Matlab code for Bayesian Network Component Analysis
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Updated
Nov 11, 2015 - MATLAB
Matlab code for Bayesian Network Component Analysis
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).
Python implementation for René Thomas's Framework
The (rendered) website of the Resendis lab. Do not send PRs here! Use https://github.com/resendislab/website instead!
Matlab code and data to reproduce results from "Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM" by Dreyfuss, Zucker, et al.
A Bio2BEL package for converting InterPro to BEL
Parsing and transformation of units of measurements
Variational Gradient Matching for Dynamical Systems
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).
Systems Biology & Machine Learning Scripts
An SBML parser written in Rust.
The Matlab tool for Prediction Uncertainty Analysis (PUA) integrates Profile Likelihood analysis with Bayesian sampling.
Utilities for working with SLV and DAT files.
Causal Inference Networks for Determining Expression Relationships Anthology
Supplementary Material for Multistate Control Paper
CBMPy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
Genome-Scale Metabolic Model of CD8+ T-Cells
Simulation of the TGF-β/SMAD pathway in single cells
PhD thesis: Molecular feedback and self-organisation in the PAR polarity network
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