Linking cis-regulatory sequences to target genes has been a long-standing challenge. In this study, we introduce CREaTor, an attention-based deep neural network designed to model cis-regulatory patterns for genomic elements up to 2 Mb from target gen...
Gene expression is regulated by transcription factors that work together to read cis-regulatory DNA sequences. The 'cis-regulatory code' - how cells interpret DNA sequences to determine when, where and how much genes should be expressed - has proven ...
Elucidating the relationship between non-coding regulatory element sequences and gene expression is crucial for understanding gene regulation and genetic variation. We explored this link with the training of interpretable deep learning models predict...
Cell-type-specific regulatory elements, cataloged through extensive experiments and bioinformatics in large-scale consortiums, have enabled enrichment analyses of genetic associations that primarily utilize positional information of the regulatory el...
BACKGROUND: A number of deep learning models have been developed to predict epigenetic features such as chromatin accessibility from DNA sequence. Model evaluations commonly report performance genome-wide; however, cis regulatory elements (CREs), whi...
Predicting molecular processes using deep learning is a promising approach to provide biological insights for non-coding single nucleotide polymorphisms identified in genome-wide association studies. However, most deep learning methods rely on superv...
The rise of large-scale, sequence-based deep neural networks (DNNs) for predicting gene expression has introduced challenges in their evaluation and interpretation. Current evaluations align DNN predictions with orthogonal experimental data, providin...
Gene regulation is inherently multiscale, but scale-adaptive machine learning methods that fully exploit this property in single-nucleus accessibility data are still lacking. Here, we develop ChromatinHD, a pair of scale-adaptive models that uses the...
Genes to cells : devoted to molecular & cellular mechanisms
39904740
Cis-regulatory elements (cREs) play a crucial role in regulating gene expression and determining cell differentiation and state transitions. To capture the heterogeneous transitions of cell states associated with these processes, detecting cRE activi...
Cis-regulatory elements (CREs), including enhancers, silencers, promoters and insulators, play pivotal roles in orchestrating gene regulatory mechanisms that drive complex biological traits. However, current approaches for CRE identification are pred...