Camiel Mannens
@camielmannens.bsky.social
Reposted by Camiel Mannens
Paper alert! 💻 How many cells do you need to train reliable deep learning models in regulatory genomics? We asked how data quality, sequencing depth, and dataset size affect training of sequence-to-function models from scATAC-seq. Out now www.nature.com/articles/s41...
(details below)
(details below)
Evaluating single-cell ATAC-seq atlasing technologies using sequence-to-function modeling - Nature Communications
Generating high-quality training data for machine learning is costly. Here, authors include sequence-to-function modeling in benchmarking of custom and commercial droplet-based scATAC platforms, and r...
www.nature.com
January 29, 2026 at 2:08 PM
Paper alert! 💻 How many cells do you need to train reliable deep learning models in regulatory genomics? We asked how data quality, sequencing depth, and dataset size affect training of sequence-to-function models from scATAC-seq. Out now www.nature.com/articles/s41...
(details below)
(details below)
Reposted by Camiel Mannens
We are thrilled to share our new pre-print: “System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development”. S2F-deeplearning models can accurately encode enhancers, yet decoding these models into human-interpretable rules remains a major challenge.
January 15, 2026 at 11:57 AM
We are thrilled to share our new pre-print: “System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development”. S2F-deeplearning models can accurately encode enhancers, yet decoding these models into human-interpretable rules remains a major challenge.
New preprint from the lab and wonderful work by Seppe de Winter:
System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development
www.biorxiv.org/content/10.6...
System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 15, 2026 at 8:31 AM
New preprint from the lab and wonderful work by Seppe de Winter:
System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development
www.biorxiv.org/content/10.6...
System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development
www.biorxiv.org/content/10.6...
Out now in Nature as part of the 'Brain Development' special issue, our perspective on the developing human and mammalian brain. www.nature.com/articles/s41...
The new frontier in understanding human and mammalian brain development - Nature
Recent studies integrating multi-omics data with cell atlases across development for brains of humans and model organisms are revealing conserved and divergent patterns of brain development at the mol...
www.nature.com
November 6, 2025 at 7:27 PM
Out now in Nature as part of the 'Brain Development' special issue, our perspective on the developing human and mammalian brain. www.nature.com/articles/s41...
Reposted by Camiel Mannens
A major KI initiative to recruit new assistant professors with outstanding proposals in all areas of medicine, biomedicine and public health. We offer an amazing research environment, great colleagues and generous startup packages. Check it out and get working on your applications! (repost please!)
Applications are now open! We are recruiting 20 Assistant Professors in a wide range of subject areas. We're looking for early-career researchers with strong scientific merits and future potential.
🔗 All positions: ki.se/en/about-ki/...
🔗 All positions: ki.se/en/about-ki/...
June 25, 2025 at 10:08 AM
A major KI initiative to recruit new assistant professors with outstanding proposals in all areas of medicine, biomedicine and public health. We offer an amazing research environment, great colleagues and generous startup packages. Check it out and get working on your applications! (repost please!)
Reposted by Camiel Mannens
Heads-up for major new faculty search at KI — with great startup packages and a wide range of subject areas.
Save the date! On 25 June, Karolinska Institutet will be starting a major recruitment drive for 20 junior researchers with a focus on excellence and mobility news.ki.se/ki-to-recruit-junior-researchers-with-a-focus-on-excellence
KI to recruit junior researchers with a focus on excellence
On 25 June, Karolinska Institutet will be starting a major recruitment drive for 20 junior researchers with a focus on excellence and mobility. As one of Europe’s leading medical universities, KI offe...
news.ki.se
June 19, 2025 at 5:50 AM
Heads-up for major new faculty search at KI — with great startup packages and a wide range of subject areas.
Reposted by Camiel Mannens
Breaking from @science.org: The Trump administration wants to kill off a host of active and healthy NASA climate and planetary spacecraft. It would be a "leaner, more focused" agency, they say -- and one far less capable of studying the Earth and exploring space.
Dozens of active and planned NASA spacecraft killed in Trump budget request
Proposal would end nearly all new major science missions
www.science.org
May 30, 2025 at 10:58 PM
Breaking from @science.org: The Trump administration wants to kill off a host of active and healthy NASA climate and planetary spacecraft. It would be a "leaner, more focused" agency, they say -- and one far less capable of studying the Earth and exploring space.
Reposted by Camiel Mannens
Check out our work on evaluating methods for predicting in vivo cell enhancer activity in the mouse cortex! Combined, scATAC peak specificity and sequence-based CREsted predictions gave the best predictive performance, aiming to advance genetic tool design for cell targeting in the brain.
Evaluating methods for the prediction of cell-type-specific enhancers in the mammalian cortex
Johansen et al. report the results of a community challenge to predict functional
enhancers targeting specific brain cell types. By comparing multi-omics machine learning
approaches using in vivo data...
www.cell.com
May 21, 2025 at 4:45 PM
Check out our work on evaluating methods for predicting in vivo cell enhancer activity in the mouse cortex! Combined, scATAC peak specificity and sequence-based CREsted predictions gave the best predictive performance, aiming to advance genetic tool design for cell targeting in the brain.
Reposted by Camiel Mannens
Our new preprint is out! We optimized our open-source platform, HyDrop (v2), for scATAC sequencing and generated new atlases for the mouse cortex and Drosophila embryo with 607k cells. Now, we can train sequence-to-function models on data generated with HyDrop v2!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
April 4, 2025 at 8:52 AM
Our new preprint is out! We optimized our open-source platform, HyDrop (v2), for scATAC sequencing and generated new atlases for the mouse cortex and Drosophila embryo with 607k cells. Now, we can train sequence-to-function models on data generated with HyDrop v2!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Camiel Mannens
Very proud of two new preprints from the lab:
1) CREsted: to train sequence-to-function deep learning models on scATAC-seq atlases, and use them to decipher enhancer logic and design synthetic enhancers. This has been a wonderful lab-wide collaborative effort. www.biorxiv.org/content/10.1...
1) CREsted: to train sequence-to-function deep learning models on scATAC-seq atlases, and use them to decipher enhancer logic and design synthetic enhancers. This has been a wonderful lab-wide collaborative effort. www.biorxiv.org/content/10.1...
CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species
Sequence-based deep learning models have become the state of the art for the analysis of the genomic regulatory code. Particularly for transcriptional enhancers, deep learning models excel at decipher...
www.biorxiv.org
April 4, 2025 at 9:04 AM
Very proud of two new preprints from the lab:
1) CREsted: to train sequence-to-function deep learning models on scATAC-seq atlases, and use them to decipher enhancer logic and design synthetic enhancers. This has been a wonderful lab-wide collaborative effort. www.biorxiv.org/content/10.1...
1) CREsted: to train sequence-to-function deep learning models on scATAC-seq atlases, and use them to decipher enhancer logic and design synthetic enhancers. This has been a wonderful lab-wide collaborative effort. www.biorxiv.org/content/10.1...
Reposted by Camiel Mannens
It’s the first time a frog—or any amphibian—has been observed pollinating a plant, researchers reported in 2023.
Learn more on #WorldFrogDay: scim.ag/4kGdvCy
Learn more on #WorldFrogDay: scim.ag/4kGdvCy
March 20, 2025 at 7:34 PM
It’s the first time a frog—or any amphibian—has been observed pollinating a plant, researchers reported in 2023.
Learn more on #WorldFrogDay: scim.ag/4kGdvCy
Learn more on #WorldFrogDay: scim.ag/4kGdvCy
Reposted by Camiel Mannens
Congrats Camiel, awesome to have you in the lab!
Congratulations to Camiel Mannens, postdoc in the Aerts lab, on obtaining an MSCA fellowship to investigate how genes control brain cell types across different species.
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February 26, 2025 at 12:17 PM
Congrats Camiel, awesome to have you in the lab!