separation-based method.
    J BIOL CHEM. 2022 Dec 20:102822. doi: 10.1016/j.jbc.2022.102822
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  • Natsume, T.
    Robotic Biology: Robotics and AI Accelerate Life Science.
    CANCER SCIENCE. 113; FEB
  • Kuroda, T; Hattori, Y; Kagami, A; Fukuda, E; Tamura, G.
    Genetic modification in the body to make friends with cancer cells?! Dreaming of cancer treatment in 100 years.
    CANCER SCIENCE. 113 1517-1517; FEB
  • Fujimoto, M; Arai, E; Nishiyama, N; Maeshima, A; Fujimoto, H; Kitamura, H; Kuno, A; Yoshida, T; Kanai, Y.
    Lectin staining analysis of protein glycosylation in urothelial carcinomas.
    CANCER SCIENCE. 113 378-378; FEB
  • Kitazume, Y; Arai, E; Matsuda, A; Kakuda, S; Ohara, K; Maeshima, A; Kuno, A; Yoshida, T; Kanai, Y.
    Alteration of protein glycosylation in renal carcinogenesis.
    CANCER SCIENCE. 113 1284-1284; FEB
  • Demachi, A; Ohte, S; Uchida, R; Shin-Ya, K; Ohshiro, T; Tomoda, H; Ikeda, H.
    Discovery of prescopranone, a key intermediate in scopranone biosynthesis.
    JOURNAL OF ANTIBIOTICS. 2022 Apr 20. doi: 10.1038/s41429-022-00521-x
  • Maeda, F; Kato, A; Takeshima, K; Shibazaki, M; Sato, R; Shibata,T; Miyake, K; Kozuka-Hata, H; Oyama, M; Shimizu, E; Imoto, S; Miyano, S; Adachi, S; Natsume, T; Takeuchi, K; Maruzuru, Y; Koyanagi, N; Jun, A; Yasushi, K.
    Role of the Orphan Transporter SLC35E1 in the Nuclear Egress of Herpes Simplex Virus 1.
    J VIROL. 2022 Apr 27:e0030622. doi: 10.1128/jvi.00306-22
  • Mohamed, HMA; Takahashi, A; Nishijima, S; Adachi, S; Murai, I; Okamura, H; Yamamoto, T.
    CNOT1 regulates circadian behaviour through Per2 mRNA decay in a deadenylation-dependent manner.
    RNA BIOL. 2022;19(1):703-718. doi: 10.1080/15476286.2022.2071026
  • Rider, SD Jr; Gadgil, RY; Hitch, DC; Damewood, FJ 4th; Zavada, N; Shanahan, M; Alhawach, V; Shrestha, R; Shin-Ya, K; Leffak, M.
    Stable G-quadruplex DNA structures promote replication-dependent genome instability.
    J BIOL CHEM. 2022 Apr 18:101947. doi: 10.1016/j.jbc.2022.101947
  • Nagata, Y; Kageyama, S; Ishikawa, T; Kokura, S; Okayama, T; Abe, T; Murakami, M; Otsuka, K; Ariyoshi, T; Kojima, T; Taniguchi, K; Kobayashi, S; Shimada, H; Yajima, S; Suzuki, T; Hirano, S; Tsuchikawa, T; Shichinohe, T; Ueda, S; Kanetaka, K; Yoneda, A; Wada, H; Doki, Y; Yamaue, H; Katsuda, M; Ohi, M; Yasuda, H; Kondo, K; Kataoka, M; Kodera, Y; Koike, M; Shiraishi, T; Miyahara, Y; Goshima,N;Fukuda, E; Yamaguchi, K; Sato, E; Ikeda, H; Yamada, T; Osako, M; Hirai, K; Miyamoto, H; Watanabe, T; Shiku, H.
    Prognostic significance of NY-ESO-1 antigen and PIGR expression in esophageal tumors of CHP-NY-ESO-1-vaccinated patients as adjuvant therapy.
    CANCER IMMUNOL IMMUNOTHER. 2022 Apr 16. doi: 10.1007/s00262-022-03194-5
  • Odaka, H; Hiemori, K; Shimoda, A; Akiyoshi, K; Tateno, H.
    CD63-positive extracellular vesicles are potential diagnostic biomarkers of pancreatic ductal adenocarcinoma.
    BMC GASTROENTEROLOGY. 2022 Mar 28;22(1):153. doi: 10.1186/s12876-022-02228-7
  • Hayashi, Y; Yimiti, D; Sanada, Y; Ding, C; Omoto, T; Ogura, T; Nakasa, T; Ishikawa, M; Hiemori, K; Tateno, H; Miyaki, S; Adachi, N.
    The therapeutic capacity of bone marrow MSC-derived extracellular vesicles in Achilles tendon healing is passage-dependent and indicated by specific glycans.
    FEBS LETTERS. 2022 Apr;596(8):1047-1058. doi: 10.1002/1873-3468.14333
  • Tasaki, M; Tateno, H; Sato, T; Tomioka, A; Kaji, H; Narimatsu, H; Saito, K; Nakagawa, Y; Aoki, T; Kamimura, M; Ushiki, T; Okada, M; Miwa, Y; Hotta, K; Yoshida, Y; Takahashi, K; Tomita, Y.
    A Novel Method of CD31-Combined ABO Carbohydrate Antigen Microarray Predicts Acute Antibody-Mediated Rejection in ABO-Incompatible Kidney Transplantation.
    TRANSPL INT. 2022 Mar 23;35:10248. doi: 10.3389/ti.2022.10248
  • Oinam, L; Hayashi, R; Hiemori, K; Kiyoi, K; Sage-Ono, K; Miura, K; Ono, M; Tateno, H.
    Quantitative evaluation of glycan-binding specificity of recombinant Concanavalin A produced in lettuce (Lactuca sativa).
    BIOTECHNOL BIOENG. 2022 Apr 8. doi: 10.1002/bit.28099
  • Nakagawa, Y; Hishida, T; Hatano, E; Sumaru, K; Morishita, K; Morimoto, M; Yokojima, S; Nakamura, S; Uchida, K.
    Photoinduced cytotoxicity of photochromic symmetric diarylethene derivatives: the relation of structure and cytotoxicity.
    ORGANIC & BIOMOLECULAR CHEMISTRY. 2022 Apr 13;20(15):3211-3217. doi: 10.1039/d2ob00224h
  • Miyazaki, Y; Mori, N; Akagi, Y; Oda, T; Kida, YS.
    Potential Metabolite Markers for Pancreatic Cancer Identified by Metabolomic Analysis of Induced Cancer-Associated Fibroblasts.
    CANCERS. 2022 Mar 8;14(6):1375. doi: 10.3390/cancers14061375
  • Santos, HJ; Hanadate, Y; Imai, K; Watanabe, H; Nozaki, T.
    Entamoeba histolytica EHD1 Is Involved in Mitosome-Endosome Contact.
    MBIO. 2022 Apr 11:e0384921. doi: 10.1128/mbio.03849-21
  • Ishii, N.
    Systematic Investigation of Lanthanoid Transition Heavy Metal Acetates as Electron Staining Reagents for Protein Molecules in Biological Transmission Electron Microscopy.
    MICROSC MICROANAL. 2022 Apr 1:1-10. doi: 10.1017/S1431927622000411
  • Suenaga, H; Matsuzawa, T; Sahara, T.
    Discovery by metagenomics of a functional tandem repeat sequence that controls gene expression in bacteria.
    FEMS MICROBIOL ECOL. 2022 Mar 28:fiac037. doi: 10.1093/femsec/fiac037

2021

  • Konishi, T; Takahashi, Y; Shiina, Y; Oike, H; Oishi, K.
    Time-of-day effects of consumption of fish oil-enriched sausages on serum lipid parameters and fatty acid composition in normolipidemic adults: A randomized, double-blind, placebo-controlled, and parallel-group pilot study.
    Nutrition. 2021;90:111247. doi: 10.1016/j.nut.2021.111247
  • Abdelhady, AM; Hirano, Y; Onizuka, K; Okamura, H; Komatsu, Y; Nagatsugi, F.
    Synthesis of Crosslinked 2-OMe RNA Duplexes Using 2-Amino-6-Vinylpurine and Their Application for Effective Inhibition of miRNA Function.
    CURR PROTOC. Mar;2(3):e386. doi: 10.1002/cpz1.386
  • Nagasaki, A; Katoh, K; Hoshi, M; Doi, M; Nakamura, C; Uyeda, TQP.
    Characterization of phalloidin-negative nuclear actin filaments in U2OS cells expressing cytoplasmic actin-EGFP.
    GENES TO CELLS. 2022 Feb 23. doi: 10.1111/gtc.12930
  • Seo, N; Nakamura, J; Kaneda, T; Tateno, H; Shimoda, A; Ichiki, T; Furukawa, K; Hirabayashi, J; Akiyoshi, K; Shiku, H.
    Distinguishing functional exosomes and other extracellular vesicles as a nucleic acid cargo by the anion-exchange method.
    J EXTRACELL VESICLES. 2022 Mar;11(3):e12205. doi: 10.1002/jev2.12205
  • Araiso, Y; Imai, K; Endo, T.
    Role of the TOM Complex in Protein Import into Mitochondria: Structural Views.
    ANNU REV BIOCHEM. 2022 Feb 14. doi: 10.1146/annurev-biochem-032620-104527
  • Tajima, K; Yagi, H; Morisaku, T; Nishi, K; Kushige, H; Kojima, H; Higashi, H; Kuroda, K; Kitago, M; Adachi, S; Natsume, T; Nishimura, K; Oya, M; Kitagawa, Y.
    An organ-derived extracellular matrix triggers in situ kidney regeneration in a preclinical model.
    NPJ REGEN MED. 2022 Feb 28;7(1):18. doi: 10.1038/s41536-022-00213-y
  • Ono, J; Koshimizu, U; Fukunishi, Y; Nakai, H.
    Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations.
    CHEM PHYS LETT. 2022 Feb 22;794:139489. doi: 10.1016/j.cplett.2022.139489
  • Radhakrishnan, N; Kaul, SC; Wadhwa, R; Sundar, D.
    Phosphatidylserine Exposed Lipid Bilayer Models for Understanding Cancer Cell Selectivity of Natural Compounds: A Molecular Dynamics Simulation Study.
    MEMBRANES 12 (1);doi: 10.3390/membranes12010064 JAN
  • Malik, V; Radhakrishnan, N; Kaul, SC; Wadhwa, R; Sundar, D.
    Computational Identification of BCR-ABL Oncogenic Signaling as a Candidate Target of Withaferin A and Withanone.
    BIOMOLECULES 12 (2);doi: 10.3390/biom12020212 FEB
  • Nagata, R; Suemune, H; Kobayashi, M; Shinada, T; Shin-Ya, K; Nishiyama, M; Hino, T; Sato, Y; Kuzuyama, T; Nagano, S.
    Structural Basis for the Prenylation Reaction of Carbazole-Containing Natural Products Catalyzed by Squalene Synthase-like Enzymes.
    ANGEW CHEM INT ED ENGL. 2022 Mar 2. doi: 10.1002/anie.202117430
  • Mitani, Y; Yasuno, R; Kihira, K; Chung, KM; Mitsuda, N; Kanie, S; Tomioka, A; Kaji, H; Ohmiya, Y.
    Host-Dependent Producibility of Recombinant Cypridina noctiluca Luciferase With Glycosylation Defects.
    FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY 10;doi: 10.3389/fbioe.2022.774786 FEB 7
  • Odaka, H; Ozaki, H; Tateno, H.
    scGR-seq: Integrated analysis of glycan and RNA in single cells.
    STAR PROTOC. 2022 Feb 18;3(1):101179. doi: 10.1016/j.xpro.2022.101179. eCollection
  • Sari, AN; Dhanjal, JK; Elwakeel, A; Kumar, V; Meidinna, HN; Zhang, H; Ishida, Y; Terao, K; Sundar, D; Kaul, SC; Wadhwa, R.
    A Low Dose Combination of Withaferin A and Caffeic Acid Phenethyl Ester Possesses Anti-Metastatic Potential In Vitro: Molecular Targets and Mechanisms.
    CANCERS (Basel). 2022 Feb 3;14(3):787. doi: 10.3390/cancers14030787
  • Irumagawa, S; Hiemori, K; Saito, S; Tateno, H; Arai, R.
    Self-Assembling Lectin Nano-Block Oligomers Enhance Binding Avidity to Glycans.
    INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 23 (2);doi: 10.3390/ijms23020676 JAN
  • Suzuki, R; Nakamura, Y; Koiwai, R; Fuseya, S; Murakami, Y; Hagiwara, K; Sato, T; Takahashi, S; Kudo, T.
    Global Loss of Core 1-Derived O-Glycans in Mice Leads to High Mortality Due to Acute Kidney Failure and Gastric Ulcers.
    INT J MOL SCI. 2022 Jan 24;23(3):1273. doi: 10.3390/ijms23031273
  • Saiki, P; Yoshihara, M; Kawano, Y; Miyazaki, H; Miyazaki, K.
    Anti-Inflammatory Effects of Heliangin from Jerusalem Artichoke (Helianthus tuberosus) Leaves Might Prevent Atherosclerosis.
    BIOMOLECULES 12 (1); doi:10.3390/biom12010091 JAN
  • Penedo, M; Miyazawa, K; Okano, N; Furusho, H; Ichikawa, T; Alam, MS; Miyata, K; Nakamura, C; Fukuma, T.
    Visualizing intracellular nanostructures of living cells by nanoendoscopy-AFM.
    SCI ADV. 2021 Dec 24;7(52):eabj4990. doi: 10.1126/sciadv.abj4990. Epub 2021 Dec 22
  • Sogabe, M; Kojima, S; Kaya, T; Tomioka, A; Kaji, H; Sato, T; Chiba, Y; Shimizu, A; Tanaka, N; Suzuki, N; Hayashi, I; Mikami, M; Togayachi, A; Narimatsu, H.
    Sensitive New Assay System for Serum Wisteria floribunda Agglutinin-Reactive Ceruloplasmin That Distinguishes Ovarian Clear Cell Carcinoma from Endometrioma.
    ANALYTICAL CHEMISTRY; doi:10.1021/acs.analchem.1c04302
  • Yamamoto, K; Yoneda, Y; Makino, A; Tanaka, Y; Meng, XY; Hashimoto, J; Shin-Ya, K; Satoh, N; Fujie, M; Toyama, T; Mori, K; Ike, M, Morikawa, M; Kamagata, Y; Tamaki, H.
    Draft Genome Sequence of Bryobacteraceae Strain F-183.
    MICROBIOL RESOUR ANNOUNC. 2022 Jan 13:e0045321. doi: 10.1128/mra.00453-21
  • Malik, V; Kumar, V; Kaul, SC; Wadhwa, R; Sundar, D.
    Potential of Withaferin-A, Withanone and Caffeic Acid Phenethyl ester as ATP-competitive inhibitors of BRAF: A bioinformatics study.
    CURR RES STRUCT BIOL. 2021 Nov 18;3:301-311. doi: 10.1016/j.crstbi.2021.11.004
  • Goel, I; Noiri, M; Yamauchi, Y; Kato, K; Chung, UI; Teramura, Y.
    Enhancement of intercellular interaction between iPSC-derived neural progenitor cells and activated endothelial cells using cell surface modification with functional oligopeptides.
    BIOMATER SCI. 2022 Jan 11. doi: 10.1039/d1bm01503f
  • Kaul, A; Kuthethur, R; Ishida, Y; Terao, K; Wadhwa, R; Kaul, SC.
    Molecular Insights into the Antistress Potentials of Brazilian Green Propolis Extract and Its Constituent Artepillin C.
    MOLECULES. 2021 Dec 23;27(1):80. doi: 10.3390/molecules27010080
  • Hori, K; Yoshimoto, S; Yoshino, T; Zako, T; Hirao, G; Fujita, S; Nakamura, C; Yamagishi, A; Kamiya, N.
    Recent advances in research on biointerfaces: From cell surfaces to artificial interfaces.
    J BIOSCI BIOENG. 2022 Jan 5:S1389-1723(21)00331-5. doi: 10.1016/j.jbiosc.2021.12.004
  • Ogata, H; Akita, S; Ikehara, S; Azuma, K; Yamaguchi, T; Maimaiti, M; Maezawa, Y; Kubota, Y; Yokote, K; Mitsukawa, N; Ikehara, Y.
    Calcification in Werner syndrome associated with lymphatic vessels aging.
    AGING (Albany NY). 2021 Dec 27;13(undefined). doi: 10.18632/aging.203789
  • Hirose, J; Watanabe, T; Futagami, T; Fujihara, H; Kimura, N; Suenaga, H; Goto, M; Suyama, A; Furukawa, K.
    A New ICEclc Subfamily Integrative and Conjugative Element Responsible for Horizontal Transfer of Biphenyl and Salicylic Acid Catabolic Pathway in the PCB-Degrading Strain Pseudomonas stutzeri KF716.
    MICROORGANISMS. 2021 Nov 29;9(12):2462. doi: 10.3390/microorganisms9122462
  • Matsuzawa, T; Watanabe, M; Nakamichi, Y; Kameyama, A; Kojima, N; Yaoi, K.
    Characterization of an extracellular α-xylosidase involved in xyloglucan degradation in Aspergillus oryzae.
    APPL MICROBIOL BIOTECHNOL. 2021 Dec 31. doi: 10.1007/s00253-021-11744-7
  • Nagai-Okatani, C; Zou, X; Matsuda, A; Itakura, Y; Toyoda, M; Zhang, Y; Kuno, A.
    Tissue Glycome Mapping: Lectin Microarray-Based Differential Glycomic Analysis of Formalin-Fixed Paraffin-Embedded Tissue Sections.
    METHODS MOL BIOL. 2022;2460:161-180. doi: 10.1007/978-1-0716-2148-6_10
  • Radhakrishnan, N; Dhanjal, JK; Sari, AN; Ishida, Y; Terao, K; Kaul, SC; Sundar, D; Wadhwa, R.
    Caffeic acid phenethyl ester (CAPE) confers wild type p53 function in p53(Y220C) mutant: bioinformatics and experimental evidence.
    DISCOVER ONCOLOGY 12 (1);doi: 10.1007/s12672-021-00461-2 DEC 20
  • Oinam, L; Tateno, H.
    Evaluation of Glycan-Binding Specificity by Glycoconjugate Microarray with an Evanescent-Field Fluorescence Detection System.
    METHODS MOL BIOL. 2022;2460:25-32. doi: 10.1007/978-1-0716-2148-6_2
  • Higashi, H; Yagi, H; Kuroda, K; Tajima, K; Kojima, H; Nishi, K; Morisaku, T; Hirukawa, K; Fukuda, K; Matsubara, K; Kitago, M; Shinoda, M; Obara, H; Adachi, S; Nishimura, K; Natsume, T; Tomi, M; Soto-Gutierrez, A; Kitagawa, Y.
    Transplantation of Bioengineered Liver Capable of Extended Function in a Preclinical Liver Failure Model.
    AM J TRANSPLANT. 2021 Dec 21. doi: 10.1111/ajt.16928
  • Aizawa, S; Nishimura, K; Mondejar, GS; Kumar, A; Bui, PL; Tran, YTH; Kuno, A; Muratani, M; Kobayashi, S; Nabekura, T; Shibuya, A; Sugihara, E; Sato, TA; Fukuda, A; Hayashi, Y; Hisatake, K.
    Early reactivation of clustered genes on the inactive X chromosome during somatic cell reprogramming.
    STEM CELL REPORTS. 2021 Nov 29:S2213-6711(21)00589-0. doi10.1016/j.stemcr.2021.11.008
  • Zhang, M; Kiyono, T; Aoki, K; Goshima, N; Kobayashi, S; Hiranuma, K; Shiraishi, K; Saya, H; Nakahara, T.
    Development of an in vitro carcinogenesis model of HPV induced cervical adenocarcinoma.
    CANCER SCI. 2021 Dec 21. doi: 10.1111/cas.15246
  • Kaifu, T; Yabe, R; Maruhashi, T; Chung, SH; Tateno, H; Fujikado, N; Hirabayashi, J; Iwakura, Y.
    DCIR and its ligand asialo-biantennary N-glycan regulate DC function and osteoclastogenesis.
    J EXP MED. 2021 Dec 6;218(12):e20210435. doi: 10.1084/jem.20210435. Epub 2021 Nov
  • Shimoda, A; Miura, R; Tateno, H; Seo, N; Shiku, H; Sawada, S; Sasaki, Y; Akiyoshi, K.
    Assessment of Surface Glycan Diversity on Extracellular Vesicles by Lectin Microarray and Glycoengineering Strategies for Drug Delivery Applications.
    SMALL METHODS; doi: 10.1002/smtd.202100785
  • Tulin, EKC; Nakazawa, C; Nakamura, T; Saito, S; Ohzono, N; Hiemori, K; Nakakita, SI; Tateno, H; Tonozuka, T; Nishikawa, A.
    Glycan detecting tools developed from the Clostridium botulinum whole hemagglutinin complex.
    SCI REP. 2021 Nov 9;11(1):21973. doi: 10.1038/s41598-021-01501-1
  • Kaigawa, H; Tateno, H; Arai, R.
    Self-Assembling Functional Complexes of Protein Nanobuilding Blocks with a Trimeric Lectin.
    PROTEIN SCIENCE 30 158-159; OCT
  • Irumagawa, S; Tateno, H; Arai, R.
    Self-Assembling Lectin Nano-Building Blocks Enhance Avidity to Glycans through Polyvalent Effect.
    PROTEIN SCIENCE 30 173-174; OCT
  • Takayanagi, S; Watanabe, K; Maruyama, T; Ogawa, M; Morishita, K; Soga, M; Hatta, T; Natsume, T; Hirano, T; Kagechika, H; Hattori, K; Naguro, I; Ichijo, H.
    ASKA technology-based pull-down method reveals a suppressive effect of ASK1 on the inflammatory NOD-RIPK2 pathway in brown adipocytes.
    SCI REP. 2021 Nov 10;11(1):22009. doi: 10.1038/s41598-021-01123-7
  • Shigi, N.
    Biosynthesis and Degradation of Sulfur Modifications in tRNAs.
    INT J MOL SCI. 2021 Nov 3;22(21):11937. doi: 10.3390/ijms222111937
  • Hurd, MD; Goel, I; Sakai, Y; Teramura, Y.
    Current status of ischemic stroke treatment: From thrombolysis to potential regenerative medicine.
    REGENERATIVE THERAPY 18 408-417; doi:10.1016/j.reth.2021.09.009 DEC
  • Queliconi BB, Kojima W, Kimura M, Imai K, Udagawa C, Motono C, Hirokawa T, Tashiro S, Caaveiro JMM, Tsumoto K, Yamano K, Tanaka K, Matsuda N.
    Unfolding is the driving force for mitochondrial import and degradation of Parkinsons disease-related protein DJ-1.
    J CELL SCI. 2021 Oct 22:jcs.258653. doi: 10.1242/jcs.258653
  • Wang, J; Zhang, H; Kaul, A; Li, K; Priyandoko, D; Kaul, SC; Wadhwa, R.
    Effect of Ashwagandha Withanolides on Muscle Cell Differentiation.
    BIOMOLECULES. 2021 Oct 4;11(10):1454. doi: 10.3390/biom11101454
  • Kumar, V; Sari, AN; Meidinna, HN; Dhanjal, JK; Subramani, C; Basu, B; Kaul, SC; Vrati, S; Sundar, D; Wadhwa, R.
    Computational and in vitro experimental analyses of the anti-COVID-19 potential of Mortaparib and MortaparibPlus.
    BIOSCI REP. 2021 Oct 29;41(10):BSR20212156. doi: 10.1042/BSR20212156
  • Adler, A; Inoue, Y; Ekdahl, KN; Baba, T; Ishihara, K; Nilsson, B; Teramura, Y.
    Effect of liposome surface modification with water-soluble phospholipid polymer chain-conjugated lipids on interaction with human plasma proteins.
    J MATER CHEM B. 2021 Oct 7. doi: 10.1039/d1tb01485d
  • Sano, M; Morishita, K; Oikawa, S; Akimoto, T; Sumaru, K; Kato, Y.
    Live-cell imaging of microRNA expression with post-transcriptional feedback control.
    MOL THER NUCLEIC ACIDS. 2021 Aug 26;26:547-556. doi: 10.1016/j.omtn.2021.08.018
  • Tsutsumi, H; Moriwaki, Y; Terada, T; Shimizu, K; Shin-Ya, K; Katsuyama, Y; Ohnishi, Y.
    Structural and Molecular Basis of the Catalytic Mechanism of Geranyl Pyrophosphate C-6 Methyltransferase: Creation of an Unprecedented Farnesyl Pyrophosphate C-6 Methyltransferase.
    ANGEW CHEM INT ED ENGL. 2021 Oct 9. doi: 10.1002/anie.202111217
  • Nakatani, E; Yamazaki, W; Sugiura, S; Kanamori, T; Ohnuma, K.
    Modeling of differentiation pattern formation in human induced pluripotent stem cells mediated by BMP4 and its inhibitor noggin secreted from cells.
    BIOCHEMICAL ENGINEERING JOURNAL 176; doi: 10.1016/j.bej.2021.108159 DEC
  • Hoshi, K; Ito, H; Abe, E; Fuwa, TJ; Kanno, M; Murakami, Y; Abe, M; Murakami, T, Yoshihara, A, Ugawa, Y, Saito, T, Saido, TC, Matsumoto, K, Yamaguchi, Y, Furukawa, K, Arai, H, Kanai, M, Miyajima, M, Arai, H, Ogawa, N, Akatsu, H, Hashizume, Y, Tateno, H, Honda, T, Hashimoto, Y.
    Transferrin Biosynthesized in the Brain Is a Novel Biomarker for Alzheimers Disease.
    METABOLITES. 2021 Sep 10;11(9):616. doi: 10.3390/metabo11090616
  • Angata, K; Wagatsuma, T; Togayachi, A; Sato, T; Sogabe, M; Tajiri, K; Ozawa, T; Nagashima, I; Shimizu, H; Iijima, S; Korenaga, M; Kuno, A; Kaji, H; Mizokami, M; Narimatsu, H.
    O-glycosylated HBsAg peptide can induce specific antibody neutralizing HBV infection.
    BIOCHIM BIOPHYS ACTA GEN SUBJ. 2021 Sep 25:130020. doi: 10.1016/j.bbagen.2021.130020
  • Fujikura, Y; Sugihara, H; Hatakeyama, M; Oishi, K; Yamanouchi, K.
    Ketogenic diet with medium-chain triglycerides restores skeletal muscle function and pathology in a rat model of Duchenne muscular dystrophy.
    FASEB J. 2021 Sep;35(9):e21861. doi: 10.1096/fj.202100629R
  • Bhargava, P; Mahanta, D; Kaul, A; Ishida, Y; Terao, K; Wadhwa, R; Kaul, SC.
    Experimental Evidence for Therapeutic Potentials of Propolis.
    NUTRIENTS. 2021 Jul 24;13(8):2528. doi: 10.3390/nu13082528
  • Kumar, A; Konar, A; Garg, S; Kaul, SC; Wadhwa, R.
    Experimental evidence and mechanism of action of some popular neuro-nutraceutical herbs.
    NEUROCHEMISTRY INTERNATIONAL 149; doi: 10.1016/j.neuint.2021.105124
  • Takeuchi, K; Kofuku, Y; Imai, S; Ueda, T; Tokunaga, Y; Toyama, Y; Shiraishi, Y; Shimada, I.
    Function-Related Dynamics in Multi-Spanning Helical Membrane Proteins Revealed by Solution NMR.
    MEMBRANES (Basel). 2021 Aug 9;11(8):604. doi: 10.3390/membranes11080604
  • Yoko-O, T; Komatsuzaki, A; Yoshihara, E; Zhao, S; Umemura, M; Gao, XD; Chiba, Y.
    Regulation of alcohol oxidase gene expression in methylotrophic yeast Ogataea minuta.
    J BIOSCI BIOENG. 2021 Aug 27:S1389-1723(21)00204-8. doi: 10.1016/j.jbiosc.2021.08.001
  • Kaul, Z; Cheung, CTY; Bhargava, P; Sari, AN ; Yu, Y; He, HF; Bid, H; Henson, JD; Groden, J; Reddel, RR; Kaul, SC; Wadhwa, R.
    Functional characterization of miR-708 microRNA in telomerase positive and negative human cancer cells.
    SCI REP. 2021 Aug 23;11(1):17052. doi: 10.1038/s41598-021-96096-y
  • Isaka, E; Sugiura, T; Hashimoto, K; Kikuta, K; Anazawa, U; Nomura, T; Kameyama, A.
    Characterization of tumor-associated MUC1 and its glycans expressed in mucoepidermoid carcinoma.
    ONCOLOGY LETTERS 22 (4);doi: 10.3892/ol.2021.12963 OCT
  • Minoshima, F; Ozaki, H; Odaka, H; Tateno, H.
    Integrated analysis of glycan and RNA in single cells.
    ISCIENCE. 2021 Jul 17;24(8):102882. doi: 10.1016/j.isci.2021.102882. eCollection
  • Funakoshi, Y; Ohji, G; Yakushijin, K; Ebisawa, K; Arakawa, Y; Saegusa, J; Matsumoto, H; Imanishi, T; Fukuda, E; Matsutani, T; Mori, Y; Iwata, K; Minami, H.
    Massive surge of mRNA expression of clonal B-cell receptor in patients with COVID-19.
    HELIYON. 2021 Aug;7(8):e07748. doi: 10.1016/j.heliyon.2021.e07748. Epub 2021 Aug 10
  • Watanabe, T; Takeda, K; Hiemori, K; Minamisawa, T; Tateno, H.
    A glycosaminoglycan microarray identifies the binding of SARS-CoV-2 spike protein to chondroitin sulfate E.
    FEBS LETT. 2021 Aug 10. doi: 10.1002/1873-3468.14173
  • Perez, CAG; Adachi, S; Nong, QD; Adhitama, N; Matsuura, T; Natsume, T; Wada, T; Kato, Y; Watanabe, H.
    Sense-overlapping lncRNA as a decoy of translational repressor protein for dimorphic gene expression.
    PLOS GENET. 2021 Jul 28;17(7):e1009683. doi: 10.1371/journal.pgen.1009683
  • Kimura, M; Imai, K; Morinaka, Y; Hosono-Sakuma, Y; Horton, P; Imamoto, N.
    Distinct mutations in importin-β family nucleocytoplasmic transport receptors transportin-SR and importin-13 affect specific cargo binding.
    SCI REP. 2021 Aug 2;11(1):15649. doi: 10.1038/s41598-021-94948-1
  • Sato, Y; Asawa, K; Huang, T; Noiri, M; Nakamura, N; Ekdahl, KN; Nilsson, B; Ishihara, K; Teramura, Y.
    Induction of Spontaneous Liposome Adsorption by Exogenous Surface Modification with Cell-Penetrating Peptide-Conjugated Lipids.
    LANGMUIR. 2021 Aug 3. doi: 10.1021/acs.langmuir.1c01072
  • Suenaga, H; Kagaya, N; Kawada, M; Tatsuda, D; Sato, T; Shin-Ya, K.
    Phenotypic screening system using three-dimensional (3D) culture models for natural product screening.
    J ANTIBIOT (Tokyo). 2021 Jul 29. doi: 10.1038/s41429-021-00457-8
  • Konno, S; Kobayashi, K; Senda, M; Funai, Y; Seki, Y; Tamai, I; Schäkel, L; Sakata, K; Pillaiyar, T; Taguchi, A; Taniguchi, A; Gütschow, M; Müller, CE; Takeuchi, K; Hirohama, M; Kawaguch,i A; Kojima, M; Senda, T; Shirasaka, Y; Kamitani, W; Hayashi, Y.
    3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents.
    J MED CHEM. 2021 Jul 27. doi: 10.1021/acs.jmedchem.1c00665
  • Motono, C; Yanagida, S; Sato, M; Hirokawa, T.
    MDContactCom: a tool to identify differences of protein molecular dynamics from two MD simulation trajectories in terms of interresidue contacts.
    BIOINFORMATICS. 2021 Jul 21:btab538. doi: 10.1093/bioinformatics/btab538
  • Adler, A; Inoue, Y; Sato, Y; Ishihara, K; Ekdahl, KN; Nilsson, B; Teramura, Y.
    Synthesis of poly(2-methacryloyloxyethyl phosphorylcholine)-conjugated lipids and their characterization and surface properties of modified liposomes for protein interactions.
    BIOMATER SCI. 2021 Jul 20. doi: 10.1039/d1bm00570g
  • Haramoto, Y.
    First person - Yoshikazu Haramoto.
    BIOLOGY OPEN 10 (4);doi: 10.1242/bio.058759 APR
  • Seimiya, H; Nagasawa, K; Shin-Ya, K.
    Chemical targeting of G-quadruplexes in telomeres and beyond for molecular cancer therapeutics.
    J ANTIBIOT (Tokyo). 2021 Jul 20. doi: 10.1038/s41429-021-00454-x
  • Mostafa, Abdelhady A; Hirano, Y; Onizuka, K; Okamura, H; Komatsu, Y; Nagatsugi, F.
    Synthesis of Crosslinked 2-OMe RNA Duplexes and Their Application for Effective Inhibition of miRNA Function.
    BIOORG MED CHEM LETT. 2021 Jul 8:128257. doi: 10.1016/j.bmcl.2021.128257
  • Iida, S; Fukunishi, Y.
    Asymmetric dynamics of dimeric SARS-CoV-2 and SARS-CoV main proteases in an apo form: Molecular dynamics study on fluctuations of active site, catalytic dyad, and hydration water.
    BBA ADV. 2021;1:100016. doi: 10.1016/j.bbadva.2021.100016. Epub 2021 Jun 20
  • Ninomiya, K; Iwakiri, J; Aly, MK; Sakaguchi, Y; Adachi, S; Natsume, T; Terai, G; Asai, K; Suzuki, T; Hirose, T.
    m(6) A modification of HSATIII lncRNAs regulates temperature-dependent splicing.
    EMBO J. 2021 Jun 29:e107976. doi: 10.15252/embj.2021107976
  • Elwakeel, A; Sari, AN; Dhanjal, JK; Meidinna, HN; Sundar, D; Kaul, SC; Wadhwa, R.
    Mutant p53(L194F) Harboring Luminal-A Breast Cancer Cells Are Refractory to Apoptosis and Cell Cycle Arrest in Response to Mortaparib(Plus), a Multimodal Small Molecule Inhibitor.
    CANCERS (Basel). 2021 Jun 18;13(12):3043. doi: 10.3390/cancers13123043
  • Noro, E; Matsuda,A; Kyoutou,T; Sato, T; Tomioka,A; Nagai,M; Sogabe,M; Tsuruno,C; Takahama,Y; Kuno, A; Tanaka,Y; Kaji, H; Narimatsu, H.
    N-glycan structures of Wisteria floribunda agglutinin-positive Mac2 binding protein in the serum of patients with liver fibrosis.
    GLYCOBIOLOGY. 2021 Jun 29:cwab060. doi: 10.1093/glycob/cwab060
  • Hashimoto, M; Murai, Y; Morita, K; Kikukawa, T; Takagi, T; Takahashi, H; Yokoyama, Y; Amii, H; Sonoyama, M.
    Comparison of functionality and structural stability of bacteriorhodopsin reconstituted in partially fluorinated dimyristoylphosphatidylcholine liposomes with different perfluoroalkyl chain lengths.
    BIOCHIM BIOPHYS ACTA BIOMEMBR. 2021 Jun 25;1863(10):183686. doi: 10.1016/j.bbamem.2021.183686
  • Ogita, Y; Tamura, K; Mawaribuchi, S; Takamatsu, N; Ito, M.
    Independent pseudogenizations and losses of sox15 during amniote diversification following asymmetric ohnolog evolution.
    BMC ECOL EVOL. 2021 Jun 30;21(1):134. doi: 10.1186/s12862-021-01864-z
  • Yamagishi, A; Ito, F; Nakamura, C.
    Study on Cancer Cell Invasiveness via Application of Mechanical Force to Induce Chloride Ion Efflux.
    ANAL CHEM. 2021 Jun 21. doi: 10.1021/acs.analchem.1c01589
  • Tomita, T; Wadhwa, R; Kaul, SC; Kurita, R; Kojima, N; Onishi, Y.
    Withanolide Derivative 2,3-Dihydro-3β-methoxy Withaferin-A Modulates the Circadian Clock via Interaction with RAR-Related Orphan Receptor α (RORa.
    J NAT PROD. 2021 Jun 21. doi: 10.1021/acs.jnatprod.0c01276
  • Kagiwada, H; Kiboku, T; Matsuo, H; Kitazawa, M; Fukui, K; Horimoto, K.
    Assessing the activation/inhibition of tyrosine kinase-related pathways with a newly developed platform.
    PROTEOMICS. 2021 Jun 21:e2000251. doi: 10.1002/pmic.202000251
  • Dhanjal, JK; Kumar, V; Garg, S; Subramani, C; Agarwal, S; Wang, J; Zhang, H; Kaul, A; Kalra, RS; Kaul, SC; Vrati, S; Sundar, D; Wadhwa, R
    Molecular mechanism of anti-SARS-CoV2 activity of Ashwagandha-derived withanolides
    Int J Biol Macromol. 2021 Jun 9:S0141-8130(21)01215-0. doi: 10.1016/j.ijbiomac.2021.06.015
  • Furuta, T; Oda, T; Kiyoi, K; Ozawa, Y; Kimura, S; Kurimori, K; Miyazaki, Y; Yu, Y; Furuya, K; Akashi, Y; Shimomura, O; Tateno, H
    Carcinoembryonic antigen as a specific glycoprotein ligand of rBC2LCN lectin on pancreatic ductal adenocarcinoma cells
    Cancer Sci. 2021 Jun 11. doi: 10.1111/cas.15023
  • Okumura, S; Hirano, Y; Komatsu, Y.
    Stable duplex-linked antisense targeting miR-148a inhibits breast cancer cell proliferation.
    SCI REP. 2021 Jun 1;11(1):11467. doi: 10.1038/s41598-021-90972-3
  • Suzuki, T; Katayama, Y; Komatsu, Y; Kamiya, H.
    Similar frequency and signature of untargeted substitutions induced by abasic site analog under reduced human APE1 conditions.
    J TOXICOL SCI. 2021;46(6):283-288. doi: 10.2131/jts.46.283
  • Numakawa, T; Odaka, H.
    Brain-Derived Neurotrophic Factor Signaling in the Pathophysiology of Alzheimers Disease: Beneficial Effects of Flavonoids for Neuroprotection.
    INT J MOL SCI. 2021 May 27;22(11):5719. doi: 10.3390/ijms22115719
  • Yoneda, Y; Yamamoto, K; Makino, A; Tanaka, Y; Meng, XY; Hashimoto, J; Shin-Ya, K; Satoh, N; Fujie, M; Toyama, T; Mori, K; Ike, M; Morikawa, M; Kamagata, Y; Tamaki, H
    Novel Plant-Associated Acidobacteria Promotes Growth of Common Floating Aquatic Plants, Duckweeds
    Microorganisms. 2021 May 24;9(6):1133. doi: 10.3390/microorganisms9061133
  • Mogi, K; Kimura, H; Kondo, Y; Inoue, T; Adachi, S; Natsume, T.
    Automatic radioisotope manipulation for small amount of nuclear medicine using an EWOD device with a dimple structure.
    R SOC OPEN SCI. 2021 May 26;8(5):201809. doi: 10.1098/rsos.201809
  • Nishimura, T; Kawahara, T; Kagaya, N; Ogura, Y; Takikawa, H; Suenaga, H; Adachi, M; Hirokawa, T; Doi, T; Shin-Ya, K.
    JBIR-155, a Specific Class D β-Lactamase Inhibitor of Microbial Origin.
    ORG LETT. 2021 May 24. doi: 10.1021/acs.orglett.1c01352
  • Kudo, K; Nishimura, T; Kozone, I; Hashimoto, J; Kagaya, N; Suenaga, H; Ikeda, H; Shin-Ya, K.
    Hemiacetal-less rapamycin derivatives designed and produced by genetic engineering of a type I polyketide synthase.
    SCI REP. 2021 May 11;11(1):9944. doi: 10.1038/s41598-021-88583-z
  • Amemiya, T; Horimoto, K; Fukui, K.
    Application of multiple omics and network projection analyses to drug repositioning for pathogenic mosquito-borne viruses.
    SCI REP. 2021 May 12;11(1):10136. doi: 10.1038/s41598-021-89171-x
  • Sakata-Matsuzawa, M; Denda-Nagai, K; Fujihira, H; Noji, M; Ishii-Schrade, KB; Matsuda, A; Kuno, A; Okazaki, M; Nakai, K; Horimoto, Y; Saito, M; Irimura, T
    Glycans unique to the relapse-prone subset within triple-negative breast cancer as revealed by lectin array-based analysis of surgical specimens
    PLoS One. 2021 May 11;16(5):e0250747. doi: 10.1371/journal.pone.0250747. eCollection
  • Baba, T; Tanimura, S; Yamaguchi, A; Horikawa, K; Yokozeki, M; Hachiya, S; Iemura, SI; Natsume, T; Matsuda, N; Takeda, K.
    Cleaved PGAM5 dephosphorylates nuclear serine/arginine-rich proteinsduring mitophagy.
    BIOCHIM BIOPHYS ACTA MOL CELL RES. 2021 Apr 16:119045. doi: 10.1016/j.bbamcr.2021.119045
  • Tokunaga, Y; Tanaka, M; Iida, H; Kinoshita, M; Tojima, Y; Takeuchi, K; Imashimizu, M.
    Nonthermal excitation effects mediated by subterahertz radiation on hydrogen exchange in ubiquitin
    BIOPHYS J. 2021 Apr 21:S0006-3495(21)00329-5. doi: 10.1016/j.bpj.2021.04.013
  • Akagi, Y; Mori, N; Kawamura, T; Takayama, Y; Kida, YS.
    Non-invasive cell classification using the Paint Raman Express Spectroscopy System (PRESS)
    SCI REP. 2021 Apr 23;11(1):8818. doi: 10.1038/s41598-021-88056-3
  • Liu, C; Hashimoto, J; Kudo, K; Shin-Ya, K; Kakeya, H.
    An Atypical Arginine Dihydrolase Involved in the Biosynthesis of Cyclic Hexapeptide Longicatenamides.
    CHEM ASIAN J. 2021 Apr 22. doi: 10.1002/asia.202100181
  • Kaneko, S; Mitsuyama, T; Shiraishi, K; Ikawa, N; Shozu, K; Dozen, A; Machino, H; Asada, K; Komatsu, M; Kukita, A; Sone, K; Yoshida, H; Motoi, N; Hayami, S; Yoneoka, Y; Kato, T; Kohno, T; Natsume, T; Keudell, GV; Saloura, V; Yamaue, H; Hamamoto, R
    Genome-Wide Chromatin Analysis of FFPE Tissues Using a Dual-Arm Robot with Clinical Potential
    Cancers (Basel). 2021 Apr 28;13(9):2126. doi: 10.3390/cancers13092126
  • Li, X; Wang, J; Zhang, H; Xiao, L; Lei, Z; Kaul, SC; Wadhwa, R; Zhang, Z.
    Low Dose of Fluoride in the Culture Medium of Cordyceps militaris Promotes Its Growth and Enhances Bioactives with Antioxidant and Anticancer Properties.
    J FUNGI (Basel). 2021 Apr 28;7(5):342. doi: 10.3390/jof7050342
  • Kohrogi, K; Hino, S; Sakamoto, A; Anan, K; Takase, R; Araki, H; Hino, Y; Araki, K; Sato, T; Nakamura, K; Nakao, M
    LSD1 defines erythroleukemia metabolism by controlling the lineage-specific transcription factors GATA1 and C/EBP
    Blood Adv. 2021 May 11;5(9):2305-2318. doi: 10.1182/bloodadvances.2020003521
  • Okubo, S; Ena, E; Okuda, A; Kozone, I; Hashimoto, J; Nishitsuji, Y; Fujie, M; Satoh, N; Ikeda, H; Shin-Ya, K.
    Identification of functional cytochrome P450 and ferredoxin from Streptomyces sp. EAS-AB2608 by transcriptional analysis and their heterologous expression.
    APPL MICROBIOL BIOTECHNOL. 2021 May 4. doi: 10.1007/s00253-021-11304-z
  • Haramoto, Y; Sakata, M; Kobayashi, S.
    Visualization of X chromosome reactivation in mouse primordial germ cells in vivo.
    BIOL OPEN. 2021 Apr 15;10(4):bio058602. doi: 10.1242/bio.058602. Epub 2021 Apr 29
  • Mori, N; Kida, YS.
    Applicability of Artificial Vascularized Liver Tissue to Proteomic Analysis.
    MICROMACHINES (Basel). 2021 Apr 11;12(4):418. doi: 10.3390/mi12040418
  • Moritsugu, K; Takeuchi, K; Kamiya, N; Higo, J; Yasumatsu, I; Fukunishi, Y; Fukuda, I.
    Flexibility and Cell Permeability of Cyclic Ras-Inhibitor Peptides Revealed by the Coupled Nosé-Hoover Equation.
    J CHEM INF MODEL. 2021 Apr 9. doi: 10.1021/acs.jcim.0c01427
  • Penedo, M; Shirokawa, T; Alam, MS; Miyazawa, K; Ichikawa, T; Okano, N; Furusho, H; Nakamura, C; Fukuma, T.
    Cell penetration efficiency analysis of different atomic force microscopy nanoneedles into living cells.
    SCI REP. 2021 Apr 8;11(1):7756. doi: 10.1038/s41598-021-87319-3
  • Ohashi, H; Watashi, K; Saso, W; Shionoya, K; Iwanami, S; Hirokawa, T; Shirai, T; Kanaya, S; Ito, Y; Kim, KS; Nomura, T; Suzuki, T; Nishioka, K; Ando, S; Ejima, K; Koizumi, Y; Tanaka, T; Aoki, S; Kuramochi, K; Suzuki, T; Hashiguchi, T; Maenaka, K; Matano, T; Muramatsu, M; Saijo, M; Aihara, K; Iwami, S; Takeda, M; McKeating, JA; Wakita, T
    Potential anti-COVID-19 agents, Cepharanthine and Nelfinavir, and their usage for combination treatment.
    ISCIENCE. 2021 Mar 26:102367. doi: 10.1016/j.isci.2021.102367
  • Hirama, H; Otahara, R; Mogi, K; Hayase, M; Torii, T; Mekaru, H.
    Rapid Prototyping of a Nanoparticle Concentrator Using a Hydrogel Molding Method.
    POLYMERS (Basel). 2021 Mar 29;13(7):1069. doi: 10.3390/polym13071069
  • Lintuluoto, M; Horioka, Y; Hongo, S; Lintuluoto, JM; Fukunishi, Y.
    Molecular Dynamics Simulation Study on Allosteric Regulation of CD44-Hyaluronan Binding as a Force Sensing Mechanism.
    ACS OMEGA. 2021 Mar 16;6(12):8045-8055. doi: 10.1021/acsomega.0c05502. eCollection
  • Kalra, RS; Kumar, V; Dhanjal, JK; Garg, S; Li, X; Kaul, SC; Sundar, D; Wadhwa, R.
    COVID19-inhibitory activity of withanolides involves targeting of the host cell surface receptor ACE2: insights from computational and biochemical assays.
    J BIOMOL STRUCT DYN. 2021 Apr 2:1-14. doi: 10.1080/07391102.2021.1902858
  • Katsuyama, Y; Sone, K; Harada, A; Kawai, S; Urano, N; Adachi, N; Moriya, T; Kawasaki, M; Shin-Ya, K; Senda, T; Ohnishi, Y
    Structural and functional analyses of the tridomain-nonribosomal peptide synthetase FmoA3 for 4-methyloxazoline ring formation
    Angew Chem Int Ed Engl. 2021 Mar 29. doi: 10.1002/anie.202102760
  • Nakamura, A; Wang, D; Komatsu, Y.
    Analysis of GTP addition in the reverse (3-5) direction by human tRNA(His) guanylyltransferase.
    RNA. 2021 Mar 23:rna.078287.120. doi: 10.1261/rna.078287.120
  • Watanabe, T; Tateno, H.
    Elimination of cells deviated from human induced pluripotent stem cells with a photoactivatable IR700-labelled antibody.
    BIOCHEM BIOPHYS RES COMMUN. 2021 Mar 25;554:13-18. doi: 10.1016/j.bbrc.2021.03.078

2020

  • Koiwai K, Morohashi K, Inaba K, Ebihara K, Kojima H, Okabe T, Yoshino R, Hirokawa T, Nampo T, Fujikawa Y, Inoue H, Yumoto F, Senda T, Niwa R
    Non-steroidal inhibitors of Drosophila melanogaster steroidogenic glutathione S-transferase Noppera-bo
    J Pestic Sci. 2021 Feb 20;46(1):75-87. doi: 10.1584/jpestics.D20-072
  • Higo J, Takashima H, Fukunishi Y, Yoshimori A
    Generalized-ensemble method study: A helix-mimetic compound inhibits protein-protein interaction by long-range and short-range intermolecular interactions.
    J COMPUT CHEM. 2021 Mar 23. doi: 10.1002/jcc.26516
  • Hayami T, Kamiya N, Kasahara K, Kawabata T, Kurita JI, Fukunishi Y, Nishimura Y, Nakamura H, Higo J
    Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities.
    SCI REP. 2021 Mar 17;11(1):6178. doi: 10.1038/s41598-021-85612-9
  • Yamamoto K, Honda T, Yokoyama S, Ma L, Kato A, Ito T, Ishizu Y, Kuzuya T, Nakamura M, Kawashima H, Ishigami M, Tsuji NM, Fujishiro M
    Microbiome, fibrosis and tumor networks in a non-alcoholic steatohepatitis model of a choline-deficient high-fat diet using diethylnitrosamine
    Dig Liver Dis. 2021 Mar 13:S1590-8658(21)00081-5. doi: 10.1016/j.dld.2021.02.013
  • Miyazaki Y, Oda T, Inagaki Y, Kushige H, Saito Y, Mori N, Takayama Y, Kumagai Y, Mitsuyama T, Kida YS
    Adipose-derived mesenchymal stem cells differentiate into heterogeneous cancer-associated fibroblasts in a stroma-rich xenograft model.
    SCI REP. 2021 Feb 25;11(1):4690. doi: 10.1038/s41598-021-84058-3
  • Kumagai Y, Hirasawa T, Wachi M
    Requirement of the LtsA Protein for Formation of the Mycolic Acid-Containing Layer on the Cell Surface of Corynebacterium glutamicum.
    MICROORGANISMS. 2021 Feb 16;9(2):409. doi: 10.3390/microorganisms9020409
  • Shinohara M, Arakawa H, Oda Y, Shiraki N, Sugiura S, Nishiuchi T, Satoh T, Iino K, Leo S, Kato Y, Araya K, Kawanishi T, Nakatsuji T, Mitsuta M, Inamura K, Goto T, Shinha K, Nihei W, Komori K, Nishikawa M, Kume S, Kato Y, Kanamori T, Sakai Y, Kimura H
    Coculture with hiPS-derived intestinal cells enhanced human hepatocyte functions in a pneumatic-pressure-driven two-organ microphysiological system
    Sci Rep. 2021 Mar 8;11(1):5437. doi: 10.1038/s41598-021-84861-y
  • Nagai-Okatani C, Zou X, Fujita N, Sogabe I, Arakawa K, Nagai M, Angata K, Zhang Y, Aoki-Kinoshita KF, Kuno A
    LM-GlycomeAtlas Ver. 2.0: An Integrated Visualization for Lectin Microarray-based Mouse Tissue Glycome Mapping Data with Lectin Histochemistry.
    J PROTEOME RES. 2021 Mar 4. doi: 10.1021/acs.jproteome.0c00907
  • Fujimoto M, Arai E, Matsuda A, Maeshima A, Fujimoto H, Kuno A, Yoshida T, Kanai Y
    Alterations of protein glycosylation and DNA methylation in urothelial carcinoma.
    CANCER SCIENCE 112 670-670; FEB
  • Sari AN, Elwakeel A, Dhanjal JK,Kumar V, Sundar D, Kaul SC, Wadhwa R
    Identification and Characterization of Mortaparib(Plus)-A Novel Triazole Derivative That Targets Mortalin-p53 Interaction and Inhibits Cancer-Cell Proliferation by Wild-Type p53-Dependent and -Independent Mechanisms.
    CANCERS (Basel). 2021 Feb 17;13(4):835. doi: 10.3390/cancers13040835
  • Bekker GJ, Fukuda I, Higo J, Fukunishi Y, Kamiya N
    Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations.
    SCI REP. 2021 Mar 3;11(1):5046. doi: 10.1038/s41598-021-84488-z
  • Furuta T, Tateno H, Kiyoi K, Miyazaki Y, Kimura S, Kurimori K, Shimomura O, Oda T
    Glycans on CEA as a targeting ligand of pancreatic ductal adenocarcinoma in novel lectin-drug conjugated therapy.
    CANCER SCIENCE 112 718-718; FEB
  • Okabe S, Shin-ya K, Dan S, Nagasawa K, Seimiya H
    Establishment of G-quadruplex ligand-resistant cancer cells and elucidation of the resistance mechanism.
    CANCER SCIENCE 112 558-558; FEB
  • Miyazaki K, Suenaga H, Oshiki M, Kawano S, Fukushima T
    Complete Genome Sequence of Thiohalobacter sp. Strain COW1, Isolated from Activated Sludge Treating Coke Oven Wastewater.
    MICROBIOL RESOUR ANNOUNC. 2021 Feb 18;10(7):e00013-21. doi: 10.1128/MRA.00013-21
  • Ueoka R, Hashimoto J, Kozone I, Hashimoto T, Kudo K, Kagaya N, Suenaga H, Ikeda H, Shin-Ya K
    A novel methymycin analog, 12-ketomethymycin N-oxide, produced by the heterologous expression of the large pikromycin/methymycin biosynthetic gene cluster of Streptomyces sp. AM4900.
    BIOSCI BIOTECHNOL BIOCHEM. 2020 Dec 22:zbaa111. doi: 10.1093/bbb/zbaa111
  • Higo J, Kusaka A, Kasahara K, Kamiya N, Hayato I, Qilin X, Takahashi T, Fukuda I, Mori K, Hata Y, Fukunishi Y
    GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics
    Biophys Physicobiol. 2020 Dec 26;17:161-176. doi: 10.2142/biophysico.BSJ-2020008
  • Malik V, Kumar V, Kaul SC, Wadhwa R, Sundar D
    Computational Insights into the Potential of Withaferin-A, Withanone and Caffeic Acid Phenethyl Ester for Treatment of Aberrant-EGFR Driven Lung Cancers.
    BIOMOLECULES. 2021 Jan 26;11(2):160. doi: 10.3390/biom11020160
  • Maejima A, Ishibashi K, Kim H, Kumagai I, Asano R
    Evaluation of intercellular cross-linking abilities correlated with cytotoxicities of bispecific antibodies with domain rearrangements using AFM force-sensing.
    BIOSENS BIOELECTRON. 2021 Jan 27;178:113037. doi: 10.1016/j.bios.2021.113037
  • Wadhwa R, Yadav NS, Katiyar SP, Yaguchi T, Lee C, Ahn H, Yun CO, Kaul SC, Sundar D
    Molecular dynamics simulations and experimental studies reveal differential permeability of withaferin-A and withanone across the model cell membrane.
    SCI REP. 2021 Jan 27;11(1):2352. doi: 10.1038/s41598-021-81729-z
  • Kojima W, Yamano K, Kosako H, Imai K, Kikuchi R, Tanaka K, Matsuda N
    Mammalian BCAS3 and C16orf70 associate with the phagophore assembly site in response to selective and non-selective autophagy.
    AUTOPHAGY. 2021 Jan 26:1-26. doi: 10.1080/15548627.2021.1874133
  • Odaka H, Numakawa T, Soga M, Kido J, Matsumoto S, Kajihara R, Okumiya T, Tani N, Tanoue Y, Fukuda T, Furuya H, Inoue T, Era T
    An iPSC-based neural model of sialidosis uncovers glycolytic impairment-causing presynaptic dysfunction and deregulation of Ca(2+) dynamics
    Neurobiol Dis. 2021 Jan 28:105279. doi: 10.1016/j.nbd.2021.105279
  • Kimura S, Oda T, Shimomura O, Enomoto T, Hashimoto S, Kuroda Y, Yu Y, Kurimori K, Furuta T, Miyazaki Y, Tateno H
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