Genome-resolved ecology and evolution of the microbiome enabled by quantitative long-read metagenomics https://www.biorxiv.org/content/10.64898/2026.09.28.754546v1
Ove Øyås 🇺🇦
@oveoyas.bsky.social
Computational systems biologist integrating data with mathematical models to explain biology. 🦠🍄🌱🐟🐮🧑 Researcher at Oslo Center for Biostatistics and Epidemiology (OCBE).
The ModelSEED Biochemistry Database, 2026 update: grading multi-source thermodynamics https://www.biorxiv.org/content/10.64898/2026.09.15.751859v1
Growth rate and yield are not constrained by a trade-off in microbes https://www.biorxiv.org/content/10.64898/2026.09.08.750265v1
www.sciencedirect.com/science/arti...
The evolution of standards in systems biology: From metabolic and multi-scale to whole-cell models
The branches of systems biology focusing on mechanistic modeling have worked on standardizing data formats and vocabularies for well over two decades,…
sciencedirect.com
www.nature.com/articles/s41...
MetaCAT enables reconstruction of high-quality microbial genomes and their association with host traits from metagenomic data - Nature Microbiology
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...
nature.com
$3.7 billion spent on APCs in 2025. That's ~1000X more than it costs to run bioRxiv/medRxiv. Worth thinking about as we consider how to fund infrastructure... arxiv.org/pdf/2608.16322
arxiv.org
www.biorxiv.org/content/10.6...
The MiDAS global genome catalog: 53,501 long-read MAGs representing all core prokaryotic genera in the global activated sludge microbiome
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...
biorxiv.org
Happy to finally share these results: Cross-feeding enables robust coexistence between four bacterial species www.biorxiv.org/content/10.6... With @saramitri.bsky.social @lambdapp.bsky.social @dan1elmachado.bsky.social @lhtxra.bsky.social Eric Ulrich, Alisson Gillon & Sam Testa #microsky
academic.oup.com/bioinformati...
WILDkCAT: Extract, retrieve, and predict enzyme turnover numbers of constraint-based metabolic models
AbstractSummary. Accurate enzyme turnover numbers are essential for building enzyme-constrained genome-scale metabolic models. However, collecting and cura
academic.oup.com
journals.plos.org/plosbiology/...
Normative assembly rule reveals fairness in microbial communities
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...
journals.plos.org
My journey with @anthropic.com's Fable 5 model has been a very short one; characterized by "No". So, in my most recent blog post, I explain why I think "Fable is not a useful model" combine-lab.github.io/blog/2026/07...
COMBINE-lab - Fable is not a useful model
COMBINE-lab develops algorithms, data structures, and software for high-throughput genomics.
combine-lab.github.io
link.springer.com/article/10.1...
Thermo-flux: generation and analysis of thermodynamic-stoichiometric metabolic network models - Molecular Systems Biology
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...
link.springer.com
Our paper on minimal metabolic pathways is finally out! 🙌 www.cell.com/cell-systems... I have summarized the new methods and some applications they enable in the thread below. 🧵 A stable version of the mptool toolbox is on PyPi and a major update is already on GitLab. 🤖 gitlab.com/csb.ethz/mpt...
Scalable enumeration and sampling of minimal metabolic pathways for organisms and communities
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...
cell.com
Ove Øyås 🇺🇦@oveoyas.bsky.social · 2y agoVery excited to share our latest preprint on metabolic pathway analysis! 📰 By focusing on minimal pathways, we can enumerate or sample pathways efficiently in large models with new methods. ⚡ This also enables some cool new applications: 🧵
It took several years, but @hmbaghdassarian.bsky.social got it working... genome scale models of human metabolism, transcription, translation, and protein secretion (ME+secretion model). Check out the preprint! www.biorxiv.org/content/10.6...
Hello #world, meet 1,000× Expansion Microscopy. A small gel would grow to the size of an Olympic swimming pool, while amino-acid-scale distances become visible with ordinary light microscopy. Led by Helena Hu from @eboyden3.bsky.social's lab, in collab with us. Story: www.biorxiv.org/content/10.6...
The tree labeling polytope: A unified approach to ancestral reconstruction problems: Cell Systems www.cell.com/cell-systems...
The tree labeling polytope: A unified approach to ancestral reconstruction problems
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...
cell.com
A Differentiable dFBA Simulator for Scalable Bayesian Inference over Microbial Metabolic Models https://www.biorxiv.org/content/10.64898/2026.05.05.722888v1
Out today in @cp-trendsecolevo.bsky.social our paper “Second Thoughts about First Principles in Biology.” www.cell.com/trends/ecolo... . We are in favour of first principles approaches in biology but we think that we need to do better in how we use them.
Second thoughts about first principles in biology
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...
cell.com
Improving metagenome binning by integrating intrinsic features and taxonomy - @ucph.bsky.social @aicentre.dk go.nature.com/3QpQ3iq
Improving metagenome binning by integrating intrinsic features and taxonomy - Nature Biotechnology
TaxVAMB combines sequence features with taxonomic information for improved metagenome binning.
go.nature.com
Direct benefits are not necessary for the evolution of multicellularity | Nature Ecology & Evolution https://www.nature.com/articles/s41559-026-03044-y
Direct benefits are not necessary for the evolution of multicellularity - Nature Ecology & Evolution
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.
nature.com
Structure-centric searching enables global mapping of the public metabolome - @pieterdorrestein.bsky.social @mingxunwang.bsky.social @yelabiead.bsky.social go.nature.com/481Sbmk
Structure-centric searching enables global mapping of the public metabolome - Nature Biotechnology
StructureMASST enables pan-repository MS/MS searches using a chemical name or structure.
go.nature.com
@shrylishreekar.bsky.social and me wrote a commentary on Chunhui Hao's and @stuwest.bsky.social et al.'s recent paper "Cooperation and the evolution of bacterial niche breadth" in PNAS. Please find our commentary here: www.pnas.org/doi/10.1073/...
1/25 New paper out in PNAS! We show that the fitness costs of reproductive specialization, where somatic cells give up reproduction, scale inversely with organism size. Larger organisms can afford far more soma, removing a key barrier to multicellular complexity.
The fitness costs of reproductive specialization scale inversely with organismal size
pnas.org
The lab of Johannes Zimmermann at Jena University has an opening for a PhD position - exciting research in a highly innovative group: www.jsmc-phd.de/admission/va...