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

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

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

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

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...

📣 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 🧩

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...

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

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

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!

Choose Science. Choose Europe. A new Marie Skłodowska-Curie Actions Postdoctoral Fellowships 2025 call is now open. With a budget of €404.3 million, it will support around 1,650 researchers from Europe and beyond. Apply by 10 September → europa.eu/!fBTMgF

Our new contribution to the quest to find causal GWAS genes! Sam Ghatan from my lab at @nygenome.org led a systematic comparison of eQTLs and CRISPRi+scRNA-seq screens. TL;DR: they provide highly complementary insights, with ortogonal pros and cons. 🧵👇 www.biorxiv.org/content/10.1...

📣📣 New postdoc in biomedical data science available in our lab!! www.jobs.cam.ac.uk/job/50966/ Flexible funding - many research areas in scope + ideas welcome Check out our group www.inouyelab.org/home And the awesome Cambridge research environment! @vpd-hlri.bsky.social @uniofcam.bsky.social

Just out! Our manuscript (led by Pauline Lanting and @robertwarmerdam.bsky.social) on the generation of pharmacogenetic passports from low-cost GSA oligonucleotide array data.

I want to share some observations from a recent recruitment process for a PhD position that may be interesting for other future candidates 🧵

In every civilization, people end up sorted into levels of socio-economic status (SES). We explore the history, present, and future of scientific research on the complicated relationship between SES and DNA in @naturehumbehav.bsky.social💰🧬🎓 Link: rdcu.be/efacK Thread below 👇🏽

Exciting day! It's the opening of the Netherlands Women's Health Research and Innovation Center @erasmusmc.bsky.social

Let me tell you a story about 2 patients we identified, both with a rare variant in TNNT2; NM_001001430.3: c.571-1G>A. Both had cardiac phenotypes and both had Oceanian ancestry Our latest in EHJ! @alexbutters25.bsky.social @escardio.bsky.social #medsky #genechat #cardiosky doi.org/10.1093/eurh...

📣 New from the lab: The contribution of genetic determinants of blood gene expression and splicing to molecular phenotypes and health outcomes www.nature.com/articles/s41... Check out the INTERVAL RNAseq portal www.intervalrna.org.uk Led by @alextokolyi.bsky.social & Elodie Persyn!

Recruitment for the EMBL International PhD Programme is officially open! 🔊 At EMBL, we train young scientists to become skilled and creative future leaders in academia, industry & other sectors. Start your career in the life sciences with us! www.embl.org/about/info/e... 🧪 #AcademicSky #careers

One more week to apply! 🧬💻

Come do a PhD with me! 🖥️🧬 We've got very exciting multiomics data coming in, you get to shape the project and there are lots of opportunities to collaborate and learn. Reach out here or via email if you have questions Please reskeet 🙏 www.werkenbijerasmusmc.nl/en/vacancy/1...

We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇 Paper: doi.org/10.1101/2024.12.20.629764 Code: github.com/saezlab/greta

🌟 Exciting news: The Leena Peltonen School of Human Genetics returns in 2025! We're excited to bring PhD students together with an all-star list of leaders in human genetics. 📅 July 27-31, 2025 📍 Wellcome Genome Campus, UK 📝 Apply by March 7 at www.lpshg.com

From next spring, the Open Targets Platform will incorporate the best of Open Targets Genetics into an integrated drug discovery platform 🧵

From GWAS variants⚡️to key-genes🧬: Downstreamer is your tool! This tool developed by (former) colleagues @patrickdeelen.bsky.social, @anniquec.bsky.social and Olivier Bakker incorporates GWAS Variants and tissue specific co-regulation to identify key genes for common diseases 👇Explainer

Proud to share my final PhD work! 🧬🖥️ This article is about finding KEY DISEASE GENES using GWAS and gene expression patterns, nicely explained in Patrick's thread below. But it's also a story about perseverence and team work across institutions, thanks to Olivier, Lude and Patrick 🙏

Does my mutation have the same impact as yours? Population genetics 🤠 🥸 🤓 🤡 meets single cell CRISPRi ⚡ ! www.biorxiv.org/content/10.1... Led by Claudia Feng, Oliver Stegle, Britta Velten, @sangerinstitute.bsky.social .

🚨 This will become a curated list of awesome tools for complex trait genetics, **add yours**! it may become a review in which case those who contribute are invited as co-authors.

Meanwhile in the Netherlands… An already hyper competitive milieu that will see its biggest cuts of recourses seen in years www.nature.com/articles/d41...

For „fun with numbers“ there’s www.graphs.world …where you guess what the underlying dataset is for a daily chart.

🎉 New blog post! Choosing colors for a #dataviz on race, ethnicity or continents can be tricky. I collected lots of examples and wrote down 6 guidelines to help ensure all your readers feel respected by your color choices: blog.datawrapper.de/colors-for-r...