A community effort to optimize sequence-based deep learning models of gene regulation
A systematic evaluation of how model architectures and training strategies impact genomics
model performance is needed. To address this gap, we held a DREAM Challenge where …
model performance is needed. To address this gap, we held a DREAM Challenge where …
Designing interpretable deep learning applications for functional genomics: a quantitative analysis
Deep learning applications have had a profound impact on many scientific fields, including
functional genomics. Deep learning models can learn complex interactions between and …
functional genomics. Deep learning models can learn complex interactions between and …
CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant
Functional enhancer annotation is critical for understanding tissue-specific transcriptional
regulation and prioritizing disease-associated non-coding variants. However, unbiased …
regulation and prioritizing disease-associated non-coding variants. However, unbiased …
[HTML][HTML] Rewriting regulatory DNA to dissect and reprogram gene expression
Regulatory DNA sequences within enhancers and promoters bind transcription factors to
encode cell type-specific patterns of gene expression. However, the regulatory effects and …
encode cell type-specific patterns of gene expression. However, the regulatory effects and …
[HTML][HTML] Just a SNP away: The future of in vivo massively parallel reporter assay
KN Degner, JL Bell, SD Jones, H Won - Cell Insight, 2024 - Elsevier
The human genome is largely noncoding, yet the field is still grasping to understand how
noncoding variants impact transcription and contribute to disease etiology. The massively …
noncoding variants impact transcription and contribute to disease etiology. The massively …
Chromatin accessibility is a two-tier process regulated by transcription factor pioneering and enhancer activation
KJ Brennan, M Weilert, S Krueger, A Pampari, HY Liu… - bioRxiv, 2022 - biorxiv.org
Chromatin accessibility is integral to the process by which transcription factors (TFs) read out
cis-regulatory DNA sequences, but it is difficult to differentiate between TFs that drive …
cis-regulatory DNA sequences, but it is difficult to differentiate between TFs that drive …
[HTML][HTML] DNA-Diffusion: Leveraging Generative Models for Controlling Chromatin Accessibility and Gene Expression via Synthetic Regulatory Elements
The challenge of systematically modifying and optimizing regulatory elements for precise
gene expression control is central to modern genomics and synthetic biology …
gene expression control is central to modern genomics and synthetic biology …
Flexible use of conserved motif vocabularies constrains genome access in cell type evolution
Cell types evolve into a hierarchy with related types grouped into families. How cell type
diversification is constrained by the stable separation between families over vast …
diversification is constrained by the stable separation between families over vast …
Molecular convergence of risk variants for congenital heart defects leveraging a regulatory map of the human fetal heart
Congenital heart defects (CHD) arise in part due to inherited genetic variants that alter
genes and noncoding regulatory elements in the human genome. These variants are …
genes and noncoding regulatory elements in the human genome. These variants are …
EPInformer: a scalable deep learning framework for gene expression prediction by integrating promoter-enhancer sequences with multimodal epigenomic data
Transcriptional regulation, critical for cellular differentiation and adaptation to environmental
changes, involves coordinated interactions among DNA sequences, regulatory proteins, and …
changes, involves coordinated interactions among DNA sequences, regulatory proteins, and …