The Bioinformatics Unit at the Department of Clinical and Experimental Medicine, University of Catania, Italy.
We develop algorithms, pipelines and applications for the analysis of biological networks and omics data — pathway analysis and simulation, drug repurposing, NGS pipelines and clinical reporting. Everything we publish is released as open source.
🌐 knowmics.it · 🏛 medclin.unict.it
- Network medicine & systems biology — pathway models carrying post-transcriptional regulation, signal propagation over integrated interactomes, disease-specific sub-structures
- Phenotype simulation — predicting the downstream effect of a perturbation before running it
- In-silico drug repurposing — ranking approved compounds by how strongly they reverse a disease signature in network space
- NGS pipelines & multi-omics integration — reproducible, containerised workflows with real user interfaces
- AI & ML for precision oncology — transformer models for reference-tissue identification, TMB, variant-to-therapy interpretation
- Text mining & biomedical knowledge graphs — literature in, knowledge graph out
| Tool | What it does |
|---|---|
| PHENSIM | Simulates how over- or under-expressing a molecule de-regulates every pathway element. Web portal, free for academic use |
| MITHrIL 2 | miRNA-enriched topological pathway analysis across 60+ species, with the SPECifIC sub-pathway extractor built in |
| PACO | Shiny app comparing perturbed pathways across phenotypes, conditions or species as a multilayer network |
| NetCoS | Network-enhanced connectivity score for drug repurposing over LINCS signatures |
| Tool | What it does |
|---|---|
| OncoReport | Solid and liquid biopsy DNA-Seq to a precision-medicine therapy report: evidence, trials, drug interactions, ESMO guidelines |
| RNAdetector | Stand-alone and cloud RNA-Seq analysis for coding genes and every major ncRNA class — no command line required |
| BacExplorer | De-novo bacterial genome annotation: AMR, virulence factors, plasmids, MLST, serotyping |
| TMBCalc | Tumour mutational burden from raw data, shipped as a Docker image |
| REFINET | Reference tissue identification with transformer autoencoders over 19,253 samples |
| Tool | What it does |
|---|---|
| NetMe 2.0 | Biomedical literature to a knowledge graph, with a Graph-RAG module. Web interface and REST API (portal temporarily offline — server migration) |
| TemporalRI | Subgraph isomorphism in temporal networks |
| GASOLINE | Local alignment of biological networks (CLI + Cytoscape app) |
| MUTClass | Identification of targeted gene panels able to classify cancer patients |
| BioTagME | Spark pipeline for large-scale biomedical entity extraction and linking |
| Tool | What it does |
|---|---|
| geneslator | Gene identifier conversion and annotation across 19 organisms |
| tRFUniverse / tRFexplorer | tRNA-derived fragments: expression, interactions and clinical correlates |
| DEGGs | Differentially expressed gene–gene pairs, with interactive regression plots |
| TACITuS | Transcriptomic data collector, integrator and selector |
| Alfredo Pulvirenti — Principal Investigator | Scholar · Profile |
| Salvatore Alaimo — Associate Professor | Scholar · @alaimos |
| Giovanni Micale — Researcher | Scholar · @GMicale |
| Grete Francesca Privitera — Post-doc | Scholar |
| Lorenzo Federico Signorini — Post-doc | Scholar |
| Alfredo Ferro — Professor Emeritus, founder | Scholar |
We organise the Lipari School — the J.T. Schwartz International School for Scientific Research, running since 1989, with tracks in Computational Life Sciences, Computer Science & Engineering, and Computational Complex & Social Systems.
Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania Torre Biologica "F. Latteri" — north side, 9th floor, Via Santa Sofia 89, 95123 Catania, Italy
Enquiries about theses, PhD projects and collaborations: write to the PI.