Robert Alan Edwards

This study investigates whether FIT samples can reveal a microbial signature of sessile serrated lesions, finding no significant differences in community structure but suggesting potential functional differences.

This paper organizes a community challenge to develop automated virus taxonomy classification tools and evaluates their performance on a combined dataset of expert-curated and metagenomic sequences.

The paper shows bacterial strain identity is the main factor determining phage infectivity in Achromobacter, with lineage and strain identity explaining 90% of variation in infection efficiency.

The paper predicts homooligomeric phage protein structures using a computational framework, confirming predictions for dimers and trimers and showing high accuracy in classifying homooligomeric states.

Baktfold improves protein functional annotation for microbial genomes using structural information, achieving higher annotation rates than existing tools for bacteria and archaea.

This study shows lithium affects behavior and physiology through the gut-brain axis by activating gut enterochromaffin cells, challenging the belief that lithium acts directly on the brain.

agtools provides a Python framework to manipulate assembly graphs across formats, enabling analysis and integration into bioinformatics workflows.

Phold pairs ProstT5-predicted 3Di tokens with Foldseek searches against 1,363,704 curated phage structures, annotating 49.4% of CDS in 1,419 INPHARED genomes versus 34.7% for Pharokka MMseqs2.

The paper proposes a roadmap for fair reuse of public microbiome data by introducing a Data Reuse Information tag (DRI) to facilitate communication between data creators and consumers.

The paper examines viral metabolism in coral reefs, finding that lytic viruses consume central carbon intermediates for virion production, while temperate viruses build them, leading to distinct ecosystem states.

Phynteny combines ESM2 protein embeddings, a BiLSTM, and circular-attention transformer layers to exploit phage gene order, assigning one of nine PHROG functional categories to unannotated genes.

This study uses structure-informed methods to annotate hypothetical proteins from Pseudomonas phages, showing that combining structural and sequence-based approaches can annotate up to 43% of previously unannotated proteins.

The paper analyzes 15,000 bacterial genomes to investigate the presence of antimicrobial resistance (AMR) genes in prophages across human body sites and regions, finding diverse AMR genes associated with prophages.

The paper identifies shared metabolic trends between degraded soils and T2D gut microbiomes, showing increased sugar metabolism and reduced lignin and branched-chain fatty acid metabolism.

Sphae is a bioinformatics pipeline that rapidly assesses phage therapeutic potential by analyzing genomic markers for safety and efficacy in under ten minutes.

Roughly 25× short-read depth polishes nearly all residual errors in Nanopore-only bacterial assemblies; new '--careful' modes in Pypolca and Polypolish largely avoid introducing low-depth errors.

The paper quantifies the compound processing potential of gut and soil metagenomes to link microbiome function to human health and ecosystem quality.

Hybracter improves bacterial genome assembly accuracy and speed, outperforming existing tools in hybrid and long-read-only modes, especially for small plasmids.

The paper predicts stop codon reassignment in bacteriophage genomes to improve functional annotation, showing significant increases in gene length and coding density.

Phables improves phage genome recovery from fragmented viral metagenome assemblies, recovering more high-quality genomes and resolving variants with high nucleotide identity.

The paper analyzes prophage DNA in human microbiome bacterial genomes, showing site- and health-related variations in prophage content and its impact on bacterial growth and microbiome structure.

The paper quantifies the benefits and costs of prophages in bacterial genomes, showing uniform prophage density and estimating their energetic contribution.

The paper introduces a machine-learning method to predict programmed ribosomal frameshifts with over 90% accuracy, addressing a gap in automated detection tools.

Hecatomb is a bioinformatics platform for viral metagenomics that enables read and contig analysis, integrating reference databases and providing tools for virome discovery.

The paper presents a gold-standard dataset of manually curated bacterial genomes and a framework to evaluate prophage prediction algorithms, showing their performance metrics across seven tools.

hafeZ identifies active prophages in bacterial genomes using read mapping, demonstrating accuracy on known datasets.

The paper introduces multiPhATE2, a tool for functional annotation and comparative genomics of bacteriophage genomes, with improved scalability and additional search algorithms.

PhANNs classifies phage ORFs into structural protein classes or 'other' with high accuracy using an artificial neural network ensemble trained on curated phage sequences.

RaFAH is a machine-learning method for virus-host prediction that outperforms existing methods with an F1-score of 0.97 at the phylum level, discovering new archaeal virus lineages and auxiliary metabolic genes.