I’m excited to announce that as of today we are officially releasing “QED for Grants” for everyone. What started off as an extension of our existing paper review platform, grew in the last few months to an entirely new design (2/16)

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

Sasha Gusev@sashagusevposts.bsky.social · 4mo ago

Monthly median Received to Accepted time (days) at Nature Genetics

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...

Genome-scale mapping of variant, enhancer and gene function in primary human CD4+ T cells https://www.biorxiv.org/content/10.64898/2026.03.09.710372v1

🧬 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

Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics - Nature Methods

This work presents SUM-seq, an ultra-high-throughput method for co-profiling chromatin accessibility and gene expression in single nuclei across multiplexed samples, advancing the study of gene regula...

nature.com

Nature Protocols@natprot.nature.com · 5mo ago

New Article! Single-cell ultra-high-throughput multiplexed chromatin accessibility and gene expression sequencing (SUM-seq)

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

bioRxiv Genomics@biorxiv-genomic.bsky.social · 6mo ago

Mapping trans-eQTLs at single-cell resolution using Latent Interaction Variational Inference. https://www.biorxiv.org/content/10.64898/2026.02.04.703363v1

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!

Robert Warmerdam@robertwarmerdam.bsky.social · 6mo ago

🧬 New preprint alert! After years of collaborative work across 52 datasets we are presenting eQTLGen phase 2: a genome-wide eQTL meta-analysis covering 43,301 blood samples: www.medrxiv.org/content/10.6... (1/8)

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

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...

Funders must recognise that great discoveries often come from studies that seeks to advance knowledge for its own sake go.nature.com/47zrzYZ

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.

go.nature.com

Really nice beginner's guide to academia in the Netherlands knaw.h5mag.com/beginners-gu...

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...

knaw.h5mag.com

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...

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...

blog.opentargets.org

📣 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 🧩

bioRxivpreprint@biorxivpreprint.bsky.social · last yr.

High-throughput single-cell CRISPRi screens stratify neurodevelopmental functions of schizophrenia-associated genes https://www.biorxiv.org/content/10.1101/2025.06.13.659629v1

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

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

And read the News & Views highlighting this work, here: www.nature.com/articles/s41...

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.

nature.com

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

Mikael Marttinen@mmarttinen.bsky.social · last yr.

SUM-seq out @natmethods.nature.com !
 🚀 Ultra-high-throughput Multiplexed snATAC+RNA Used to: ⏳ link temporal macrophage GRNs to immune disease genetics 🩸 map T cell regulatory landscapes 🧬✂️ dissect TF function in hiPSC differentiation via CRISPRi/a screens doi.org/10.1038/s41592-025-02700-8 🧵

For those who just attended my talk at #ESHG2025: embargo on SUM-seq has lifted! www.nature.com/articles/s41...

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.

nature.com

Annique Claringbould @anniquec.bsky.social is talking about CRISPR interference in primary CD4 T cells for ~1000 GWAS-implicated enhancers, reading out ~2000 genes. Interfering with some key enhancers (CD28, IL2RA) impact basically every CD4-expressed gene. #eshg2025

Today I'm presenting some unpublished work of a CRISPRi screen targeting T-cell-specific enhancers that overlap immune disease GWAS hits in session S14 at #ESHG2025 - hope to see you there!

Ciao Milano! Looking forward to #eshg2025 these next days

Wonderful resource if you're looking to catch up on sequence language models in genomics!

Michel Nivard@michelnivard.bsky.social · last yr.

🚨 I just released the alpha-version of my AI in Genomics textbook! It covers (so far!) sequence language models & deep learning for DNA/RNA/proteins. Check it out: biobook.michel.science