Xiaofang Jiang

The paper identifies SpiE as a gut microbial enzyme that, along with SpiR, converts cholesterol to coprostanol, and shows its correlation with stool coprostanol levels and antibiotic impact.

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

This study determines the structure of Bap1 bound to VPS and shows how it facilitates biofilm adhesion and VPS organization through a conserved β-propeller interaction.

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

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.

The paper investigates how a Vibrio cholerae peptide binds lipids through a β-hairpin conformation, contributing to biofilm adhesion and host colonization.

The paper improves microbial phylogenetic analysis by selecting tailored marker genes from functional databases, enhancing tree accuracy across genomes and metagenomes.

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

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 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.

This study shows that only a limited number of gut bacteria can metabolize D-allulose via AlsE, suggesting its potential as a low-impact sweetener.

This study analyzes the distribution, diversity, and evolution of biofilm matrix clusters and proteins across Vibrio species, revealing structural and evolutionary patterns of key genes.

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

This study expands the number of complete temperate phage genomes by over 100-fold using a novel computational method applied to bacterial NGS data.

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.

The paper identifies transcriptional regulatory sequences in coronaviruses and finds recombination hotspots are more frequently co-located with TRS-B sites.

The paper characterizes mobile genetic elements in the gut microbiome, revealing phylum-level adaptive gene pools and their role in horizontal gene transfer.