Niklas Kempynck
@niklaskemp.bsky.social
PhD Student at the Stein Aerts Lab of Computational Biology. Studying brain genomics
Reposted by Niklas Kempynck
Relieved to finally post my whole developing brain evolutionary "theory of everything" preprint!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
ANTIPODE Provides a Global View of Cell Type Homology and Transcriptomic Divergence in the Developing Mammalian Brain
Diverse neurons and glia are generated in conserved spatial and temporal sequences during mammalian brain development. Divergence in gene regulatory networks can alter brain composition, scaling, timi...
www.biorxiv.org
October 20, 2025 at 2:50 AM
Relieved to finally post my whole developing brain evolutionary "theory of everything" preprint!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Niklas Kempynck
We have two open positions for a ML and a LLM engineer to launch a machine learning expertise unit in our center @vibai.bsky.social, see vib.ai/en/opportuni...
vib.ai
September 23, 2025 at 11:21 AM
We have two open positions for a ML and a LLM engineer to launch a machine learning expertise unit in our center @vibai.bsky.social, see vib.ai/en/opportuni...
Reposted by Niklas Kempynck
We will have our next community meeting on Tuesday, 2025-09-16 at 18:00 CEST! Niklas Kempynck will be presenting on CREsted, a package for training enhancer models on scATAC-seq data.
(Zoom registration link and more information in thread!)
🧵
(Zoom registration link and more information in thread!)
🧵
September 10, 2025 at 3:02 PM
We will have our next community meeting on Tuesday, 2025-09-16 at 18:00 CEST! Niklas Kempynck will be presenting on CREsted, a package for training enhancer models on scATAC-seq data.
(Zoom registration link and more information in thread!)
🧵
(Zoom registration link and more information in thread!)
🧵
Reposted by Niklas Kempynck
I wrote a quick application note on Tomtom-lite, a Python implementation of the Tomtom algorithm for comparing PWMs against each other. This implementation can be 10-1000x faster and, as a Python function, can be integrated into your workflows easier.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Tomtom-lite: Accelerating Tomtom enables large-scale and real-time motif similarity scoring
Summary Pairwise sequence similarity is a core operation in genomic analysis, yet most attention has been given to sequences made up of discrete characters. With the growing prevalence of machine lear...
www.biorxiv.org
June 3, 2025 at 6:02 PM
I wrote a quick application note on Tomtom-lite, a Python implementation of the Tomtom algorithm for comparing PWMs against each other. This implementation can be 10-1000x faster and, as a Python function, can be integrated into your workflows easier.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Niklas Kempynck
One thousand candidate enhancers tested in vivo in the mouse brain! A massive resource and oh so useful as validation set for genome-wide enhancer prediction methods. Super fun to be involved in one of the papers: ‘the prediction challenge paper’ by Nelson&Niklas et al www.cell.com/cell-genomic...
May 21, 2025 at 4:50 PM
One thousand candidate enhancers tested in vivo in the mouse brain! A massive resource and oh so useful as validation set for genome-wide enhancer prediction methods. Super fun to be involved in one of the papers: ‘the prediction challenge paper’ by Nelson&Niklas et al www.cell.com/cell-genomic...
Make sure to also check out the other studies part of the larger effort on identifying and validating enhancer tools.
In the battle against brain disease, researchers can now rely on a new arsenal of genetic tools – The Armamentarium.
Together with scientists from across the NIH BRAIN Initiative, we’ve created and published over 1000 new enhancer AAV vectors.
🧠📈
Together with scientists from across the NIH BRAIN Initiative, we’ve created and published over 1000 new enhancer AAV vectors.
🧠📈
May 21, 2025 at 4:51 PM
Make sure to also check out the other studies part of the larger effort on identifying and validating enhancer tools.
This study was done together with Nelson Johansen and supervised by Trygve Bakken at the @alleninstitute.org. Thanks to all co-authors for the great inter-lab collaboration! Also a personal shoutout to the members in @steinaerts.bsky.social lab for a nice team effort and to Stein for guidance.
May 21, 2025 at 4:48 PM
This study was done together with Nelson Johansen and supervised by Trygve Bakken at the @alleninstitute.org. Thanks to all co-authors for the great inter-lab collaboration! Also a personal shoutout to the members in @steinaerts.bsky.social lab for a nice team effort and to Stein for guidance.
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 Niklas Kempynck
Calling someone bird-brained is, in fact, a way of calling someone highly intelligent. @yaseminsaplakoglu.bsky.social reports: www.quantamagazine.org/intelligence...
Intelligence Evolved at Least Twice in Vertebrate Animals | Quanta Magazine
Complex neural circuits likely arose independently in birds and mammals, suggesting that vertebrates evolved intelligence multiple times.
www.quantamagazine.org
April 7, 2025 at 2:28 PM
Calling someone bird-brained is, in fact, a way of calling someone highly intelligent. @yaseminsaplakoglu.bsky.social reports: www.quantamagazine.org/intelligence...
Reposted by Niklas Kempynck
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...
Also check out Hannah’s thread on our latest preprint on HyDrop v2, an open-source platform for scATAC-sequencing, and a great, cost-efficient way of generating data for S2F models. 🙌
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 10:37 AM
Also check out Hannah’s thread on our latest preprint on HyDrop v2, an open-source platform for scATAC-sequencing, and a great, cost-efficient way of generating data for S2F models. 🙌
CREsted is available at github.com/aertslab/CRE.... Analysis notebooks can be found at github.com/aertslab/CRE.... All models developed for this preprint and in previous work are available in CREsted through crested.get_model(). We look forward to your feedback!
April 3, 2025 at 2:36 PM
CREsted is available at github.com/aertslab/CRE.... Analysis notebooks can be found at github.com/aertslab/CRE.... All models developed for this preprint and in previous work are available in CREsted through crested.get_model(). We look forward to your feedback!
This was a big collaborative effort, together with @seppedewinter.bsky.social , and with great contributions from @casblaauw.bsky.social , Vasilis and many others. A special shoutout to @lukasmahieu.bsky.social who professionalized the package, and to @steinaerts.bsky.social for supervising.
April 3, 2025 at 2:35 PM
This was a big collaborative effort, together with @seppedewinter.bsky.social , and with great contributions from @casblaauw.bsky.social , Vasilis and many others. A special shoutout to @lukasmahieu.bsky.social who professionalized the package, and to @steinaerts.bsky.social for supervising.
Finally, we train a model on a full-development zebrafish scATAC-seq atlas, and use it to design and in vivo validate cell type- and timepoint-specific enhancers with a high success rate. We also attempt to modulate reporter strength over two cell types.
April 3, 2025 at 2:34 PM
Finally, we train a model on a full-development zebrafish scATAC-seq atlas, and use it to design and in vivo validate cell type- and timepoint-specific enhancers with a high success rate. We also attempt to modulate reporter strength over two cell types.
In a new functionality to CREsted, we explore Borzoi fine-tuning to mouse motor cortex scATAC-seq data. We show that fine-tuned models and smaller models from scratch have a near-identical performance.
April 3, 2025 at 2:34 PM
In a new functionality to CREsted, we explore Borzoi fine-tuning to mouse motor cortex scATAC-seq data. We show that fine-tuned models and smaller models from scratch have a near-identical performance.
We also study enhancer code inside human cancer cell lines and glioma biopsies and find that enhancer codes between Mesenchymal-like glioblastoma and melanoma states are more similar compared to glioblastoma biopsy data.
April 3, 2025 at 2:33 PM
We also study enhancer code inside human cancer cell lines and glioma biopsies and find that enhancer codes between Mesenchymal-like glioblastoma and melanoma states are more similar compared to glioblastoma biopsy data.
Next, we validated CREsted-identified motif instances from a human PBMC model with ChIP-seq data. We further show that gene locus predictions can be used to simulate the effect of TF degradation on chromatin accessibility.
April 3, 2025 at 2:32 PM
Next, we validated CREsted-identified motif instances from a human PBMC model with ChIP-seq data. We further show that gene locus predictions can be used to simulate the effect of TF degradation on chromatin accessibility.
We use the mouse cortex model to highlight CREsted’s gene locus prediction capabilities, both in unseen chromosomes and across species. This presents a powerful tool for potentially annotating genomes across species at high resolution.
April 3, 2025 at 2:32 PM
We use the mouse cortex model to highlight CREsted’s gene locus prediction capabilities, both in unseen chromosomes and across species. This presents a powerful tool for potentially annotating genomes across species at high resolution.
We first demonstrate CREsted’s functionality by providing a complete data-driven analysis of mouse motor cortex enhancer codes across cell types. Through matched scRNA-seq data, we link motifs to likely TF candidates.
April 3, 2025 at 2:31 PM
We first demonstrate CREsted’s functionality by providing a complete data-driven analysis of mouse motor cortex enhancer codes across cell types. Through matched scRNA-seq data, we link motifs to likely TF candidates.
CREsted starts from the outputs of established scATAC preprocessing pipelines, and trains sequence-to-function models on chromatin accessibility per cell type. It provides complete motif analysis tools to infer cell type-specific enhancer codes and holds a comprehensive
enhancer design toolbox.
enhancer design toolbox.
April 3, 2025 at 2:31 PM
CREsted starts from the outputs of established scATAC preprocessing pipelines, and trains sequence-to-function models on chromatin accessibility per cell type. It provides complete motif analysis tools to infer cell type-specific enhancer codes and holds a comprehensive
enhancer design toolbox.
enhancer design toolbox.
We released our preprint on the CREsted package. CREsted allows for complete modeling of cell type-specific enhancer codes from scATAC-seq data. We demonstrate CREsted’s robust functionality in various species and tissues, and in vivo validate our findings: www.biorxiv.org/content/10.1...
April 3, 2025 at 2:30 PM
We released our preprint on the CREsted package. CREsted allows for complete modeling of cell type-specific enhancer codes from scATAC-seq data. We demonstrate CREsted’s robust functionality in various species and tissues, and in vivo validate our findings: www.biorxiv.org/content/10.1...
Reposted by Niklas Kempynck
Very excited to share our new preprint together with @daniedaaboul.bsky.social, where we studied the gene regulatory code that hippocampal granule cells (GCs) use during synapse formation (1/n)
A dynamic gene regulatory code drives synaptic development of hippocampal granule cells https://www.biorxiv.org/content/10.1101/2025.03.27.645686v1
March 31, 2025 at 5:58 AM
Very excited to share our new preprint together with @daniedaaboul.bsky.social, where we studied the gene regulatory code that hippocampal granule cells (GCs) use during synapse formation (1/n)
Reposted by Niklas Kempynck
How does gene regulation shape brain evolution? Our new preprint dives into this question in the context of mammalian cerebellum development! rb.gy/dbcxjz
Led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social
Led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social
March 16, 2025 at 10:31 AM
How does gene regulation shape brain evolution? Our new preprint dives into this question in the context of mammalian cerebellum development! rb.gy/dbcxjz
Led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social
Led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social
Reposted by Niklas Kempynck
The latest Discover ASAP episode dives into "Cell Type Directed Design of Synthetic Enhancers," a study published in Nature by CRN Team Voet. They discuss how machine learning enables precise enhancer design for targeted gene expression 🧬
Watch: www.youtube.com/watch?v=Qcms...
Watch: www.youtube.com/watch?v=Qcms...
February 13, 2025 at 4:47 PM
The latest Discover ASAP episode dives into "Cell Type Directed Design of Synthetic Enhancers," a study published in Nature by CRN Team Voet. They discuss how machine learning enables precise enhancer design for targeted gene expression 🧬
Watch: www.youtube.com/watch?v=Qcms...
Watch: www.youtube.com/watch?v=Qcms...
Reposted by Niklas Kempynck
We wrote a review article on modelling and design of transcriptional enhancers using sequence-to-function models.
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
Modelling and design of transcriptional enhancers - Nature Reviews Bioengineering
Enhancers are genomic elements critical for regulating gene expression. In this Review, the authors discuss how sequence-to-function models can be used to unravel the rules underlying enhancer activit...
www.nature.com
February 28, 2025 at 2:45 PM
We wrote a review article on modelling and design of transcriptional enhancers using sequence-to-function models.
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...