Armando J. Pinho

GeAnno improves gene annotation in complex plant genomes using supervised machine learning, achieving high precision and transferability across species.

This paper introduces FALCON2, a metagenomic classifier for ancient viral DNA that outperforms existing tools on short and degraded reads.

This paper optimizes genomic sequence compression using genetic algorithms, achieving high compression rates on large datasets like the human genome.

AlcoR is a tool for simulating, mapping, and visualizing low-complexity regions in genomic and proteomic sequences, demonstrating high efficiency and accuracy on synthetic and natural data.

GTO is a toolkit that unifies pipelines in genomic and proteomic research by combining specialized tools for data analysis, simulation, compression, and visualization.

Smash++ identifies genomic rearrangements without sequence alignment, using data compression, and validates results against existing methods and FISH analysis.

FALCON-meta infers metagenomic composition from ancient DNA samples using an alignment-free compression-based method, avoiding overestimation and computational inefficiencies.