Robert D. Finn

The paper introduces BioSIFTR, a tool that uses shallow shotgun sequencing and biome-specific databases to generate accurate taxonomic and functional profiles, validated against deep sequencing data.

MAP annotates mobilome elements and their functional cargo in prokaryotic (meta)genomic assemblies, enabling identification of composite elements like ARG-carrying integrons.

The paper identifies a new transposable element, Tangerine, in the lichen fungus Xanthoria parietina, showing evidence of horizontal gene transfer and potential role in lichen genome evolution.

The paper introduces CABBAGE, a large-scale AMR genotype-phenotype database linking bacterial genomes to antibiotic susceptibility data and metadata, enabling analysis of resistance trends and predictive method benchmarks.

The paper introduces a fast clustering tool for bacterial genomes, enabling efficient analysis of millions of genomes and revealing taxonomic insights.

The paper shows that biological meaning in protein embeddings depends on resolution, with different levels of organisation preserving distinct biological relationships.

This study analyzes gut microbiome and resistome diversity in Indigenous Orang Asli communities in Malaysia, finding that urbanization reduces microbial diversity but increases antibiotic resistance gene diversity.

This study develops a machine learning framework to predict memory requirements for metagenomic assembly, improving efficiency in high-performance computing environments.

This study uses long-read metagenomic sequencing to analyze Peltigerales lichen symbionts, revealing high transposable element content and their potential role in lichenization evolution.

The paper introduces a scalable pipeline for grouping protein sequences into families, showing it matches curated databases and scales linearly with input size.

PIMENTO identifies and removes primer sequences from amplicon sequencing data to enable large-scale variant calling.

The paper identifies millions of new protein families from global metagenomic data, expanding the known repertoire of protein families and revealing potential novel functions.

RNAcentral integrates literature and gene-level data to enhance non-coding RNA sequence analysis and functional understanding.

The paper studies seasonal changes in a modern microbialite reef, finding that environmental fluctuations drive microbial community shifts and mineralization patterns, indicating metabolic drivers over taxonomy in carbonate precipitation.

The paper develops EVADES, a database of phage anti-defence proteins, predicts mechanisms for 21 uncharacterized ADPs, and explores their evolutionary and functional relationships.

Mettannotator is a scalable Nextflow pipeline for prokaryotic genome annotation, capable of handling both known and novel taxa, and it produces GFF files for downstream analysis.

CODARFE predicts continuous environmental variables from microbiome data, outperforming existing tools in correlation and prediction accuracy across multiple datasets.

CELEBRIMBOR improves core gene identification in metagenome-assembled genomes by adjusting frequency thresholds based on genome completeness.

This study compares molecular functions and biosynthetic gene clusters in cyanobacterial genomes to identify specializations associated with symbiotic lifestyles.

plastiC recovers and characterizes plastid genomes from metagenomic datasets, demonstrating its utility in recovering algal plastid MAGs from lichen metagenomes.

VIRify identifies and classifies viral contigs and prophages from metagenomic data with high accuracy across prokaryotic and eukaryotic viruses.

This paper introduces SanntiS, a machine learning tool for identifying biosynthetic gene clusters in genomic and metagenomic data, and demonstrates its ability to predict a large number of novel BGCs with experimental validation.

The paper describes the Ensembl COVID-19 resource, which integrates SARS-CoV-2 genomic data and variant annotations to support research on virus variants and their impact on therapeutics and vaccines.

R2DT generates standardised 2D RNA structure diagrams for diverse ncRNA types using a template library, producing a large dataset of visualisations.

The paper analyzes 1,167 archaeal genomes from the human gut to reveal novel species, genomic adaptations, and correlations with socio-demographic factors.

The paper assesses the value and sustainability of ELIXIR Core Data Resources, showing their critical role in preserving biological data and highlighting funding challenges.

The paper introduces EukCC, a tool for estimating eukaryotic genome quality in metagenomic data, showing it outperforms existing methods and identifies novel genomes from two biomes.

The paper evaluates metagenome and amplicon analysis tools by meta-analyzing benchmarking studies to identify accurate sequence-to-taxonomy mapping software.