Denis Thieffry

TabularQual provides a spreadsheet-based format for annotating logical models, with tools to convert between spreadsheets and SBML-qual, enhancing model reuse and interoperability.

AstroLogics analyzes Boolean model ensembles to identify differences in dynamics and regulation through simulation-based clustering and visualization.

This tutorial demonstrates how to use the CoLoMoTo software suite to perform reproducible dynamical analyses of logical models of biological networks.

The paper introduces forkedTF, a tool to create FPWM and F-Logos for modeling TF dimer binding sites, and provides precomputed resources in MethMotif 2024.

UPMaBoSS simulates cell population dynamics by extending MaBoSS to model interactions and death/division, revealing TNF-induced resistance mechanisms.

Eoulsan 2 updates a workflow manager to support bulk, long-read, and single-cell transcriptomics analyses with improved infrastructure and module development.

This study benchmarks four single-cell network inference methods using real data to assess their reproducibility across different conditions and parameters, finding GENIE3 to be the most consistent.

The paper quantifies how cis-acting genetic variation affects chromatin accessibility, histone modifications, and gene expression in Drosophila embryos, finding that much of this variation does not propagate to gene expression.

This study benchmarks nine joint multi-omics dimensionality reduction methods using simulated and real cancer data, finding intNMF excels in clustering and MCIA shows consistent performance across contexts.

The paper introduces two computational methods for analyzing complex biological models and applies them to predict T cell responses to checkpoint inhibitors.

The paper develops a computational model of the Nodal and BMP2/4 signaling pathways in sea urchin embryos, showing BMP dominance and the importance of Smad activation rates in dorsal-ventral patterning.

The paper introduces Var-tools, a framework for predicting the impact of regulatory variants on transcription factor binding, with four case studies demonstrating its functionality.

The paper demonstrates the use of the CoLoMoTo Interactive Notebook to analyze a Boolean model of tumor cell invasion, predicting mutations associated with metastasis.

The paper introduces a framework for reproducible analysis of qualitative biological networks using an interactive notebook environment.

The paper introduces GINsim 3.0, a software tool for modeling and analyzing cellular regulatory networks using logical formalism, with a focus on the p53-Mdm2 network.

The paper introduces matrix-clustering, a tool that reduces redundancy and clusters transcription factor binding motifs from multiple sources, improving interpretation of motif collections.

The paper outlines the logical modelling framework and achievements of the Consortium for Logical Models and Tools, emphasizing model reusability and interoperability.

The paper uses symbolic model checking to analyze T-helper cell plasticity by examining attractor switches in a logical model of their differentiation network.