Open position at the Swiss Institute of Bioinformatics: We are looking for a Director of the Center of Pathogen Bioinformatics apply.refline.ch/499599/0346/... I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and

Only 48% of US high schools offer calculus. This seems like a huge problem and an easy place where high schools embracing online courses (+/- AI) could easily benefit students.

Excited to share our newest manuscript on antigen discovery and vaccine design for tuberculosis lead by Owen Leddy (everyone hiring new faculty in a few years, remember this name!) www.science.org/doi/10.1126/... #TBsky

If you're looking for a faculty position at the intersection of ecology and computing (both broadly defined), please apply to this joint search between the CEE Department and the College of Computing at MIT: cee.mit.edu/people/share...

Want to make some new conceptual graphics. Tried to give Powerpoint's AI 'copilot' a spin. Asked it to make me a slide with 100 circle shape objects randomly distributed. Was excited when it made me a pptx to download... except this is what it came up with. Why can't we have nice things?

New study of 800K+ genomes from gnomAD reveals most “pathogenic” variants in healthy people aren’t truly disease-tolerant. They are explained by annotation errors, mosaicism, or compensatory variants. 🧬 A big step for precision medicine! www.nature.com/articles/s41...

Academics in Assyria in the 7th c BC complain that admin is preventing them from doing research and teaching

New online! Microbial genomics for antimicrobial resistance ecology and action

When ChatGPT was asked to rate 40,000 résumés, it ranked the older male candidates as better quality than the younger female applicants.

We are racing to find antibiotics with AI, but what if we're ignoring the obvious? 🤔 This paper proves basic science is still here. No AI, Just one gene deletion revealed an intermediate 10-100x more potent against MRSA than the final drug. pubs.acs.org/doi/10.1021/... @challis-group.bsky.social

Remember the single most important think you can do is bring a friend to vote! Chris Cullen put together this great graph.

New preprint out! 📣🚨 We found that loss-of-function mutations in the carbapenem entry porin OprD of Pseudomonas aeruginosa do more than confer #AntibioticResistance: they reshape the bacterial membrane and interaction with the host, enhancing epithelial colonization capacity 🦠 #Microsky

*NEW PAPER* How much of a threat are within-organism conflicts, really? In Biology & Philosophy, @martijnschenkel.bsky.social, Manus Patten, and I present a mathematical framework to measure evolutionary individuality in the face of internal conflicts. link.springer.com/article/10.1...

The Kim Lab (sskimlab.org) at UC Irvine is recruiting motivated grad students interested in uncovering how transcriptional regulators direct cell fates. We accept students through the CMB (cmb.uci.edu) and MCSB (ccbs.uci.edu/education/mcsb/) PhD programs. Please share with prospective grad students!

Followers who live in Cambridge MA-- Please vote in the city council election. After the citywide repeal of single family zoning this past year (!), the NIMBYs are expected to turn out. You can vote early at any of the 3 locations through Friday, or in person on Tuesday.

Analysis of essential genes in Clostridioides difficile by CRISPRi and Tn-seq | Journal of Bacteriology journals.asm.org/doi/10.1128/...

I've been using chatgpt to improve my understanding of mammalian physiology and metabolic regulation, and I must admit its very useful.

Our new preprint, led by Martin (@mfenk.bsky.social), is online. We address the microbiome’s role as a source and incubator of acute infections by combining prospective collection of native samples with population-wide, culture-based sequencing. Please check out Martin’s wonderful thread. ⬇️🧵🎉

During an 𝘌𝘯𝘵𝘦𝘳𝘰𝘣𝘢𝘤𝘵𝘦𝘳 𝘩𝘰𝘳𝘮𝘢𝘦𝘤𝘩𝘦𝘪 infection, we observe a short-lived, non-synonymous mutation in the fimbriae regulator gene 𝘧𝘪𝘮𝘡 [F126L] that is first observed in the gut, before being associated with HAI but subsequently swiftly replaced by repeated body-wide sweeps of independent genotypes.

But were those pathogens acquired within the hospital or outside? Inferring the time to the most common recent ancestor reveals, that some lineages arose from a recent bottleneck during the hospital stay, while others have been colonizing the patient already before hospitalization.

Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it: www.biorxiv.org/content/10.1... Want to get started? github.com/rickbeeloo/b...

Hot take: In the era of LLMs, there is really no excuse for demanding that speakers provide a bio for an invited talk for the purpose of advertisement. Some people might want to control their bios, so perhaps a draft could be provided for the speakers to approve, edit, ore replace.

For 10 weeks starting in mid-July, NIH went on a tear. They issued 23,436 grants worth $14.9 billion—5k grants & $5 billion more than the same 10 weeks in FY24. In fiscal week 46 alone (mid-Aug), they awarded $2.1 billion in grants, nearly double their best week in FY24. NIH staff are amazing. 🤩

Monty Python understood p-hacking

Excited to share our preprint led by Carlos Voogdt et al We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera. www.biorxiv.org/content/10.1...

A fun little side project I've been working on with @stepadenisov.bsky.social , Mato Lagator, and Andreas Wagner: "Strong promoters are mutationally robust". Briefly... www.biorxiv.org/content/10.1...

Evolution of One Species Increases Resistance to Invasion in a Simple Synthetic Community Microbial Ecology link.springer.com/article/10.1...

“Food allergies in children dropped sharply in the years after new guidelines encouraged parents to introduce infants to peanuts, a study has found… a 36 percent reduction in all food allergies, driven largely by a 43 percent drop in peanut allergies” in children under 3 years old.

www.pnas.org/doi/10.1073/... #phagesky #phage defence #synbio #microsky

Its that time of year again when I become obsessed with delicata squash.

So, in my view, handedness is a great example of a trait where the relationship between genotype and phenotype is just inherently probabilistic. What you inherit is a likelihood, but how that plays out depends significantly on chance. (No hidden variables).

Paper is finally out!! Thanks to reviewers we dig deeper on the differences between domestication events -spoiler alert: it doesn't matter that much. nph.onlinelibrary.wiley.com/doi/full/10....

OUT TODAY: SimHumanity, a SLiM 5 model of the human genome, replete with demography, autosomes, X/Y & mtDNA. A shared starting point for reproducible evolutionary simulations. Huge thanks to coauthors Ben Haller, @mufernando.bsky.social & Philipp Messer. 🔗 www.pivotscipub.com/hpgg/5/4/0006

Exciting news! 🎉 In Jan 2026, I’ll be starting as an Assistant Professor at Mass General Hospital in Boston. The lab will study host–pathogen co-adaptation during chronic lung infections, and how it shapes treatment outcomes and disease progression. 🔗 Check out open positions: meirelleslab.org

Very cool phage study from @jeremyjbarr.bsky.social's lab. Isolation, engineering and ecology of temperate phages from the human gut #microbiomesky #phagesky

onlinelibrary.wiley.com/doi/full/10.... Remember -- it's easy to speculate that trait X imposes a fitness cost (but that's basically the biologist's version of drunk-uncle-whinging). Attacking with the T6SS doesn't impose a fitness cost.

We are recruiting new faculty in IMES at MIT! IMES (Institute for Medical Engineering and Science) is the MIT home of the famous HST program. As faculty are also appointed in a department at MIT, we have diverse research programs, all focused on human health. faculty-searches.mit.edu/imes-search/

Registration and abstract submission for the Probabilistic Modeling in Genomics Conference in Berkeley, March 2026, is open. Keynotes by Sally Otto and Jonathan Pritchard. Details: https://probgen2026.github.io/registration.html #conference

www.biorxiv.org/content/10.1... #microsky #phagesky #phage

Phages evolve fast, or do they? In oysters, some stay identical for years. With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements. Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...

I'm very excited to announce that UNC Biology has 6 faculty positions open this year! The first is for an Asst Professor who studies organismal resilience using an integrative approach 1/n unc.peopleadmin.com/postings/307...

This means that we can screen for potential novel drugs for schizophrenia and bipolar disorder in easily-grown skin cells, using mitochondria as a simple readout. In fact, a team at NIH’s NCATS is working on this now! Stay tuned.

Is a healthy microbiome one that is rich in phages? 🦠 Excited to share our paper out in Lancet Microbe with @bkoskella.bsky.social & @dholtappels.bsky.social where we test whether virome diversity can be used a broad signature of microbiome health 📈

The other day a student asked me about the prevalence of insider trading in prediction markets. I now have an answer.

I almost forgot I wrote a short review in 2019 saying this. genomemedicine.biomedcentral.com/articles/10.... The new supplementary notes have useful maths and historical references though.

Blog post: Ancestry and Education Indirect, direct, confounded and quasi-causal. I write about a preprint by Wang et al, in which they look for associations with genetic ancestry in an admixed Mexican population. They found genetic effects for height and Type-II diabetes, but not for education.

...or (2) the observation of driver mutations in normal tissues "proves" that non-mutational factors are needed to explain cancer (epigenetics, promotion, etc). Of course, many other factors are important, but ... [2/4]

A short thread. For years, I have been surprised by how much confusion our discovery of clones carrying cancer-driver mutations in normal tissues has caused in the cancer community. Typical questions like: (1) if you see these mutations in normal cells, are they really cancer drivers?... [1/4]

In our latest paper, I wrote 2 supplementary notes (5 and 6) to briefly recap classical models, starting with Armitage&Doll and moving onto models with different types of clonal expansions. Some readers may find them of interest. [4/4] static-content.springer.com/esm/art%3A10...