Anna Grandchamp

DeNoFo provides a standardised format and toolkit for reproducible de novo gene annotation, enabling consistent documentation and comparison across studies.

DESwoMAN identifies and characterizes novel open reading frames in transcriptomes and analyzes their mutation patterns across species.

This study identifies convergent genomic changes in socially parasitic ants, showing gene loss, innovation, and network rewiring in parasites compared to hosts.

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 estimates de novo transcript turnover rates in Drosophila melanogaster using long and short reads, finding a high turnover rate suggesting frequent exploration of new genomic sequences.

The paper identifies de novo transcripts in Drosophila melanogaster and shows they are associated with transposable elements and enriched transcription factor motifs.

This study identifies proto-genes in Drosophila melanogaster, showing they arise rapidly, are frequently lost, and are driven by transposable elements and ORF formation.

This study examines properties of human proto-genes, finding correlations between their genomic origin and features like introns, regulatory motifs, and domains.

This study identifies a de novo gene, atlas, essential for male fertility in Drosophila by facilitating chromatin condensation in spermatids, and reveals its complex evolutionary history.