Loïc Paulevé

The paper introduces scBOLT, a framework for inferring Boolean networks from multi-condition single-cell transcriptomes, improving computational tractability for large-scale models.

The paper surveys Boolean network control tools, identifies inconsistencies in their results, and introduces a metric to prioritize mutations based on predicted phenotypic impact.

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

The paper introduces BoNesis, a tool for inferring Boolean networks from transcriptome data to model cellular differentiation and reprogramming, demonstrating its application in hematopoiesis and adipocyte/osteoblast differentiation.

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

The paper infers ecological networks and dynamics using Boolean models from observations and prior knowledge, demonstrating its ability to recover essential interactions in a protist system.

Seed2LP predicts nutritional requirements (seeds) for microorganisms using hybrid metabolic modeling, improving seed inference over graph-based methods in genome-scale metabolic networks.

This paper introduces a method to link scRNA-Seq data with Boolean gene activation states, enabling both binarisation of real data and generation of synthetic data for model validation.

The paper creates a merged SBGN PD map of the circadian clock and cell cycle, validates its dynamics, and identifies NR1D1's role in regulating cell cycle progression.

This paper introduces Most Permissive Boolean Networks (MPBNs) to improve the modeling of biological networks by avoiding spurious behaviors and reducing computational complexity for genome-scale analysis.

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.