* We generated a 700K scATAC-seq atlas of the entire adult fly, which we combined with our previously published scRNA-seq adult Fly Cell Atlas (Can Eksi et al, in preparation).
* To optimize the cost and efficiency of sampling enough cells over 10 days of development, we combined commercial platforms (10x Genomics) with a newly developed HyDrop-v2 scATAC protocol. A first bioRxiv preprint was released to describe HyDrop-v2, alongside a 600K cells atlas of the last four hours of embryo development (Dickmancken et al., BioRxiv 2025).
* We developed a new software framework to train deep learning enhancer models, called CREsted, and released the codebase on GitHub (Kempynck & De Winter et al., BioRxiv 2025).
* We trained and validated a series of CREsted models on diverse systems and shared them through a model repository. This includes a zebrafish development model, that we also used to design synthetic enhancers that we tested in vivo in zebrafish (Kempynck & De Winter et al., BioRxiv 2025).
* We trained CREsted models on the entire adult fly scATAC-seq atlas. We also trained the first ‘foundation model’ of the fruit fly, from scratch, using the Borzoi framework, on 11,000 genomic tracks that we curated from public data bases, combined with our full scRNA-seq and scATAC-seq adult atlases (Can Eksi et al, in preparation).
* We discovered and published similarities of enhancer codes between all cell types in the vertebrate pallium, particularly in the human and mouse cortex, and the chicken telencephalon. For the latter, we created the first sc-multiome and spatial atlas. We trained CREsted models for all species and devised three new metrics to compare enhancer logic. We validated several chicken enhancers in the mouse brain using AAV enhancer-reporter assays. Hecker & Kempynck, Science 2025.
* We participated in and won a computational challenge to predict cell type specific enhancers in the mouse brain, led by the Allen Institute, and co-published the results (Johansen & Kempynck, Cell Genomics 2025).
* We analyzed a human embryonic brain sc-multiome atlas and compared it to human neural tube organoids, generating a compendium of enhancer codes. We compared these to zebrafish neural tube, and validated enhancers in chicken embryos and zebrafish embryos (De Winter, in preparation).
* To compare gene loci between species, we generated a mouse sc-multiome atlas during development and curated a human counterpart from public data sets, compared trajectories using gene warping, and trained CREsted models on human and mouse to study changes in enhancer-promoter interactions between species (Abaffyova et al., in preparation).
* We developed computational models and tools to design synthetic enhancers, including generative adversarial networks, and tested in Drosophila brains and human melanoma cells (Taskiran, Nature 2025)
* We published a review paper on enhancer design (De Winter, Nat Rev Bioengineering 2025).
* We developed HyDrop-v2, a new version of our custom droplet microfluidics technique for scATAC-seq that achieves higher sensitivity and scale. We generated a large Drosophila embryo atlas and a mouse brain atlas with HyDrop-v2, and benchmarked it against commercial methods (10x Genomics) using sequence-to-function models. This technique is used to improve our atlasing efforts of the entire fruit fly. (Dickmancken et al., BioRxiv 2025).
* We developed Nova-ST, a new spatial transcriptomics technique using Illumina chips. We use this to localize and validate cell types in other species’ brains (Poovathingal et al., Cell Reports Methods 2024)
