Tom A. Williams

The paper identifies a nucleolus-like condensate in E. coli that forms during cold adaptation to enhance ribosome biogenesis.

This paper improves ancestral genome reconstruction by incorporating gene-content grammar, leading to more accurate and consistent reconstructions across different methods.

The paper uses phylogenetic methods to determine the root of the Archaea, finding support for a methanogenic ancestor and a derived origin for host-associated lineages.

This paper shows that adding noise to gene content data improves machine learning predictions of bacterial phenotypes across evolutionary time, concluding the last bacterial common ancestor was anaerobic, double-membraned, and moderately thermophilic.

This study identifies bacterial and archaeal ancestors of eukaryotic COMMD proteins through structural and phylogenetic analysis, showing their origin from a single bacterial gene.

This study investigates the temperature dependence of triosephosphate isomerase activity using experiments and simulations, revealing non-Arrhenius behavior and dynamical differences between enzymes from different organisms.

The paper traces the evolutionary divergence of ribosomal drug-binding residues across eukaryotic clades to assess similarities and differences with humans and bacteria.

This study investigates the evolutionary relationships and halophilic adaptations of Nanohaloarchaeota and related DPANN archaea, identifying Caliditerrarchaeota as a new sister group and revealing distinct halophily mechanisms.

The paper identifies a new VPS29 isoform, VPS29C, which exhibits auto-inhibition limiting its association with Retriever and Retromer accessory proteins, revealing new complexity in Retromer function.

The paper investigates the evolutionary diversity of drug-binding residues in bacterial ribosomes to determine if divergence from E. coli is common or rare.

The paper investigates the evolutionary origins of central carbon metabolism in eukaryotes, revealing a chimeric gene repertoire with contributions from Asgardarchaeota and Alphaproteobacteria.

This study resolves the phylogenetic position of Njordarchaeales and Panguiarchaeales, placing them as a new class Njordarchaeia within Asgard archaea and identifying Panguiarchaeum as a metabolically reduced, potentially symbiotic lineage.

The paper identifies evolutionarily conserved principles of ESCRT-III-mediated membrane remodeling using an Asgard archaeal two-subunit system, showing homology to eukaryotic ESCRT-IIIB and IIIA.

This study sequenced the transcriptome of Pseudotrichomonas keilini, a free-living parabasalid, and compared its genome to parasitic relatives to understand evolutionary adaptations to anaerobic lifestyles.

AleRax estimates gene and species trees together using a probabilistic model of gene duplication, transfer, and loss, achieving higher speed and robustness than existing methods.

This paper isolates a new Streptomyces species from a deep-sea sponge and identifies six unique biosynthetic gene clusters through comparative analysis.

Asteroid is a new supertree algorithm that improves robustness to missing data and speed compared to existing methods like ASTRAL and ASTRID.

SpeciesRax infers species trees from gene family trees, accounting for duplication, transfer, and loss, and is accurate and faster than existing methods.