Annique Claringbould
@anniquec.bsky.social
Assistant Professor 👩🏼💻 at Erasmus Medical Center Rotterdam researching genetics & gene regulation 🧬🖥 in the context of disease 🥼💉📊
Pinned
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
🧵
🚀 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
SUM-seq is now out 🤩
See Mikael's thread below for paper highlights
See Mikael's thread below for paper highlights
Reposted by Annique Claringbould
Funders must recognise that great discoveries often come from studies that seeks to advance knowledge for its own sake
go.nature.com/47zrzYZ
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
October 29, 2025 at 12:11 PM
Funders must recognise that great discoveries often come from studies that seeks to advance knowledge for its own sake
go.nature.com/47zrzYZ
go.nature.com/47zrzYZ
Reposted by Annique Claringbould
Reposted by Annique Claringbould
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 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
September 18, 2025 at 10:39 AM
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 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...
Reposted by Annique Claringbould
📣 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
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
July 31, 2025 at 4:12 PM
📣 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
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
Reposted by Annique Claringbould
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
Thanks, everyone, for submitting, attending, presenting, and organizing @iscb.bsky.social @eccb-europe.bsky.social
July 24, 2025 at 7:00 PM
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
Thanks, everyone, for submitting, attending, presenting, and organizing @iscb.bsky.social @eccb-europe.bsky.social
Reposted by Annique Claringbould
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...
www.iscb.org/ismbeccb2025...
RegSys
ISCB - International Society for Computational Biology
www.iscb.org
July 21, 2025 at 8:02 AM
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...
www.iscb.org/ismbeccb2025...
Reposted by Annique Claringbould
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
June 25, 2025 at 2:29 PM
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 🧩
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 🧩
High-throughput single-cell CRISPRi screens stratify neurodevelopmental functions of schizophrenia-associated genes https://www.biorxiv.org/content/10.1101/2025.06.13.659629v1
June 19, 2025 at 10:13 AM
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 🧩
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 🧩
Reposted by Annique Claringbould
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
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
June 18, 2025 at 5:56 PM
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
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
Reposted by Annique Claringbould
Your genome is not a blueprint. A thread about misleading metaphors in science communication. 🧬🧪 1/n
June 14, 2025 at 3:50 PM
Your genome is not a blueprint. A thread about misleading metaphors in science communication. 🧬🧪 1/n
Reposted by Annique Claringbould
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...
www.nature.com/articles/s41...
May 27, 2025 at 3:45 PM
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...
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"
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"
May 27, 2025 at 12:39 PM
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"
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"
Reposted by Annique Claringbould
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!
A detailed protocol is in the works for release. For now, check out the paper!
May 26, 2025 at 9:33 AM
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!
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
See Mikael's thread below for paper highlights
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
🧵
🚀 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
May 26, 2025 at 9:36 AM
SUM-seq is now out 🤩
See Mikael's thread below for paper highlights
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...
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
May 26, 2025 at 9:21 AM
For those who just attended my talk at #ESHG2025: embargo on SUM-seq has lifted!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Annique Claringbould
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
May 26, 2025 at 8:01 AM
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!
May 26, 2025 at 6:00 AM
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!
Wonderful resource if you're looking to catch up on sequence language models in genomics!
🚨 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
May 12, 2025 at 1:10 PM
Wonderful resource if you're looking to catch up on sequence language models in genomics!
Reposted by Annique Claringbould
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
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
May 8, 2025 at 10:12 AM
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
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
Reposted by Annique Claringbould
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...
www.biorxiv.org/content/10.1...
May 6, 2025 at 5:01 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Annique Claringbould
📣📣 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
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
April 8, 2025 at 11:50 AM
📣📣 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
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
Reposted by Annique Claringbould
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.
📣New from Lanting et al.
📄Low-cost generation of clinical-grade, layperson-friendly pharmacogenetic passports using oligonucleotide arrays
#PGx
📄Low-cost generation of clinical-grade, layperson-friendly pharmacogenetic passports using oligonucleotide arrays
#PGx
Low-cost generation of clinical-grade, layperson-friendly pharmacogenetic passports using oligonucleotide arrays
Almost all individuals will carry a genetic marker that affects their drug response
and warrants therapy adjustments. This study demonstrates the feasibility of a low-cost,
pre-emptive pharmacogenetic...
www.cell.com
April 4, 2025 at 10:08 AM
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 🧵
April 4, 2025 at 7:19 AM
I want to share some observations from a recent recruitment process for a PhD position that may be interesting for other future candidates 🧵