João Luís Reis-Cunha

The paper identifies three proteins that negatively regulate ESAG transcripts through specialised RNA decay in Trypanosoma brucei, revealing a novel post-transcriptional regulatory mechanism.

The paper analyzes Leishmania guyanensis population genomics to show human-driven emergence of a city-proximal population distinct from ancestral sylvatic lineage.

This study shows that the Leishmania donovani species complex dispersed globally within the last 2,000 years, aligning with human migration and colonization.

The paper estimates the rate of sexual reproduction and inbreeding rate in Leishmania using population genomic data and a Moran model approach.

The paper develops a phylogeny-aware model to predict linear B-cell epitopes for Monkeypox virus, identifying nine specific peptides as potential diagnostic targets.

The paper analyzes aneuploidy patterns across 866 Trypanosomatid isolates, finding aneuploidies are ancestral and an ancient duplication is maintained in some species.

This paper presents a multi-objective approach to prioritize epitopes for diagnostic tests, balancing immunogenicity and cross-reactivity, and identifies 20 new potential epitopes across three pathogens.

The paper presents an improved genome assembly of Trypanosoma cruzi and reveals a unique genomic structure involving subtelomeric regions and retrotransposons contributing to antigenic variation.

ProphET identifies prophages in bacterial genomes with higher precision than existing tools and includes a self-updating reference database.