MASASHI FUJII

Last Updated :2024/04/04

Affiliations, Positions
Graduate School of Integrated Sciences for Life, Assistant Professor
Web Site
E-mail
m-fujii0123hiroshima-u.ac.jp
Self-introduction
I specialize in multi-scale simulation from atoms and molecules to cells and tissues and statistical analysis. I build models for phenomena that are difficult to observe directly due to temporal, spatial, and experimental constraints, leading to new discoveries!

Basic Information

Major Professional Backgrounds

  • 2010/04/01, 2013/03/31, JSPS, Research fellow (DC1)
  • 2013/04/01, 2014/03/31, University of Tokyo, Department of Biophysics and Biochemistry, Graduate School of Science, Research fellow
  • 2014/04/01, 2016/11/30, University of Tokyo, Department of Biological Sciences, Graduate School of Science, Project Research Associate
  • 2016/12/01, 2019/03/31, University of Tokyo, Molecular Genetics Research Laboratory, Graduate School of Science, Research Associate
  • 2019/04/01, Hiroshima University, Graduate School of Integrated Sciences for Life, Research Associate

Educational Backgrounds

  • Hiroshima University, Graduate School of Science, Department of Mathematical and Life Sciences, Japan, 2010/04/01, 2013/03/23
  • Hiroshima University, Graduate School of Science, Department of Mathematical and Life Sciences, Japan, 2008/04/01, 2010/03/23
  • Hiroshima University, Faculty of Science, Japan, 2004/04, 2008/03

Academic Degrees

  • Hiroshima University
  • Hiroshima University

Educational Activity

  • [Bachelor Degree Program] School of Science : Mathematics : Mathematics
  • [Master's Program] Graduate School of Integrated Sciences for Life : Division of Integrated Sciences for Life : Program of Mathematical and Life Sciences
  • [Doctoral Program] Graduate School of Integrated Sciences for Life : Division of Integrated Sciences for Life : Program of Mathematical and Life Sciences

In Charge of Primary Major Programs

  • Mathematics
  • Life Sciences

Research Fields

  • Mathematical and physical sciences;Physics;Biological physics / Chemical physics / Soft matter physics
  • Biological Sciences;Genome science;System genome science
  • Informatics;Human informatics;Kansei informatics
  • Biology;Biological Science;Biophysics

Research Keywords

  • Theoretical Biophysics
  • Systems Biology

Affiliated Academic Societies

Educational Activity

Course in Charge

  1. 2024, Undergraduate Education, 2Term, Exercises in Mathematical Software
  2. 2024, Undergraduate Education, 4Term, Exercises in Mathematics for Computation
  3. 2024, Undergraduate Education, 1Term, Exercises in Mathematics for Computation A
  4. 2024, Undergraduate Education, First Semester, Special Study of Mathematics and Informatics for Graduation
  5. 2024, Undergraduate Education, Second Semester, Special Study of Mathematics and Informatics for Graduation
  6. 2024, Graduate Education (Master's Program) , 3Term, Research Methods in Life Science
  7. 2024, Graduate Education (Master's Program) , Academic Year, Research for Academic Degree Dissertation in Mathematical and Life Sciences
  8. 2024, Graduate Education (Master's Program) , 1Term, Computational Mathematics A
  9. 2024, Graduate Education (Master's Program) , 2Term, Topical Seminar in Mathematical Science A
  10. 2024, Graduate Education (Master's Program) , 4Term, Topical Seminar in Mathematical Science B
  11. 2024, Graduate Education (Master's Program) , First Semester, Exercises in Applied Mathematics and Computational Science A
  12. 2024, Graduate Education (Master's Program) , Second Semester, Exercises in Applied Mathematics and Computational Science B

Research Activities

Academic Papers

  1. Characteristic growth of chemical gardens from mixtures of two salts, Physical Chemistry Chemical Physics, 25(18), 12974-12978, 20230510
  2. Identification of aberrant transcription termination at specific gene loci with DNA hypomethylated transcription termination sites caused by DNA methyltransferase deficiency, Genes & Genetic Systems, 97(3), 139-152, 202206
  3. Methylome data derived from maternal-zygotic DNA methyltransferase 3aa(-/-) zebrafish, Data in Brief, 44, 202210
  4. In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states, Scientific Reports, 12(1), 2022
  5. Epigenetic-structural changes in X chromosomes promote Xic pairing during early differentiation of mouse embryonic stem cells, Biophysics and Physicobiology, 19, 2022
  6. Partial exogastrulation due to apical-basal polarity of F-actin distribution disruption in sea urchin embryo by omeprazole., Genes to cells : devoted to molecular & cellular mechanisms, 27(6), 1-17, 2022
  7. Mathematical model of chromosomal dynamics during DNA double strand break repair in budding yeast, Biophysics and Physicobiology, 19, 2022
  8. Self-Organization of Diverse Directional Hierarchical Networks in Simple Coupled Maps with Connection Changes, Journal of The Physical Society of Japan, 91(2), 20220215
  9. Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans, npj Systems Biology and Applications, 8(1), 20220208
  10. Fat Induces Glucose Metabolism in Nontransformed Liver Cells and Promotes Liver Tumorigenesis., Cancer research, 81(8), 1988-2001, 2021
  11. Trans-omic Analysis Reveals ROS-Dependent Pentose Phosphate Pathway Activation after High-Frequency Electrical Stimulation in C2C12 Myotubes, iScience, 23(10), 101558, 20201023
  12. Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle., iScience, 24(3), 2021
  13. Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity, Science Signaling, 13(660), 20201201
  14. Spontaneous Organizations of Diverse Network Structures in Coupled Logistic Maps with a Delayed Connection Change, Journal of The Physical Society of Japan, 89(11), 20201115
  15. Monitoring and mathematical modeling of mitochondrial ATP in myotubes at single-cell level reveals two distinct population with different kinetics, Quantitative Biology, 8(3), 228-237, 202009
  16. Single-Cell Information Analysis Reveals That Skeletal Muscles Incorporate Cell-to-Cell Variability as Information Not Noise, Cell Reports, 32(9), 20200901
  17. Affinity of rhodopsin to raft enables the aligned oligomer formation from dimers: Coarse-grained molecular dynamics simulation of disk membranes., PloS one, 15(2), 2020
  18. Ultrasensitive Change in Nucleosome Binding by Multiple Phosphorylations to the Intrinsically Disordered Region of the Histone Chaperone FACT, Journal of Molecular Biology, 432(16), 4637-4657, 20200724
  19. Robustness against additional noise in cellular information transmission., Physical review. E, 100(4-1), 042403, 2019
  20. Logical design of oral glucose ingestion pattern minimizing blood glucose in humans., npj Systems Biology and Applications, 5, 31, 2019
  21. NMDAR-Mediated Ca2+ Increase Shows Robust Information Transfer in Dendritic Spines., Biophysical journal, 116(9), 1748-1758, 2019
  22. Increase in hepatic and decrease in peripheral insulin clearance characterize abnormal temporal patterns of serum insulin in diabetic subjects., NPJ systems biology and applications, 4(1), 14, 2018
  23. Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data., Genes to cells : devoted to molecular & cellular mechanisms, 24(1), 82-93, 2019
  24. Trans-omic Analysis Reveals Selective Responses to Induced and Basal Insulin across Signaling, Transcriptional, and Metabolic Networks., iScience, 7, 212-229, 2018
  25. System identification of signaling dependent gene expression with different time-scale data., PLoS computational biology, 13(12), e1005913, 2017
  26. Small-Volume Effect Enables Robust, Sensitive, and Efficient Information Transfer in the Spine, Biophysical Journal, 112(4), 813-826, 2017
  27. Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin., Science signaling, 9(455), ra112, 2016
  28. Laguerre Filter Analysis with Partial Least Square Regression Reveals a Priming Effect of ERK and CREB on c-FOS Induction., PloS one, 11(8), e0160548, 2016
  29. Glucose Homeostatic Law: Insulin Clearance Predicts the Progression of Glucose Intolerance in Humans., PloS one, 10(12), e0143880, 2015
  30. Stochasticity in Ca2+ increase in spines enables robust and sensitive information coding., PloS one, 9(6), e99040, 2014
  31. Influences of Excluded Volume of Molecules on Signaling Processes on the Biomembrane, PLoS ONE, 8(5), e62218, 2013
  32. Segregation-pattern reorientation of a granular mixture on a horizontally oscillating tray, Physical Review E, 85(4), 041304, 2012
  33. Saddle-node bifurcation to jammed state for quasi-one-dimensional counter-chemotactic flow, Physical Review E, 82(2), 015102, 2010
  34. Counter Chemotactic Flow in Quasi-One-Dimensional Path, Journal of the Physical Society of Japan, 78(7), 073801, 2009

External Funds

Acceptance Results of Competitive Funds

  1. KAKENHI, Construction of a Framework for Large-Scale Coarse-Grained Molecular Dynamics Simulation, 2024/04/01, 2029/03/31
  2. KAKENHI, 2019/04/01, 2023/03/31
  3. KAKENHI, 2016/04/04, 2019/03/31
  4. KAKENHI, 2010/04/01, 2013/03/31