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)

I did not know Taylor Swift was moonlighting in soliciting contributions for fake journals!

Check out my talented colleagues' study, profiling hundreds of CRISPRa-responsive regulatory elements surrounding PHOX2B, a key player in neuroblastoma, using a targeted scRNA-seq screen in a neuroblastoma cell line.

Our first Fall #tidyomics meeting will be this Wed 10 September, early in US / noon in Europe / late in Australia. Feel free to join if you're interested in what we are doing to make omics data more amenable to tidy data analysis. Organized with Stefano @stemang.bsky.social

L’effet Matilda n’est pas une fiction. Il est inscrit dans l’histoire scientifique. Il a éclipsé des femmes comme Marthe Gautier, née il y a cent ans, pionnière oubliée de la trisomie 21. ➡️ https://l.franceculture.fr/1LI

Are electronic health records (EHR) more predictive of disease onset than polygenic scores? Can we transfer EHR-based prediction models between countries? Our study on these questions using 3 biobank-based studies with N>845K, is out in @natgenet.nature.com today: www.nature.com/articles/s41...

Last year I met a bunch of great researchers who work with high-dimensional data at a Dagstuhl seminar. This week we put out a preprint about the history and philosophy of low-dimensional embedding methods, their applications, their challenges, and their possible future arxiv.org/abs/2508.15929

We spent a year writing this review of low-dim embeddings and arguing about things like epistemic roles and best practices :-) 20+ authors are all participants of the Dagstuhl seminar we held last year: www.dagstuhl.de/24122. Led by @alexandr.bsky.social and Cyril de Bodt. arxiv.org/abs/2508.15929

We're committed to support as many attendees as possible join us at #scverse2025 - feel free to reach out if you have questions!

Antibodies are highly diverse, but most possible sequences are unstable or polyreactive. In this work, just published in Cell Syst., we propose a new source of data for modeling constraints from these properties. Our models show clear improvements in predicting Ab dysfunction. (1/n) t.co/qCZERPUMPF

Excited to share our latest paper @natmethods.nature.com We present a high-throughput framework to map cellular interactions at ultra-high scale – broadly applicable from whole-organism immune response mapping to personalized therapy response prediction (1/4). www.nature.com/articles/s41...

This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...

Evaluating something like batch correction requires looking at the data, and picking metrics that capture what you care about. Great work @prauten.bsky.social and @uweohler.bsky.social

Shortcomings of silhouette in single-cell integration benchmarking - @uweohler.bsky.social @prauten.bsky.social @mdc-bimsb.bsky.social @mdc-berlin.bsky.social @humboldtuni.bsky.social go.nature.com/4fcQzZr

Truly grateful for the exceptional opportunity to participate in #LPSHG2025 last week, featuring a stellar ✨ lineup of leading researchers who doubled as tutors, alongside inspiring fellow PhD students. Excited to apply my learnings and see where this collaborative spirit takes genomics next!

*Easter egg alert* NOT in the published paper. We also benchmarked Evo 2 and while it did better than other gLMs (consistent that scale can improve gLMs), it still falls short of a basic CNN trained using one-hot sequences and far short of supervised SOTA

The duplication crisis: the other replication crisis - www.worksinprogress.news/p/the-duplic...

The deadline for the VIB.AI group leader positions is approaching - send in your CV and short research plan before 14th June to start your BioML research lab in Leuven or Ghent

Excited to share my first contribution here at Illumina! We developed PromoterAI, a deep neural network that accurately identifies non-coding promoter variants that disrupt gene expression.🧵 (1/)

We finally concluded the meeting. Thanks to all attendees for their scientific contributions and for traveling (near or far) to the meeting! Thanks to the local organizers for the infrastructure and catering, and thanks to the co-organizers @yaronorenstein.bsky.social @camillemrcht.bsky.social!

When investors learn that the trait for green eyes is also ~20 SNPs

1. LLM-generated code tries to run code from online software packages. Which is normal but 2. The packages don’t exist. Which would normally cause an error but 3. Nefarious people have made malware under the package names that LLMs make up most often. So 4. Now the LLM code points to malware.

40 days until #RECOMB2025 in Seoul! 523 attendees confirmed—thank you! 🥳 For those who haven't registered yet, we have great news! 📢 Early bird deadline is extended to Friday, March 21st 📢 Register now at recomb2025.com 🎟️

Last day to apply ⏰😱! If you haven’t already done so, now is the time! Apply to be one of the speakers at the #SoapboxScience summer event and present your research in a fun and relaxed atmosphere ✨ #WomenInSTEM #WomenInScience #Scicomm

Look for the bare necessities with manifold learning... 🐻🎶 Data science meets Disney in the most unexpected places! Credits to the scikit-learn docs: scikit-learn.org/stable/modul... #DataScience #ManifoldLearning #TechHumor

Join us to connect with the vibrant #singlecell community. 📢Register for the #ISCO'25 Conference "Innovations in #SingleCell #OMICS" in Berlin! 🗓️ 12-13 May 2025 🎤 Fantastic Keynote and Invited Speakers 🫵🏿 Many slots for talks: submit your abstract 🔗http://isco-conference.eu Please spread the word!

1/4 🧵 Preprint alert: In "Metrics Matter: Why We Need to Stop Using Silhouette in #SingleCell #Benchmarking," we reveal critical flaws in common #Evaluation metrics for #Integration and propose robust alternatives. @uweohler.bsky.social www.biorxiv.org/content/10.1...