Bas van Steensel lab (NKI)

Bas van Steensel lab (NKI)

@basvansteensellab.bsky.social

We are a research lab at the Netherlands Cancer Institute. We develop and apply new genomics tools to study genome biology and gene regulation.

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Bas van Steensel lab (NKI)
@basvansteensellab.bsky.social

Inferring transcription factor activity: use ATAC-seq, reporter assays, or both? link.springer.com/article/10.1...

link.springer.comSystematic comparison of estimates of transcription factor activity by ATAC-seq and multiplexed reporter assays - Molecular Systems BiologyTranscription factors (TFs) are central to gene regulation and play critical roles in development, cellular homeostasis and disease. The ability to accurately measure TF activity is essential to under...
Bas van Steensel lab (NKI)
@basvansteensellab.bsky.social

Our reporter hopping scaled up to thousands of integrations in a single locus, to produce high-resolution functional maps, with plenty of interesting insights: www.science.org/doi/10.1126/...

science.orgFunctional maps of a genomic locus reveal confinement of an enhancer by its target geneGenes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...
Bas van Steensel lab (NKI)
@basvansteensellab.bsky.social

Together with the De Ridder lab www.deridderlab.nl we just published a review on deep learning as a tool for gene expression analysis/ prediction: rdcu.be/elQCc.

rdcu.bePredicting gene expression from DNA sequence using deep learning modelsNature Reviews Genetics - Barbadilla-Martínez et al. review recent progress in deep-learning-based sequence-to-expression models, which predict gene expression levels solely from DNA sequence....

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