Annique Claringbould @anniquec.bsky.social · 01/10/2026🎯 Testing the predictions will show what these models get right and where they fall short, shaping experimental design and research questions in the future. Google Deepmind's new AlphaGenome Atlas couldn't have come out at a better time. Exciting times ahead! 010
Annique Claringbould @anniquec.bsky.social · 01/10/2026 🧬 With the recent development of AI sequence-to-function models, I wondered: can we combine variant-level predictions into a patient-specific regulatory profile for type 2 diabetes risk, and then test it in the lab in human β-cells 🧫? 111
Annique Claringbould @anniquec.bsky.social · 01/10/2026Very happy that my grant proposal "From polygenic scores to regulatory profiles: Evaluating sequence-based AI in human β-cells" is funded by ZonMw's Off Road grant! 🎉 www.zonmw.nl/en/news/road... @erasmusmc.bsky.sociallnkd.inLinkedInThis link will take you to a page that’s not on LinkedIn 140
Reposted by Annique ClaringbouldOded Rechavi @odedrechavi.bsky.social · 05/05/2026I’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) 2143
Reposted by Annique ClaringbouldSasha Gusev @sashagusevposts.bsky.social · 01/04/2026Here's a little widget to play with the data across journals (as well as download the raw CSVs). sashagusev.github.io/Genetics_Pub... 32913
Reposted by Annique ClaringbouldOpen Targets @opentargets.org · 12/03/2026Out 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...biorxiv.org 1143
Annique Claringbould @anniquec.bsky.social · 12/03/2026🤝 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! 020
Reposted by Annique ClaringbouldbioRxiv Genetics @biorxiv-genetic.bsky.social · 11/03/2026Genome-scale mapping of variant, enhancer and gene function in primary human CD4+ T cells www.biorxiv.org/content/10.64898/20… 011
Annique Claringbould @anniquec.bsky.social · 12/03/2026🎯 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) 120
Annique Claringbould @anniquec.bsky.social · 12/03/2026🧪 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 120
Annique Claringbould @anniquec.bsky.social · 12/03/2026🔢 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 eQTLsnature.comTargeted Perturb-seq enables genome-scale genetic screens in single cells - Nature MethodsTargeted 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... 110
Annique Claringbould @anniquec.bsky.social · 12/03/2026🧬 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 12811
Annique Claringbould @anniquec.bsky.social · 26/02/2026Did 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 Protocolsnature.comSingle-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics - Nature MethodsThis 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... 073
Reposted by Annique ClaringbouldDanai Vagiaki @danaivagiaki.bsky.social · 08/02/2026Delighted 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 12713
Annique Claringbould @anniquec.bsky.social · 11/02/2026For 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! 091
Reposted by Annique ClaringbouldPieter T. L. Beck @ptrbck.bsky.social · 13/01/2026The 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/eugenicshumanitiesacademie.ugent.beEugenics: Critical Perspectives on a Creeping Concept Between Science and Ideology | Humanities Academie 14925
Reposted by Annique ClaringbouldSaloni @scientificdiscovery.dev · 09/12/2025Big 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... 28802312
Reposted by Annique ClaringbouldNature @nature.com · 29/10/2025Funders must recognise that great discoveries often come from studies that seeks to advance knowledge for its own sake go.nature.com/47zrzYZgo.nature.comFrom MRI to Ozempic: breakthroughs that show why fundamental research must be protectedIn these financially straitened times, funders must recognize that great discoveries often arise from work that was looking for something completely different. 118082
Annique Claringbould @anniquec.bsky.social · 13/10/2025Hi @apnet.bsky.social, I tried to RSVP to your email but it seems my emails are getting bounced. 110
Reposted by Annique ClaringbouldEiko Fried @eikofried.bsky.social · 08/10/2025Really nice beginner's guide to academia in the Netherlands knaw.h5mag.com/beginners-gu...knaw.h5mag.comIntroduction - beginners-guideIn 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... 0156
Reposted by Annique ClaringbouldOpen Targets @opentargets.org · 18/09/2025The 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...blog.opentargets.orgOpen 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... 1229
Reposted by Annique ClaringbouldNicky Whiffin @nickywhiffin.bsky.social · 31/07/2025📣 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 14443
Reposted by Annique ClaringbouldAnthony Mathelier @amathelier.bsky.social · 24/07/2025What 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 294
Reposted by Annique ClaringbouldAnthony Mathelier @amathelier.bsky.social · 21/07/2025The #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...iscb.orgRegSysISCB - International Society for Computational Biology 064
Reposted by Annique ClaringbouldŽiga Avsec @avsecz.bsky.social · 25/06/2025Excited 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 521982
Annique Claringbould @anniquec.bsky.social · 19/06/2025How 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 🧩 0112
Reposted by Annique ClaringbouldAxel Visel @axelvisel.bsky.social · 18/06/2025Textbooks: “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 216379
Reposted by Annique ClaringbouldSimon Fisher @profsimonfisher.bsky.social · 14/06/2025Your genome is not a blueprint. A thread about misleading metaphors in science communication. 🧬🧪 1/n 919866
Reposted by Annique ClaringbouldNature Methods @natmethods.nature.com · 27/05/2025And read the News & Views highlighting this work, here: www.nature.com/articles/s41...nature.comMethods for multiplexing single-cell multi-omics - Nature MethodsAdvances in single-cell multi-omics assays that co-detect two or more modalities enable a new frontier in resolving cellular heterogeneity and gene regulation. 095
Reposted by Annique ClaringbouldNature Methods @natmethods.nature.com · 27/05/2025SUM-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... 1124
Annique Claringbould @anniquec.bsky.social · 27/05/2025Justified 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" 0438
Reposted by Annique ClaringbouldMikael Marttinen @mmarttinen.bsky.social · 26/05/2025This 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! 021
Annique Claringbould @anniquec.bsky.social · 26/05/2025SUM-seq is now out 🤩 See Mikael's thread below for paper highlights 0112
Annique Claringbould @anniquec.bsky.social · 26/05/2025For those who just attended my talk at #ESHG2025: embargo on SUM-seq has lifted! www.nature.com/articles/s41...nature.comMethods for multiplexing single-cell multi-omics - Nature MethodsAdvances in single-cell multi-omics assays that co-detect two or more modalities enable a new frontier in resolving cellular heterogeneity and gene regulation. 1163
Reposted by Annique ClaringbouldLuke Jostins-Dean @lukejostins.bsky.social · 26/05/2025Annique 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 122
Annique Claringbould @anniquec.bsky.social · 26/05/2025Today 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! 070
Annique Claringbould @anniquec.bsky.social · 24/05/2025Ciao Milano! Looking forward to #eshg2025 these next days 0120
Annique Claringbould @anniquec.bsky.social · 12/05/2025Wonderful resource if you're looking to catch up on sequence language models in genomics! 031
Annique Claringbould @anniquec.bsky.social · 12/05/2025Some 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>" 020
Annique Claringbould @anniquec.bsky.social · 12/05/2025Yes, the letters become so much less informative! I wrote a thread about this a couple of weeks ago bsky.app/profile/anni... 010
Reposted by Annique ClaringbouldEuropean Commission @ec.europa.eu · 08/05/2025Choose 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 15947556
Reposted by Annique ClaringbouldTuuli Lappalainen @tuuliel.bsky.social · 06/05/2025Our 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... 19842
Reposted by Annique ClaringbouldMike Inouye @mikeinouye.bsky.social · 08/04/2025📣📣 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 02422
Reposted by Annique ClaringbouldJelle Slager @jslager.bsky.social · 04/04/2025Just out! Our manuscript (led by Pauline Lanting and @robertwarmerdam.bsky.social) on the generation of pharmacogenetic passports from low-cost GSA oligonucleotide array data. 074
Annique Claringbould @anniquec.bsky.social · 04/04/2025My recommendations 💡 add some personality or info to your letter that is not obvious from your CV 💡 use AI tools for brainstorming, drafting, and improving flow and grammar, but DO NOT let it write the entire letter 💡 remember that vacancies are about people, and hiring committees want to see you 👉 043
Annique Claringbould @anniquec.bsky.social · 04/04/2025🙅♀️ Does this mean you should not use these tools when you are applying? Of course not! I know it's not easy to find a position, and when applying you may not be able to spend hours specifically tailoring each letter. 110
Annique Claringbould @anniquec.bsky.social · 04/04/2025But having read so many of the same letters, the power of that conviction sank. To the point where I rated "flawed" letters, those clearly written by a person because there were small errors, higher than those obviously produced by AI 📝 120