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oveoyas.bsky.social
Ove Øyås 🇺🇦
@oveoyas.bsky.social
560 followers 1.4K following 62 posts
Computational systems biologist integrating data with mathematical models to explain biology. 🦠🍄🌱🐟🐮🧑 Researcher at Oslo Center for Biostatistics and Epidemiology (OCBE). Currently on paternity leave 🫐👶.
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oveoyas.bsky.social
Ove Øyås 🇺🇦 @oveoyas.bsky.social · Nov 1
Very 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: 🧵
Reposted by Ove Øyås 🇺🇦
harriswang.bsky.social
📢 Our Dept. of Systems Biology at Columbia University has an open tenure-track Assistant Professor position in the broad area of quantitative biology. Come join our awesome department in NYC! Please circulate.
apply.interfolio.com/177622
Suggested deadline: 12/15/2025.
@columbiasysbio.bsky.social
November 15, 2025 at 4:02 AM
Reposted by Ove Øyås 🇺🇦
hansonmark.bsky.social
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 11, 2025 at 11:52 AM
Reposted by Ove Øyås 🇺🇦
nilsgilman.bsky.social
You can’t really blame arXiv for the decision to stop publishing computer science stuff (given the flood of slop) but this is also a textbook example of a global public good being gratuitously degraded www.nature.com/articles/d41...
Preprint site arXiv is banning computer-science reviews: here’s why
The repository is taking steps to tackle a surge in low quality, AI-generated content.
www.nature.com
November 7, 2025 at 11:28 PM
Reposted by Ove Øyås 🇺🇦
tsbschm.bsky.social
Great to see this finally published!

Metalog: curated and harmonised contextual data for global metagenomics samples

now out in @narjournal.bsky.social

academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data
academic.oup.com
October 31, 2025 at 3:16 PM
Reposted by Ove Øyås 🇺🇦
ewanbirney.bsky.social
Definitely a good use of AI!
mbeisen.bsky.social Michael Eisen @mbeisen.bsky.social · Oct 15
Finally, someone has solved a real problem with AI! No more having to take a paper in the format for a journal that rejected you, and reformat it for a new journal. Well done!! formatmypaper.com
October 15, 2025 at 6:39 AM
Reposted by Ove Øyås 🇺🇦
cmkobel.bsky.social
Finally got my tool published!
October 9, 2025 at 6:22 PM
oveoyas.bsky.social
www.cell.com/cell-systems...
Accelerated design of Escherichia coli reduced genomes using a whole-cell model and machine learning
A machine learning model trained on whole-cell simulations predicts gene deletion effects on cell division. This approach enables rapid genome minimization and the design of a viable reduced E. coli g...
www.cell.com
September 25, 2025 at 8:31 AM
Reposted by Ove Øyås 🇺🇦
paulvilloutreix.bsky.social
Very happy to introduce jsPCA, a fast and interpretable computational framework for spatial transcriptomics that simultaneously identifies spatial domains and variable genes across multi-slice and multi-sample data.
September 19, 2025 at 6:50 AM
Reposted by Ove Øyås 🇺🇦
nature.com
Nature research paper: Learning the natural history of human disease with generative transformers

go.nature.com/4gzhLCo
Learning the natural history of human disease with generative transformers - Nature
Delphi-2M forecasts a person’s future health, covering more than 1,000 diseases, provides insights into co-morbidity dynamics and generates synthetic data for the training of AI models that have never seen actual data.
go.nature.com
September 18, 2025 at 9:06 AM
Reposted by Ove Øyås 🇺🇦
keenancrane.bsky.social
I got tired of mashing together tools to write long threads with 𝐫𝐢𝐜𝐡 𝑓𝑜𝑟𝑚𝑎𝑡𝑡𝑖𝑛𝑔 and ℳα†ℏ—so I wrote La𝑇𝑤𝑒𝑒𝑡!

It converts Markdown and LaTeX to Unicode that can be used in “tweets”, and automatically splits long threads. Try it out!

keenancrane.github.io/LaTweet/
September 11, 2025 at 1:28 PM
Reposted by Ove Øyås 🇺🇦
sulheim.bsky.social
Excited to share the first results from my postdoc at @dmf-unil.bsky.social with @saramitri.bsky.social
www.biorxiv.org/content/10.1...
Microbes release lower-value metabolites at higher rates
Microbes release a wide range of metabolites into their environment, yet the reasons for this release and the factors that influence release rates are not well understood. Here, using a combination of...
www.biorxiv.org
August 20, 2025 at 8:31 AM
Reposted by Ove Øyås 🇺🇦
symbionticism.bsky.social
We published a new lane of research today on human gut fungi. Shout out to 1st author @emilyvansyoc.bsky.social sky.social & @erdavenport.bsky.social For 20 years, bacteria received the lion's share of interest in the human gut. Yet we know little about the gut mycobiome. doi.org/10.1371/jour...
Gut fungi are associated with human genetic variation and disease risk
In contrast to decades of research on gut bacteria, human genetic determinants of the gut fungal community (mycobiome) remain understudied. This investigation presents the first GWAS on the number and...
doi.org
September 2, 2025 at 7:31 PM
Reposted by Ove Øyås 🇺🇦
sirileknes.bsky.social
Will they ever fix these issues?
We pay to publish
Pay to read
Write for free
Edit for free
Proofread for free
And they won’t even give us a single login across journals 🤪
vborghesani.bsky.social Valentina Borghesani @vborghesani.bsky.social · Aug 27
You know why my review is late. You know.
Login Failed message from an Editorial Manager
August 27, 2025 at 9:05 AM
Reposted by Ove Øyås 🇺🇦
mdg.no
Din stemme til MDG kan avgjøre om Sylvi Listhaug eller Jonas Gahr Støre styrer landet. Valget kan bli det jevneste på mange tiår, og om MDG havner under sperregrensen øker faren for et Frp-styrt Norge dramatisk. Stem allerede i dag: mdg.no/stem
Stopp FrP Stem MDG MDG over sperregrensen redder rødgrønt flertall. Bilde av alvorlig Arild Hermstad MDG-logo
August 26, 2025 at 7:39 AM
Reposted by Ove Øyås 🇺🇦
milocco.bsky.social
🚨 We're hiring!
PhD position in Evolutionary Systems Biology at Stockholm University & SciLifeLab

🎓 Focus: evolution, development, computational & mathematical modeling, prediction
📍 Stockholm, Sweden
🕒 4 years, fully-funded
🔍 Details: su.varbi.com/en/what:job/...

Please share!
August 25, 2025 at 9:01 AM
oveoyas.bsky.social
www.nature.com/articles/s41...
Quantifying large language model usage in scientific papers - Nature Human Behaviour
Liang et al. estimate the prevalence of text modified by large language models in recent scientific papers and preprints, finding widespread use (up to 17.5% of papers in computer science).
www.nature.com
August 16, 2025 at 11:16 PM
Reposted by Ove Øyås 🇺🇦
yoakiyama.bsky.social
Excited to share work with
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Scaling down protein language modeling with MSA Pairformer
Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...
biorxiv.org
August 5, 2025 at 6:31 AM
Reposted by Ove Øyås 🇺🇦
erictopol.bsky.social
Scientific fraud through paper mills and targeted journals is already occurring at scale. It is organized, orchestrated, and rapidly growing, far outpacing legitimate science
www.pnas.org/doi/abs/10.1...
August 4, 2025 at 8:00 PM
Reposted by Ove Øyås 🇺🇦
gibbological.bsky.social
You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements.

Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal.

journals.asm.org/doi/10.1128/...
🧵
Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems
In this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, ...
journals.asm.org
July 31, 2025 at 3:33 PM
Reposted by Ove Øyås 🇺🇦
richardsever.bsky.social
bioRxiv bat signal going up. We have a big backlog of submissions. If any affiliates have time to do some screening, we (and all the authors) would be immensely grateful! 🙏
July 31, 2025 at 12:32 PM
Reposted by Ove Øyås 🇺🇦
siribirkeland.bsky.social
New paper with @peter-hoitinga.bsky.social ! Fun little project we started a while back :)
cp-trendsgenetics.bsky.social Trends in Genetics @cp-trendsgenetics.bsky.social · Jul 29
"Pathway-level convergence: an underexplored aspect of convergent evolution"
by Peter Hoitinga (@peter-hoitinga.bsky.social)
& Siri Birkeland (@siribirkeland.bsky.social)‬

"The extent to which evolution is repeatable at the genetic level remains a central question in biology..."

shorturl.at/NXF4k
Figure 1. Types and examples of pathway convergence.
July 30, 2025 at 6:37 AM
Reposted by Ove Øyås 🇺🇦
pacyc184.bsky.social
Degradation of extracellular polymeric substances shapes microbial community diversity | PLOS Biology https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003287
Degradation of extracellular polymeric substances shapes microbial community diversity
Cross-feeding of small metabolites is known to drive carbon exchange among microbial species, but the role of extracellular polymeric substances (EPS) has been poorly understood. This study shows that EPS, formed during chitin degradation, drives microbial diversity by acting as a major, sequentially degraded, carbon source.
journals.plos.org
July 29, 2025 at 9:46 PM
Reposted by Ove Øyås 🇺🇦
greening.bsky.social
Our article showing energy production from air alone is in PNAS today. This paper provides an ultimate biochemical proof that microbes can survive simply by 'making' energy from air (making two ATP per molecule atmospheric H2 consumed) and has biotech applications. www.pnas.org/doi/10.1073/...
ATP synthesis driven by atmospheric hydrogen concentrations | PNAS
All cells require a continuous supply of the universal energy currency, adenosine triphosphate (ATP), to drive countless cellular reactions. The un...
www.pnas.org
July 25, 2025 at 12:54 AM
Reposted by Ove Øyås 🇺🇦
microbesrule.bsky.social
Back in 1962 microscopy was used to pen a hypothesis about eukaryote-microbe relationships. ~65 years later we have coupled the latest advancements in long read MetaG, MetaP and EUK SAGs to help explain what this means for wider rumen microbiome function www.nature.com/articles/s41...
Protozoal populations drive system-wide variation in the rumen microbiome - Nature Communications
Here, the authors reveal that protozoal communities shape rumen microbiome structure, offering fresh insights into how these complex communities coordinate essential metabolic tasks across multiple mi...
www.nature.com
July 25, 2025 at 7:19 AM
Reposted by Ove Øyås 🇺🇦
gretchentg.bsky.social
We are six months into the second Trump administration and the scale and severity of its assault on our nation's science and democracy has been unrelenting.

Today, @ucs.org releases a detailed assessment of the damage so far and where we go from here: www.ucs.org/resources/sc... #ProtectScience
Science and Democracy Under Siege
Documenting Six Months of the Trump Administration’s Destructive Actions
www.ucs.org
July 21, 2025 at 12:38 PM