Computational Methods in Systems Biology

.- Boolean and Qualitative Networks

.- Source-Target Control of Boolean Networks with Minimal Edge Perturbations.
.- Modulation-Reaction Networks.
.- Inference of Qualitative Models from Steady-State Data via Weighted MaxSMT.
.- pyModRev: a Python Tool for Model Revision of Boolean Networks.

.- Rule-Based and Stochastic Models

.- Statistical model checking for rule-based models in the Kappa language.
.- Efficient Stochastic Trace Generation for Transcriptio.
.- Mamdani-Driven Fuzzy Reaction Systems.
.- Incremental KaSa: Static Analysis of Kappa Models at Edit Time.

.- Constraint-Based Modeling and Molecular Computation

.- Inferring Minimal Culture Media using Biologically Constrained Combinatorial Optimization.
.- On the Design of an Analog-Dyadic Converter CRN.
.- Analog computation with transcriptional networks.
.- Metabolic Transformation Algorithm: A Systems Biology Approach to Aging and Alzheimer’s Disease.

.- Causal Inference and Multi-Omics Integration

.- Metabolic Flux Inference in a Cheese Microbial Community via comFI: a Biology-informed Approach for Time-resolved Multi-omics Integration.
.- GRNgen: a Generator of Gene Regulatory Networks Fitting Graph and Motif Properties.
.- Consensus Enhances Individual Causal Models: a Use Case on Lung Cancer Driven by Cellular Pathways.
.- Graph Learning Models for Temporal Gene Expression Prediction and the Role of Interactions Topology.
.- Multi-view Clustering of Transcriptomics and Methylomics Data Elucidates Glioma Molecular Stratification.