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Structure-based development of novel substrate-type G9a inhibitors as epigenetic modulators for sickle cell disease treatment. Bioorg Med Chem Lett. 2024 110:129856. doi: 10.1016/j.bmcl.2024.129856.
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Catalytic Aerobic Carbooxygenation for Construction of Vicinal Tetrasubstituted Centers: Application to the Synthesis of Hexa-substituted γ-Lactones. Angewandte Chemie International Edition. 2024 doi: 10.1002/anie.202405876.
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Design of an Artificial Peptide Inspired by Transmembrane Mitochondrial Protein for Escorting Exogenous DNA into the Mitochondria to Restore their Functions by Simultaneous Multiple Gene Expression. Adv Funct Mater. 2023 34:2306070. doi: 10.1002/adfm.202306070.
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Acidic extracellular pH drives accumulation of N1-acetylspermidine and recruitment of protumor neutrophils. PNAS Nexus. 2023 2(10):pgad306. doi: 10.1093/pnasnexus/pgad306.
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UBL3 Interacts with Alpha-Synuclein in Cells and the Interaction Is Downregulated by the EGFR Pathway Inhibitor Osimertinib. Biomedicines. 2023 11 (6): 1685. doi: 10.3390/biomedicines11061685.
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Identification of triazenyl indoles as inhibitors of fungal fatty acid biosynthesis with broad-spectrum activity. Cell Chem Biol. 2023 30:1-16. doi: 10.1016/j.chembiol.2023.06.005.
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A set of vectors and strains for chromosomal integration in fission yeast. Scientific reports. 2023 13(1):9295. doi: 10.1038/s41598-023-36267-1.
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Identification of small-molecule inhibitors against the interaction of RNA-binding protein PSF and its target RNA for cancer treatment. PNAS Nexus. 2023 2: 1-10. doi: 10.1093/pnasnexus/pgad203.
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Lysine long-chain fatty acylation regulates the TEAD transcription factor. Cell Reports. 2023 42(4):112388. doi: 10.1016/j.celrep.2023.112388.
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Discovery of Novel Substrate-Competitive Lysine Methyltransferase G9a Inhibitors as Anticancer Agents. J Med Chem. 2023 66(6):4059–4085. doi: 10.1021/acs.jmedchem.2c02059.
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Identification of Fungal and Bacterial Denitrification Inhibitors Targeting Copper Nitrite Reductase. J Agric Food Chem. 2023 71(13):5172–5184. doi: 10.1021/acs.jafc.3c00896.
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Identification of a derivative of the alkaloid emetine as an inhibitor of the YAP-TEAD interaction and its potential as an anticancer agent. Biosci Biotechnol Biochem. 2023 98(5):501–510. doi: 10.1093/bbb/zbad022.
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RNAi screening reveals a synthetic chemical‐genetic interaction between ATP synthase and PFK1 in cancer cells. CANCER SCIENCE. 2023 00:1-9. doi: 10.1111/cas.15713.
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A specific G9a inhibitor unveils BGLT3 lncRNA as a universal mediator of chemically induced fetal globin gene expression. NATURE COMMUNICATIONS. 2023 14:23. doi: 10.1038/s41467-022-35404-0.
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MDMX elevation by a novel Mdmx–p53 interaction inhibitor mitigates neuronal damage after ischemic stroke. Scientific Reports. 2022 12:21110. doi: 10.1038/s41598-022-25427-4.
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FK506 binding protein, FKBP12, promotes serine utilization and negatively regulates threonine deaminase in fission yeast. iScience. 2022 25:105659. doi: 10.1016/j.isci.2022.105659.
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Isoquercitrin from Apocynum venetum L. produces an anti-obesity effect on obese mice by targeting C-1-tetrahydrofolate synthase, carbonyl reductase, and glutathione S-transferase P and modification of the AMPK/SREBP-1c/FAS/CD36 signaling pathway in mice in vivo. Food & Function. 2022 13:10923-10936. doi: 10.1039/d2fo02438a.
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Genome-based discovery and total synthesis of janustatins, potent cytotoxins from a plant-associated bacterium. Nature chemistry. 2022 14:1193–1201. doi: 10.1038/s41557-022-01020-0.
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Discovery of Benzylpiperazine Derivatives as CNS-Penetrant and Selective Histone Deacetylase 6 Inhibitors. ACS Medicinal Chemistry Letters. 2022 13(7):1077–1082. doi: 10.1021/acsmedchemlett.2c00081.
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A Novel Class of HIV-1 Inhibitors Targeting the Vpr-Induced G2-Arrest in Macrophages by New Yeast- and Cell-Based High-Throughput Screening. Viruses. 2022 14(6):1321. doi: 10.3390/v14061321.
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Improving Measures of Chemical Structural Similarity Using Machine Learning on Chemical-Genetic Interactions. Journal of chemical information and modeling. 2021 61(9):4156-4172. doi: 10.1021/acs.jcim.0c00993.
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Improved development of mouse somatic cell nuclear transfer embryos by chlamydocin analogues, class I and IIa histone deacetylase inhibitors. BIOLOGY OF REPRODUCTION. 2021 105(2):543-553. doi: 10.1093/biolre/ioab096.
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Targeting Epigenetic and Posttranscriptional Gene Regulation by PSF Impairs Hormone Therapy-Refractory Cancer Growth. CANCER RESEARCH. 2021 81(13):3495-3508. doi: 10.1158/0008-5472.CAN-20-3819.
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The Insulin Receptor: A Potential Target of Amarogentin Isolated from Gentiana rigescens Franch That Induces Neurogenesis in PC12 Cells. BIOMEDICINES. 2021 9(5):581. doi: 10.3390/biomedicines9050581.
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Mechanism-based inhibitors of SIRT2: structure–activity relationship, X-ray structures, target engagement, regulation of α-tubulin acetylation and inhibition of breast cancer cell migration. RSC Chemical Biology. 2021 2:612-626. doi: 10.1039/d0cb00036a.
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Spliceostatin A interaction with SF3B1 limits U1 snRNP availability and causes premature cleavage and polyadenylation. Cell Chemical Biology. 2021 28(9):1356-1365. doi: 10.1016/j.chembiol.2021.03.002.
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PKC downregulation upon rapamycin treatment attenuates mitochondrial disease. Nature Metabolism. 2020 2:1472–1481.
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A novel GSK3 inhibitor that promotes self-renewal in mouse embryonic stem cells. Biosci Biotechnol Biochem. 2020 84(10):2113-2120. doi: 10.1080/09168451.2020.1789445.
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A nonrandomized study of single oral supplementation within the daily tolerable upper level of nicotinamide affects blood nicotinamide and NAD+ levels in healthy subjects. Translational Medicine of Aging. 2020 4:45-54. https://doi.org/10.1016/j.tma.2020.04.002
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Genome-wide Survey of Ribosome Collision. Cell Rep. 2020 31(5):107610. doi: 10.1016/j.celrep.2020.107610.
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Design and Discovery of an Orally Efficacious Spiroindolinone-Based Tankyrase Inhibitor for the Treatment of Colon Cancer. J Med Chem. 2020 23;63(8):4183-4204. doi: 10.1021/acs.jmedchem.0c00045.
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Design, Synthesis and Structure-Activity Relationship Study of Pyrilamine Derivatives as Histone Deacetylase Inhibitors. Heterocycles. 2020 101(2):26-737 DOI:10.3987/COM-19-S(F)52.
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Targeting the N Terminus of eIF4AI for Inhibition of Its Catalytic Recycling. Cell Chem Biol. 2019 26(10):1417-1426.e5. doi: 10.1016/j.chembiol.2019.07.010.
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Mechanism of Action of Prethioviridamide, an Anticancer Ribosomally Synthesized and Post-Translationally Modified Peptide with a Polythioamide Structure. ACS Chem Biol. 2019 14(8):1819-1828. doi: 10.1021/acschembio.9b00410.
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Integrating yeast chemical genomics and mammalian cell pathway analysis. Acta Pharmacol Sin. 2019 May 28. doi: 10.1038/s41401-019-0231-y.
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Nakajima Y, Kawamura T, Maeda K, Ichikawa H, Motoyama T, Kondoh Y, Saito T, Kobayashi T, Yoshida M, Osada H, Kimura M.
Identification and characterization of an inhibitor of trichothecene 3-O-acetyltransferase, TRI101, by the chemical array approach. Biosci Biotechnol Biochem. 2013;77(9):1958-60.
Deshpande R, Asiedu MK, Klebig M, Sutor S, Kuzmin E, Nelson J, Piotrowski J, Shin SH, Yoshida M, Costanzo M, Boone C, Wigle DA, Myers CL.
A comparative genomic approach for identifying synthetic lethal interactions in human cancer. Cancer Res. 2013 Oct 15;73(20):6128-36.
Kumar A, Ito A, Hirohama M, Yoshida M, Zhang KY.
Identification of quinazolinyloxy biaryl urea as a new class of SUMO activating enzyme 1 inhibitors. Bioorg Med Chem Lett. 2013 Sep 15;23(18):5145-9.
Arai T, Ashraful Hoque M, Nishino N, Kim HJ, Ito A, Yoshida M.
Cyclic tetrapeptides with -SS- bridging between amino acid side chains for potent histone deacetylases' inhibition. Amino Acids. 2013 Oct;45(4):835-43.
Egawa N, Kitaoka S, Tsukita K, Naitoh M, Takahashi K, Yamamoto T, Adachi F, Kondo T, Okita K, Asaka I, Aoi T, Watanabe A, Yamada Y, Morizane A, Takahashi J, Ayaki T, Ito H, Yoshikawa K, Yamawaki S, Suzuki S, Watanabe D, Hioki H, Kaneko T, Makioka K, Okamoto K, Takuma H, Tamaoka A, Hasegawa K, Nonaka T, Hasegawa M, Kawata A, Yoshida M, Nakahata T, Takahashi R, Marchetto MC, Gage FH, Yamanaka S, Inoue H.
Response to comment on "Drug screening for ALS using patient-specific induced pluripotent stem cells". Sci Transl Med. 2013 Jun 5;5(188):188lr2.
Das J, Vo TV, Wei X, Mellor JC, Tong V, Degatano AG, Wang X, Wang L, Cordero NA, Kruer-Zerhusen N, Matsuyama A, Pleiss JA, Lipkin SM, Yoshida M, Roth FP, Yu H.
Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways. Sci Signal. 2013 May 21;6(276):ra38.
Guo TT, Yu YN, Cheong Yip GW, Matsumoto K, Bay BH.
Silencing the YB-1 gene inhibits cell migration in gastric cancer in vitro. Anat Rec (Hoboken). 2013 Jun;296(6):891-8.
Ling F, Hori A, Yoshitani A, Niu R, Yoshida M, Shibata T.
Din7 and Mhr1 expression levels regulate double-strand-break-induced replication and recombination of mtDNA at ori5 in yeast. Nucleic Acids Res. 2013 Jun;41(11):5799-816.
Matsushita K, Tamura M, Tanaka N, Tomonaga T, Matsubara H, Shimada H, Levens D, He L, Liu J, Yoshida M, Nomura F.
Interactions between SAP155 and FUSE-binding protein-interacting repressor bridges c-Myc and P27Kip1 expression. Mol Cancer Res. 2013 Jul;11(7):689-98.
Matsubara K, Lee AR, Kishigami S, Ito A, Matsumoto K, Chi H, Nishino N, Yoshida M, Hosoi Y.
Dynamics and regulation of lysine-acetylation during one-cell stage mouse embryos. Biochem Biophys Res Commun. 2013 Apr 26;434(1):1-7.
Kumar A, Ito A, Hirohama M, Yoshida M, Zhang KY.
Identification of sumoylation activating enzyme 1 inhibitors by structure-based virtual screening. J Chem Inf Model. 2013 Apr 22;53(4):809-20.
Espiritu RA, Matsumori N, Murata M, Nishimura S, Kakeya H, Matsunaga S, Yoshida M.
Interaction between the marine sponge cyclic peptide theonellamide A and sterols in lipid bilayers as viewed by surface plasmon resonance and solid-state (2)H nuclear magnetic resonance. Biochemistry. 2013 Apr 9;52(14):2410-8.
Kawaguchi M, Yasumasu S, Shimizu A, Kudo N, Sano K, Iuchi I, Nishida M.
Adaptive evolution of fish hatching enzyme: one amino acid substitution results in differential salt dependency of the enzyme. J Exp Biol. 2013 May 1;216(Pt 9):1609-15.
Narita K, Fukui Y, Sano Y, Yamori T, Ito A, Yoshida M, Katoh T.
Total synthesis of bicyclic depsipeptides spiruchostatins C and D and investigation of their histone deacetylase inhibitory and antiproliferative activities. Eur J Med Chem. 2013 Feb;60:295-304.
Ishfaq M, Maeta K, Maeda S, Natsume T, Ito A, Yoshida M.
The role of acetylation in the subcellular localization of an oncogenic isoform of translation factor eIF5A. Biosci Biotechnol Biochem. 2012;76(11):2165-7.
Hoque MA, Arai T, Nishino N, Kim HJ, Ito A, Yoshida M.
Cyclic tetrapeptides with thioacetate tails or intramolecular disulfide bridge as potent inhibitors of histone deacetylases. Bioorg Med Chem Lett. 2012 Nov 1;22(21):6770-2.
Takahashi H, Sun X, Hamamoto M, Yashiroda Y, Yoshida M.
The SAGA histone acetyltransferase complex regulates leucine uptake through the Agp3 permease in fission yeast. J Biol Chem. 2012 Nov 2;287(45):38158-67.
Cho HS, Shimazu T, Toyokawa G, Daigo Y, Maehara Y, Hayami S, Ito A, Masuda K, Ikawa N, Field HI, Tsuchiya E, Ohnuma S, Ponder BA, Yoshida M, Nakamura Y, Hamamoto R.
Enhanced HSP70 lysine methylation promotes proliferation of cancer cells through activation of Aurora kinase B. Nat Commun. 2012;3:1072.
Bauer F, Matsuyama A, Yoshida M, Hermand D.
Determining proteome-wide expression levels using reverse protein arrays in fission yeast. Nat Protoc. 2012 Oct;7(10):1830-5.
Dancy BM, Crump NT, Peterson DJ, Mukherjee C, Bowers EM, Ahn YH, Yoshida M, Zhang J, Mahadevan LC, Meyers DJ, Boeke JD, Cole PA.
Live-cell studies of p300/CBP histone acetyltransferase activity and inhibition. Chembiochem. 2012 Sep 24;13(14):2113-21.
Egawa N, Kitaoka S, Tsukita K, Naitoh M, Takahashi K, Yamamoto T, Adachi F, Kondo T, Okita K, Asaka I, Aoi T, Watanabe A, Yamada Y, Morizane A, Takahashi J, Ayaki T, Ito H, Yoshikawa K, Yamawaki S, Suzuki S, Watanabe D, Hioki H, Kaneko T, Makioka K, Okamoto K, Takuma H, Tamaoka A, Hasegawa K, Nonaka T, Hasegawa M, Kawata A, Yoshida M, Nakahata T, Takahashi R, Marchetto MC, Gage FH, Yamanaka S, Inoue H.
Drug screening for ALS using patient-specific induced pluripotent stem cells. Sci Transl Med. 2012 Aug 1;4(145):145ra104.
Niu R, Yoshida M, Ling F.
Increases in mitochondrial DNA content and 4977-bp deletion upon ATM/Chk2 checkpoint activation in HeLa cells. PLoS One. 2012;7(7):e40572.
Ishfaq M, Maeta K, Maeda S, Natsume T, Ito A, Yoshida M.
Acetylation regulates subcellular localization of eukaryotic translation initiation factor 5A (eIF5A). FEBS Lett. 2012 Sep 21;586(19):3236-41.
Bauer, F., Matsuyama, A., Candiracci, J., Dieu, M., Scheliga, J., Wolf, D. A., Yoshida, M., and Hermand, D.
Translational control of cell division by Elongator. Cell Rep. 2012 May 31;1(5):424-33.
Isozaki Y, Hoshino I, Nohata N, Kinoshita T, Akutsu Y, Hanari N, Mori M, Yoneyama Y, Akanuma N, Takeshita N, Maruyama T, Seki N, Nishino N, Yoshida M, Matsubara H.
Identification of novel molecular targets regulated by tumor suppressive miR-375 induced by histone acetylation in esophageal squamous cell carcinoma. Int J Oncol. 2012 Oct;7(10):1830-5.
Yoshihara H, Fukushima T, Hakuno F, Saeki Y, Tanaka K, Ito A, Yoshida M, Iemura S, Natsume T, Asano T, Chida K, Girnita L, Takahashi S.
Insulin/insulin-like growth factor (IGF) stimulation abrogates an association between a deubiquitinating enzyme USP7 and insulin receptor substrates (IRSs) followed by proteasomal degradation of IRSs. Biochem Biophys Res Commun. 2012 Jun 22;423(1):122-7.
Bradshaw E, Yoshida M, Ling F.
Mitochondrial fission proteins Fis1 and Mdv1, but not Dnm1, play a role in maintenance of heteroplasmy in budding yeast. FEBS Lett. 2012 Sep;41(3):985-94.
Kamemura K, Ogawa M, Ohkubo S, Ohtsuka Y, Shitara Y, Komiya T, Maeda S, Ito A, Yoshida M.
Depression of mitochondrial metabolism by downregulation of cytoplasmic deacetylase, HDAC6. FEBS Lett. 2012 May 7;586(9):1379-83.
Matsushita, K., Kajiwara, T., Tamura, M., Satoh, M., Tanaka, N., Tomonaga, T., Matsubara, H., Shimada, H., Yoshimoto, R., Ito, A., Kubo, S., Natsume, T., Levens, D., Yoshida, M., and Nomura, F.
SAP155-mediated splicing of FUSE-binding protein-interacting repressor (FIR) serves as a molecular switch for c-myc gene expression. Mol. Cancer Res. 2012 Apr 11.
Kobayashi H, Harada H, Nakamura M, Futamura Y, Ito A, Yoshida M, Iemura S, Shin-Ya K, Doi T, Takahashi T, Natsume T, Imoto M, Sakakibara Y.
Comprehensive predictions of target proteins based on protein-chemical interaction using virtual screening and experimental verifications. BMC Chem Biol. 2012 Apr 5;12:2.
Piotrowski JS, Nagarajan S, Kroll E, Stanbery A, Chiotti KE, Kruckeberg AL, Dunn B, Sherlock G, Rosenzweig F.
Different selective pressures lead to different genomic outcomes as newly-formed hybrid yeasts evolve. BMC Evol Biol. 2012 Apr 2;12:46.
Takahashi, M., Takemoto, Y., Shimazu, T., Kawasaki, H., Tachibana, M., Shinkai, Y., Takagi, M., Shin-Ya, K., Igarashi, Y., Ito, A., and Yoshida, M.
Inhibition of histone H3K9 methyltransferases by gliotoxin and related epipolythiodioxopiperazines. J. Antibiot. 2012 Feb 15.
Matsuyama, A. and Yoshida, M.
Heterologous gene expression by chromosomal integration in fission yeast. Methods Mol. Biol. 2012;824:433-50.
Sun, Y., Takada, K., Takemoto, Y., Yoshida, M., Nogi, Y., Okada, S., and Matsunaga, S.
Gliotoxin analogues from a marine-derived fungus, Penicillium sp., and their cytotoxic and histone methyltransferase inhibitory activities. J. Nat. Prod. 2012 Jan 27;75(1):111-4.
Williams DE, Dalisay DS, Patrick BO, Matainaho T, Andrusiak K, Deshpande R, Myers CL, Piotrowski JS, Boone C, Yoshida M, Andersen RJ.
Padanamides A and B, highly modified linear tetrapeptides produced in culture by a Streptomyces sp. isolated from a marine sediment. Org Lett. 2011 Aug 5;13(15):3936-9.
Fukushima T, Okajima H, Yamanaka D, Ariga M, Nagata S, Ito A, Yoshida M, Asano T, Chida K, Hakuno F, Takahashi S.
HSP90 interacting with IRS-2 is involved in cAMP-dependent potentiation of IGF-I signals in FRTL-5 cells. Mol Cell Endocrinol. 2011 Mar 4;406(1):42-6.
Tsuiji, H., Yoshimoto, R., Hasegawa, Y., Furuno, M., Yoshida, M., and Nakagawa, S.
Competition between a noncoding exon and introns: Gomafu contains tandem UACUAAC repeats and associates with splicing factor-1. Genes Cells. 2011 May;16(5):479-90.
Takahashi, H., Suzuki, T., Shirai, A., Matsuyama, A., Dohmae, N., and Yoshida, M.
Mitochondrial localization of fission yeast manganese superoxide dismutase is required for its lysine acetylation and for cellular stress resistance and respiratory growth. Biochem. Biophys. Res. Commun. 2011 Mar 4;406(1):42-6.
Schmidt, U., Basyuk, E., Robert, M.-C., Yoshida, M., Villemin, J.-P., Auboeuf, D., Aitken, S., and Bertrand, E.
Real-time imaging of cotranscriptional splicing reveals a kinetic model that reduces noise: implications for alternative splicing regulation. J. Cell Biol. 2011 May 30;193(5):819-29.
Oiso, H., Furukawa, N., Suefuji, M., Shimoda, S., Ito, A., Furumai, R., Nakagawa, J., Yoshida, M., Nishino, N., and Araki, E.
The role of class I histone deacetylase (HDAC) on gluconeogenesis in liver. Biochem. Biophys. Res. Commun. 2011 Jan 7;404(1):166-72.
Martins, S. B., Rino, J., Carvalho, T., Carvalho, C., Yoshida, M., Klose, J. M., Almeida, S. F. d., and Carmo-Fonseca, M.
Spliceosome assembly is coupled to RNA polymerase II dynamics at the 3′ end of human genes. Nat. Str. Mol Biol. 2011 Sep 4;18(10):1115-23.
Kizuka, Y., Kitazume, S., Yoshida, M., and Taniguchi, N.
Brain-specific Expression of N-Acetylglucosaminyltransferase IX (GnT-IX) Is Regulated by Epigenetic Histone Modifications. J. Biol. Chem. 2011 Sep 9;286(36):31875-84.
Ito, T., Umehara, T., Sasaki, K., Nakamura, Y., Nishino, N., Terada, T., Shirouzu, M., Padmanabhan, B., Yokoyama, S., Ito, A., and Yoshida, M.
Real-time imaging of histone H4K12-specific acetylation determines the modes of action of histone deacetylase and bromodomain inhibitors. Chem. Biol. 2011 Apr 22;18(4):495-507.
Islam, M. S., Bhuiyan, M. P., Islam, M. N., Nsiama, T. K., Oishi, N., Kato, T., Nishino, N., Ito, A., and Yoshida, M.
Evaluation of functional groups on amino acids in cyclic tetrapeptides in histone deacetylase inhibition. Amino Acids. 2011 Jun 3.
Hori, A., Yoshida, M., and Ling, F.
Mitochondrial fusion increases the mitochondrial DNA copy number in budding yeast. Genes Cells. 2011 May;16(5):527-44.
Hasegawa, M., Miura, T., Kuzuya, K., Inoue, A., Ki, S. W., Horinouchi, S., Yoshida, T., Kunoh, T., Koseki, K., Mino, K., Sasaki, R., Yoshida, M., and Mizukami, T.
Identification of SAP155 as the target of GEX1A (Herboxidiene), an antitumor natural product. ACS Chem. Biol. 2011 Sep 4;18(10):1115-23.
Furumai, R., Ito, A., Ogawa, K., Maeda, S., Saito, A., Nishino, N., Horinouchi, S., and Yoshida, M.
Histone deacetylase inhibitors block NF-κB−dependent transcription by interfering with RNA polymerase II recruitment. Cancer Sci. 2011 May;102(5):1081-7.
Furukawa, K., Abe, H., Tamura, Y., Yoshimoto, R., Yoshida, M., Tsuneda, S., and Ito, Y.
Fluorescence detection of intron lariat RNA with reduction-triggered fluorescent probes. Angew. Chem. Int. Ed. 2011 Dec 9;50(50):12020-3.
Arita, Y., Nishimura, S., Matsuyama, A., Yashiroda, Y., Usui, T., Boone, C., and Yoshida, M.
Microarray-based target identification using drug hypersensitive fission yeast expressing ORFeome. Mol. BioSyst. 2011 May;7(5):1463-72.
Furumai R, Uchida K, Komi Y, Yoneyama M, Ishigami K, Watanabe H, Kojima S, Yoshida M
Spliceostatin A blocks angiogenesis by inhibiting global gene expression including VEGF. Cancer Sci. 2010 Nov;101(11).
Iwasa, E., Hamashima, Y., Fujishiro, S., Higuchi, E., Ito, A., Yoshida, M., and Sodeoka, M.
Total synthesis of (+)-chaetocin and its analogs: Their histone methyltransferase G9a inhibitory activity. J Am Chem Soc. 2010 Mar 31;132(12):4078-9.
Jung, I., Matsuyama, A., Yoshida, M., and Kim, D.
PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship. BMC Bioinformatics. 2010 Jan 18;11.
Islam, N. M., Kato, T., Nishino, N., Kim, H.-J., Ito, A., and Yoshida, M.
Bicyclic peptides as potent inhibitors of histone deacetylases: Optimization of alkyl loop length. Bioorg Med Chem Lett. 2010 Feb 1;20(3):997-9.
Yashiroda, Y., Okamoto, R., Hatsugai, K., Takemoto, Y., Goshima, N., Saito, T., Hamamoto, M., Sugimoto, Y., Osada, H., Seimiya, H., and Yoshida, M.
A novel yeast cell-based screen identifies flavone as a tankyrase inhibitor. Biochem Biophys Res Commun. 2010 Apr 9;394(3):569-73.
Murakami, K., Matsubara, H., Hoshino, I., Akutsu, Y., Miyazawa, Y., Matsushita, K., Sakata, H., Nishimori, T., Usui, A., Kano, M., Nishino, N., and Yoshida, M.
CHAP31 induces apoptosis only via the intrinsic pathway in human esophageal cancer cells. Oncology. 2010;78(1):62-74. Epub 2010 Mar 6.
Nishimura, S., Arita, Y., Honda, M., Iwamoto, K., Matsuyama, A., Shirai, A., Kawasaki, H., Kakeya, H., Kobayashi, T., Matsunaga, S., and Yoshida, M.
Marine antifungal theonellamides target 3b-hydroxysterol to activate Rho1 signaling. Nature Chem. Biol. 2010 Jul;6(7).
Yoshida, M., Takeuchi, H., Ishida, Y., Yashiroda, Y., Yoshida, M., Takagi, M., Shin-Ya, K., and Doi, T.
Synthesis, structure determination, and biological evaluation of destruxin E. Org. Lett. 2010 Sep 3;12(17):3792-5.
Izawa, M., Takekawa, O., Arie, T., Teraoka, T., Yoshida, M., Kimura, M., and Kamakura, T.
Inhibition of histone deacetylase causes reduction of appressorium formation in the rice blast fungus Magnaporthe oryzae. J. Gen. Appl. Microbiol. 2009 Sep 22;106(38):16257-62.
Sato, M., Okada, N., Kakui, Y., Yamamoto, M., Yoshida, M., and Toda, T.
Nucleocytoplasmic transport of Alp7/TACC organizes spatiotemporal microtubule formation in fission yeast. EMBO Rep. 2009 Aug 21.
Ho CH, Magtanong L, Barker SL, Gresham D, Nishimura S, Natarajan P, Koh JL, Porter J, Gray CA, Andersen RJ, Giaever G, Nislow C, Andrews B, Botstein D, Graham TR, Yoshida M, Boone C.
A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds. Nat Biotechnol. 2009 Apr;27(4):369-77.
Ueda JY, Hwang JH, Maeda S, Kato T, Ochiai A, Isshiki K, Yoshida M, Takagi M, Shin-Ya K.
JBIR-17, a novel trichostatin analog from Streptomyces sp. 26634. J Antibiot (Tokyo). 2009 May;62(5):283-5.
Fukuda I, Ito A, Hirai G, Nishimura S, Kawasaki H, Saitoh H, Kimura K, Sodeoka M, Yoshida M.
Ginkgolic acid inhibits protein SUMOylation by blocking formation of the E1-SUMO intermediate. Chem Biol. 2009 Feb 27;16(2):133-40.
Ueoka R, Ito A, Izumikawa M, Maeda S, Takagi M, Shin-Ya K, Yoshida M, van Soest RW, Matsunaga S.
Isolation of azaspiracid-2 from a marine sponge Echinoclathria sp. as a potent cytotoxin. Toxicon. 2009 May;53(6):680-4.
Zhou J, Vos CC, Gjyrezi A, Yoshida M, Khuri FR, Tamanoi F, Giannakakou P.
The protein farnesyltransferase regulates HDAC6 activity in a microtubule-dependent manner. J Biol Chem. 2009 Apr 10;284(15):9648-55.
Ling F, Yoshida M, Shibata T.
Heteroduplex joint formation free of net topological change by Mhr1, a mitochondrial recombinase. J Biol Chem. 2009 Apr 3;284(14):9341-53.
Hori A, Yoshida M, Shibata T, Ling F.
Reactive oxygen species regulate DNA copy number in isolated yeast mitochondria by triggering recombination-mediated replication. Nucleic Acids Res. 2009 Feb;37(3):749-61.
Matsuyama, A. and Yoshida, M.
Systematic cloning of an ORFeome using the Gateway system. Methods Mol. Biol. 2009;577:11-24.
Dohi Y, Ikura T, Hoshikawa Y, Katoh Y, Ota K, Nakanome A, Muto A, Omura S, Ohta T, Ito A, Yoshida M, Noda T, Igarashi K.
Bach1 inhibits oxidative stress-induced cellular senescence by impeding p53 function on chromatin. Nat Struct Mol Biol. 2008 Dec;15(12):1246-54.
Hoshino I, Matsubara H, Komatsu A, Akutsu Y, Nishimori T, Yoneyama Y, Murakami K, Sakata H, Matsushita K, Miyazawa Y, Brooks R, Yoshida M, Ochiai T.
Combined effects of p53 gene therapy and leptomycin B in human esophageal squamous cell carcinoma. Oncology. 2008 75(1-2):113-9.
Tokai T, Takahashi-Ando N, Izawa M, Kamakura T, Yoshida M, Fujimura M, Kimura M.
4-O-acetylation and 3-O-acetylation of trichothecenes by trichothecene 15-O-acetyltransferase encoded by Fusarium Tri3. Biosci Biotechnol Biochem. 2008 Sep;72(9):2485-9.
Crabb SJ, Howell M, Rogers H, Ishfaq M, Yurek-George A, Carey K, Pickering BM, East P, Mitter R, Maeda S, Johnson PW, Townsend P, Shin-ya K, Yoshida M, Ganesan A, Packham G.
Characterisation of the in vitro activity of the depsipeptide histone deacetylase inhibitor spiruchostatin A. Biochem. Pharmacol. 2008 Aug 15;76(4):463-75.
Kamemura K, Ito A, Shimazu T, Matsuyama A, Maeda S, Yao TP, Horinouchi S, Khochbin S, Yoshida M.
Effects of downregulated HDAC6 expression on the proliferation of lung cancer cells. Biochem Biophys Res Commun. 2008 Sep 12;374(1):84-9.
Matsuyama A, Shirai A, Yoshida M.
A series of promoters for constitutive expression of heterologous genes in fission yeast. Yeast. 2008 May;25(5):371-6.
Nakao Y, Narazaki G, Hoshino T, Maeda S, Yoshida M, Maejima H, Yamashita JK.
Evaluation of antiangiogenic activity of azumamides by the in vitro vascular organization model using mouse induced pluripotent stem (iPS) cells. Bioorg Med Chem Lett. 2008 May 1;18(9):2982-4.
Kimata Y, Matsuyama A, Nagao K, Furuya K, Obuse C, Yoshida M, Yanagida M.
Diminishing HDACs by drugs or mutations promotes normal or abnormal sister chromatid separation by affecting APC/C and adherin. J Cell Sci. 2008 Apr 1;121(Pt 7):1107-18.
Shirai A, Matsuyama A, Yashiroda Y, Hashimoto A, Kawamura Y, Arai R, Komatsu Y, Horinouchi S, Yoshida M.
Global analysis of gel mobility of proteins and its use in target identification. J Biol Chem. 2008 Apr 18;283(16):10745-52. Epub 2008 Feb 21.
Takahashi-Ando N, Ochiai N, Tokai T, Ohsato S, Nishiuchi T, Yoshida M, Fujimura M, Kimura M.
A screening system for inhibitors of trichothecene biosynthesis: hydroxylation of trichodiene as a target. Biotechnol Lett. 2008 Jun;30(6):1055-9.
Nishino N, Shivashimpi GM, Soni PB, Bhuiyan MP, Kato T, Maeda S, Nishino TG, Yoshida M.
Interaction of aliphatic cap group in inhibition of histone deacetylases by cyclic tetrapeptides. Bioorg Med Chem. 2008 Jan 4;365(1): 183-8.
Lo CW, Kaida D, Nishimura S, Matsuyama A, Yashiroda Y, Taoka H, Ishigami K, Watanabe H, Nakajima H, Tani T, Horinouchi S, Yoshida M.
Inhibition of splicing and nuclear retention of pre-mRNA by spliceostatin A in fission yeast. Biochem Biophys Res Commun. 2007 Dec 21;364(3): 573-7.
Yurek-George A, Cecil AR, Mo AH, Wen S, Rogers H, Habens F, Maeda S, Yoshida M, Packham G, Ganesan A.
The first biologically active synthetic analogues of FK228, the depsipeptide histone deacetylase inhibitor. J Med Chem. Nov 15;50(23):5720-6. Epub 2007 Oct 24.
Kaida D, Motoyoshi H, Tashiro E, Nojima T, Hagiwara M, Ishigami K, Watanabe H, Kitahara T, Yoshida T, Nakajima H, Tani T, Horinouchi S, Yoshida M.
Spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA. Nat Chem Biol. 2007 Sep;3(9):576-83. Epub 2007 Jul 22.
Ling F, Hori A, Yoshida M, Shibata T.
Rolling circle replication: a universal model for controlling mechanisms of mitochondrial DNA copy number. Tanpakushitsu Kakusan Koso. 2007 Jul;52(8):886-92. Review. Japanese.
Hoshino H, Nishino TG, Tashiro S, Miyazaki M, Ohmiya Y, Igarashi K, Horinouchi S, Yoshida M.
Co-repressor SMRT and class II histone deacetylases promote Bach2 nuclear retention and formation of nuclear foci that are responsible for local transcriptional repression. J Biochem (Tokyo). 2007 May;141(5):719-27. Epub 2007 Mar 23.
Tsuchiya A, Tashiro E, Yoshida M, Imoto M.
Involvement of protein phosphatase 2A nuclear accumulation and subsequent inactivation of activator protein-1 in leptomycin B-inhibited cyclin D1 expression. Oncogene. 2007 Mar 8;26(11):1522-32. Epub 2006 Sep 11.
Jang BC, Sung SH, Park JG, Park JW, Suh MH, Choi IH, Yoshida M, Yoo SK, Suh SI.
Leptomycin B, a metabolite of Streptomyces, inhibits the expression of inducible nitric oxide synthase in BV2 microglial cells. Int J Oncol. 2006 Dec;29(6):1509-15.
Inoue K, Kobayashi M, Yano K, Miura M, Izumi A, Mataki C, Doi T, Hamakubo T, Reid PC, Hume DA, Yoshida M, Aird WC, Kodama T, Minami T.
Histone deacetylase inhibitor reduces monocyte adhesion to endothelium through the suppression of vascular cell adhesion molecule-1 expression. Arterioscler Thromb Vasc Biol. 2006 Dec;26(12):2652-9. Epub 2006 Sep 28.
Sasaki K, Yoshida M.
Histone modification enzymes. Tanpakushitsu Kakusan Koso, 2006 Nov;51(14 Suppl):2069-75. Review. Japanese.
Suzuki T, Kouketsu A, Itoh Y, Hisakawa S, Maeda S, Yoshida M, Nakagawa H, Miyata N.
Highly potent and selective histone deacetylase 6 inhibitors designed based on a small-molecular substrate. J Med Chem. 2006 Aug 10;49(16):4809-12.
Shinji C, Maeda S, Imai K, Yoshida M, Hashimoto Y, Miyachi H.
Design, synthesis, and evaluation of cyclic amide/imide-bearing hydroxamic acid derivatives as class-selective histone deacetylase (HDAC) inhibitors. Bioorg Med Chem. 2006 Nov 15;14(22):7625-51. Epub 2006 Jul 31.
Matsuyama A, Arai R, Yashiroda Y, Shirai A, Kamata A, Sekido S, Kobayashi Y, Hashimoto A, Hamamoto M, Hiraoka Y, Horinouchi S, Yoshida M.
ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe. Nat. Biotechnol. 2006 Jul;24(7):841-7. Epub 2006 Jun 25.
Tomono A, Mashiko M, Shimazu T, Inoue H, Nagasawa H, Yoshida M, Ohnishi Y, Horinouchi S.
Self-activation of serine/threonine kinase AfsK on autophosphorylation at threonine-168. J Antibiot (Tokyo). 2006 Feb;59(2):117-23.
Kataoka M, Hashimoto KI, Yoshida M, Nakamatsu T, Horinouchi S, Kawasaki H.
Gene expression of Corynebacterium glutamicum in response to the conditions inducing glutamate overproduction. Lett Appl Microbiol. 2006 May;42(5):471-6.
Jeon EJ, Lee KY, Choi NS, Lee MH, Kim HN, Jin YH, Ryoo HM, Choi JY, Yoshida M, Nishino N, Oh BC, Lee KS, Lee YH, Bae SC.
Bone morphogenetic protein-2 stimulates Runx2 acetylation. J Biol Chem. 2006 Jun 16;281(24):16502-11. Epub 2006 Apr 13.
Masumi A, Fukazawa H, Shimazu T, Yoshida M, Ozato K, Komuro K, Yamaguchi K.
Nucleolin is involved in interferon regulatory factor-2-dependent transcriptional activation. Oncogene. 2006 Aug 24;25(37):5113-24. Epub 2006 Apr 3.
Tokunaga K, Shibuya T, Ishihama Y, Tadakuma H, Ide M, Yoshida M, Funatsu T, Ohshima Y, Tani T.
Nucleocytoplasmic transport of fluorescent mRNA in living mammalian cells: nuclear mRNA export is coupled to ongoing gene transcription. Genes Cells. 2006 Mar;11(3):305-17.
Margolis SS, Perry JA, Weitzel DH, Freel CD, Yoshida M, Haystead TA, Kornbluth S.
A role for PP1 in the Cdc2/Cyclin B-mediated positive feedback activation of Cdc25. Mol Biol Cell. 2006 Apr;17(4):1779-89. Epub 2006 Feb 8.
Lee KH, Nishimura S, Matsunaga S, Fusetani N, Ichijo H, Horinouchi S, Yoshida M.
Induction of a ribotoxic stress response that stimulates stress-activated protein kinases by 13-deoxytedanolide, an antitumor marine macrolide. Biosci Biotechnol Biochem. 2006 Jan;70(1): 161-71.
Hirokawa Y, Nheu T, Grimm K, Mautner V, Maeda S, Yoshida M, Komiyama K, Maruta H.
Sichuan pepper extracts block the PAK1/cyclin D1 pathway and the growth of NF1-deficient cancer xenograft in mice. Cancer Biol Ther. 2006 Mar;5(3):305-9. Epub 2006 Mar 12.
Cheng Q, Balzer E, Miller S M, Yoshida M, and Wong J C
Effect of histone deacetylase inhibitors on tubulin acetylation and development in Volvox carteri (Volvocales). J. Phycol. 2006 42: 417-422
Tsuchiya A, Tashiro E, Yoshida M, Imoto M.
Involvement of nuclear accumulation of heat shock protein 27 in leptomycin B-induced apoptosis in HeLa cells. J Antibiot (Tokyo). 2005 Dec;58(12):810-6.
Barnfield PC, Zhang X, Thanabalasingham V, Yoshida M, Hui CC.
Negative regulation of Gli1 and Gli2 activator function by Suppressor of fused through multiple mechanisms. Differentiation. 2005 Oct;73(8):397-405.
Iwabata H, Yoshida M, Komatsu Y.
Proteomic analysis of organ-specific post-translational lysine-acetylation and -methylation in mice by use of anti-acetyllysine and -methyllysine mouse monoclonal antibodies. Proteomics. 2005 Dec;5(18):4653-64.
Shinji C, Nakamura T, Maeda S, Yoshida M, Hashimoto Y, Miyachi H.
Design and synthesis of phthalimide-type histone deacetylase inhibitors. Bioorg Med Chem Lett. 2005 Oct 15;15(20):4427-31.
Col E, Caron C, Chable-Bessia C, Legube G, Gazzeri S, Komatsu Y, Yoshida M, Benkirane M, Trouche D, Khochbin S.
HIV-1 Tat targets Tip60 to impair the apoptotic cell response to genotoxic stresses. EMBO J. 2005 Jul 20;24(14):2634-45. Epub 2005 Jul 7.
Lee KH, Nishimura S, Matsunaga S, Fusetani N, Horinouchi S, Yoshida M.
Inhibition of protein synthesis and activation of stress-activated protein kinases by onnamide A and theopederin B, antitumor marine natural products. Cancer Sci. 2005 Jun;96(6):357-64.
Kovacs JJ, Murphy PJM, Gaillard S, Zhao X, Wu JT, Nicchitta CV, Yoshida M, Toft DO, Pratt WB, Yao TP.
HDAC6 regulates Hsp90 acetylation and chaperone-dependent activation of clucocorticoid receptor. Mol Cell. 2005 May 27;18(5):601-7.
Tatematsu K, Yoshimoto N, Koyanagi T, Tokunaga C, Tachibana T, Yoneda Y, Yoshida M, Okajima T, Tanizawa K, Kuroda S.
Nuclear-cytoplasmic shuttling of a RING-IBR protein RBCK1 and its functional interaction with nuclear body proteins. J Biol Chem. 2005 Jun 17;280(24):22937-44. Epub 2005 Apr 15.
Saji S, Kawakami M, Hayashi S, Yoshida N, Hirose M, Horiguchi S, Itoh A, Funata N, Schreiber SL, Yoshida M, Toi M.
Significance of HDAC6 regulation via estrogen signaling for cell motility and prognosis in estrogen receptor-positive breast cancer. Oncogene. 2005 Jun 30;24(28):4531-9.
Nishimura S, Matsunaga S, Yoshida M, Hirota H, Yokoyama S, Fusetani N.
13-Deoxytedanolide, a marine sponge-derived antitumor macrolide, binds to the 60S large ribosomal subunit. Bioorg Med Chem. 2005 Jan 17;13(2):449-54.
Matsuyama A, Shirai A, Yashiroda Y, Kamata A, Horinouchi S, Yoshida M.
pDUAL, a multipurpose, multicopy vector capable of chromosomal integration in fission yeast. Yeast. 2004 Nov;21(15):1289-305.
Kamura T, Hara T, Matsumoto M, Ishida N, Okumura F, Hatakeyama S, Yoshida M, Nakayama K, Nakayama KI.
Cytoplasmic ubiquitin ligase KPC regulates proteolysis of p27(Kip1) at G1 phase. Nat Cell Biol. 2004 Dec;6(12):1229-35. Epub 2004 Nov 7.
Motoyoshi H, Horigome M, Ishigami K, Yoshida T, Horinouchi S, Yoshida M, Watanabe H, Kitahara T.
Structure-activity relationship for FR901464: a versatile method for the conversion and preparation of biologically active biotinylated probes. Biosci Biotechnol Biochem. 2004 Oct;68(10):2178-82.
Nishino N, Jose B, Shinta R, Kato T, Komatsu Y, Yoshida M.
Structure-activity relationship for FR901464: a versatile method for the conversion and preparation of biologically active biotinylated probes. Bioorg Med Chem. 2004 Nov 15;12(22):5777-84.
Heltweg B, Dequiedt F, Marshall BL, Brauch C, Yoshida M, Nishino N, Verdin E, Jung M.
Subtype selective substrates for histone deacetylases. J Med Chem. 2004 Oct 7;47(21):5235-43.
Jose B, Oniki Y, Kato T, Nishino N, Sumida Y, Yoshida M.
Novel histone deacetylase inhibitors: cyclic tetrapeptide with trifluoromethyl and pentafluoroethyl ketones. Bioorg. Med. Chem. Lett. 2004 Nov 1;14(21):5343-6.
Jang BC, Paik JH, Jeong HY, Oh HJ, Park JW, Kwon TK, Song DK, Park JG, Kim SP, Bae JH, Mun KC, Suh MH, Yoshida M, Suh SI.
Leptomycin B-induced apoptosis is mediated through caspase activation and down-regulation of Mcl-1 and XIAP expression, but not through the generation of ROS in U937 leukemia cells. Biochem Pharmacol. 2004 Jul 15;68(2):263-74.
Suzuki H, Tashiro S, Hira S, Sun J, Yamazaki C, Zenke Y, Ikeda-Saito M, Yoshida M, Igarashi K.
Heme regulates gene expression by triggering Crm1-dependent nuclear export of Bach1. EMBO J. 2004 Jul 7;23(13):2544-53. Epub 2004 Jun 3.
Yoshida M, Sazer S.
Nucleocytoplasmic transport and nuclear envelope integrity in the fission yeast Schizosaccharomyces pombe. Methods, 2004 Jul;33(3):226-38.
Nishino N, Yoshikawa D, Watanabe LA, Kato T, Jose B, Komatsu Y, Sumida Y, Yoshida M.
Synthesis and histone deacetylase inhibitory activity of cyclic tetrapeptides containing a retrohydroxamate as zinc ligand. Bioorg. Med. Chem. Lett. 2004 May 17;14(10):2427-31.
Tashiro S, Muto A, Tanimoto K, Tsuchiya H, Suzuki H, Hoshino H, Yoshida M, Walter J, Igarashi K.
Repression of PML nuclear body-associated transcription by oxidative stress-activated Bach2. Mol Cell Biol. 2004 Apr;24(8):3473-84.
Jose B, Okamura S, Kato T, Nishino N, Sumida Y, Yoshida M.
Toward an HDAC6 inhibitor: synthesis and conformational analysis of cyclic hexapeptide hydroxamic acid designed from alpha-tubulin sequence. Bioorg. Med. Chem. 2004 Mar 15;12(6):1351-6.
Uchida S, Ohtsubo M, Shimura M, Hirata M, Nakagama H, Matsunaga T, Yoshida M, Ishizaka Y, Yamashita K.
Nuclear export signal in CDC25B. Biochem Biophys Res Commun. 2004 Mar 26;316(1):226-32.
Watanabe LA, Jose B, Kato T, Nishino N, and Yoshida M.
Synthesis of L-a-amino-w-bromoalkanoic acid for side chain modification. Tetrahedron Lett. 45: 491-494, 2004.
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