Annique Claringbould

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

Thank you so much!

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.

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!

Some examples:

"I am writing to express my strong interest in <position>. With a <Masters program>, I am eager to contribute to <goal/project>"

"My academic journey"

"Your lab's innovative approach"

"While I have foundational proficiency in <skill>, I am highly motivated to <required skill>"

Yes, the letters become so much less informative! I wrote a thread about this a couple of weeks ago

bsky.app/profile/anni...

A graphic for the Marie Skłodowska-Curie Actions (MSCA), showing a historical portrait of Marie Skłodowska-Curie overlaid with an image of four young researchers walking down a hallway. The European Commission logo is in the top left. Text reads: "Marie Skłodowska-Curie Actions – €404.3 million to support postdoctoral researchers”

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