John Mattick

This paper introduces a phylogenetic occupancy model to infer gene presence in incomplete genomes, outperforming existing methods and enabling ancestral-state reconstruction.

This paper investigates the evolutionary origin of eukaryotic spliceosomal introns by analyzing group II introns in asgard archaea and proposes that introns originated from the archaeal genome, not mitochondria.

The paper predicts bacterial and archaeal transcripts using ONT direct RNA sequencing and public data, revealing novel and previously characterized transcripts across multiple strains.

This study evaluates the impact of read length and pairing on differential expression analysis in host-pathogen interactions, finding 54-bp paired reads most robust and 36-bp single reads suitable for bacterial samples.