Collaborative research projects in life sciences increasingly need to integrate private, embargoed consortium data with public reference databases in order to reach statistically meaningful interpreta...

Microbial communities often maintain ecosystem functions despite environmental fluctuations and compositional turnover. This robustness is frequently …

Viral mutation forecasting plays a key role in pandemic preparedness by enabling researchers to anticipate novel variants and design proactive interventions. Evolutionary histories, represented as phy...

The branches of systems biology focusing on mechanistic modeling have worked on standardizing data formats and vocabularies for well over two decades,…

MetaCAT is a computational framework to assess host–microbiome interaction via a combination of high-accuracy and efficient microbial genome reconstruction and metagenome-wide association studies with...

The current best bounds on the matrix multiplication exponent $ω$ are obtained through a refinement of the laser method called combination loss analysis (Duan et al., 2022; Williams et al., 2024; Alma...

Wastewater treatment relies on complex microbial communities, yet existing genome-resolved references for this essential engineered ecosystem remain dominated by short-read assemblies, limiting genome...

Nature Methods - Getting over ANOVA: estimation graphics for multi-group comparisons

AbstractSummary. Accurate enzyme turnover numbers are essential for building enzyme-constrained genome-scale metabolic models. However, collecting and cura

Is microbial ecology fair? This study uses an ecological ‘Game of Growth’ to explore how fair ecological dynamics is as a distribution rule of biomass, revealing the degree of meritocracy found in the...

COMBINE-lab develops algorithms, data structures, and software for high-throughput genomics.

Metabolic modeling with stoichiometric models and flux balance analysis (FBA) has greatly advanced our understanding of metabolism. However, valid FBA predictions require mechanistically correct const...

Networks of metabolic exchanges are essential for multicellular systems and microbial consortia. Øyås et al. introduce minimal pathways, which generalize concepts of metabolic pathway analysis. By com...

Schmidt et al. introduce the tree labeling polytope, a mathematical framework to infer the ancestral states on a phylogenetic tree. This framework enables researchers to infer the routes of metastases...

First-principles approaches, based on physics or chemistry, are key pillars of biological theory. Despite their value, there are recurrent problems with many first-principles approaches in biology: th...

TaxVAMB combines sequence features with taxonomic information for improved metagenome binning.

A model for the evolution of multicellularity in a spatially heterogeneous environment shows that indirect mechanisms such as escape from competition and increased environmental exploitation can drive the evolution of multicellularity in the absence of direct benefits.

StructureMASST enables pan-repository MS/MS searches using a chemical name or structure.

Progress toward a true virtual cell will depend on uniting AI’s pattern-finding power with the causal rigor of mechanistic models.

Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.

AbstractAims. Attribution-based explainability methods are widely used in electrocardiogram (ECG) analysis to interpret predictions from ‘black-box’ deep n

Using individual-level data from the Swedish Prescribed Drug Register and fecal metagenomes of 14,979 individuals in Sweden, the authors examined the association between oral antibiotic use over 8 yea...

Job title: Postdoctoral position in Machine Learning and Computational Biology (296798), Employer: University of Oslo, Deadline: Friday, April 10, 2026

Sequencing of marine sediments finds 136 newly identified Heimdallarchaeia and several novel lineages, and indicates that Heimdallarchaeia evolved distinct metabolic capabilities from other Asgardarchaeota, in conditions that may have given rise to early eukaryotes.

Nature Reviews Genetics - In this Review, Ji et al. overview how rapidly advancing experimental and computational methods are enabling improved and automated annotation of gene structure and...

We are seeking two ambitious Postdoctoral Researchers to join the Köhn-Luque group at the Oslo University Hospital. These 3-year positions are part of a high-impact project funded by the Norwegia...

Job title: 4-year PhD position in Biostatistics (292171), Employer: University of Oslo, Deadline: Thursday, February 12, 2026

Here, with metagenomic analyses on longitudinal samples collected from 195 mother-infant pairs, the authors show that the breast milk microbiome contributes to infant gut assembly through bacterial st...

Download the updated bacterial and archaeal reference genome collection! We built this collection of 22,307 genomes by selecting the “best” genome assembly for each species among the 450,000+ prokaryo...

Abstract. Despite an ever-expanding number of bacterial taxa being discovered, many of these taxa remain uncharacterized with unknown traits and environmen

Comprehensive large-scale studies of multi-national populations identified microbiome species consistently associated with favourable and unfavourable health markers, informing future studies of the human gut microbiome and its association with diet and cardiometabolic conditions.

In this work, we present a manually curated genome-scale metabolic model for Ruminiclostridium cellulolyticum, one of the few species known to fully degrade cellulose and hemicellulose. The model was ...

Author summary Microbial communities, vital for human and environmental health, are complex systems whose quantitative behaviors are not yet fully understood. Scientists employ mathematical models to ...

Glycolysis is a fundamental metabolic pathway central to the bioenergetics and physiology of virtually all living organisms. In this comprehensive review, we explore the intricate biochemical princip....