Keith Dufault‐Thompson

Ancestral proteins trace the emergence of substrate specificity and oligomerization within bacterial DEDDy dinucleases

This study reconstructs ancestral bacterial DEDDy dinucleases to trace the evolution of substrate specificity and oligomerization from a dimeric ancestor with intermediate preferences.

LAMBDA: A Prophage Detection Benchmark for Genomic Language Models

The paper introduces LAMBDA, a benchmark to evaluate genomic language models' ability to detect prophage sequences across four complexity levels.

Discovery of BilV reveals a multienzymatic basis for bilirubin reduction across vertebrate gut microbiomes

The paper identifies BilV, a novel enzyme that works with BilR to reduce bilirubin to urobilinogen, and shows its distribution varies across vertebrate gut microbiomes.

Gut Bacteria Metabolize Natural and Synthetic Steroid Hormones via the Reductive OsrABC Pathway

The paper identifies a novel gut bacterial pathway for steroid hormone metabolism and shows its impact on drug efficacy in Crohn's disease.

The Impact of Tokenizer Selection in Genomic Language Models

This study evaluates the impact of tokenizer selection on genomic language models, finding that character tokenization outperforms sub-word methods for nucleotide-level tasks, but byte-pair encoding performs better for SARS-CoV-2 variant classification.

Gut Bacteria Encode Reductases that Biotransform Steroid Hormones

Gut bacteria encode 5β-reductase, fused 3β-HSDH/Δ5-4 isomerase and Δ6-3-ketosteroid reductase enzymes acting on steroid hormones; two of these genes are enriched in female gut metagenomes.

Deciphering Phage-Host Specificity Based on the Association of Phage Depolymerases and Bacterial Surface Glycan with Deep Learning

The paper develops SpikeHunter, a deep learning model to identify tailspike proteins from prophages, revealing associations between these proteins and bacterial serotypes.

Reconstruction and analysis of thermodynamically-constrained models reveal metabolic responses of a deep-sea bacterium to temperature perturbations

This study uses thermodynamically-constrained genome-scale models to simulate metabolic responses of a deep-sea bacterium to different temperatures, revealing changes in metabolic efficiency and pathway utilization.

Putative host-derived insertions in the genome of circulating SARS-CoV-2 variants

The paper identifies two host-derived insertions in SARS-CoV-2 genomes using RNA sequencing and GISAID data, showing integration of human rRNA fragments into viral genomes.

Diversity and Function of the Eastern Oyster (Crassostrea virginica) Microbiome

This study characterizes the microbiome of the eastern oyster using 16S rRNA profiling, shotgun metagenomics, and metabolic reconstruction, revealing a dominant Mollicutes taxon with unique metabolic functions.