新潟大学　医歯学系　システム生化学分野 / 大学院医歯学総合研究科　オミクス生物学分野

Department of Omics and Systems Biology Niigata University

2026

• Zinc-redox crosstalk regulates proteostasis in the endoplasmic reticulum.
  Amagai Y, Arai C, Yamamoto W, Watanabe S, Kowada T, Sitia R, Hoseki J, Mizukami S, Matsumoto M, Inaba K.
  Nature Commun., 2026, Online ahead of print.
  
• Global loss of metabolic responsiveness and elevated enzyme in leptin deficient obese mice during starvation
  Li D, Morita K, Kokaji T, Hatano A, Hirayama A, Soga T, Suzuki Y, Matsumoto M, Tsuchiya T, Ozaki H, Ohno S, Inoue H, Inaba Y, Maehara H, Sugimoto H, Pan Y, Kuroda S.
  NPJ Syst. Biol. Appl., 12(1):53, 2026.
  
• Inflammatory markers link steroid profiles to bone status in patients with autonomous cortisol secretion.
  Kitamura Y, Yokomoto-Umakoshi M, Nakano Y, Nakatani K, Umakoshi H, Nakao H, Kaneko H, Iwahashi N, Fujita M, Ogasawara T, Fukumoto T, Sakamoto R, Izumi Y, Bamba T, Ogawa Y.
  J. Clin. Endocrinol. Metab., 111(5):1299-310, 2026.
  
• Multi-condition machine learning models for understanding retention mechanisms and predicting retention time in supercritical fluid chromatography/mass spectrometry.
  Heravizadeh O, Nakatani K, Tomiyasu N, Torigoe T, Yamashita T, Takahashi M, Izumi Y, Bamba T.
  Anal. Chim. Acta., 1385:345026, 2026.
  

2025

• Characterizing lipoprotein profiles in coronary atherosclerosis development through quantitative lipidomics and proteomics approaches.
  Takeda H, Izumi Y, Koike Y, Koike T, Nakatani K, Hata K, Matsumoto M, Shiomi M, Bamba T.
  NPJ Cardiovasc. Health, 2(1):55, 2025.
  
• eIF2D promotes 40S ribosomal subunit recycling during intrinsic ribosome destabilization.
  Ichihara K, Shiraishi T, Chadani Y, Kito Y, Shiraishi C, Hirata M, Takahashi Y, Kobo A, Hatano A, Matsumoto M, Machida K, Imataka H, Toyoda A, Mishiro-Sato E, Nojima T, Ito T, Taguchi H, Nakayama KI, Matsumoto A.
  Nucleic Acids Res., 53(22):gkaf1322, 2025,
  
• Chemical Digestion-Assisted Proteomics Reveals the Extracellular Matrix Profile of Human Periodontal Ligament and Its Alterations in Cultured Cell-derived Extracellular Matrix.
  Thant L, Dobashi A, Kitami M, Phyu HP, Kobayashi M, Ono Y, Kakihara Y, Matsumoto M, Kaku M.
  Mol. Cell. Proteomics, 24(12):101460, 2025.
  
• Transomic analysis reveals DNA methylation and transcription factor roles in obese liver protein expression.
  Maehara H, Hatano A, Shirai M, Kokaji T, Suzuki Y, Matsumoto M, Egami R, Kubota H, Araki H, Miura F, Ito T, Kuroda S.
  NPJ Syst. Biol. Appl., 11(1):130, 2025.
  
• A robust protocol for proteomic profiling of secreted proteins in conditioned culture medium.
  Otsuka T, Hatano A, Matsumoto M, Matsui H.
  Biol. Methods Protoc., 10(1):bpaf068, 2025,
  
• Plasma steroid profiles in individuals with class II/III obesity: Association with weight loss after metabolic surgery.
  Ibusuki M*, Nakatani K*, Matsuda Y, Umakoshi H, Yokomoto-Umakoshi M, Takayanagi H, Sakamoto R, Kawazoe T, Oki E, Yoshizumi T, Izumi Y, Bamba T, Ogawa Y. (*contributed equally authors)
  J. Endocr. Soc., 9(11):bvaf151, 2025.
  
• Amino acid-dependent TSC2 dephosphorylation by lysosome-PP2A regulates mTORC1 signaling transduction.
  Nakamura T, Nada S, Matsumoto M, Loling Othman N, Kosako H, Ikeda K, Koshikawa N, Masumoto J, Sawasaki T, Takekawa M, Suzuki T, Okada M.
  Life Sci. Alliance., 8(11):e202503206, 2025.
  
• Data-Independent Acquisition (DIA)-Based Label-Free Redox Proteomics (DIALRP) Identifies Prominent Cysteine Oxidations in Translation Machinery in Prostate Cancer Cells Under Oxidative Stress.
  Kobayashi D, Takami T, Matsumoto M.
  J Proteome Res., 24(9):4597-610, 2025.
  
• BCG-derived acellular membrane vesicles elicit antimycobacterial immunity and innate immune memory.
  Yamaguchi T, Samukawa N, Matsumoto S, Shiota M, Matsumoto M, Nakao R, Hirayama S, Yoshida Y, Nishiyama A, Ozeki Y, Tomita S.
  Front Immunol., 16:1534615, 2025.
  
• Alternative Splicing of FBLN2 Generates a Prometastatic Extracellular Matrix in Gastrointestinal Cancers by Determining N-Glycosylation of Fibulin 2.
  Funayama R, Wang Y, Hosogane M, Kao WC, Toyama S, Ohira M, Matsumoto M, Aizawa T, Kobayashi M, Karasawa H, Ohnuma S, Nakayama KI, Unno M, Nakayama K.
  Genes Cells, 30(3):e70027, 2025.
  
• CARM1/PRMT4 facilitates XPF–ERCC1 heterodimer assembly and maintains nucleotide excision repair activity.
  Niida H, Ito M, Iijima K, Motegi A, Ogihara R, Akiyama H, Uchida C, Sakai S, Ohhata T, Hatano A, Hirose M, Ogura A, Matsumoto M, McDonald NQ, Kitagawa M.
  Nucleic Acids Res., 53(8):gkaf355, 2025.
  
• Structural robustness and temporal vulnerability of the starvation-responsive metabolic network in healthy and obese mouse liver.
  Morita K, Hatano A, Kokaji T, Sugimoto H, Tsuchiya T, Ozaki H, Egami R, Li D, Terakawa A, Ohno S, Inoue H, Inaba Y, Suzuki Y, Matsumoto M, Takahashi M, Izumi Y, Bamba T, Hirayama A, Soga T, Kuroda S.
  Sci. Signal., 18(883):eads2547, 2025.
  
• WDR74-mediated ribosome biogenesis and proteome dynamics during mouse preimplantation development.
  Kakihara A, Maemura M, Hatano A, Matsumoto M*, Tsukada Y*. (*corresponding authors)
  Genes Cells, 30(1):e70001, 2025.
  
• jPOST environment accelerates the reuse and reanalysis of public proteome mass spectrometry data.
  Okuda S, Yoshizawa AC, Kobayashi D, Takahashi Y, Watanabe Y, Moriya Y, Hatano A, Takami T, Matsumoto M, Araki N, Tabata T, Iwasaki M, Sugiyama N, Kodera Y, Tanaka S, Goto S, Kawano S, Ishihama Y.
  Nucleic Acids Res., 53(D1):D462-7, 2025.
  

2024

• Time-series transcriptomics reveals distinctive mRNA expression dynamics associated with gene ontology specificity and protein expression in skeletal muscle after electrical stimulation-induced resistance exercise.
  Kusano T, Sotani Y, Takeda R, Hatano A, Kawata K, Kano R, Matsumoto M, Kano Y, Hoshino D.
  FASEB J., 38(22):e70153, 2024.
  
• Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver.
  Pan Y*, Hatano A*, Ohno S, Morita K, Kokaji T, Bai Y, Sugimoto H, Egami R, Terakawa A, Li D, Uematsu S, Maehara H, Fujita S, Inoue H, Inaba Y, Nagano AJ, Hirayama A, Soga T, Kuroda S. (*contributed equally authors)
  NPJ Syst. Biol. Appl., 10(1):107, 2024.
  
• iMPAQT reveals that adequate mitohormesis from TFAM overexpression leads to life extension in mice.
  Igami K, Kittaka H, Yagi M, Gotoh K, Matsushima Y, Ide T, Ikeda M, Ueda S, Nitta SI, Hayakawa M, Nakayama KI, Matsumoto M, Kang D, Uchiumi T.
  Life science alliance, 7(7):e202302498, 2024.
  
• Trans-omic analysis reveals opposite metabolic dysregulation between feeding and fasting in liver associated with obesity.
  Bai Y, Morita K, Kokaji T, Hatano A, Ohno S, Egami R, Pan Y, Li D, Yugi K, Uematsu S, Inoue H, Inaba Y, Suzuki Y, Matsumoto M, Takahashi M, Izumi Y, Bamba T, Hirayama A, Soga T, Kuroda S.
  iScience, 27(3):109121, 2024.
  
• PRMT1 sustains de novo fatty acid synthesis by methylating PHGDH to drive chemoresistance in triple-negative breast cancer.
  Yamamoto T, Hayashida T, Masugi Y, Oshikawa K, Hayakawa N, Itoh M, Nishime C, Suzuki M, Nagayama A, Kawai Y, Hishiki T, Matsuura T, Naito Y, Kubo A, Yamamoto A, Yoshioka Y, Kurahori T, Nagasaka M, Takizawa M, Takano N, Kawakami K, Sakamoto M, Wakui M, Yamamoto T, Kitagawa Y, Kabe Y, Horisawa K, Suzuki A, Matsumoto M, Suematsu M.
  Cancer Res., 84(7):1065-83, 2024.
  
• Effect of Sparc knockout on the extracellular matrix of mouse periodontal ligament cells.
  Arai M, Kaku M, Thant L, Kitami M, Ono Y, Dobashi A, Iwama H, Mizukoshi M, Kitami K, Matsumoto M, Saito I, Uoshima K.
  Biochem. Biophys. Res. Commun., 692:149364, 2024.
• Multiomics analysis of cultured mouse periodontal ligament cell-derived extracellular matrix.
  Kaku M, Thant L, Dobashi A, Ono Y, Kitami M, Mizukoshi M, Arai M, Iwama H, Kitami K, Kakihara Y, Matsumoto M, Saito I, Uoshima K.
  Sci. Rep., 14(1):354, 2024.

2023

• DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle.
  Maehara H, Kokaji T, Hatano A, Suzuki Y, Matsumoto M, Nakayama KI, Egami R, Tsuchiya T, Ozaki H, Morita K, Shirai M, Li D, Terakawa A, Uematsu S, Hironaka KI, Ohno S, Kubota H, Araki H, Miura F, Ito T, Kuroda S.
  Sci. Rep., 13(1):19118, 2023.
• A stepwise and digital pattern of RSK phosphorylation determines the outcome of thymic selection.
  Funasaki S, Hatano A, Nakatsumi H, Koga D, Sugahara O, Yumimoto K, Baba M, *Matsumoto M, *Nakayama KI.　(*corresponding authors)
  iScience, 26(9):107552, 2023.
• The ASC-1 complex promotes translation initiation by scanning ribosomes.
  Kito Y, Matsumoto A, Ichihara K, Shiraishi C, Tang R, Hatano A, Matsumoto M, Han P, Iwasaki S, Nakayama KI.
  EMBO J., 42(12):e112869, 2023.
• RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function.
  Shiraishi C, Matsumoto A, Ichihara K, Yamamoto T, Yokoyama T, Mizoo T, Hatano A, Matsumoto M, Tanaka Y, Matsuura-Suzuki E, Iwasaki S, Matsushima S, Tsutsui H, Nakayama KI.
  Nature Commun., 14(1):2131, 2023.
• Monitoring autophagic flux in vivo revealed its physiological response and significance of heterogeneity in pancreatic beta cells.
  Aoyama S, Nishida Y, Uzawa H, Himuro M, Kanai A, Ueki K, Ito M, Iida H, Tanida I, Miyatsuka T, Fujitani Y, Matsumoto M, Watada H.
  Cell Chem. Biol. , 30(6):658-71.e4, 2023.
• In situ digestion of alcohol-fixed cells for quantitative proteomics.
  Hatano A, Takami T, Matsumoto M.
  J Biochem. , 173(4):243-54, 2023.
• Phosphorylation of PBX2, a novel downstream target of mTORC1, is determined by GSK3 and PP1.
  Wada R, Fujinuma S, Nakatsumi H, Matsumoto M, Nakayama KI.
  J Biochem. , 173(2):129-38, 2023.

2022

• LIGHTHOUSE illuminates therapeutics for a variety of diseases including COVID-19.
  Shimizu H, Kodama M, Matsumoto M, Orba Y, Sasaki M, Sato A, Sawa H, Nakayama KI.
  iScience 25(11): 105314, 2022.
• AT-hook DNA-binding motif-containing protein one knockdown downregulates EWS-FLI1 transcriptional activity in Ewing's sarcoma cells.
  Kitagawa T, Kobayashi D, Baron B, Okita H, Miyamoto T, Takai R, Paudel D, Ohta T, Asaoka Y, Tokunaga M, Nakagawa K, Furutani-Seiki M, Araki N, Kuramitsu Y, Kobayashi M.
  PLoS One 17(10):e0269077, 2022.
• SPP1 Derived from Macrophages Is Associated with a Worse Clinical Course and Chemo-Resistance in Lung Adenocarcinoma.
  Matsubara E, Komohara Y, Esumi S, Shinchi Y, Ishizuka S, Mito R, Pan C, Yano H, Kobayashi D, Fujiwara Y, Ikeda K, Sakagami T, Suzuki M.
  Cancers 14(18):4374, 2022.
• Water droplet-in-oil digestion method for single-cell proteomics.
  Masuda T, Inamori Y, Furukawa A, Yamahiro M, Momosaki K, Chang CH, Kobayashi D, Ohguchi H, Kawano Y, Ito S, Araki N, Ong SE, Ohtsuki S.
  Anal. Chem. 94(29):10329-36, 2022.
• HSF1 phosphorylation establishes an active chromatin state via the TRRAP–TIP60 complex and promotes tumorigenesis.
  Fujimoto M, Takii R, Matsumoto M, Okada M, Nakayama KI, Nakato R, Fujiki K, Shirahige K, Nakai A.
  Nature Commun. 13(1):4355, 2022.
• In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states.
  Kokaji T, Eto M, Hatano A, Yugi K, Morita K, Ohno S, Fujii M, Hironaka KI, Ito Y, Egami R, Uematsu S, Terakawa A, Pan Y, Maehara H, Li D, Bai Y, Tsuchiya T, Ozaki H, Inoue H, Kubota H, Suzuki Y, Hirayama A, Soga T, Kuroda S.
  Sci. Rep. 12(1):13719, 2022.
• Multi-omics-based label-free metabolic flux inference reveals obesity-associated dysregulatory mechanisms in liver glucose metabolism.
  Uematsu S, Ohno S, Tanaka KY, Hatano A, Kokaji T, Ito Y, Kubota H, Hironaka KI, Suzuki Y, Matsumoto M, Nakayama KI, Hirayama A, Soga T, Kuroda S.
  iScience 25(2):103787, 2022.
• Meta-analysis of transcriptional regulatory networks for lipid metabolism in neural cells from schizophrenia patients based on an open-source intelligence approach.
  Okamoto L, Watanabe S, Deno S, Nie X, Maruyama J, Tomita M, Hatano A, Yugi K.
  Neurosci. Res. 175:82-97, 2022.

2021

• Candesartan prevents arteriopathy progression in cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy model.
  Kato T, Manabe RI, Igarashi H, Kametani F, Hirokawa S, Sekine Y, Fujita N, Saito S, Kawashima Y, Hatano Y, Ando S, Nozaki H, Sugai A, Uemura M, Fukunaga M, Sato T, Koyama A, Saito R, Sugie A, Toyoshima Y, Kawata H, Murayama S, Matsumoto M, Kakita A, Hasegawa M, Ihara M, Kanazawa M, Nishizawa M, Tsuji S, Onodera O.
  J. Clin. Invest. 131(22):e140555, 2021.
• The bioactive peptide SL-13R expands human umbilical cord blood hematopoietic stem and progenitor cells in vitro.
  Nii T, Konno K, Matsumoto M, Bhukhai K, Borwornpinyo S, Sakai K, Hongeng S, Sugiyama D.
  Molecules 26(7):1995, 2021.
• An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liver.
  Matsuzaki F, Uda S, Yamauchi Y, Matsumoto M, Soga T, Maehara K, Ohkawa Y, Nakayama KI, Kuroda S, Kubota H.
  Cell Reports 36(8):109569, 2021.
• A ubiquitin-like protein encoded by the "noncoding" RNA TINCR promotes keratinocyte proliferation and wound healing.
  Nita A, Matsumoto A, Tang R, Shiraishi C, Ichihara K, Saito D, Suyama M, Yasuda T, Tsuji G, Furue M, Katayama B, Ozawa T, Murata T, Dainichi T, Kabashima K, Hatano A, Matsumoto M, Nakayama KI.
  PLoS Genet. 17(8):e1009686, 2021.
• Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle.
  Egami R, Kokaji T, *Hatano A, Yugi K, Eto M, Morita K, Ohno S, Fujii M, Hironaka K, Uematsu S, Terakawa A, Bai Y, Pan Y, Tsuchiya T, Ozaki H, Inoue H, Uda S, Kubota H, Suzuki Y, Matsumoto M, Nakayama KI, Hirayama A, Soga T, Kuroda S. (*co-first author)
  iScience 24(3):102217, 2021.
• Senolysis by glutaminolysis inhibition ameliorates various age-associated disorders.
  Johmura Y, Yamanaka T, Omori S, Wang T, Sugiura Y, Matsumoto M, Suzuki N, Kumamoto S, Yamaguchi K, Hatakeyama S, Takami T, Yamaguchi R, Shimizu E, Ikeda K, Okahashi N, Mikawa R, Suematsu M, Arita M, Sugimoto M, Nakayama KI, Furukawa Y, Imoto S, Nakanishi M.
  Science 371(6526): 265-70, 2021.

2020

• Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity.
  Kokaji T, *Hatano A, Ito Y, Yugi K, Eto M, Morita K, Ohno S, Fujii M, Hironaka KI, Egami R, Terakawa A, Tsuchiya T, Ozaki H, Inoue H, Uda S, Kubota H, Suzuki Y, Ikeda K, Arita M, Matsumoto M, Nakayama KI, Hirayama A, Soga T, Kuroda S. (*co-first author)
  Sci. Signal. 13(660):eaaz1236, 2020.
• Trans-omic Analysis Reveals ROS-Dependent Pentose Phosphate Pathway Activation after High-Frequency Electrical Stimulation in C2C12 Myotubes.
  Hoshino D, Kawata K, Kunida K, Hatano A, Yugi K, Wada T, Fujii M, Sano T, Ito Y, Furuichi Y, Manabe Y, Suzuki Y, Fujii NL, Soga T, Kuroda S.
  iScience 23(10): 101558, 2020.
• A phospho-switch controls RNF43-mediated degradation of Wnt receptors to suppress tumorigenesis.
  Tsukiyama T, Zou J, Kim J, Ogamino S, Shino Y, Masuda T, Merenda A, Matsumoto M, Fujioka Y, Hirose T, Terai S, Takahashi H, Ishitani T, Nakayama KI, Ohba Y, Koo BK. and Hatakeyama S.
  Nature Commun. Article number: 4586, 2020.
• Chemical acetylation of mitochondrial transcription factor A occurs on specific lysine residues and affects its ability to change global DNA topology.
  Fang Y, Akimoto M, Mayanagi K, Hatano A, Matsumoto M, Matsuda S, Yasukawa T, Kang D.
  Mitochondrion 53:99-108, 2020.
• The Autism-Related Protein SETD5 Controls Neural Cell Proliferation through Epigenetic Regulation of rDNA Expression.
  Nakagawa T, Hattori S, Nobuta R, Kimura R, Nakagawa M, Matsumoto M, Nagasawa Y, Funayama R, Miyakawa T, Inada T, Osumi N, Nakayama KI, Nakayama K.
  iScience 23(4), 2020.
• FTO Demethylates Cyclin D1 mRNA and Controls Cell-Cycle Progression.
  Hirayama M, Wei FY, Chujo T, Oki S, Yakita M, Kobayashi D, Araki N, Takahashi N, Yoshida R, Nakayama H, Tomizawa K.
  Cell Rep. 31(1):107464, 2020.
• Cell cycle-dependent localization of the proteasome to chromatin.
  Kito Y, *Matsumoto M, Hatano A, Takami T, Oshikawa K, Matsumoto A, *Nakayama KI. (*corresponding authors)
  Sci. Rep. 10(1):5801, 2020.
• Cell Stress Induced Stressome Release Including Damaged Membrane Vesicles and Extracellular HSP90 by Prostate Cancer Cells.
  Eguchi T, Sogawa C, Ono K, Matsumoto M, Tran MT, Okusha Y, Lang BJ, Okamoto K, Calderwood SK.
  Cells. 9(3):755, 2020.
• A shift in glutamine nitrogen metabolism contributes to the malignant progression of cancer.
  Kodama M, Oshikawa K, Shimizu H, Yoshioka S, Takahashi M, Izumi Y, Bamba T, Tateishi C, Tomonaga T, *Matsumoto M, *Nakayama KI. (*corresponding authors)
  Nature Commun. 11(1):1320, 2020. PDF
• Tyrosine pre-transfer RNA fragments are linked to p53-dependent neuronal cell death via PKM2.
  Inoue M, Hada K, Shiraishi H, Yatsuka H, Fujinami H, Morisaki I, Nishida Y, Matsubara E, Ishitani T, Hanada R, Matsumoto M, Penninger JM, Ihara K, Hanada T.
  Biochem. Biophys. Res. Commun. 525(3):726-32, 2020.
• The role of Mediator and Little Elongation Complex in transcription termination.
  Takahashi H, Ranjan A, Chen S, Suzuki H, Shibata M, Hirose T, Hirose H, Sasaki K, Abe R, Chen K, He Y, Zhang Y, Takigawa I, Tsukiyama T, Watanabe M, Fujii S, Iida M, Yamamoto J, Yamaguchi Y, Suzuki Y, Matsumoto M, Nakayama KI, Washburn MP, Saraf A, Florens L, Sato S, Tomomori-Sato C, Conaway RC, Conaway JW, Hatakeyama S.
  Nature Commun. 11(1):1063, 2020.
• Novel localizations and interactions of intercellular bridge proteins revealed by proteomic profiling.
  Iwamori T, Iwamori N, Matsumoto M, Imai H, Ono E.
  Biol. Reprod. 102(5):1134-44, 2020.
• In-line sample processing system with an immobilized trypsin-packed fused-silica capillary tube for proteomic analysis of a small number of mammalian cells.
  Hata K, *Izumi Y, Hara T, *Matsumoto M, Bamba T. (*corresponding authors)
  Anal. Chem. 92(4):2997-3005, 2020.
• A fail-safe system to prevent oncogenesis by senescence is targeted by SV40 small T antigen.
  Oshikawa K, *Matsumoto M, Kodama M, Shimizu H, *Nakayama KI. (*corresponding authors)
  Oncogene 39(10):2170-86, 2020. PDF
• Production of BBF2H7‐derived small peptide fragments via endoplasmic reticulum stress‐dependent regulated intramembrane proteolysis.
  Matsuhisa K, Saito A, Cai L, Kaneko M, Okamoto T, Sakaue F, Asada R, Urano F, Yanagida K, Okochi M, Kudo Y, Matsumoto M, Nakayama KI, Imaizumi K.
  FASEB J. 34(1):865-80, 2020.

2019

• The pericentromeric protein shugoshin 2 cooperates with HSF1 in heat shock response and RNA Pol II recruitment.
  Takii R, Fujimoto M, Matsumoto M, Srivastava P, Katiyar A, Nakayama KI, Nakai A.
  EMBO J. 38(24):e102566, 2019.
• Frequent detection of pituitary-derived PrPres in human prion diseases.
  Honda H, Matsumoto M, Shijo M, Hamasaki H, Sadashima S, Suzuki SO, Aishima S, Kai K, Nakayama KI, Sasagasako N, Iwaki T.
  J. Neuropathol. Exp. Neurol. 78(10): 922-9, 2019.
• Tricarboxylic acid cycle activity suppresses acetylation of mitochondrial proteins during early embryonic development in Caenorhabditis elegans.
  Hada K, Hirota K, Inanobe A, Kako K, Miyata M, Araoi S, Matsumoto M, Ohta R, Arisawa M, Daitoku H, Hanada T, Fukamizu A.
  J. Biol. Chem. 294(9): 3091-9, 2019.
• Identification of a specific translational machinery via TCTP-EF1A2 interaction regulating NF1-associated tumor growth by affinity purification and data-independent mass spectrometry acquisition (AP-DIA).
  Kobayashi D, Tokuda T, Sato K, Okanishi H, Nagayama M, Hirayama-Kurogi M, Ohtsuki S, Araki N.
  Mol. Cell. Proteomics 18: 245-62, 2019.
• Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data.
  Kawata K, Yugi K, Hatano A, Kokaji T, Tomizawa Y, Fujii M, Uda S, Kubota H, Matsumoto M, Nakayama KI, Kuroda S.
  Genes Cells 24(1): 82-93, 2019.

2018

• Bcl11b sets pro-T cell fate bysite-specific cofactor recruitment and by repressing Id2 and Zbtb16.
  Hosokawa H, Romero-Wolf M, Yui MA, Ungerbäck J, Quiloan MLG, Matsumoto M, Nakayama KI, Tanaka T, Rothenberg EV.
  Nature Immunol. 19: 1427-40, 2018.
• Transcription factor PU.1 represses and activates gene expression in early T cells by redirecting partner transcription factor binding.
  Hosokawa H, Ungerbäck J, Wang X, Matsumoto M, Nakayama KI, Cohen SM, Tanaka T, Rothenberg EV.
  Immunity 48(6): 1119-34, 2018.
• Identification of the physiological substrates of PDIp, apancreas-specific protein disulfide isomerase family member.
  Fujimoto T, Nakamura O, Saito M, Tsuru A, Matsumoto M, Kohno K, Inaba K, Kadokura H.
  J. Biol. Chem. 293(48): 18421-33, 2018.
• The promise of targeted proteomics for quantitative network biology.
  Matsumoto M (Corresponding author), Nakayama KI.
  Curr. Opin. Biotechnol. 54:88-97, 2018.
• The jPOST environment: an integrated proteomics data repository and database.
  Moriya Y, Kawano S, Okuda S, Watanabe Y, Matsumoto M, Takami T, Kobayashi D, Yamanouchi Y, Araki N, Yoshizawa AC, Tabata T, Iwasaki M, Sugiyama N, Tanaka S, Goto S, Ishihama Y.
  Nucleic Acids Res. 47(D1): D1218-24, 2018.
• Isocitrate dehydrogenase gene mutations and 2-Hydroxyglutarate accumulation in esophageal squamous cell carcinoma.
  Keisuke M, Baba Y, Ishimoto T, Hiyoshi Y, Iwatsuki M, Miyamoto Y, Yoshida N, Watanabe M, Ogata Y, Nagayama M, Silsirivanit A, Kobayashi D, Araki N, Baba H.
  Med. Oncol. 36: 11, 2018.
• Trans-omic analysis reveals selective responses to induced and basal insulin across signaling, transcriptional, and metabolic networks.
  Kawata K, Hatano A, Yugi K, Kubota H, Sano T, Fujii M, Tomizawa Y, Kokaji T, Tanaka KY, Uda S, Suzuki Y, Matsumoto M, Nakayama KI, Saitoh K, Kato K, Ueno A. Ohishi M, Hirayama A, Soga T, Kuroda S.
  iScience 7: 212-29, 2018.
• GRWD1 regulates ribosomal protein L23 levels via the ubiquitin-proteasome system.
  Watanabe S, Fujiyama H, Takafuji T, Kayama K, Matsumoto M, Nakayama KI, Yoshida K, Sugimoto N, Fujita M.
  J. Cell Sci. 131: pii: jcs213009, 2018.
• Insulin-like growth factor 1 receptor stabilizes the ETV6-NTRK3 chimeric oncoprotein by blocking its KPC1/Rnf123-mediated proteasomal degradation.
  Tognon CE, Rafn B, Cetinbas NM, Kamura T, Trigo G, Rotblat B, Okumura F, Matsumoto M, Chow C, Davare M, Pollak M, Mayor T, Sorensen PH.
  J. Biol. Chem. 293: 12502-15, 2018.
• Artesunate and chloroquine induce cytotoxic activity on cholangiocarcinoma cells via different cell death mechanisms.
  Guragain D, Seubwai W, Kobayashi D, Silsinivanit A, Vaeteewoottacharn K, Sawanyawisuth K, Wongkham C, Wongkham S, Araki N, Cha'on U.
  Cell. Mol. Biol. 64: 113-8, 2018.
• SIRT7 has a critical role in bone formation by regulating lysine acylation of SP7/Osterix.
  Fukuda M, Yoshizawa T, Karim MF, Sobuz SU, Korogi W, Kobayashi D, Okanishi H, Tasaki M, Ono K, Sawa T, Sato Y, Chirifu M, Masuda T, Nakamura T, Tanoue H, Nakashima K, Kobashigawa Y, Morioka H, Bober E, Ohtsuki S, Yamagata Y, Ando Y, Oike Y, Araki N, Takeda S, Mizuta H, Yamagata K.
  Nature Commun. 9: 2833, 2018.
• PKM1 confers metabolic advantages and promotes cell-autonomous tumor cell growth.
  Morita M, Sato T, Nomura M, Sakamoto Y, Inoue Y, Tanaka R, Ito S, Kurosawa K, Yamaguchi K, Sugiura Y, Takizaki H, Yamashita Y, Katakura R, Sato I, Kawai M, Okada Y, Watanabe H, Kondoh G, Matsumoto S, Kishimoto A, Obata M, Matsumoto M, Fukuhara T, Motohashi H, Suematsu M, Komatsu M, Nakayama KI, Watanabe T, Soga T, Shima H, Maemondo M, Tanuma N.
  Cancer Cell 33: 355-67.e7, 2018.
• Brain-derived neurotrophic factor improves limited exercise capacity in mice with heart failure.
  Matsumoto J, Takada S, Kinugawa S, Furihata T, Nambu H, Kakutani N, Tsuda M, Fukushima A, Yokota T, Tanaka S, Takahashi H, Watanabe M, Hatakeyama S, Matsumoto M, Nakayama KI, Otsuka Y, Sabe H, Tsutsui H, Anzai T.
  Circulation 138: 2064-6, 2018.
• Ribosome Incorporation into Somatic Cells Promotes Lineage Transdifferentiation towards Multipotency.
  Ito N, Katoh K, Kushige H, Saito Y, Umemoto T, Matsuzaki Y, Kiyonari H, Kobayashi D, Soga M, Era T, Araki N, Furuta Y, Suda T, Kida Y, Ohta K.
  Sci. Rep. 8: 1634, 2018.

2017

• Noncanonical pathway for regulation of CCL2 expression by an mTORC1-FOXK1 axis promotes recruitment of tumor-associated macrophages.
  Nakatsumi H, Matsumoto M, Nakayama KI.
  Cell Rep. 21: 2471-86, 2017.
• Sez6l2 regulates phosphorylation of ADD and neuritogenesis.
  Yaguchi H, Yabe I, Takahashi H, Watanabe M, Nomura T, Kano T, Matsumoto M, Nakayama KI, Watanabe M, Hatakeyama S.
  Bioche. Biophys. Res. Commun. 494: 234-41, 2017.
• Heat shock protein 70 inhibitors suppress androgen receptor expression in LNCaP95 prostate cancer cells.
  Kita K, Shiota M, Tanaka M, Otsuka A, Matsumoto M, Kato M, Tamada S, Iwao H, Miura K, Nakatani T, Tomita S.
  Cancer Sci. 108: 1820-7, 2017.
• Robotic crowd biology with Maholo LabDroids.
  Yachie N; Robotic Biology Consortium (Inc. Matsumoto M), Natsume T.
  Nature Biotechnol. 35: 310-2, 2017.
• Small nucleolar noncoding RNA SNORA23, up-regulated in human pancreatic ductal adenocarcinoma, regulates expression of spectrin repeat-containing nuclear envelope 2 to promote growth and metastasis of xenograft tumors in mice.
  Cui L, Nakano K, Obchoei S, Setoguchi K, Matsumoto M, Yamamoto T, Obika S, Shimada K, Hiraoka N.
  Gastroenterology 153: 292-306.e2, 2017.
• A large-scale targeted proteomics assay resource based on an in vitro human proteome.
  Matsumoto M, Matsuzaki F, Oshikawa K, Goshima N, Mori M, Kawamura Y, Ogawa K, Fukuda E, Nakatsumi H, Natsume T, Fukui K, Horimoto K, Nagashima T, Funayama R, Nakayama K, Nakayama KI.
  Nature Methods 14: 251-8, 2017.
• Identification of KIAA1210 as a novel X-chromosome-linked protein that localizes to the acrosome and associates with the ectoplasmic specialization in testes.
  Iwamori T, Iwamori N, Matsumoto M, Ono E, Matzuk MM.
  Biol. Reprod. 96: 469-77, 2017.
• mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide.
  Matsumoto A, *Pasut A, *Matsumoto M (*equally contributed), *Yamashita R, Fung J, Monteleone E, Saghatelian A, Nakayama KI, Clohessy JG, Pandolfi PP.
  Nature 541: 228-32, 2017.
• jPOSTrepo: an international standard data repository for proteomes.
  Okuda S, Watanabe Y, Moriya Y, Kawano S, Yamamoto T, Matsumoto M, Takami T, Kobayashi D, Araki N, Yoshizawa AC, Tabata T, Sugiyama N, Goto S, Ishihama Y.
  Nucleic Acids Res. 45(D1): D1107-11, 2017.
• GRWD1 negatively regulates p53 via the RPL11-MDM2 pathway and promotes tumorigenesis.
  Kayama K, Watanabe S, Takafuji T, Tsuji T, Hironaka K, Matsumoto M, Nakayama KI, Enari M, Kohno T, Shiraishi K, Kiyono T, Yoshida K, Sugimoto N, Fujita M.
  EMBO Rep. 18: 123-37, 2017.

2016

• The novel heart-specific RING finger protein 207 is involved in energy metabolism in cardiomyocytes.
  Mizushima W, Takahashi H, Watanabe M, Kinugawa S, Matsushima S, Takada S, Yokota T, Furihata T, Matsumoto J, Tsuda M, Chiba I, Nagashima S, Yanagi S, Matsumoto M, Nakayama KI, Tsutsui H, Hatakeyama S.
  J. Mol. Cell. Cardiol. 100: 43-53, 2016.
• Phosphoproteomics analyses show subnetwork systems in T-cell receptor signaling.
  Hatano A, Matsumoto M, Nakayama KI.
  Genes Cells 21: 1095-112, 2016.
• Inhibition of the Arabidopsis bHLH transcription factor by monomerization through abscisic acid-induced phosphorylation.
  Takahashi Y, Kinoshita T, Matsumoto M, Shimazaki K.
  Plant J. 87: 559-67, 2016.
• Protection of stromal cell-derived factor 2 by heat shock protein 72 prevents oxaliplatin-induced cell death in oxaliplatin-resistant human gastric cancer cells.
  Takahashi K, Tanaka M, Yashiro M, Matsumoto M, Ohtsuka A, Nakayama KI, Izumi Y, Nagayama K, Miura K, Iwao H, Shiota M.
  Cancer Lett. 378: 8-15, 2016.
• Akt1-mediated Gata3 phosphorylation controls the repression of IFNγ in memory-type Th2 cells.
  Hosokawa H, Tanaka T, Endo Y, Kato M, Shinoda K, Suzuki A, Motohashi S, Matsumoto M, Nakayama KI, Nakayama T.
  Nature Commun. 7: 11289, 2016.
• Ribophorin II is involved in the tissue factor expression mediated by phosphatidylserine-dependent antiprothrombin antibody on monocytes.
  Fujieda Y, Amengual O, Matsumoto M, Kuroki K, Takahashi H, Kono M, Kurita T, Otomo K, Kato M, Oku K, Bohgaki T, Horita T, Yasuda S, Maenaka K, Hatakeyama S, Nakayama KI, Atsumi T.
  Rheumatology (Oxford) 55: 1117-26, 2016.
• Identification of low-abundance proteins in serum via the isolation of HSP72 complexes.
  Tanaka M, Shiota M, Nakao T, Uemura R, Nishi S, Ohkawa Y, Matsumoto M, Yamaguchi M, Osada-Oka M, Inagaki A, Takahashi K, Nakayama KI, Gi M, Izumi Y, Miura K, Iwao H.
  J. Proteomics 136: 214-21, 2016.
• Truncation mutants of ASXL1 observed in myeloid malignancies are expressed at detectable protein levels.
  Inoue D, Matsumoto M, Nagase R, Saika M, Fujino T, Nakayama KI, Kitamura T.
  Exp. Hematol. 44: 172-6, 2016.
• Trans-omics: how to reconstruct biochemical networks across multiple ‘omic’layers.
  Yugi K, Kubota H, Hatano A, Kuroda S.
  Trends. Biotechnol. 34 (4), 276-90, 2016.
• Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin.
  Sano T, Kawata K, Ohno S, Yugi K, Kakuda H, Kubota H, Uda S, Fujii M, Kunida K, Hoshino D, Hatano A, Ito Y, Sato M, Suzuki Y, Kuroda S.
  Sci. Signal. 22(9): ra112, 2016.

2015

• UV damage-induced phosphorylation of HBO1 triggers CRL4DDB2-mediated degradation to regulate cell proliferation.
  Matsunuma R, Niida H, Ohhata T, Kitagawa K, Sakai S, Uchida C, Shiotani B, Matsumoto M, Nakayama KI, Ogura H, Shiiya N, Kitagawa M.
  Mol. Cell Biol. 36: 394-406, 2015.
• Tissue-specific expression of histone H3 variants diversified after species separation.
  Maehara K, Harada A, Sato Y, Matsumoto M, Nakayama KI, Kimura H, Ohkawa Y.
  Epigenetics Chromatin 8: 35, 2015.
• Methylation of Gata3 protein at Arg-261 regulates transactivation of the Il5 gene in T helper 2 cells.
  Hosokawa H, Kato M, Tohyama H, Tamaki Y, Endo Y, Kimura MY, Tumes DJ, Motohashi S, Matsumoto M, Nakayama KI, Tanaka T, Nakayama T.
  J. Biol. Chem. 290: 13095-103, 2015.
• Overexpression of Ephrin A2 receptors in cancer stromal cells is a prognostic factor for the relapse of gastric cancer.
  Kikuchi S, Kaibe N, Morimoto K, Fukui H, Niwa H, Maeyama Y, Takemura M, Matsumoto M, Nakamori S, Miwa H, Hirota S, Sasako M.
  Gastric Cancer 18: 485-94, 2015.
• Up-regulation of DRP-3 long isoform during the induction of neural progenitor cells by glutamate treatment in the ex vivo rat retina.
  Tokuda K, Kuramitsu Y, Byron B, Kitagawa T, Tokuda N, Kobayashi D, Nagayama M, Araki N, Sonoda KH, Nakamura K.
  Biochem. Biophys. Res. Commun. 463: 593-9, 2015.

2014

• Reconstruction of insulin signal flow from phosphoproteome and metabolome data.
  Yugi K, Kubota H, Toyoshima Y, Noguchi R, Kawata K, Komori Y, Uda S, Kunida K, Tomizawa Y, Funato Y, Miki H, Matsumoto M, Nakayama KI, Kashikura K, Endo K, Ikeda K, Soga T, Kuroda S.
  Cell Rep. 8: 1171-83, 2014.
• ZFP36L1 and ZFP36L2 control LDLR mRNA stability via the ERK-RSK pathway.
  Adachi S, Homoto M, Tanaka R, Hioki Y, Murakami H, Suga H, Matsumoto M, Nakayama KI, Hatta T, Iemura S, Natsume T.
  Nucleic Acids Res. 42: 10037-49, 2014.
• Translationally controlled tumor protein is a novel biological target for neurofibromatosis type 1(NF1)-associated tumors.
  Kobayashi D, Hirayama M, Komohara Y, Mizuguchi S, Wilson Morifuji M, Ihn H, Takeya M, Kuramochi A, Araki N.
  J. Biol. Chem. 289(38): 26314-26, 2014.
• Fbw7 targets GATA3 through cyclin-dependent kinase 2-dependentproteolysis and contributes to regulation of T-cell development.
  Kitagawa K, Shibata K, Matsumoto A, Matsumoto M, Ohhata T, Nakayama KI, Niida H, Kitagawa M.
  Mol. Cell Biol. 34: 2732-44, 2014.
• Structural elucidation of an asparagine-linked oligosaccharide from the hyperthermophilic archaeon, Pyrococcus furiosus.
  Fujinami D, Matsumoto M, Noguchi T, Sonomoto K, Kohda D.
  Carbohydr Res. 387: 30-6, 2014.
• Identification of anti-Sez6l2 antibody in a patient with cerebellar ataxia and retinopathy.
  Yaguchi H, Yabe I, Takahashi H, Okumura F, Takeuchi A, Horiuchi K, Kano T, Kanda A, Saito W, Matsumoto M, Nakayama KI, Hatakeyama S, Sasaki H.
  J. Neurol. 261: 224-6, 2014.

2013

• Phosphorylation of Noxo1 at threonine 341 regulates its interaction with Noxa1 and the superoxide-producing activity of Nox1.
  Yamamoto A, Takeya R, Matsumoto M, Nakayama KI, Sumimoto H.
  FEBS J. 280: 5145-59, 2013.
• F-box and WD repeat domain-containing-7 (Fbxw7) protein targets endoplasmic reticulum-anchored osteogenic and chondrogenic transcriptional factors for degradation.
  Yumimoto K, Matsumoto M, Onoyama I, Imaizumi K, Nakayama KI.
  J. Biol. Chem. 288: 28488-502, 2013.
• Integrated proteomics identified novel activation of dynein IC2-GR-COX-1 signaling in neurofibromatosis type I (NF1) disease model cells.
  *Hirayama M, *Kobayashi D(*co-first authors), Mizuguchi S, Morikawa T, Nagayama M, Midorikawa U, Wilson MM, Nambu AN, Yoshizawa AC, Kawano S, Araki N.
  Mol. Cell. Proteomics 12: 1377-94, 2013.
• FBXL21 regulates oscillation of the circadian clock through ubiquitination and stabilization of cryptochromes.
  Hirano A, Yumimoto K, Tsunematsu R, Matsumoto M, Oyama M, Kozuka-Hata H, Nakagawa T, Lanjakornsiripan D, Nakayama KI, Fukada Y.
  Cell 152: 1106-18, 2013.
• Glioma initiaing cells form a differentiation niche via the induction of extra cellular matrices and integrin alpha V.
  Niibori-Nambu A, Midorikawa U, Mizuguchi S, Hide T, Nagai M, Komohara Y, Nagayama M, Hirayama M, Kobayashi D, Tsubota N, Takezaki T, Makino K, Nakamura H, Takeya M, Kuratsu J, Araki N.
  PLOS ONE 8: e59558, 2013.

2012

• A strategy for large-scale phosphoproteomics and SRM-based validation of human breast cancer tissue samples.
  Narumi R, Murakami T, Kuga T, Adachi J, Shiromizu T, Muraoka S, Kume H, Kodera Y, Matsumoto M, Nakayama K, Miyamoto Y, Ishitobi M, Inaji H, Kato K, Tomonaga T.
  J. Proteome Res. 11: 5311-22, 2012.
• Crystal structure of the C-terminal globular domain of oligosaccharyltransferase from Archaeoglobus fulgidus at 1.75 Å resolution.
  Matsumoto S, Igura M, Nyirenda J, Matsumoto M, Yuzawa S, Noda N, Inagaki F, Kohda D.
  Biochemistry 51: 4157-66, 2012.
• Comprehensive identification of substrates for F-box proteins by differential proteomics analysis.
  Yumimoto K, Matsumoto M, Oyamada K, Moroishi T, Nakayama KI.
  J. Proteome Res. 11: 3175-85, 2012.
• Chk1 phosphorylates the tumour suppressor Mig-6, regulating the activation of EGF signaling.
  Liu N, Matsumoto M, Kitagawa K, Kotake Y, Suzuki S, Shirasawa S, Nakayama KI, Nakanishi M, Niida H, Kitagawa M.
  EMBO J. 31: 2365-77, 2012.
• Genetic reevaluation of the role of F-box proteins in cyclin D1 degradation.
  Kanie T, Onoyama I, Matsumoto A, Yamada M, Nakatsumi H, Tateishi Y, Yamamura S, Tsunematsu R, Matsumoto M, Nakayama KI.
  Mol. Cell. Biol. 32: 590-605, 2012.
• Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin.
  Oshikawa K, Matsumoto M, Oyamada K, Nakayama KI.
  J. Proteome Res. 11: 796-807, 2012.

2011

• Protrudin serves as an adaptor molecule that connects KIF5 and its cargoes in vesicular transport during process formation.
  Matsuzaki F, Shirane M, Matsumoto M, Nakayama KI.
  Mol. Biol. Cell 22: 4602-20, 2011.
• TRIM8 regulates Nanog via Hsp90β-mediated nuclear translocation of STAT3 in embryonic stem cells.
  Okumura F, Okumura AJ, Matsumoto M, Nakayama KI, Hatakeyama S.
  Biochim. Biophys. Acta. 181: 1784-92, 2011.
• Functional analyses of the activation loop of phototropin2 in Arabidopsis.
  Inoue S, Matsushita T, Tomokiyo Y, Matsumoto M, Nakayama KI, Kinoshita T, Shimazaki K.
  Plant Physiol. 156: 117-28, 2011.
• Proteome of ubiquitin/MVB pathway: possible involvement of iron-induced ubiquitylation of transferrin receptor in lysosomal degradation.
  Tachiyama R, Ishikawa D, Matsumoto M, Nakayama KI, Yoshimori T, Yokota S, Himeno M, Tanaka Y, Fujita H.
  Genes Cells 16: 448-66, 2011.
• Plasma gelsolin facilitates interaction between β2 glycoprotein I and α5β1 integrin.
  Bohgaki M, Matsumoto M, Atsumi T, Kondo T, Yasuda S, Horita T, Nakayama KI, Okumura F, Hatakeyama S, Koike T.
  J. Cell Mol. Med. 15: 141-51, 2011

2010

• Human proteins that specifically bind to 8-oxoguanine-containing RNA and their responses to oxidative stress.
  Hayakawa H, Fujikane A, Ito R, Matsumoto M, Nakayama KI, Sekiguchi M.
  Biochem Biophys Res. Commun. 403: 220-4, 2010.
• Comparative analysis of human SRC-family kinase substrate specificity in vitro.
  Takeda H, Kawamura Y, Miura A, Mori M, Wakamatsu A, Yamamoto J, Isogai T, Matsumoto M, Nakayama KI, Natsume T, Nomura N, Goshima N.
  J. Proteome Res. 9: 5982-93, 2010.
• Nedd4-interacting protein 2, a short half-life membrane protein degraded in lysosomes, negatively controls down-regulation of connexin43.
  Ohzono C, Etoh S, Matsumoto M, Nakayama KI, Hirota Y, Tanaka Y, Fujita H.
  Biol. Pharm. Bull. 33: 951-7, 2010.
• Fbxo45, a novel ubiquitin ligase, regulates synaptic activity.
  Tada H, Okano HJ, Takagi H, Shibata S, Yao I, Matsumoto M, Saiga T, Nakayama KI, Kashima H, Takahashi T, Setou M, Okano H.
  J. Biol. Chem. 285: 3840-9, 2010.
• Phosphorylation of the chromodomain changes the binding specificity of Cbx2 for methylated histone H3.
  Hatano A, Matsumoto M, Higashinakagawa T, Nakayama KI.
  Biochem. Biophys. Res. Commun. 397: 93-9, 2010.

1993-2009

• Large-scale proteomic analysis of tyrosine-phosphorylation induced by T-cell receptor or B-cell receptor activation reveals new signaling pathways.
  Matsumoto M, Oyamada K, Takahashi H, Sato T, Hatakeyama S, Nakayama KI.
  Proteomics 9: 3549-63, 2009.
• An integrated approach of differential mass spectrometry and gene ontology analysis identified novel proteins regulating neuronal differentiation and survival.
  Kobayashi D, Kumagai J, Morikawa T, Wilson-Morifuji M, Wilson A, Irie A, Araki N.
  Mol. Cell. Proteomics 8: 2350-67, 2009.
• Fbxo45 forms a novel ubiquitin ligase complex and is required for neuronal development.
  Saiga T, Fukuda T, Matsumoto M, Tada H, Okano HJ, Okano H, Nakayama KI.
  Mol. Cell Biol. 29: 3529-43, 2009.
• Nucleolar structure and function are regulated by the deubiquitylating enzyme USP36.
  Endo A, Matsumoto M, Inada T, Yamamoto A, Nakayama KI, Kitamura N, Komada M.
  J. Cell Sci. 122 (Pt 5): 678-86, 2009.
• oleed, a medaka Polycomb group gene, regulates ciliogenesis and left–right patterning.
  Arai D, Hatano A, Higashinakagawa T.
  Genes Cells 14(12): 1359-67, 2009.
• CHD8 suppresses p53-mediated apoptosis through histone H1 recruitment during early embryogenesis.
  Nishiyama M, Oshikawa K, Tsukada Y, Nakagawa T, Iemura S, Natsume T, Fan Y, Kikuchi A, Skoultchi AI, Nakayama KI.
  Nature Cell Biol. 11(2): 172-82, 2009.
• Dynamic regulation of ubiquitylation and deubiquitylation at the central spindle during cytokinesis.
  Mukai A, Mizuno E, Kobayashi K, Matsumoto M, Nakayama KI, Kitamura N, Komada M.
  J. Cell Sci. 121 (Pt 8):1325-33, 2008.
• Blue light-induced autophosphorylation of phototropin is a primary step for signaling.
  Inoue S, Kinoshita T, Matsumoto M, Nakayama KI, Doi M, Shimazaki K.
  Proc. Natl. Acad. Sci. U. S. A. 105: 5626-31, 2008.
• Neurofibromatosis type 1 (NF1) tumor suppressor, neurofibromin, regulates the neuronal differentiation of PC12 cells via its associating protein, CRMP-2.
  Patrakitkomjorn S, Kobayashi D, Morikawa T, Wilson MM, Tsubota N, Irie A, Ozawa T, Aoki M, Arimura N, Kaibuchi K, Saya H, Araki N.
  J. Biol. Chem. 283(14): 9399-413, 2008.
• Alteration of intra-pancreatic target-organ specificity by abrogation of Aire in NOD mice.
  Niki S, Oshikawa K, Mouri Y, Hirota F, Matsushima A, Yano M, Han H, Bando Y, Izumi K, Matsumoto M, Nakayama KI, Kuroda N, Matsumoto M.
  J. Clin. Invest. 116: 1292-301, 2006.
• Mapping of ubiquitination sites on target proteins.
  Hatakeyama S, Matsumoto M, Nakayama KI.
  Methods Enzymol. 399: 277-86, 2005.
• Mammalian E4 is required for cardiac development and maintenance of the nervous system.
  Kaneko-Oshikawa C, Nakagawa T, Yamada M, Yoshikawa H, Matsumoto M, Yada M, Hatakeyama S, Nakayama K, Nakayama KI.
  Mol. Cell Biol. 25: 10953-64, 2005.
• Large-scale analysis of the human ubiquitin-related proteome.
  Matsumoto M, Hatakeyama S, Oyamada K, Oda Y, Nishimura T, Nakayama KI.
  Proteomics 5: 4145-51, 2005.
• VHL-box and SOCS-box domains determine binding specificity for Cul2-Rbx1 and Cul5-Rbx2 modules of ubiquitin ligases.
  Kamura T, Maenaka K, Kotoshiba S, Matsumoto M, Kohda D, Conaway RC, Conaway JW, Nakayama KI.
  Genes Dev. 18: 3055-65, 2004.
• Cytoplasmic ubiquitin ligase KPC regulates proteolysis of p27(Kip1) at G1 phase.
  Kamura T, Hara T, Matsumoto M, Ishida N, Okumura F, Hatakeyama S, Yoshida M, Nakayama K, Nakayama KI.
  Nature Cell Biol. 6: 1229-35, 2004.
• U-box protein carboxyl terminus of Hsc70-interacting protein (CHIP) mediates poly-ubiquitylation preferentially on four-repeat Tau and is involved in neurodegeneration of tauopathy.
  Hatakeyama S, Matsumoto M, Kamura T, Murayama M, Chui DH, Planel E, Takahashi R, Nakayama KI, Takashima A.
  J. Neurochem. 91: 299-307, 2004.
• Functional regulation of FEZ1 by the U-box-type ubiquitin ligase E4B contributes to neuritogenesis.
  Okumura F, Hatakeyama S, Matsumoto M, Kamura T, Nakayama KI.
  J. Biol. Chem. 279: 53533-43, 2004.
• Interaction of U-box-type ubiquitin-protein ligases (E3s) with molecular chaperones.
  Hatakeyama S, Matsumoto M, Yada M, Nakayama KI.
  Genes Cells 9: 533-48, 2004.
• Molecular clearance of ataxin-3 is regulated by a mammalian E4.
  Matsumoto M, Yada M, Hatakeyama S, Ishimoto H, Tanimura T, Tsuji S, Kakizuka A, Kitagawa M, Nakayama KI.
  EMBO J. 23: 659-69, 2004.
• Preferential interaction of TIP120A with Cul1 that is not modified by NEDD8 and not associated with Skp1.
  Oshikawa K, Matsumoto M, Yada M, Kamura T, Hatakeyama S, Nakayama KI.
  Biochem. Biophys. Res. Commun. 303: 1209-16, 2003
• Characterization of the mouse gene for the U-box-type ubiquitin ligase UFD2a.
  Kaneko C, Hatakeyama S, Matsumoto M, Yada M, Nakayama K, Nakayama KI.
  Biochem. Biophys. Res. Commun. 300: 297-304, 2003.
• Genomic cloning of ribonucleases in Nicotiana glutinosa leaves, as induced in response to wounding or to TMV-infection, and characterization of their promoters.
  Hayashi T, Kobayashi D, Kariu T, Tahara M, Hada K, Kouzuma Y, Kimura M.
  Biosci. Biotechnol. Biochem. 67: 2574-83, 2003.
• U box proteins as a new family of ubiquitin-protein ligases.
  Hatakeyama S, Yada M, Matsumoto M, Ishida N, Nakayama KI.
  J. Biol. Chem. 276: 33111-20, 2001.
• Protein engineering of novel proteinase inhibitors and their effects on the growth of Spodoptera exigua larvae.
  Inanaga H, Kobayashi D, Kouzuma Y, Aoki-Yasunaga C, Iiyama K, Kimura M.
  Biosci. Biotechnol. Biochem. 65: 2259-64, 2001.
• Cell cycle-dependent expression of mammalian E2-C regulated by the anaphase-promoting complex/cyclosome.
  Yamanaka A, Hatakeyama S, Kominami K, Kitagawa M, Matsumoto M, Nakayama K.
  Mol. Biol. Cell 11: 2821-31, 2000.
• Targeted disruption of Skp2 results in accumulation of cyclin E and p27(Kip1), polyploidy and centrosome overduplication.
  Nakayama K, Nagahama H, Minamishima YA, Matsumoto M, Nakamichi I, Kitagawa K, Shirane M, Tsunematsu R, Tsukiyama T, Ishida N, Kitagawa M, Nakayama K, Hatakeyama S.
  EMBO J. 19: 2069-81, 2000.
• High pressure sensitizes murine erythroleukemia cells to caffeine-induced premature mitosis.
  Matsumoto M, Yamaguchi T, Nakazono K, Fukumaki Y, Terada S.
  Jpn. J. Physiol. 50: 329-36, 2000.
• Molecular dissection of the interactions among IkappaBalpha, FWD1, and Skp1 required for ubiquitin-mediated proteolysis of IkappaBalpha.
  Hattori K, Hatakeyama S, Shirane M, Matsumoto M, Nakayama K.
  J. Biol. Chem. 274: 29641-7, 1999.
• An F-box protein, FWD1, mediates ubiquitin-dependent proteolysis of beta-catenin.
  Kitagawa M, Hatakeyama S, Shirane M, Matsumoto M, Ishida N, Hattori K, Nakamichi I, Kikuchi A, Nakayama K, Nakayama K.
  EMBO J. 18: 2401-10, 1999.
• Ubiquitin-dependent degradation of IkappaBalpha is mediated by a ubiquitin ligase Skp1/Cul 1/F-box protein FWD1.
  Hatakeyama S, Kitagawa M, Nakayama K, Shirane M, Matsumoto M, Hattori K, Higashi H, Nakano H, Okumura K, Onoé K, Good RA, Nakayama K.
  Proc. Natl. Acad. Sci. U.S.A. 96: 3859-63, 1999.
• Effects of chemical modification of cysteines 201 and 317 of band 3 on hemolytic properties of human erythrocytes under hydrostatic pressure.
  Yamaguchi T, Nakano T, Matsumoto M, Terada S.
  Jpn. J. Physiol. 48: 205-10, 1998.
• High pressure induces G2 arrest in murine erythroleukemia cells.
  Matsumoto M, Yamaguchi T, Fukumaki Y, Yasunaga R, Terada S.
  J. Biochem. 123: 87-93,1998.
• Effects of intracellular pH on high pressure-induced hemolysis of anion transport inhibitor-treated erythrocytes.
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