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...

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.

Improving metagenome binning by integrating intrinsic features and taxonomy - @ucph.bsky.social @aicentre.dk go.nature.com/3QpQ3iq

Direct benefits are not necessary for the evolution of multicellularity | Nature Ecology & Evolution https://www.nature.com/articles/s41559-026-03044-y

Structure-centric searching enables global mapping of the public metabolome - @pieterdorrestein.bsky.social @mingxunwang.bsky.social @yelabiead.bsky.social go.nature.com/481Sbmk

@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 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...

Fantastic new paper casting doubt on explainability of explainable AI. To explain complex machine learning algorithms you need reproducibility of the explanation at a minimum academic.oup.com/ehjdh/articl... #machinelearning #Statistics #StatsSky @maartenvsmeden.bsky.social

A relic at risk: Genomic evidence for an early-diverging domesticated lineage in Norwegian farmhouse yeast https://www.biorxiv.org/content/10.64898/2026.03.16.711853v1

🚨 New paper! Very excited to have been part of this collaborative work looking at the effect of antibiotics on the gut microbiota even years after prescription. Amazing effort led by Gabriel @tovefall.bsky.social and many others published today in Nature Medicine! 🔗 www.nature.com/articles/s41...

Open postdoctoral position (3-years) in Machine Learning and Computational Biology! www.jobbnorge.no/en/available... Job conditions are great 🏥💶 The scientific environment is top-notch 🧬 Oslo is a fantastic place to live ⛷️🏔️ ☀️ 🌲 Please, get in touch if you have questions

Nature research paper: Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor go.nature.com/4rSfRRw

Our new review on genome annotation just appeared in @naturerevgenet.bsky.social, with a particular focus on the human genome, with Hayden Ji and Mihaela Pertea: rdcu.be/e4mI1

Happy to announce that CarveMe is now running online at usegalaxy.eu and usegalaxy.no 🙂

We are hiring! Seeking two ambitious postdoc to work at intersection of math modeling and machine learning for personalize breast cancer treatment. 2411.webcruiter.no/Main2/Recrui... Great conditions, top-notc scientific environment and a fantastic place to live. Please, get in touch for more

They can hide, censor, and deny #climate change science but that doesn't change the #science. They can try to repeal the #Endangerment Finding but that doesn't change the danger. Reality will always win and history will never forget what they're doing and who is doing it.

We’re hiring: Research Group Leader in computational biology. Are you generating more research ideas than you can explore? Lead cutting-edge AI & biology research at EMBL-EBI. Apply by 11 April 2026: embl.wd103.myworkdayjobs.com/en-US/EMBL/j... #ScienceCareers @ewaldlab.org @embl.org

Only a few days left to apply for this interesting PhD position in biostatistics at OCBE: www.jobbnorge.no/en/available... @jmgran.bsky.social

Breast milk isn't just nutrition – it delivers live bacterial strains that colonize the infant gut and persist for months. Happy to share our new paper, where we used metagenomics to track bacterial strains between 195 mother-infant pairs over the first 6 months of life: doi.org/10.1038/s414...

From #NCBI Insight | Updated Bacterial and Archaeal Reference Genome Collection is now available | #Bioinformatics #Genomics #OpenScience #OpenData 🧬 🖥️ 🧪 ⬇️ ncbiinsights.ncbi.nlm.nih.gov/2026/01/13/a...

New paper up - inspired by the periodic table of the elements, we attempted to organize bacterial diversity in genome-inferred trait space academic.oup.com/ismej/advanc...

A database of over 15.000 strain design publications reveals a conserved set of metabolic engineering targets across microbial hosts and products https://www.biorxiv.org/content/10.64898/2025.12.15.694291v1

Nature research paper: Gut micro-organisms associated with health, nutrition and dietary interventions go.nature.com/4oODWqv

Our new genome-scale model for R. cellulolyticum is out on mSystems: journals.asm.org/doi/10.1128/... Very proud of the hard work of my PhD student, Idun Burgos 😊

Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬 www.nature.com/articles/s41...

"Our results enable us to reject mitochondrion-early scenarios of eukaryogenesis, instead supporting a complexified-archaean, late-mitochondrion sequence for the assembly of eukaryote characteristics" www.nature.com/articles/s41...

Revealing the dynamical time course of physiological changes before, during and after menopause. This revealed sudden changes at menopause in nearly all physiological systems. (2/2) arxiv.org/abs/2511.05906

Gift link for NY Times article on cuts at NIH and NSF: www.nytimes.com/interactive/...

I am very excited to announce that a fully funded PhD position is available in my group. Topic: Synergistic coevolution in mono-specific and multi-species microbial consortia Please RT or forward this information to interested candidates. Deadline: 11.01.26 More info: shorturl.at/f1TuF

Don't miss out on our free virtual symposium (Dec. 12th) focused on microbial metabolites and their effects on the host. Sponsors: @amiposts.bsky.social, Pendulum, & Liv (@zymoresearch.bsky.social) Registrants will receive free memberships to Applied Microbiology International. Details below 👇

📢 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

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/...

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...

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-...

Definitely a good use of AI!

Finally got my tool published!

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.

Nature research paper: Learning the natural history of human disease with generative transformers go.nature.com/4gzhLCo

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/

Excited to share the first results from my postdoc at @dmf-unil.bsky.social with @saramitri.bsky.social www.biorxiv.org/content/10.1...

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...

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 🤪