okadalabipr/context-dependent-GRNs Fork of Masaaaato/context-dependent-GRNs

This repository provides reproducible code for the study by Tsutsui M. et al. (2025), focused on constructing and analyzing context-aware gene regulatory networks (GRNs) derived from biomedical literature.

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okadalabipr/text2model-from-knowledge

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

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okadalabipr/cREscENDO

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okadalabipr/DynProfiler Fork of Masaaaato/DynProfiler

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okadalabipr/HER2_Cellcycle

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okadalabipr/inflammatory-aging

Tabata, S. et al.

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okadalabipr/py2jl 📦

Converting Python code to Julia for ODE model construction

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okadalabipr/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).

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okadalabipr/cancer_modeling

Modeling signaling networks in cancer

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okadalabipr/Haga2023

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okadalabipr/periodontitis

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okadalabipr/intro_to_param_estim 📦

Parameter estimation of ODE models describing biological processes

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okadalabipr/sensitivity_analysis 📦

Calculation of sensitivity coefficients and visualization

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okadalabipr/Nakakuki2010

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

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okadalabipr/BioMASS.jl Fork of biomass-dev/BioMASS.jl

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

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okadalabipr/ASURAT Fork of keita-iida/ASURAT

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

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okadalabipr/ccle_extractor

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

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okadalabipr/Wibisana2021

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

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okadalabipr/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).

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okadalabipr/findfoci Fork of johannesnicolaus/findfoci

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

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okadalabipr/biomass Fork of biomass-dev/biomass

A Python Framework for Modeling and Analysis of Signaling Systems

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okadalabipr/pasmopy Fork of pasmopy/pasmopy

Patient-Specific Modeling in Python

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okadalabipr/egf_signaling

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

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okadalabipr/Kanazawa2021

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

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okadalabipr/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).

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okadalabipr/Inoue2016

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

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okadalabipr/Birtwistle2007

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

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okadalabipr/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).

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okadalabipr/Michida2020

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

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okadalabipr/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).

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okadalabipr/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).

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