Publications
2026
demultiplexing and basecalling pipeline for Nanopore sequencing runs with dual-indexed Illumina-style barcodes, packaged as a reproducible Nextflow workflow.
TreeProfiler is a command-line tool that annotates any phylogenetic tree with metadata (ecology, taxonomy, phenotypes) and lets researchers visualise and query patterns across thousands of tips at once.
eggNOG v7 expands the gold-standard database of orthologous genes to cover 12,000+ species, adding phylogeny-aware functional predictions that help scientists interpret what newly sequenced genes do.
2025
The soil fungus Penicillium melinii boosts root growth in crops by producing specific metabolites; the study maps the molecular mechanisms behind this plant-growth promotion.
A global atlas mapping gene expression across the full tree of life at the single-cell level, revealing universal and lineage-specific cell-type programmes from microbes to animals.
A deep dive into environmental DNA databases reveals that chemoreceptor genes—bacterial sensors for chemical signals—are far more diverse and widespread in rare microbial communities than previously thought.
A step-by-step protocol for RNA-seq differential expression analysis using the Galaxy computational platform, accessible without programming skills.
2024
Faecal microbiota transplantation (FMT) in HIV patients reshapes the gut immune environment by changing which proteins are produced, pointing to microbiome-based strategies to reduce chronic inflammation.
A perspective on how the surge in biodiversity genomics—sequencing organisms across the full tree of life—is transforming our ability to detect and study orthologous genes at an unprecedented scale.
Machine learning scans millions of metagenome sequences and discovers thousands of previously unknown antimicrobial peptides with activity against drug-resistant bacteria.
A new large-scale phylogeny of salt-loving archaea shows that extreme halophily evolved independently multiple times, and identifies dozens of new lineages in hypersaline environments.
Analysing nearly one million prokaryotic genomes, the study maps how ecological pressures and evolutionary history jointly shape genome size, gene content, and metabolic diversity.
2023
Tens of millions of genes in environmental metagenomes lack any functional annotation. This study shows many of these 'unknown' genes are ancient, conserved, and likely encode novel essential functions.
Different criteria used to cluster genes into ortholog groups give different results; the study benchmarks them systematically and shows that no single method is universally best.
A computational pipeline screens environmental microbiome data for natural antibiotic compounds, identifying promising leads against resistant pathogens.
A comprehensive atlas of mRNA translation and decay rates across hundreds of bacterial species, revealing universal regulatory principles and species-specific adaptations.
proGenomes3 provides nearly one million consistently annotated prokaryotic genomes with curated taxonomy and habitat labels, enabling large-scale comparative genomics.
eggNOG 6.0 updates the comprehensive orthology database to cover 12,535 organisms with improved functional annotations, enabling comparative genomics at scale.
2022
Discovery of new bacterial phyla within the FCB superphylum using metagenome-assembled genomes, expanding our understanding of microbial diversity.
A multi-omics study of Earth's diverse microbiomes finds conserved metabolic functions and microbial markers shared across very different environments.
GeCoViz is a web tool to visualise the genomic neighbourhood of prokaryotic genes, helping researchers understand gene function through their genomic context.
PhyloCloud is an online platform to store, visualise, and share large phylogenomic trees and their associated metadata.
2021
Analysing thousands of prokaryotic genomes, this study maps the global biogeography of microbial genes and shows that geography and ecology both shape gene distributions.
eggNOG-mapper v2 greatly expands the functional annotation pipeline, adding domain predictions, GO terms, and KEGG pathway assignments for any protein or gene set.
Single-cell sequencing of sponges—among the earliest animals—reveals the origins of nervous system cell types and sheds light on animal evolution.
A survey of chemoreceptor repertoires in plant-associated bacteria shows that microbial sensory capacity is highly tuned to the plant environment.
A 10-year retrospective on the Quest for Orthologs community effort, summarising achievements, remaining challenges, and future directions in orthology research.
2020
The Quest for Orthologs community benchmarks 15 orthology methods on reference datasets, providing a consensus guide for researchers choosing tools.
A large-scale comparison disentangles how environmental conditions versus evolutionary history drive differences in prokaryotic genome content and metabolic potential.
proGenomes2 improves the database of annotated prokaryotic genomes with better taxonomy, habitat labels, and consistency checks across one million entries.
2019
Analysing global ocean metagenomes over time, the study separates gene-expression changes (within species) from community turnover (species replacement) as drivers of ecosystem-level shifts.
A review of the advances and biological applications enabled by accurate orthology prediction tools over the past decade.
NG-meta-profiler uses NGLess—a domain-specific language for NGS data—to process metagenomes faster and more reproducibly than general-purpose tools.
mOTUs2 profiles the abundance of microbial species from shotgun metagenome data using marker genes, enabling culture-independent community comparisons.
Treatment with broad-spectrum antibiotics can allow a single rare bacterial order to take over the gut, demonstrating how antibiotics disrupt microbial balance.
STRING v11 updates the comprehensive protein interaction database to cover more organisms and interaction evidence types, enabling network-based functional analysis.
eggNOG 5.0 builds a hierarchical database of orthologous genes across 4,445 organisms, with functional annotations at each taxonomic level.
2018
A comprehensive review of J-domain proteins (co-chaperones), covering their structure, evolutionary history, and roles in protein folding and cellular stress.
Shotgun sequencing and analysis of global topsoil samples reveals an enormous diversity of microbial life and its role in nutrient cycling.
A perspective on how the mosaic nature of microbial genomes—driven by horizontal gene transfer—complicates orthology inference and what strategies help.
2017
Analysis of metagenomic data from the global Human Microbiome Project identifies consistent subspecies within major gut bacterial species.
eggNOG-mapper performs rapid genome-wide functional annotation by assigning orthologs from the eggNOG database and propagating their functional terms.
A critical analysis of how support values (bootstrap, posterior probability) are displayed and interpreted in phylogenetic tree-viewing software.
Metabolic engineering of a 'anchor reaction' strategy to maintain stable performance in microbial cell factories.
proGenomes provides a curated collection of prokaryotic genomes with consistent functional and taxonomic annotations for comparative genomics.
2016
MOCAT2 is a pipeline for assembling, annotating, and profiling microbial genes from shotgun metagenome data.
ETE 3 is a Python toolkit for phylogenetic tree handling, offering analysis and publication-quality visualisation of large trees and their metadata.
ArthropodaCyc provides metabolic pathway databases for arthropod genomes, built on the CycADS automated annotation system.
After faecal microbiota transplantation, donor bacteria can stably coexist with the recipient's own bacteria for years, demonstrating lasting microbiome engraftment.
A standardised benchmarking framework for orthology methods, providing reference datasets and metrics to compare tools on equal footing.
eggNOG 4.5 restructures the orthology database into a hierarchical framework with improved functional coverage and updated annotations.