Hamano Lab

Peer-reviewed paper
  1. H. Yoshimura, Y. Takeda, Y. Shirai, M. Yamamoto, D. Nakatsubo, S. Amiya, T. Enomoto, R. Hara, Y. Adachi, R. Edahiro, M. Yaga, K. Masuhiro, T. Koba, M. Itoh-Takahashi, M. Nakayama, S. Takata, Y. Hosono, S. Obata, M. Nishide, A. Hata, M. Yanagawa, S. Namba, M. Iwata, M. Hamano, H. Hirata, S, Koyama, K. Iwahori, I. Nagatomo, Y. Suga, K. Miyake, T. Shiroyama, K. Fukushima, S. Futami, Y. Naito, T. Kawasaki, K. Mizuguchi, Y. Kawashima, Y. Yamanishi, J. Adachi, M. Nogami-Itoh, S. Ueki, A. Kumanogoh,Galectin-10 in serum extracellular vesicles reflects asthma pathophysiology. J Allergy Clin Immunol., 14:S0091-6749(24)00128-3. (2024)
  2. M. Hamano, T. Nakamura, R. Ito, Y. Shimada, M. Iwata, J. Takeshita, R. Eguchi, Y. Yamanishi*, DIRECTEUR: Transcriptome-based prediction of small molecules that replace transcription factors for direct cell conversion. Bioinformatics, 25:btae048 (2024)
  3. MM Rashid, M. Hamano, M. Iida, M. Iwata, T. Ko, S. Nomura, I. Komuro, Y. Yamanishi*, Network-based identification of diagnosis-specific trans-omic biomarkers via integration of multiple omics data, Biosystems, 236:105122 (2024)
  4. Z. Dai, T. Ko, K. Fujita, S. Nomura, Y. Uemura, K. Onoue, M. Hamano, M. Katoh, S. Yamada, M. Katagiri, B. Zhang, S. Hatsuse, T. Yamada, S. Inoue, M. Kubota, K. Sawami, T. Heryed, M. Ito, E. Amiya, M. Hatano, N. Takeda, H. Morita, Y. Yamanishi, Y. Saito, I. Komuro*, Myocardial DNA Damage Predicts Heart Failure Outcome in Various Underlying Diseases. JACC Heart Fail. 28:S2213-1779(23)00680-7 (2023)
  5. M. Hamano*, T. Ichinose, T. Yasuda, T. Ishijima, S. Okada, K. Abe, K. Tashiro, S. Furuya*, Bioinformatics Analysis of the Molecular Networks Associated with the Amelioration of Aberrant Gene Expression by a Tyr-Trp Dipeptide in Brains Treated with the Amyloid-β Peptide. (Nutrients. 13;15(12):2731(2023))
  6. S. Yamada†, T. Ko†, M. Ito†, T. Sassa†, S. Nomura†, H. Okuma†, M. Sato†, T. Imasaki, S. Kikkawa, B. Zhang, T. Yamada, Y. Seki, K. Fujita, M. Katoh, M. Kubota, S. Hatsuse, M. Katagiri, H. Hayashi, M. Hamano, N. Takeda, H. Morita, S. Takada, M. Toyoda, M. Uchiyama, M. Ikeuchi, K. Toyooka, A. Umezawa, Y. Yamanishi, R. Nitta, H. Aburatani, I. Komuro*, TEAD1 trapping by the Q353R–Lamin A/C causes dilated cardiomyopathy (Science Advances, 9(15) eade7047(2023))(† co-first author)
  7. Y. Takashima†, M. Hamano†, K. Yoshii†, A. Hayano, J. Fukai, Y. Iwadate, K. Kajiwara, H. Hondoh, R. Yamanaka*, Reciprocal expression of the immune response genes CXCR3 and IFI44L as module hubs are associated with patient survivals in primary central nervous system lymphoma（Int J Clin Oncol., 28(3):468-481(2023)）(† co-first author)
  8. T. Nakamura, M. Iwata, M. Hamano, R. Eguchi, Jun-Ichi Takeshita, Y. Yamanishi*, Small compound-based direct cell conversion with combinatorial optimization of pathway regulations. （Bioinformatics, 38(2): ii99-ii105(2022)）
  9. R. Eguchi, M. Hamano, M. Iwata, T. Nakamura, S. Oki, Y. Yamanishi*, TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach. （Bioinformatics, 13;38(10):2839-2846 (2022)）
  10. M. Hamano，S. Nomura，M. Iida，I. Komuro，Y. Yamanishi*, Prediction of single-cell mechanisms for disease progression in hypertrophic remodelling by a trans-omics approach, (Scientific Reports, 14;11(1):8112 (2021))
  11. M. Hamano*, K. Esaki, K. Moriyasu, T. Yasuda, S. Mohri, K. Tashiro, Y. Hirabayashi and S. Furuya*, Hepatocyte-specific Phgdh deficient mice culminate in mild obesity, insulin resistance, and enhanced vulnerability to protein starvation. (Nutrients, 29;13(10):3468 (2021))
  12. M. Hamano*, S. Tomonaga, Y. Osaki, H. Oda, H. Kato and S. Furuya*, Transcriptional activation of Chac1 and other Atf4-target genes induced by extracellular L-Serine depletion is negated with glycine consumption in Hepa1-6 hepatocarcinoma cells. (Nutrients, 12(10), 3018 (2020))
  13. Y. Takashima, M. Hamano, J. Fukai, Y. Iwadate, K.Kajiwara, T. Kobayashi, H. Hondoh and R. Yamanaka*, GSEA-associated gene signatures are valid for diagnosis of cell-types and prognosis prediction in PCNLS (Scientific Reports, in press (2020))
  14. M. Iwata, L. Yuan, Q. Zhao, Y. Tabei, F. Berenger, R. Sawada, S. Akiyoshi, M. Hamano and Y. Yamanishi*, Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm (Bioinformatics, 15;35(14)191-199, (2019))
  15. M. Hamano*, Y. Haraguchi, T. Sayano, C. Zyao, Y. Arimoto, K. Moriyasu, M. Udono, Y. Katakura, T. Ogawa, H. Kato and S. Furuya, Enhanced vulnerability to oxidative stress and induction of inflammatory gene expression in Phgdh-deficient fibroblasts, (FEBS Open Bio, 8(6):914-922, (2018))
  16. M. Hamano, T. Sayano,W. Kusada, H. Kato, S. Furuya*, Microarray data on altered transcriptional program of Phgdh-deficient mouse embryonic fibroblasts caused by L-serine depletion, (Data in Brief, 7:1598-1601, (2016))
  17. T. Sayano, Y. Kawano,W. Kusada, Y. Arimoto, K. Esaki, M. Hamano, M. Udono, Y. Katakura, T. Ogawa,H. Kato, Y. Hirabayashi, S. Furuya*, Adaptive response to L-serine deficiency is mediated by p38 MAPK activation via 1-deoxysphinganine in normal fibroblasts, (FEBS Open Bio, 6(4):303-316, (2016))

    18. * Corresponding author

Peer-reviewed proceeding paper
    　　　　　　
  1. T. Nakamura, M. Iwata, M. Hamano, R. Eguchi, J. Takeshita, and Y. Yamanishi, Small compound-based direct cell conversion with combinatorial optimization of pathway regulations, 21th European Conference on Computational Biology (Spain, Sep.(2022))
  2. M. Iwata, L. Yuan, Q. Zhao, Y. Tabei, F. Berenger, R. Sawada, S. Akiyoshi, M. Hamano, and Y. Yamanishi, Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm, The 27rd International Conference on Intelligent Systems for Molecular Biology & 18th European Conference on Computational Biology (Switzerland, Jul.(2019))

Book chapter
    　　　　　　
  1. 濱野桃子，岩田通夫，山西芳裕，マルチオミクス解析による細胞リプログラミング誘導因子の推定―パイオニア因子を考慮したデータ駆動型ダイレクトリプログラミング（データ駆動時代の疾患研究 : がん、老化、生活習慣病 : 最新のオミクス統合で挑む標的探索と病態解明 (羊土社) (2023年)）
  2. 江口凌平，濱野桃子，岩田通夫，中村透，山西芳裕，データ駆動型ダイレクトリプログラミング（ダイレクトリプログラミング最前線 (株式会社エヌ・ティー・エヌ) (2020年)）

Available code
    　　　　　　

  1. DIRECTEUR