Selected publications on computational biology, microbial ecology, and protein science.
Protein sequence similarity search is fundamental to biology research, but current methods are typically not able to consider crucial genomic context information. Gaia is a sequence annotation platform that enables rapid, context-aware protein sequence search across genomic datasets.
[FeFe] hydrogenases, previously thought to be exclusive to bacteria and eukaryotes, are present in diverse, active, and ancient lineages within anaerobic archaea. This study identifies and characterizes hybrid complexes formed by the fusion of [FeFe] and [NiFe] hydrogenases.
This study uses genome curation to complete metagenome-derived sequences that encode predicted proteins of up to 85,804 amino acids. Many giant genes in newly complete Omnitrophota genomes are located near genes homologous to type II secretion systems.
Borgs are remarkably large, divergent archaeal extrachromosomal elements with metabolic genes linked to the methane cycle. We identified at least 19 different Borg types coexisting with Methanoperedens spp. in four distinct ecosystems.