Decima learns to predict cell-type-specific gene expression based on DNA sequences, contributing to the analysis of gene regulation and design of context-specific regulatory elements.

Nature Methods - Decima learns to predict cell-type-specific gene expression based on DNA sequences, contributing to the analysis of gene regulation and design of context-specific regulatory elements.

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The development of modern genome editing and DNA synthesis has enabled researchers to edit DNA sequences with high precision but has left unsolved the problem of designing these edits. We introduce Le...

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gReLU advances deep-learning-based modeling and analysis of DNA sequences with comprehensive toolsets and versatile applications.

gReLU advances deep-learning-based modeling and analysis of DNA sequences with comprehensive toolsets and versatile applications.

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The design of regulatory elements is pivotal in gene and cell therapy, where DNA sequences are engineered to drive elevated and cell-type specific expression. However, the systematic assessment of synthetic DNA sequences without robust metrics and easy-to-use software remains challenging. Here, we introduce Polygraph, a Python framework that evaluates synthetic DNA elements, based on features like diversity, motif and k-mer composition, similarity to endogenous sequences, and screening with predictive and foundational models. Polygraph is the first instrument for assessing synthetic regulatory sequences, enabling faster progress in therapeutic interventions and improving our understanding of gene regulatory mechanisms.

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Sequence-to-function models that predict gene expression from genomic DNA sequence have proven valuable for many biological tasks, including understanding cis-regulatory syntax and interpreting non-co...