Software

Tools I lead, co-develop or contribute to. Three of them use AI — and each is built so you can check what the AI claimed.
SQANTI-epi
Lead developer
Transcript structure and chromatin state on one coordinate system, with a machine-learning model scoring accessibility per molecule.
Rust, Python · machine learning · ISMB 2026 HiTSeq talk · not yet public
PaintOmics AI
Lead developer
Multi-omics on KEGG, Reactome and MapMan pathways. An agent reads your results and drafts the biology with citations you can open and check.
Python, JavaScript · AI agent · paintomics.org · successor to PaintOmics 4
TELLME
Lead developer
Pathway explanation that earns its claims: keeps only the links your data confirms, and strips everything the evidence does not support.
Python · LLM with grounding checks · ELIXIR Science Tier project · not yet public
TUSCO
Lead developer
Single-isoform control genes for human and mouse. Any extra isoform called at one of them is a false discovery by construction.
Python, R · the evaluation layer inside SQANTI3 · Nature Communications 2026
SQANTI3
Contributor
The standard quality-control tool for long-read transcriptomes: classifies transcript models, flags artefacts, rescues real ones.
Python, R · 280 stars · ConesaLab · Nature Methods 2024
MirCure
Co-developer
Curation for microRNA annotations in animals and plants, scored on expression, biogenesis and conservation.
R · 7 stars · ConesaLab · Bioinformatics 2020