Late-onset Alzheimer's disease (LOAD) is the most common multifactorial neurodegenerative disease among elderly people. LOAD is heterogeneous, and the symptoms vary among patients. Genome-wide association studies (GWAS) have identified genetic risk f...
Deep learning models such as convolutional neural networks (CNNs) excel in genomic tasks but lack interpretability. We introduce ExplaiNN, which combines the expressiveness of CNNs with the interpretability of linear models. ExplaiNN can predict TF b...
Despite the continued efforts, a batch-insensitive tool that can both infer and predict the developmental dynamics using single-cell genomics is lacking. Here, I present scTour, a novel deep learning architecture to perform robust inference and accur...
A novel framework for the automated evaluation of various deep learning-based splice site detectors is presented. The framework eliminates time-consuming development and experimenting activities for different codebases, architectures, and configurati...
BACKGROUND: The diagnosis of rare genetic diseases is often challenging due to the complexity of the genetic underpinnings of these conditions and the limited availability of diagnostic tools. Machine learning (ML) algorithms have the potential to im...
Computer methods and programs in biomedicine
Jun 17, 2023
BACKGROUND AND OBJECTIVE: Mechanistic-based Model simulations (MM) are an effective approach commonly employed, for research and learning purposes, to better investigate and understand the inherent behavior of biological systems. Recent advancements ...
Super-enhancers are large domains on the genome where multiple short typical enhancers within a specific genomic distance are stitched together. Typically, they are cell type-specific and responsible for defining cell identity and regulating gene tra...
The advance of sequencing technologies has enabled a thorough molecular characterization of the genome in human cancers. To improve patient prognosis predictions and subsequent treatment strategies, it is imperative to develop advanced computational ...
IEEE/ACM transactions on computational biology and bioinformatics
Jun 5, 2023
Genomic selection (GS) is expected to accelerate plant and animal breeding. During the last decade, genome-wide polymorphism data have increased, which has raised concerns about storage cost and computational time. Several individual studies have att...
High-throughput profiling methods (such as genomics or imaging) have accelerated basic research and made deep molecular characterization of patient samples routine. These approaches provide a rich portrait of genes, molecular pathways and cell types ...
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