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Annique Claringbould

@anniquec.bsky.social

730 followers 690 following 30 posts

Assistant Professor 👩🏼‍💻 at Erasmus Medical Center Rotterdam researching genetics & gene regulation 🧬🖥 in the context of disease 🥼💉📊

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Annique Claringbould @anniquec.bsky.social · May 26

SUM-seq is now out 🤩

See Mikael's thread below for paper highlights

Mikael Marttinen @mmarttinen.bsky.social · May 26

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
🧵

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...

doi.org

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Reposted by Annique Claringbould

Eiko Fried @eikofried.bsky.social · 21h

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

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Reposted by Annique Claringbould

Open Targets @opentargets.org · 20d

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

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Reposted by Annique Claringbould

Nicky Whiffin @nickywhiffin.bsky.social · Jul 31

📣 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

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'

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Reposted by Annique Claringbould

Anthony Mathelier @amathelier.bsky.social · Jul 24

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

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Reposted by Annique Claringbould

Anthony Mathelier @amathelier.bsky.social · Jul 21

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...

RegSys

ISCB - International Society for Computational Biology

www.iscb.org

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Reposted by Annique Claringbould

Žiga Avsec @avsecz.bsky.social · Jun 25

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

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Annique Claringbould @anniquec.bsky.social · Jun 19

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 · Jun 16

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

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Reposted by Annique Claringbould

Axel Visel @axelvisel.bsky.social · Jun 18

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 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.

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Reposted by Annique Claringbould

Simon Fisher @profsimonfisher.bsky.social · Jun 14

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

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Reposted by Annique Claringbould

Nature Methods @natmethods.nature.com · May 27

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.

www.nature.com

5 9

Reposted by Annique Claringbould

Nature Methods @natmethods.nature.com · May 27

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...

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Annique Claringbould @anniquec.bsky.social · May 27

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"

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Reposted by Annique Claringbould

Mikael Marttinen @mmarttinen.bsky.social · May 26

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!

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Annique Claringbould @anniquec.bsky.social · May 26

SUM-seq is now out 🤩

See Mikael's thread below for paper highlights

Mikael Marttinen @mmarttinen.bsky.social · May 26

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

doi.org

2 11

Annique Claringbould @anniquec.bsky.social · May 26

Thank you so much!

Annique Claringbould @anniquec.bsky.social · May 26

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.

www.nature.com

1 3 16

Reposted by Annique Claringbould

Luke Jostins-Dean @lukejostins.bsky.social · May 26

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

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Annique Claringbould @anniquec.bsky.social · May 26

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!

Annique Claringbould @anniquec.bsky.social · May 24

Ciao Milano! Looking forward to #eshg2025 these next days

Annique Claringbould @anniquec.bsky.social · May 12

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

Michel Nivard @michelnivard.bsky.social · May 12

🚨 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

Sequence Language Models & Deep Learning in Genomics

biobook.michel.science

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Annique Claringbould @anniquec.bsky.social · May 12

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>"

Annique Claringbould @anniquec.bsky.social · May 12

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

bsky.app/profile/anni...

Annique Claringbould @anniquec.bsky.social · Apr 4

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

Reposted by Annique Claringbould

European Commission @ec.europa.eu · May 8

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

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Reposted by Annique Claringbould

Tuuli Lappalainen @tuuliel.bsky.social · May 6

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...

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Annique Claringbould @anniquec.bsky.social · Apr 24

Congratulations, cool story!