Anne Lopes

DENSE is an automated pipeline for identifying de novo emerged genes, offering flexible strategies and a database of predictions across seven model organisms.

The paper shows that cytoplasmic lncRNAs in yeast are translated, affecting their abundance and post-transcriptional regulation through mechanisms involving NMD and ribosome binding.

SURFMAP maps protein surface features into 2D projections for visual and quantitative analysis.

The paper develops a theoretical framework to analyze how protein interaction energy landscapes are shaped by both functional and non-functional partners through cross-docking simulations.