Great to see this from @vmetzis.bsky.social & co published Dissection of CDX2 regulatory elements identifies a repressive element that converts to an enhancer with a nuclear receptor motif switch www.cell.com/developmenta...

✨Exciting news: the main story of my PhD is out in Science! Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation. 📖 Read the full story here: www.science.org/doi/10.1126/...

This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)

🚨🚨🚨🧪 H1B scientists who are traveling outside the USA. Please be aware that current advice is to return to the USA IMMEDIATELY

this is wild - i was aware of Mary-Claire King's absurdly important discoveries on BRCA / inherited breast cancer but I had no idea that her first PhD paper (King & Wilson 1975, Science, not bad lol) is the "99% of protein coding shared btwn chimps and humans" result www.science.org/doi/abs/10.1...

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

🚨 New preprint We present an extended version of ScAPE, the method that won one of the prizes 🏆 in the @neuripsconf.bsky.social 2023 Single-Cell Perturbation Prediction challenge. 📄 preprint: doi.org/10.1101/2025... 🧬 code: github.com/scapeML/scape

New preprint from our lab! What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells? Find out here: www.biorxiv.org/content/10.1... 👇 1/

Our paper Genomic diversity of the African malaria vector Anopheles funestus was published in Science today! It features inversions, selection in action, museum specimens and putative new ecotypes. doi.org/10.1126/scie...

Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome: The E2G Portal! e2g.stanford.edu This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues. Uses cases 👇 1/

Cool work from @ewanbirney.bsky.social Moritz Gerstung, Tom Fitzgerald about modeling health trajectories with generative AI! www.nature.com/articles/s41...

With two months to go, @alwaysrong.bsky.social is dominating the Genomic History Inference Strategies Tournament leaderboards. Jump into the competition to help dethrone Stephen! Glory, money, and authorship are all on the line! ghi.st

super excited to share this big project with @daeaton.bsky.social out now in Systematic Biology! We derived distributions for -- given an arbitrary species tree model -- how far you have to move along a genome before observing a change in the underlying genealogy: doi.org/10.1093/sysb...

This is a Melissa Hortman appreciation account for the next 24 hours.

SINGER, our ARG inference method, is finally published and freely available online: doi.org/10.1038/s415... It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...

Jasmin Rees PhD chapter as a paper just out at the AJHG @ajhgnews.bsky.social, with Sergi Castellano, who first envisioned the study. Jas investigated signatures of human local genetic adaptation in hundreds of micronutrient-associated genes.

Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when @shenwei356.bsky.social joined our group for a year on an @embl.org sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n www.nature.com/articles/s41...

The constant barrage of terrible news on bluesky has made me feel weird about promoting papers, but people in the lab have been doing so much amazing work over the past few months that I want to share a few brief teasers/links:

Large AI models are reported to achieve high accuracy (AUROC) predicting pathogenic variants across the genome. A preprint reports that the predictions are based on splice variants. Using only this info (no sequences, no AI) achieves AUROC=0.944 across noncoding variants. 1/2

The GRFP lives!! (due end of October) www.nsf.gov/funding/oppo...

woah this is genuinely, utterly WILD Ant queens of one species produce males of another species, so she can then mate with them and produce hybrid workers! This is so gloriously weird I can't quite compute it 🤯🧪🐜 www.nature.com/articles/d41...

*Postdoc in Evolutionary genomics at Stockholm University* We are recruiting a postdoc for a large interdisciplinary project to investigate evolutionary drivers and genomic consequences of pollen evolution in response to pollination mode shifts in flowering plants. 1/5 su.varbi.com/what:job/job...

The scent of silence! Cool research in Cell @cellpress.bsky.social to brighten up your day🌹. The mystery of why some roses are fragrant and others aren't has an answer. It's called SCREP: a rose-specific gene that evolved from non-coding DNA 16.8 million years ago 👇

To all post-docs: The Genome Biology dept ‪@embl.org has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

1. 🚨New preprint: tinyurl.com/tenk10k-causal. We explored causal effects of gene expression in immune cell types on complex traits and diseases by combining single-cell expression quantitative trait loci (sc-eQTL) mapping in 5M+ cells from 1,925 donors in TenK10K study and GWAS. 🧵

I went to work on my lecture over some ramen and the server asked if I worked in healthcare, because she’s a cancer bioinformatician who can’t find a job and is in now in tenuous visa territory. I’m so sad and angry about this country, and it keeps hitting me at the moments I don’t expect it

This story has it all: aquaculture, Black Flag, Bernie Sanders, Star Trek as policy, John Hodgman, male tears, and a candidate citing Luthen’s monologue from Andor. Meet Graham Platner, the Maine oysterman trying to crack the senate. @grahamformaine.bsky.social newrepublic.com/article/1996...

Excited / nervous to share the “magnum opus” of my postdoc in Andreas Wagner’s lab! "De-novo promoters emerge more readily from random DNA than from genomic DNA" This project is the accumulation of 4 years of work, and lays the foundation for my future group. In short, we… (1/4)

1) I am delighted to present this terrific tour de force research conducted by my post-doc Dr. Gayani Senevirathne @gayani.bsky.social and published today in Nature - www.nature.com/articles/s41...

Another truly amazing work by the Capellini lab

I need more faculty members to be talking to students about the likely long term impacts on our field from the Trump Administration's growing fascism.

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...

Denisovans or their close relatives identified in the fossil record using a gene regulatory phenotyping method. Now out: www.pnas.org/doi/10.1073/...

I led a “punk science” activity for our incoming freshman biology majors at our orientation event. They made zines and fliers on any topic they chose. Here’s a sample:

New paper from our lab! We found that LINE-1 transposons contribute to early human brain development. Funded by @asapresearch.parkinsonsroadmap.org www.cell.com/cell-genomic...

With #eseb2025 coming to a close, it is time to start making plans for 2026. Interested in the interface of evolution 🧬 and ecology 🌳? Come to our #ExE conference hosted by @uniexecec.bsky.social in beautiful #Cornwall. Leave your email address at tinyurl.com/EvolxEcol to join our mailing list!

Our paper on the evolution of MUC19 in humans, Neanderthals, and Denisovans is finally out today in Science! This has been a six-year effort by 13 authors to weave together 3 separate but related evolutionary stories around this one gene (more on thread 🧵). www.science.org/doi/10.1126/...

The Hibbins Lab at the University of Rochester seeks a postdoctoral researcher in Phylogenomics. Ideal candidates should have experience in phylogenetics and strong computational skills. Details: https://mhibbins.github.io/research/ #postdoc

I'm hiring a postdoc to work in theoretical / computational phylogenomics! More info at tinyurl.com/63hb5ew8. Please share!

@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease. Details below careersearch.stanford.edu/jobs/computa... Plz RT

💻🧬 The Swedish Museum of Natural History is seeking a bioinformatician. Permanent position, 70-80% of the time should be dedicated to supporting day-to-day activities and long-term research of research groups. 20-30% for their own research. Please share widely! arbetsformedlingen.se/platsbanken/...

Are you ready to boost your research career? Apply with @uniGoettingen for an #MSCA postdoctoral fellowship! We’ll gladly support your application, so get in touch asap: www.uni-goettingen.de/en/671766.html #EarlyCareerResearcher #PostdocCareers #Mobility #WeAreInternational Deadline 10 Sept.

Our latest research is out today on ‪@medrxivpreprint.bsky.social: www.medrxiv.org/content/10.1... Saturation genome editing of BRCA1 across cell types accurately resolves cancer risk. Led by the amazing Phoebe Dace. This one’s packed full of data, so check out the paper. Quick highlights… 🧵 1/n

Last chance to register for this brilliant international #BioHackathon 8-10 Sep £35 for 3 days, inc. team or individual coding and problem solving, refreshments, dinner and quiz! 2025.biohack.live Join us at venues in #Cambridge #Newcastle #Antwerp

Latest on Waddington Landscapes: Computational methods to fit dynamical landscapes directly to single cell data Applied to neural tube patterning shows morphogen-signalling landscapes can be linearly interpolated Connects interpretable landscape models with data www.biorxiv.org/content/10.1...

Big news! We are recruiting a postdoc to work on tomatillo evolution: jobs.colorado.edu/jobs/JobDeta.... The clade containing tomatillos and its allies (ca 300 spp) has evolved lantern fruits at least 25 times - we want to know why! Join us @rociodeanna.bsky.social & @caschenck-bio.bsky.social

Excited to share the latest work from the lab led by @eharo84.bsky.social, in which we have used synthetic biology to explore the mechanisms by which different types of long-range enhancers ensure robust and precise developmental gene expression www.biorxiv.org/content/10.1...

I just got the notice that all the FlyBase people at Harvard, including me, will be laid off on October 12. I'm devastated.

Important new document available regarding SCOTUS and NIH grants. scienceandfreedomalliance.substack.com/p/tell-the-s... 1/2