Computational Tools
Our computational activity is tightly integrated with experimental research and is driven by biological questions rather than by standardised pipelines
We develop and adapt analytical frameworks to address specific challenges in RNA biology, cancer genomics, and transcript-resolved analysis, with a particular focus on long-read sequencing, RNA regulation, and multi-omics integration.
Infrastructure
Computational workflows are supported by scalable HPC and data infrastructure developed at IIT (DSC), enabling the analysis of large-scale sequencing datasets and the integration of multi-layered genomic information.
These frameworks are continuously updated to support emerging technologies, including long-read and direct RNA sequencing, single-cell multi-omics, and 3D genomic analyses.
Tools
A number of tools and analytical frameworks have been developed within the group to support different aspects of genomic and transcriptomic analysis:
- Nanocompore / NanocomporeV2 – detection of RNA modifications from direct RNA sequencing data from Nanopore data
- INSPEcT+ / INSPEcT- / INSPEcT-GUI – modelling and quantification of RNA dynamics
- compEpiTools – integrative analysis of epigenomic data
- Onassis – semantic-driven integration of multi-omics datasets
- ChroKit – interactive analysis and visualisation of chromatin data
- IsomiRage – analysis of miRNA expression and isoforms
- TDMDfinder – a catalogue of miRNA:Target pairs with TDMD features