computational-systems-biology

Python package for multi-omic trajectory inference from paired single-cell RNA-seq and ATAC-seq data.

Fast and Accurate LSTM Meta-modeling of TNF-induced Tumor Resistance In Vitro.

rLotos: deep reinforcement learning for design space exploration of simulated epithelial sheet biofabrication.

Spike train scalograms with fine-tuned CNNs for neuronal cell type classification from electrophysiological recordings.

Genomic Annotated Gene Activity Matrix (GAGAM) for integrating scATAC-seq accessibility and scRNA-seq expression.

Curated intracellular Boolean models and multiscale simulation trajectories for computational biology benchmarking.

META² is a meta-model for predicting the performance of meta-heuristic algorithms on arbitrary optimization problems. This repository provides instructions to build, use, and extend the model.

Neuronal Spike Shapes (NSS): analysis of electrophysiological cell profiles from action potential waveforms.

Meta-analysis of scRNA-seq markers for mammalian cortex interneuron subtype discrimination.

NWN model for simulating microbiota dynamics under antibiotic resistance scenarios.

Code and workflows to reproduce the results from the ATLAS multi-omic trajectory inference paper.

A paper on using event sourcing in computational systems biology.

Sample size enrichment for single-cell multimodal low-throughput Patch-seq datasets.

PhysiS&S implements the Start & Stop add-on for PhysiCell and PhysiBoSS, enabling simulations to pause based on time or cell conditions, save system-state snapshots, and resume from saved states. This repository includes code and instructions to reproduce the results from the Start&Stop paper.

Gene Regulation Accessibility Integrating GeneHancer (GRAIGH): integrating GeneHancer elements with scATAC-seq data.

Reinforcement learning for optimizing synthetic oscillatory biological networks.

Nets-within-Nets Petri net model of C. elegans vulval precursor cell specification.

Meta-analysis of gene activity (MAGA) contributions and correlation with gene expression through GAGAM.

Coherence: evolutionary design space exploration and co-simulation for optimized biofabrication protocols.

Computational pipeline to perform miRNA targets enrichment in pathways involved in Bronchiolitis Obliterates Syndrome development.