Katie E. Shalvarjian

Efficient biological design via genomic in-context learning

This paper demonstrates that in-context learning in the genome language model Evo 2 enables efficient biological sequence design without additional training.

Genus-specific remodeling of carbon and energy metabolism facilitates acetoclastic methanogenesis in Methanosarcina spp. and Methanothrix spp.

This study investigates the modular genetic pathways for acetoclastic methanogenesis in Methanosarcina and Methanothrix species, showing that gene modules are not interchangeable between the two genera.

The Ambiguous Genetic Code of Methanogenic Archaea that Grow on Methylamines

This study shows that methanogenic archaea use an ambiguous genetic code where the stop codon UAG can encode pyrrolysine, and that Pyl biosynthesis is regulated to manage this ambiguity.

Methanogenesis marker 16 metalloprotein is the primary coenzyme M synthase in Methanosarcina acetivorans

This study demonstrates that MMP16 is the primary CoM synthase in Methanosarcina acetivorans, showing that its deletion leads to CoM-dependent growth and transcriptomic changes, supporting its role as a bona fide ComF.