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)

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...

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...

nature.com

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!)

Karolinska Institutet@ki.se · last yr.

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/...

Heads-up for major new faculty search at KI — with great startup packages and a wide range of subject areas.

Karolinska Institutet@ki.se · last yr.

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

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

science.org

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...

cell.com

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...

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...

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...

biorxiv.org

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

Congrats Camiel, awesome to have you in the lab!

VIB.AI@vibai.bsky.social · last yr.

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. 👏