Peter Florian Stadler

The paper introduces bi-alignments to model incongruent evolution of RNA sequence and structure, showing they are a special case of 4-way alignments and finding such incongruence is not rare in the Rfam database.

The paper identifies 27 new telomerase RNAs in Saccharomycetacea but finds that most Saccharomycotina genomes lack annotated telomerase RNA due to sequence variability.

The paper analyzes protein domain distributions across eukaryotes to identify evolutionary patterns and finds widespread avoidance of certain domains associated with specific gene ontology terms.

The paper reviews methods to represent regulatory feedback in cellular processes and discusses their implications for synthetic biology.