Modelling and design of transcriptional enhancers

2025/02/28 by Seppe De Winter, Vasileios Konstantakos, Stein Aerts · 1 voice · 2 citations
Biochemistry, Genetics and Molecular Biology · #DNA and Nucleic Acid Chemistry #Genomics and Chromatin Dynamics #RNA Research and Splicing

paper · pdf · doi:10.1038/s44222-025-00280-y

crossref issued 2025/02/28 · crossref published 2025/02/28 · crossref published-online 2025/02/28 · openalex publication_date 2025/02/28 · crossref created 2025/02/28 · crossref deposited 2025/05/09 · openalex created_date 2025/10/10 · crossref indexed 2026/07/27 · openalex updated_date 2026/07/28

Citations

• Categorical Reparameterization with Gumbel-Softmax
• Deep learning: new computational modelling techniques for genomics
• Denoising Diffusion Probabilistic Models
• DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
• Effective gene expression prediction from sequence by integrating long-range interactions
• Generative Adversarial Networks
• Analog Bits: Generating Discrete Data using Diffusion Models with Self-Conditioning
• Hyena Hierarchy: Towards Larger Convolutional Language Models
• Data navigation on the ENCODE portal
• HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution
• Exploiting Generative AI to Scale up Intelligent Tutoring Systems
• SiT: Exploring Flow and Diffusion-based Generative Models with Scalable Interpolant Transformers
• Dirichlet Flow Matching with Applications to DNA Sequence Design
• DiscDiff: Latent Diffusion Model for DNA Sequence Generation
• Accurate structure prediction of biomolecular interactions with AlphaFold 3
• scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution
• Enhancer cooperativity can compensate for loss of activity over large genomic distances
• ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants
• Genomic Language Models: Opportunities and Challenges

Cited by

• Biological Reasoning-Informed Regression for Interpretable Regulatory DNA Activity Prediction
• Toward Interpretable and Generalizable AI in Regulatory Genomics

Discussions

• Check out this excellent review. ➡️ De Winter, S., Konstantakos, V. & Aerts, S. Modelling and design of transcriptional enhancers. Nat Rev Bioeng (2025). DOI: doi.org/10.1038/s442... [bsky, 2 points, 0 comments]