This is the Github page of the Systems Biology group in the Department of Informatics at King's College London, led by Dr Sophia Tsoka.
Our group develops algorithmic and machine-learning methods to understand complex biological systems — from metabolic and protein–protein interaction networks to multi-omic patient data — with a strong emphasis on interpretability and translational impact in precision medicine and drug discovery.
"Bridging algorithmic innovation with biological insight."
Genome and disease data mining · network analysis & reconstruction · metabolic & PPI networks · evolutionary genome dynamics Quantitative structure–activity relationships · piecewise & network-based regression · lead optimisation · ChEMBL/RDKit workflows | Optimisation-based deep learning · pathway activity autoencoders · supervised feature selection · interpretable patient stratification Network embedding · drug–target interaction prediction · pathway activity inference · clinical & translational applications |
| Repository | Description | Language |
|---|---|---|
| OPLRAreg | Mixed-integer piecewise regression with regularisation | Python |
| modSAR | Network-based piecewise linear regression for QSAR | Jupyter |
| qsar-models | Data and regression models for QSAR | HTML |
| qsar-tutorial | QSAR tutorial — ChEMBL data & RDKit | Jupyter |
| network-multi-omics | SCONE: subset-contrastive multi-omics network embedding (paper) | Python |
| DT2Vec | Drug–target interaction via link prediction & embedding | Jupyter |
| pathwayae | Pathway activity inference (paper) | Jupyter |
| CGM | Multi-gene ML risk classification for breast cancer prognosis | Jupyter |
📂 All repositories
| Repository | Description |
|---|---|
| DIOPTRA | Optimisation-based pathway activity inference |
| coxae | Cox survival models with pathway activity encoding |
| DT2VecPlus | Extended drug–target embedding framework |
| modsar-for-malaria | modSAR applied to antimalarial lead discovery |
| Optimisation-based-Modelling-for-Explainable-Lead-Discovery-in-Malaria | Explainable lead discovery in malaria |
| Similarity-Fusion-GRMF | Graph regularised matrix factorisation |
| melanoma-ig | B-cell response analysis in melanoma |
 Dr Sophia Tsoka Group Leader · Reader in Bioinformatics Computational genome analysis, network reconstruction, and explainable AI for biomedicine. Leads the Algorithms & Data Analysis research strand. |  Modest Lungociu PhD Student AI for drug discovery and ML-driven methods for biodosimetry |  Xinyue Chen PhD Student Computational methods for biological data analysis within the Systems Biology group. |
 Sabaoon Zeb PhD Student Computational biology and data-driven methods for systems-level analysis. |  lws2022 PhD Student Machine learning and bioinformatics research in the Systems Biology group. | |
 Jon Cardoso-Silva Former PhD Student Now at · London School of Economics Creator of modSAR and OPLRAreg. Network-based piecewise regression for QSAR. |  Pedro Henrique da Costa Avelar Former PhD Student Now at · University of Manchester Pathway activity inference and multi-omics integration. Author of pathwayae and network-multi-omics (SCONE). |  Ruby Li Former PhD Student Now at · University College London Optimisation-based modelling for explainable drug discovery and graph embedding methods. |
 Lili Chen Former PhD Student Machine learning and bioinformatics research in the Systems Biology group. |
Recent research from the group (auto-updated monthly from Dr Sophia Tsoka's Google Scholar profile; last sync: 2026-08-01).
Source: openalex · View full publication list on Google Scholar →
- ⭐ Star a repository if you find our tools useful
- 🐛 Open an issue for bugs, questions, or feature requests
- 🔀 Submit a PR — we welcome contributions and tutorials
- 📧 Contact:sophia.tsoka@kcl.ac.uk
Systems Biology · Department of Informatics · King's College London · London, UK