Journal papers

Characteristic growth of chemical gardens from mixtures of two salts;
Y. Kubodera, Y. Xu, Y. Yamaguchi, M. Matsuo, M. Fujii, M. Kageyama, O. Steinbock, S. Nakata,
Phys. Chem. Chem. Phys. (2023) Vol.25, 12974–12978

Methylome data derived from maternal-zygotic DNA methyltransferase 3aa-/- zebrafish;
M. Shirai, K. Takayama, H. Takahashi, Y. Hirose, M. Fujii, A. Awazu, N. Shimoda, Y. Kikuchi,
Data in Brief (2022) Vol.44, 108514

In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states;
T. Kokaji, M. Eto, A. Hatano, K. Yugi, K. Morita, S. Ohno, M. Fujii, K. Hironaka, Y. Ito, R. Egami, S. Uematsu, A. Terakawa, Y. Pan, H. Maehara, D. Li, Y. Bai, T. Tsuchiya, H. Ozaki, H. Inoue, H. Kubota, Y. Suzuki, A. Hirayama, T. Soga, S. Kuroda,
Scientific Report (2022) Vol.12, 13719

Identification of aberrant transcription termination at specific gene loci with DNA hypomethylated transcription termination sites caused by DNA methyltransferase deficiency;
M. Shirai, T. Nara, H. Takahashi, K. Takayama, Y. Chen, Y. Hirose, M. Fujii, A. Awazu, N. Shimoda, Y. Kikuchi,
Biophysics and Genes & Genetic Systems (2022) 21-00092

Epigenetic-structural changes in X chromosomes promote Xic pairing during early differentiation of mouse embryonic stem cells;
T. Komoto, M. Fujii, A. Awazu,
Biophysics and Physicobiology (2022) Vol.19, e190018

Mathematical model of chromosomal dynamics during DNA double strand break repair in budding yeast;
S. Nakahata, T. Komoto, M. Fujii, A. Awazu,
Biophysics and Physicobiology (2022) Vol.19, e190012

Partial exogastrulation due to apical-basal polarity of F-actin distribution disruption in sea urchin embryo by omeprazole;
K. Watanabe, Y. Yasui, Y. Kurose, M. Fujii, T. Yamamoto, N. Sakamoto, A. Awazu,
Genes to Cells (2022) 1-17

Self-Organization of Diverse Directional Hierarchical Networks in Simple Coupled Maps with Connection Changes;
T. Nakanishi, M. Fujii, A. Awazu,
Journal of the Physical Society of Japan (2022) Vol.91, 023801

Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans;
S. Fujita, Y. Karasawa, M. Fujii, K. Hironaka, S. Uda, H. Kubota, H. Inoue, Y. Sumitomo, A. Hirayama, T. Soga, S. Kuroda,
npj Systems Biology and Applications (2022) Vol.8, 1-16

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)