Luca Parmigiani

On Deriving Synteny Blocks by Compacting Elements

This paper introduces a formal framework for deriving synteny blocks directly from sequence data to better capture genomic rearrangements without obscuring structural variation.

Interpolating and Extrapolating Node Counts in Colored Compacted de Bruijn Graphs for Pangenome Diversity

The paper introduces a method to interpolate and extrapolate node counts in colored compacted de Bruijn graphs to compare pangenomes while accounting for genome number variability and rare sequence influence.

EasyCircR:Detection and reconstruction of circular RNAs post-transcriptional regulatory interaction networks

EasyCircR detects and reconstructs circRNA-miRNA-mRNA regulatory networks through post-transcriptional analysis and visualization.

Panacus: fast and exact pangenome growth and core size estimation

Panacus quantifies core genome size and pangenome growth from pangenome graphs, processing large datasets efficiently.

Revisiting pangenome openness with k-mers

The paper estimates pangenome openness using k-mers instead of genes and compares the results, providing an efficient implementation.