🌟 Applications for the 2026 Leena Peltonen School of Human Genetics are open! Back after a great 2025 edition: ~20 global leaders and ~20 PhD students shaping the future of genomics. 📅 July 26–30, 2026 📍 Wellcome Genome Campus, UK 📝 Apply by March 6 → www.lpshg.com

Thrilled to announce that I’ve just opened my research lab at @helmholtz-hiri.bsky.social ! A huge thank you to my mentor Roi Avraham (and lab members!) for the incredible training and support that made this possible.

There is the obvious fraud potential, but I think something much more fundamental is going to happen, too. It will change the meaning of what a "research publication" is. The reason why people read papers is to learn something that they couldn't reproduce in seconds by pushing a few buttons.

Raphael Wimmer@raphaelwimmer.bsky.social · 6mo ago

OpenAI just released Prism, a LaTeX editor with embedded ChatGPT for free. Writing a paper has never been easier. Clogging the scientific publishing pipeline has never been easier. It took me 54 seconds to write up an experiment I did not actually conduct. prism.openai.com

How many high-impact developmental variants are we missing by relying only on adult splicing annotations? We address this in our preprint “Aberrant splicing prediction during human organ development”: www.biorxiv.org/content/10.1...

I'm excited to announce we're recruiting a PhD student in Machine Learning for Immunology within the Einstein Center for Early Disease Interception, together with Simon Haas!

🧠 The Lipid #Brain Atlas is out now! If you think #lipids are boring and membranes are all the same, prepare to be surprised. Led by @lucafusarbassini.bsky.social with Giovanni D'Angelo's lab, we mapped membrane lipids in the mouse brain at high resolution. www.biorxiv.org/cgi/content/...

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.

Dubravka Vucicevic@dr-dusa.bsky.social · 11mo ago

I am so happy to share that our paperis officially published in Cell Genomics! In this paper, we describe TESLA-seq, which combines pooled CRISPR activation with targeted single-cell RNA-seq to map enhancer-gene connections at high sensitivity. Link to the full story: www.cell.com/cell-genomic...

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...

Cross-biobank generalizability and accuracy of electronic health record-based predictors compared to polygenic scores - Nature Genetics

Comparison of electronic health record-based phenotype risk scores (PheRS) and polygenic scores (PGS) across 13 common diseases and three biobank-based studies indicates that PheRS and PGS may provide...

nature.com

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!

scverse@scverse.bsky.social · 12mo ago

💰 Travel Grants Available for scverse conference 2025! 💰 Did you know we are offering grants to help anyone in financial need attend our annual conference? 🌍 🧵 #scverse #scverse2025 #SingleCell #Conference #StanfordUniversity #TravelGrant

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...

Protein language models reveal evolutionary constraints on synonymous codon choice

Evolution has shaped the genetic code, with subtle pressures leading to preferences for some synonymous codons over others. Codons are translated at different speeds by the ribosome, imposing constrai...

biorxiv.org

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

Nature Biotechnology@natbiotech.nature.com · last yr.

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

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

Shortcomings of silhouette in single-cell integration benchmarking - Nature Biotechnology

Silhouette score is unsuitable as a metric for single-cell data integration.

go.nature.com

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!

Andrea Ganna@andganna.bsky.social · last yr.

Leena Peltonen School of Human Genetics in full-swing! @gosiatrynka.bsky.social @dgmacarthur.bsky.social @bpasaniuc.bsky.social @tuuliel.bsky.social @hilarycmartin.bsky.social @sashagusevposts.bsky.social @zkutalik.bsky.social @mashaals.bsky.social @alemedinarivera.bsky.social

*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

Peter Koo@pkoo562.bsky.social · last yr.

Our work on "Evaluating the representational power of pre-trained DNA language models for regulatory genomics" led by @AmberZqt with help from @NiraliSomia & @stevenyuyy is finally published in Genome Biology! Check it out! genomebiology.biomedcentral.com/articles/10....

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

The duplication crisis: the other replication crisis

How bad publishing incentives hinder long-term thinking in computational biology research

worksinprogress.news

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

VIB.AI@vibai.bsky.social · last yr.

We want to connect: To link model builders with data generators. To bring together scientists asking why cells behave the way they do, and others figuring out how to model that behavior. If you're working on AI in biology, consider joining! https://tinyurl.com/y35m6khy

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.

David D. Levine@daviddlevine.com · last yr.

LLMs hallucinating nonexistent software packages with plausible names leads to a new malware vulnerability: "slopsquatting."

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

Soapbox Science Berlin@berlin-soapbox.bsky.social · last yr.

Only five days left to apply!😱 Don't miss your chance to be one of the speakers at our Soapbox Science event. You will really enjoy it! ☺️ #WomenInSTEM #WomenInScience #scicomm @soapboxscience.bsky.social Apply here👇🏼 berlinsoapboxscience.wordpress.com/2025/01/15/c...