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 🤪

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

🚨 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!

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🧵

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...

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/... 🧵

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! 🙏

New paper with @peter-hoitinga.bsky.social ! Fun little project we started a while back :)

Degradation of extracellular polymeric substances shapes microbial community diversity | PLOS Biology https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003287

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/...

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...

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

New online! The global burden of inflammatory bowel disease: from 2025 to 2045

NIH advisory councils are being gutted - reviewers were ousted before starting. NIH staff were told to nominate Trump-loyal scientists, and warned that even those could be replaced by handpicked cronies. What’s happening at Trump’s NIH is a hostile takeover of science. zurl.co/WQS6B

I love that the title uses "delve": Delving into LLM-assisted writing in biomedical publications through excess vocabulary www.science.org/doi/10.1126/...

The 3-decade-old competition that enabled the emergence and evaluate of AlphaFold has run out of NIH funding. The program will be terminated in weeks. This is terminating success. www.science.org/content/arti...

🌳 In Europa bedroht ein neu eingeführter Pilz die heimische Esche ernsthaft. 🇬🇧 Ein Forschungsteam aus GB hat nun bewiesen, dass sich eine Population wilder Eschen in nur einer Generation genetisch an die Epidemie anpasst. 🧵 1/7

Metabolic modeling reveals determinants of synbiotic efficacy in a human intervention trial. https://www.medrxiv.org/content/10.1101/2025.06.24.25330246v1

1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬 www.science.org/doi/full/10....

New Consensus Statement in Nature Microbiology! Working with low-biomass microbiome samples? From deep subsurface rocks to human lungs, contamination is a major challenge. We offer field-to-data analysis guidelines to help keep your results clean. 📖 doi.org/10.1038/s415...

Has someone found a good way of getting money out of research? Don't stop it. Copy it. APC charges cost billions. MDPI leads with over $1.7bn (est. 2015-2023). Springer-Nature ‘only’ got $1.1bn and so what do they do? They copy MDPI. the-strain-on-scientific-publishing.github.io/website/post...

Thrilled to share our new paper in @science.org describing our discovery that bacteria can switch from competitors to bonafide predators when resources run dry—arming nanoscale “spears” (T6SS) to stab & consume neighbours. www.science.org/doi/10.1126/... #MicroSKy #Microbiology

Identification of dynamic models of microbial communities https://www.biorxiv.org/content/10.1101/2025.06.09.658565v1

A genomic catalog of Earth's bacterial and archaeal symbionts (bioRxiv pdf): www.biorxiv.org/content/10.1...