Obtaining genetics insights from deep learning via explainable artificial intelligence
Artificial intelligence (AI) models based on deep learning now represent the state of the art
for making functional predictions in genomics research. However, the underlying basis on …
for making functional predictions in genomics research. However, the underlying basis on …
Applying interpretable machine learning in computational biology—pitfalls, recommendations and opportunities for new developments
Recent advances in machine learning have enabled the development of next-generation
predictive models for complex computational biology problems, thereby spurring the use of …
predictive models for complex computational biology problems, thereby spurring the use of …
Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation
Sequence-based machine-learning models trained on genomics data improve genetic
variant interpretation by providing functional predictions describing their impact on the cis …
variant interpretation by providing functional predictions describing their impact on the cis …
Sequence determinants of human gene regulatory elements
DNA can determine where and when genes are expressed, but the full set of sequence
determinants that control gene expression is unknown. Here, we measured the …
determinants that control gene expression is unknown. Here, we measured the …
Cell-type-directed design of synthetic enhancers
Transcriptional enhancers act as docking stations for combinations of transcription factors
and thereby regulate spatiotemporal activation of their target genes. It has been a long …
and thereby regulate spatiotemporal activation of their target genes. It has been a long …
[HTML][HTML] Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation
C Bravo Gonzalez-Blas, I Matetovici, H Hillen… - Nature Cell …, 2024 - nature.com
In the mammalian liver, hepatocytes exhibit diverse metabolic and functional profiles based
on their location within the liver lobule. However, it is unclear whether this spatial variation …
on their location within the liver lobule. However, it is unclear whether this spatial variation …
Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation
KJ Brennan, M Weilert, S Krueger, A Pampari, H Liu… - Developmental cell, 2023 - cell.com
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 …
Multiplexed single-cell characterization of alternative polyadenylation regulators
Most mammalian genes have multiple polyA sites, representing a substantial source of
transcript diversity regulated by the cleavage and polyadenylation (CPA) machinery. To …
transcript diversity regulated by the cleavage and polyadenylation (CPA) machinery. To …
The genetic and biochemical determinants of mRNA degradation rates in mammals
Background Degradation rate is a fundamental aspect of mRNA metabolism, and the factors
governing it remain poorly characterized. Understanding the genetic and biochemical …
governing it remain poorly characterized. Understanding the genetic and biochemical …
Machine-guided design of cell-type-targeting cis-regulatory elements
Cis-regulatory elements (CREs) control gene expression, orchestrating tissue identity,
developmental timing and stimulus responses, which collectively define the thousands of …
developmental timing and stimulus responses, which collectively define the thousands of …