Publications

Journal papers

Fat Induces Glucose Metabolism in Nontransformed Liver Cells and Promotes Liver Tumorigenesis;
L. A. Broadfield, J. A. G. Duarte, R. Schmieder, D. Broekaert, K. Veys, M. Planque, K. Vriens, Y. Karasawa, F. Napolitano, S. Fujita, M. Fujii, M. Eto, B. Holvoet, R. Vangoitsenhoven, J. Fernandez-Garcia, J. van Elsen, J. Dehairs, J. Zeng, J. Dooley, R. Alba Rubio, J. van Pelt, T. G.P. Grünewald, A. Liston, C. Mathieu, C. M. Deroose, J. V. Swinnen, D. Lambrechts, D. D. Bernardo, S. Kuroda, K. De Bock, S. Fendt,
Cancer Research (2021) Vol.81, 1988
Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle;
R. Egami, T. Kokaji, A. Hatano, K. Yugi, M. Eto, K. Morita, S. Ohno, M. Fujii, K. Hironaka, S. Uematsu, A. Terakawa, Y. Bai, Y. Pan, T. Tsuchiya, H. Ozaki, H. Inoue, S. Uda, H. Kubota, Y. Suzuki, M. Matsumoto, K. I. Nakayama, A. Hirayama, T. Soga, S. Kuroda,
iScience (2021) Vol.24, 102217
Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity;
T. Kokaji, A. Hatano, Y. Ito, K. Yugi, M. Eto, K. Morita, S. Ohno, M. Fujii, K. Hironaka, R. Egami, A. Terakawa, T. Tsuchiya, H. Ozaki, H. Inoue, S. Uda, H. Kubota, Y. Suzuki, K. Ikeda, M. Arita, M. Matsumoto, K. I. Nakayama, A. Hirayama, T. Soga, S. Kuroda,
Science Signaling (2020) Vol.13, eaaz1236
Spontaneous organizations of diverse network structures in coupled logistic maps with a delayed connection change;
A. Ohara, M. Fujii, A. Awazu,
Journal of Physical Society of Japan (2020) Vol.89, 114801
Single-cell information analysis reveals that skeletal muscles incorporate cell-to-cell variability as information not noise;
T. Wada, K. Hironaka, M. Wataya, M. Fujii, M. Eto, S. Uda, D. Hoshino, K. Kunida, H. Inoue, H. Kubota, T. Takizawa, Y. Karasawa, H. Nakatomi, N. Saito, H. Hamaguchi, Y. Furuichi, Y. Manabe, N. L. Fujii, S. Kuroda,
Cell Reports (2020) Vol. 32, 108051
Trans-omic analysis reveals Ros-dependent pentose phosphate pathway activation after high-frequency electrical stimulation in C2C12 myotubes;
D. Hoshino, K. Kawata, K. Kunida, A. Hatano, K. Yugi, T. Wada, M. Fujii, T. Sano, Y. Ito, Y. Furuichi, Y. Manabe, Y. Suzuki, N. L. Fujii, T. Soga, S. Kuroda,
iScience (2020) Vol. 23, 101558
Monitoring and mathematical modeling of mitochondrial ATP in myotubes at single-cell level reveals two distinct population with different kinetics;
N. Matsuda, K. Hironaka, M. Fujii, T. Wada, K. Kunida, H. Inoue, M. Eto, D. Hoshino, Y. Furuichi, Y. Manabe, N. Fujii, H. Noji, H. Imamura, S. Kuroda,
Quantitative Biology (2020) Vol. 8, 228-237
Ultrasensitive change in nucleosome binding by multiple phosphorylations to the intrinsically disordered region of the histone chaperone FACT;
D. Aoki, A. Awazu, M. Fujii, J. Uewaki, M. Hashimoto, N. Tochio, T. Umehara, S. Tate,
Journal of Molecular Biology (2020) Vol. 432, 4637–4657
Affinity of rhodopsin to raft enables the aligned oligomer formation from dimers: Coarse-grained molecular dynamics simulation of disk membranes; 
Y. Kaneshige, F. Hayashi, K. Morigaki, Y. Tanimoto, H. Yamashita, M. Fuji, A. Awazu,
PLoS One (2020) Vol. 15, e0226123
Robustness against additional noise in cellular information transmission;
T. Tottori, M. Fujii, S. Kuroda,
Physical Review E (2019) Vol. 100, 042403
Logical design of oral glucose ingestion pattern minimizing blood glucose in humans;
M. Fujii, Y. Murakami, Y. Karasawa, Y. Sumitomo, S. Fujita, M. Koyama, S. Uda, H. Kubota, H. Inoue, K. Konishi, S. Oba, S. Ishii, S. Kuroda, npj Systems Biology and Applications (2019) Vol. 5, 31
NMDAR-mediated Ca2+ increase shows robust information transfer in dendritic spines;
T. Tottori, M. Fujii, S. Kuroda,
Biophysical Journal (2019) Vol. 116, 1748–1758, 
Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data;
K. Kawata, K. Yugi, A. Hatano, T. Kokaji, Y. Tomizawa, M. Fujii, S. Uda, H. Kubota, M. Matsumoto, K. I. Nakayama, S. Kuroda,
Genes to Cells (2018) Vol. 24, 82–93
Trans-omic analysis reveals fed and fasting insulin signal across phosphoproteome, transcriptome, and metabolome;
K. Kawata, A. Hatano, K. Yugi, H. Kubota, T. Sano, M. Fujii, Y. Tomizawa, T. Kokaji, K. Y. Tanaka, S. Uda, Y. Suzuki, M. Matsumoto, K. I. Nakayama, K. Saitoh, K. Kato, A. Ueno, M. Ohishi, A. Hirayama, T. Soga, S. Kuroda,
iScience (2018) Vol. 7, 212
Increase in hepatic and decrease in peripheral insulin clearance characterize abnormal temporal patterns of serum insulin in diabetic subjects;
K. Ohashi, M. Fujii, S. Uda, H. Kubota, H. Komada, K. Sakaguchi, W. Ogawa, S. Kuroda,
npj Systems Biology and Applications (2018) Vol. 4, 14
System identification of signaling dependent gene expression with different time-scale data;
T. Tsuchiya, M. Fujii, N. Matsuda, K. Kunida, S. Uda, H. Kubota, K. Konishi, S. Kuroda,
PLoS Computational Biology (2017) Vol. 13(12), e1005913
Small-volume effect enables robust, sensitive and efficient information transfer in the spine;
M. Fujii, K. Ohashi, Y. Karasawa, M. Hikichi, S. Kuroda,
Biophysical Journal (2017) Vol. 112(4), 813
Selective control of upregulated and downregulated genes by temporal patterns and doses of insulin;
T. Sano, K. Kawata, S. Ohno, K. Yugi, H. Kakuda, H. Kubota, S. Uda, M. Fujii, K. Kunida, D. Hoshino, A. Hatano, Y. Ito, M. Sato, Y. Suzuki, S. Kuroda,
Science Signaling (2016) Vol. 22(9), ra112
Laguerre filter analysis with partial least square regression reveals a priming effect of ERK and CREB on c-FOS induction;
T. Kudo, S. Uda , T. Tsuchiya, T. Wada, Y. Karasawa, M. Fujii, T. H. Saito, S. Kuroda,
PLoS ONE (2016) Vol. 11(8), e0160548
Glucose homeostatic law: insulin clearance predicts the progression of glucose intolerance in humans;
K. Ohashi, H. Komada, S. Uda, H. Kubota, T. Iwaki, H. Fukuzawa, Y. Komori, M. Fujii, Y. Toyoshima, K. Sakaguchi, W. Ogawa, S. Kuroda,
PLoS ONE (2015) Vol. 10(12), e0143880
Stochasticity in Ca2+ increase in spines enables robust and sensitive information coding;
T. Komura, H. Urakubo, K. Ohashi, M. Fujii, S. Kuroda,
PLoS ONE (2013) Vol. 9(6), e99040
Influences of excluded volume of molecules on signaling process on biomembrane;
M. Fujii, H. Nishimori, A. Awazu,
PLoS ONE (2013) Vol. 8(5), e62218
Segregation pattern reorientation of granular mixture on horizontally oscillating tray;
M. Fujii, A. Awazu, H. Nishimori,
Physical Review E (2012) Vol. 85, 041304
Saddle-node bifurcation to jammed state for quasi-one-dimensional counter chemotactic flow;
M. Fujii, A. Awazu, H. Nishimori,
Physical Review E (2010) 8 Vol. 2, 015102(R)
Counter chemotactic flow in quasi-one-dimensional path;
M. Fujii, A. Awazu, H. Nishimori,
Journal of Physical Society of Japan (2009) Vol. 78, 073801

Proceeding (Japanese)

Model of Signaling Pathway on Cell Membrane Including Effect of Molecular Crowding,
Proceedings of the 17th Symposium on Simulation of Traffic Flow (2011)
Model of Signaling Pathway on Cell Membrane Including Excluded Volume Effect,
Proceedings of the 16th Symposium on Simulation of Traffic Flow (2010)
Relation between Flux and Growth of Cluster for Counter CHemotactic Flow in Quasi-One-Dimensional Path,
Proceedings of the 15th Symposium on Simulation of Traffic Flow (2009)
Multiple Lanes Traffic Flow including the Effect of Chemotaxis,
Proceedings of the 14th Symposium on Simulation of Traffic Flow (2008)

Department of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University