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...

There are 2 previous historical cases of countries destroying their science and universities, crippling them for decades: Lysenkoism in the USSR and Nazi Germany. The Trump administration will be the 3rd. It's not just budgets but research, institutions, expertise, and training the next generation.

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

JOBS ALERT! PhD position & 3-y postdoc position in statistics within my research group at @ocbe.bsky.social @uio.no Both are linked to a project funded from the Research Council of Norway on Integrative Bayesian clustering for high-dim data in omics Deadline: 13 June 2025 More info & links below!

Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.biorxiv.org/content/10.1...

Only 4 days left to the deadline: Become our new colleague as associate professor in biostatistical machine learning at Oslo Centre for Biostatistics and Epidemiology @ocbe.bsky.social and our Centre of Knowledge-driven Machine Learning Integreat! www.jobbnorge.no/en/available...

What is possible in the space of organs, organoids and organisms? How can synthetic biology help designing new types of tissues and even novel organs? How can cognition be engineered from scratch? Check our paper @jordiplam.bsky.social @drmichaellevin.bsky.social www.nature.com/articles/s41...

Europe will always stand for science and the freedom to learn and invent. As of 11 am, tune in, and discover how the @ec.europa.eu wants to help the best and brightest ‘Choose Europe’. → europa.eu/!Tx43kH

I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers, www.biorxiv.org/content/10.1... and tell you just a little bit about it in the following 🧵

GEMsembler: cross-tool structural comparison and ensemble modeling improve metabolic model performance https://www.biorxiv.org/content/10.1101/2025.04.09.647174v1

Is the genome just a bag of genes? A new paper in Science now reports that for two thirds of an organisms' genes the position along the chromosome is actually very tightly constrained! Amazing work from my favorite night scientist Martin Lercher and his team! www.science.org/doi/10.1126/...

www.nature.com/articles/s42... Metabolites are not genes. repeat, please!

Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social: rdcu.be/eg4OA 1/