Here's a little widget to play with the data across journals (as well as download the raw CSVs).

sashagusev.github.io/Genetics_Pub...

Out now on bioRxiv! 🧬🖥️

Dewi Moonen, @anniquec.bsky.social and a team led by Lars Steinmetz and Daniel Schraivogel at EMBL have mapped the downstream regulatory networks of thousands of immune disease-relevant variants in CD4+ T cells

www.biorxiv.org/content/10.6...

🤝 This was a truly collaborative effort bringing together experimental & computational expertise. Many thanks to the team - esp. my co-lead @dewimoonen.bsky.social; @danielschraivogel.bsky.social and Lars Steinmetz for excellent supervision; and @argschwind.bsky.social, Stefan Schrod +many others!

Genome-scale mapping of variant, enhancer and gene function in primary human CD4+ T cells www.biorxiv.org/content/10.64898/2026.03...

🎯 The results help resolve individual immune-related loci (TYK2, DEXI/CLEC16A) and combined disease-relevant biological processes

🦠 We observe shared core immune programs (response to virus, T cell activation), but also disease-specific enrichments (tight junction organisation in celiac disease)

🧪 We performed genome-wide Perturb-seq on >7500 genes; 12% modulated expression of >10 genes

Variant ➡️ CRE ➡️ gene ➡️ network: we constructed regulatory cascades from disease-associated variants by integrating both screens, which connected 85 enhancer-like elements to 56% of all genes in two steps

Targeted Perturb-seq enables genome-scale genetic screens in single cells - Nature Methods Targeted sequencing of perturbation effects offers a sensitive approach to capture genes of interest in CRISPR-mediated screens, enabling genome-scale screens at higher scale and lower cost than whole...

🔢 We overlapped 4,724 genetic variants across 14 immune diseases with cis-regulatory elements that were accessible in CD4+ T cells

⚡️ Perturbing these elements with TAP-seq (tinyurl.com/TAPseq) revealed the genes they regulate. Best computational predictors? ENCODE-rE2G and eQTLs

🧬 How do immune disease-relevant variants affect gene regulatory networks in CD4+ T cells?

🧪🖥️ We coupled two large-scale CRISPRi screens (>4M cells) to map the downstream cascades of thousands of SNPs

More details in the thread below 👇 or in the article 📖 on biorxiv tinyurl.com/CD4screens

Did you read our paper applying SUM-seq in macrophages, T-cells and iPSCs (www.nature.com/articles/s41...) and think: I want to try this cost-effective single cell RNA & ATAC-seq method myself? 🧬

Find the complete protocol including tips, troubleshooting and timing now in Nature Protocols

Delighted to present Latent Interaction Variational Inference (LIVI), a framework for trans-eQTL mapping at single-cell resolution that I developed during my PhD together with colleagues from @steglelab.bsky.social 1/n

For anyone who asked "Do you have genome-wide trans-eQTLs?" when we published the first eQTLGen paper: we do now! 💫

See Robert's thread for details on eQTLGen phase 2, including finemapped cis-eQTLs, cis-trans gene pairs and integration of GWAS to identify trait-relevant pathways 🧬🖥

Congrats team!

The department of Philosophy and Moral Sciences at Ghent University is proud to present a lecture series on the topic of eugenics. As philosophers and ethicists, we are concerned about the revival and normalization of eugenic discourse.

humanitiesacademie.ugent.be/eugenics

screenshot of my post

Big new blogpost!

My guide to data visualization, which includes a very long table of contents, tons of charts, and more.

--> Why data visualization matters and how to make charts more effective, clear, transparent, and sometimes, beautiful.
www.scientificdiscovery.dev/p/salonis-gu...

From MRI to Ozempic: breakthroughs that show why fundamental research must be protected In these financially straitened times, funders must recognize that great discoveries often arise from work that was looking for something completely different.

Funders must recognise that great discoveries often come from studies that seeks to advance knowledge for its own sake

go.nature.com/47zrzYZ

thank you!

Hi @apnet.bsky.social, I tried to RSVP to your email but it seems my emails are getting bounced.

Introduction - beginners-guide In this edition: A beginner’s guide to Dutch academia This guide, an introduction to Dutch research and higher education, serves as a support document for researchers and instructors who are unfamil...

Really nice beginner's guide to academia in the Netherlands

knaw.h5mag.com/beginners-gu...

Open Targets Platform 25.09 has been released! The September 25 release includes enhancer-gene data predicted by ENCODE-rE2G, molQTL credible sets for targets, new options for the variant structural viewer, and a number of data updates from GWAS C...

The Open Targets Platform autumn release is out! 🍂

We have ingested the full dataset of over 13 million enhancer-gene regulatory interactions in the human genome across 1,458 DNase-seq experiments covering 369 cell types and tissues from the ENCODE-rE2G model

blog.opentargets.org/open-targets...

Image of an old building in Oxford with the heading 'postdoc opportunities' and the text 'computational approaches to improve rare disease diagnosis and treatment' and 'Big Data Institute, University of Oxford'

📣 We are recruiting! Please share!!

Are you a bioinformatician / computational scientist who wants to apply your skills to understanding regulatory biology and improving rare disease diagnosis and treatment? 🧠 💻 🧬 🩺

We have two roles available 👇

🧵 1/4

What a fantastic #ISMBECCB2025 conference it has been, with an outstanding #RegSys @iscb-regsys.bsky.social COSI track!

Thanks, everyone, for submitting, attending, presenting, and organizing @iscb.bsky.social @eccb-europe.bsky.social

The #RegSys @iscb-regsys.bsky.social track is gonna be outstanding again this year with a great selection of talks and keynotes @verapancaldi.bsky.social, Mafalda Dias, Roser Vento-Tormo, and @lucapinello.bsky.social !

www.iscb.org/ismbeccb2025...

Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind

How do schizophrenia-linked transcription factors and chromatin regulators affect gene regulation in neurons? 🧬🧠

We assess the functional consequences of
❌knocking down❌ 65 SCZ genes and find that they disrupt neurodevelopmental timing ➡️🕐

See paper for GRNs 🖥️, validation screens ✅ & mechanisms 🧩

A meme-style comic panel with three parts. Left: A stylized enhancer with a mutation, surrounded by colored blocks representing functional motifs, a neural network diagram, chromatin accessibility signal traces, and a sequence motif. Two cartoon mouse embryos below show different LacZ reporter activity patterns. Top right: A hand hovers anxiously between two red buttons labeled “Experiments” and “AI,” with the caption “HOW DO ENHANCERS REALLY WORK?” Bottom right: A sweating superhero wipes his forehead, looking stressed about the difficult choice.

Textbooks: “Enhancers are just a bunch of TFBSs”

But how do they REALLY work?

New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social

A 🧵 (1/n)

Free access link: rdcu.be/erD22

A blueprint for the batmobile.

Your genome is not a blueprint. A thread about misleading metaphors in science communication. 🧬🧪 1/n

Methods for multiplexing single-cell multi-omics - Nature Methods Advances in single-cell multi-omics assays that co-detect two or more modalities enable a new frontier in resolving cellular heterogeneity and gene regulation.

And read the News & Views highlighting this work, here:

www.nature.com/articles/s41...

SUM-seq is an ultra-high-throughput method for co-profiling chromatin accessibility and gene expression in single nuclei. @anniquec.bsky.social

www.nature.com/articles/s41...

Justified standing ovation for Nobel laureate Katalin Karikó at #ESHG2025
She shared her adventurous scientific life and life lessons like "If you want to do something, you find a way. If not, you find excuses", and reminded us scientists to thank our near and dear because "they suffer a little bit"

This was a long, fun project, which took the effort of many talented people (Sara Lobato, Umut Yildiz, @anniquec.bsky.social et al.) from the Zaugg and Noh labs! @embl.org @unibas.ch

A detailed protocol is in the works for release. For now, check out the paper!

SUM-seq is now out 🤩

See Mikael's thread below for paper highlights