DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers
BP de Almeida, F Reiter, M Pagani, A Stark - Nature genetics, 2022 - nature.com
Enhancer sequences control gene expression and comprise binding sites (motifs) for
different transcription factors (TFs). Despite extensive genetic and computational studies, the …
different transcription factors (TFs). Despite extensive genetic and computational studies, the …
HEAP: a task adaptive-based explainable deep learning framework for enhancer activity prediction
Y Liu, Z Wang, H Yuan, G Zhu… - Briefings in …, 2023 - academic.oup.com
Enhancers are crucial cis-regulatory elements that control gene expression in a cell-type-
specific manner. Despite extensive genetic and computational studies, accurately predicting …
specific manner. Despite extensive genetic and computational studies, accurately predicting …
An intrinsically interpretable neural network architecture for sequence-to-function learning
Motivation Sequence-based deep learning approaches have been shown to predict a
multitude of functional genomic readouts, including regions of open chromatin and RNA …
multitude of functional genomic readouts, including regions of open chromatin and RNA …
DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of enhancers
BP de Almeida, F Reiter, M Pagani, A Stark - bioRxiv, 2021 - biorxiv.org
Enhancer sequences control gene expression and comprise binding sites (motifs) for
different transcription factors (TFs). Despite extensive genetic and computational studies, the …
different transcription factors (TFs). Despite extensive genetic and computational studies, the …
[HTML][HTML] SEAMoD: A fully interpretable neural network for cis-regulatory analysis of differentially expressed genes
A common way to investigate gene regulatory mechanisms is to identify differentially
expressed genes using transcriptomics, find their candidate enhancers using epigenomics …
expressed genes using transcriptomics, find their candidate enhancers using epigenomics …
Transcriptional regulatory genomics: from mechanistic modeling to causal inference
P Dibaeinia - 2023 - ideals.illinois.edu
Gene transcription refers to the process in which coding regions on the genome are copied
into mRNA molecules through complex cellular mechanisms. This process is regulated …
into mRNA molecules through complex cellular mechanisms. This process is regulated …