Publications

Presenting argNorm, a command line tool and Python library to normalize antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO)

We discuss challenges and opportunities for orthology inference in the context of the ongoing biodiversity genomics revolution.

We constructed a global microbial smORFs catalog (GMSC), demonstrating the immense and underexplored diversity of small proteins in the microbiome.

AMPSphere is an exploration of the antimicrobial peptides (AMPs) of the global microbiome.

We propose a framework for categorizing research software by its intended use and maintenance level and share seven practices for ensuring long-term maintenance, including reproducible research methods and public support forums. We call for the bioinformatics community to institutionalize software maintenance commitments through funders, peer reviewers, and journals, similar to data sharing mandates, to ensure software's long-term viability and reproducibility.

We studied horizontal gene transfer (HGT) using tree reconcilation between gene and species trees, which enabled us to observe different profiles for recent versus old events. For example, genes transferred earlier in evolution tend to be more ubiquitous within present-day species. We also found that co-occurring, interacting, and high-abundance species tend to exchange more genes.

Using a multitude of imaging methods, we cover 5 orders of magnitude to reveal that gelatinous organisms represent 30% of the total marine plantkon biovolume.

Thousands of previously-ignored protein families are found across the global microbiome.

SPIRE is a Searchable Planetary-scale mIcrobiome REsource that integrates various consistently processed metagenome-derived microbial data modalities across habitats, geography and phylogeny.

Environmental monitoring of antimicrobial resistance could help fight the resistance crisis, but some challenges remain

SemiBin2 uses self-supervised learning to improve on SemiBin1. It additionally adds support for long-read sequencing data.

ResFinderFG version 2

Baterial diversity in healthy female urinary tract

A machine-learning based tool for identifying and correcting misassemblies in metagenomic assemblies.

Transfer Learning-enabled context-aware microbial source tracking

What happens after a fecal microbiota transplantation (FMT)? Which microbes stay and which get replaced?

SemiBin is a semi-supervised binning method for metagenomes that improves on the state of the art across multiple environments.

Here, we report seven recommendations that help researchers implement software testing in microbial bioinformatics.

Segregate IHD-specific changes in gut microbial and metabolomic features from potential confounders.

Strategies combining biotin and prebiotic supplementation could help prevent the deterioration of metabolic states in severe obesity.

Presents the GMGC and concludes that the vast genomic diversity observed is driven by neutral evolution (not adaptation).

Conditional pledges can solve the collective action problem of code sharing (in neuroscience).

GUNC is a tool for finding chimeric genomes.

mBodyMap is a curated database for microbes across the human body and their associations with health and diseases.

Our results hint towards the strong role of environmental filtering in structuring cross-habitat bacterial but not fungal communities.

Macrel is a tool for finding AMPs in (meta)genomes

We explored the global principles of pangenome evolution, quantified the influence of habitat, and phylogenetic inertia on the evolution of pangenomes and identified criteria governing species ubiquity and habitat specificity.

NGLess is a tool for processing metagenomes. See more at https://ngless.embl.de

We show that mOTUs, which are based on essential housekeeping genes, are demonstrably well-suited for quantification of basal transcriptional activity of community members.

A New Meta-omics Resource for Global Ocean Microbiome Research

Our results should therefore be seen as a baseline and a framework for testing new hypotheses about changes in diversity within the whole plankton community across the global ocean, identifying the most vulnerable areas, and to better appreciate and anticipate functional and socio-economic consequences.

Progenomes2 is a collection of well-annotated, high quality prokaryotic isolate genomes.

Through extensive validations, this meta-analysis firmly establishes globally generalizable, predictive taxonomic and functional microbiome CRC signatures as a basis for future diagnostics.

We found that transmission to, and subsequent colonization of, the large intestine by oral microbes is common and extensive among healthy individuals.

We conclude that findings in dogs may be predictive of human microbiome results. In particular, a novel finding is that overweight or obese dogs experience larger compositional shifts than lean dogs in response to a high-protein diet.

Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.