Okada Lab's Projects
Ando, M. et al. IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells. npj Syst Biol Appl 7, 42 (2021).
ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes
A Python Framework for Modeling and Analysis of Signaling Systems
Julia interface to BioMASS, tailored to parameter estimation in systems biology models
Birtwistle, M. R. et al. Ligand-dependent responses of the ErbB signaling network: Experimental and modeling analyses. Mol. Syst. Biol. 3, (2007).
Modeling signaling networks in cancer
Python script for extracting dataset from CCLE (Cancer Cell Line Encyclopedia)
Chiang, S., Shinohara, H., Huang, J. H., Tsai, H. K. & Okada, M. Inferring the transcriptional regulatory mechanism of signal-dependent gene expression via an integrative computational approach. FEBS Lett. (2020).
Computational modeling of the short term pattern of cellular responses to epidermal growth factor
ImageJ2 and R package for quantitative analysis of NF-κB foci
Hatakeyama, M. et al. A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling. Biochem. J. 373, 451–463 (2003).
Imoto, H. & Okada, M. Signal-dependent regulation of early-response genes and cell cycle: a quantitative view. Curr. Opin. Syst. Biol. 15, 100–108 (2019).
Imoto, H., Zhang, S. & Okada, M. A Computational Framework for Prediction and Analysis of Cancer Signaling Dynamics from RNA Sequencing Data—Application to the ErbB Receptor Signaling Pathway. Cancers (Basel). 12, 2878 (2020).
Tabata, S. et al.
Inoue, K. et al. Oscillation dynamics underlie functional switching of NF-κB for B-cell activation. npj Syst. Biol. Appl. 2, 16024 (2016).
Parameter estimation of ODE models describing biological processes
Cell shape‐based chemical screening reveals an epigenetic network mediated by focal adhesions
Michida, H. et al. The number of transcription factors at an enhancer determines switch-like gene expression.
Nakakuki, T. et al. Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics. Cell 141, 884–896 (2010).
Patient-Specific Modeling in Python
Converting Python code to Julia for ODE model construction
Calculation of sensitivity coefficients and visualization
Shinohara, H. et al. Positive feedback within a kinase signaling complex functions as a switch mechanism for NF-κB activation. Science (80-. ). 344, 760–764 (2014).
Extending BioMASS to construct mathematical models from external knowledge (Arakane et al., 2024)
Imaging and single cell sequencing analyses of super-enhancer activation mediated by NF-κB in B cells (Wibisana, JN et al., 2021)