Okada Lab

intro_to_param_estim

Parameter estimation of ODE models describing biological processes

ccle_extractor

Python script for extracting dataset from CCLE (Cancer Cell Line Encyclopedia)

Wibisana2021

Imaging and single cell sequencing analyses of super-enhancer activation mediated by NF-κB in B cells (Wibisana, JN et al., 2021)

cancer_modeling

Modeling signaling networks in cancer

biomass

A Python Framework for Modeling and Analysis of Signaling Systems

Birtwistle2007

Birtwistle, M. R. et al. Ligand-dependent responses of the ErbB signaling network: Experimental and modeling analyses. Mol. Syst. Biol. 3, (2007).

Michida2020

Michida, H. et al. The number of transcription factors at an enhancer determines switch-like gene expression.

py2jl

Converting Python code to Julia for ODE model construction

Ando2021

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

ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes

BioMASS.jl

Julia interface to BioMASS, tailored to parameter estimation in systems biology models

findfoci

ImageJ2 and R package for quantitative analysis of NF-κB foci

Haga2023

inflammatory-aging

Tabata, S. et al.

Kanazawa2021

Cell shape‐based chemical screening reveals an epigenetic network mediated by focal adhesions

pasmopy

Patient-Specific Modeling in Python

periodontitis

Chiang2020

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).

DynProfiler

egf_signaling

Computational modeling of the short term pattern of cellular responses to epidermal growth factor

Hatakeyama2003

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).

HER2_Cellcycle

Imoto2019

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_Cancers_2020

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).

Inoue2016

Inoue, K. et al. Oscillation dynamics underlie functional switching of NF-κB for B-cell activation. npj Syst. Biol. Appl. 2, 16024 (2016).

Nakakuki2010

Nakakuki, T. et al. Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics. Cell 141, 884–896 (2010).

sensitivity_analysis

Calculation of sensitivity coefficients and visualization

Shinohara2014

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).

text2model-from-knowledge

Extending BioMASS to construct mathematical models from external knowledge (Arakane et al., 2024)