TAKASHI OKADA

Last Updated :2026/05/08

Affiliations, Positions
Graduate School of Integrated Sciences for Life, Associate Professor
Web Site
https://scholar.google.com/citations?user=OmVWsEsAAAAJ&hl=en
https://t-okadalab.github.io/

Basic Information

Major Professional Backgrounds

  • 2018/09/01, 2022/03/31, University of California, Berkeley, VIsiting Researcher
  • 2018/04/01, 2022/03/31, RIKEN, iTHEMS, Senior Research Scientist
  • 2022/04/01, 2023/03/31, Kyoto University, Lime, Program-Specific Associate Professor
  • 2023/04/01, 2026/03/31, Kyoto University, Lime, Associate Professor

Educational Backgrounds

  • Ph.D. in Physics, Graduate School of Science, Kyoto University, 2013/03
  • M.S. in Physics, Graduate School of Science, The University of Tokyo, 2009/03
  • Mar 2007 B.S. in Physics, Faculty of Science, The University of Tokyo, 2007/03

Academic Degrees

  • Kyoto University
  • The University of Tokyo

Research Keywords

  • Machine Learning
  • Statistical Physics
  • Neuronal networks
  • Population genetics
  • network science

Educational Activity

Course in Charge

  1. 2026, Undergraduate Education, 4Term, Mathematics for Computation
  2. 2026, Undergraduate Education, First Semester, Special Study of Mathematics and Informatics for Graduation
  3. 2026, Undergraduate Education, Second Semester, Special Study of Mathematics and Informatics for Graduation

Research Activities

Academic Papers

  1. Inferring Migration Networks with Time-Lagged F 2 Statistics, 20260312
  2. Uncovering heterogeneous intercommunity disease transmission from neutral allele frequency time series, Proceedings of the National Academy of Sciences, 20251202
  3. Identifying Phenotype-Indicative Molecules from the Structure of Biochemical Reaction Networks, bioRxiv, 20251023
  4. Uncovering bifurcation behaviors of biochemical reaction systems from network topology, SCIENTIFIC REPORTS, 2025
  5. Uncovering the causal relationships in plant-microbe ecosystems: A time series analysis of the duckweed cultivation system for biomass production and wastewater treatment, Science of The Total Environment, 202412
  6. BayesianSSA: a Bayesian statistical model based on structural sensitivity analysis for predicting responses to enzyme perturbations in metabolic networks, BMC BIOINFORMATICS, 20240316
  7. Stable States of a Microbial Community Are Formed by Dynamic Metabolic Networks with Members Functioning to Achieve Both Robustness and Plasticity, Microbes and Environments, 2024
  8. Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England, PLOS PATHOGENS, 2024
  9. Patterns of change in regulatory modules of chemical reaction systems induced by network modification, PNAS NEXUS, 20231221
  10. Patterns of change in regulatory modules of chemical reaction systems induced by network modification, bioRxiv, 20231124
  11. Finding regulatory modules of chemical reaction systems, Physical Review Research, 20231016
  12. Information-transfer characteristics in network motifs, PHYSICAL REVIEW RESEARCH, 20230124
  13. Information-transfer characteristics in network motifs, Physical Review Research, 20230124
  14. Origin of diverse phosphorylation patterns in the ERBB system, Biophysical Journal, 202202
  15. Structural Reduction of Hypergraphs Based on Topology, Proceedings of Blockchain in Kyoto 2021 (BCK21), 20211110
  16. Flux-augmented bifurcation analysis in chemical reaction network systems, Physical Review E, 20210615
  17. Flux-augmented bifurcation analysis in chemical reaction network systems, PHYSICAL REVIEW E, 20210615
  18. Dynamic sampling bias and overdispersion induced by skewed offspring distributions, Genetics, 219(4), 20210310
  19. Diagrammatic expansion of information flows in stochastic Boolean networks, PHYSICAL REVIEW RESEARCH, 2(4), 20201229
  20. Pyrophosphate inhibits gluconeogenesis by restricting UDP-glucose formation in vivo, Scientific Reports, 20181002
  21. Structural bifurcation analysis in chemical reaction networks, Physical Review E, 20180730
  22. Sensitivity and network topology in chemical reaction systems, PHYSICAL REVIEW E, 2017
  23. Ligand-concentration sensitivity of a multi-state receptor, Arxiv, 2017
  24. Law of localization in chemical reaction networks, Arxiv, 2016
  25. Defect branes as Alice strings, JOURNAL OF HIGH ENERGY PHYSICS, 2015
  26. Emergent bubbling geometries in the plane wave matrix model, Arxiv, 2014
  27. Exact results for perturbative partition functions of theories with SU(2|4) symmetry, JOURNAL OF HIGH ENERGY PHYSICS, 2013
  28. Solving the Naturalness Problem by Baby Universes in the Lorentzian Multiverse, PROGRESS OF THEORETICAL PHYSICS, 2012
  29. Large-N reduction for N=2 quiver Chern-Simons theories on S3 and localization in matrix models, PHYSICAL REVIEW D, 2012
  30. Rotating string in doubled geometry with generalized isometries, PHYSICAL REVIEW D, 2012
  31. Evidence for duality of conifold from fundamental string, JOURNAL OF HIGH ENERGY PHYSICS, 2011
  32. A realistic extension of gauge-mediated SUSY-breaking model with superconformal hidden sector, Physics Letters B, 200903
  33. Analysis on a relation between enterprise profit and financial state by using data mining techniques, NEW FRONTIERS IN ARTIFICIAL INTELLIGENCE, 2007