Ocular gene therapy offers a promising approach for treating various eye diseases, centered on the process of transfection, including delivery, cellular uptake and gene expression. This study addresses anatomical and physiological barriers, such as t...
Recent associations between Major Depressive Disorder (MDD) and measures of premature aging suggest accelerated biological aging as a potential biomarker for MDD susceptibility or MDD as a risk factor for age-related diseases. Residuals or "gaps" bet...
Anoikis-related genes (ANRGs) are crucial in the invasion and metastasis of breast cancer (BC). The underlying role of ANRGs in the prognosis of breast cancer patients warrants further study. The anoikis-related prognostic signature (ANRS) was gene...
Transcriptome-wide association studies (TWAS) aim to uncover genotype-phenotype relationships through a two-stage procedure: predicting gene expression from genotypes using an expression quantitative trait locus (eQTL) data set, then testing the pred...
Given the extensive heterogeneity and variability, understanding cellular functions and regulatory mechanisms through the analysis of multi-omics datasets becomes extremely challenging. Here, a comprehensive modeling framework of multi-omics machine ...
N-terminal coding sequence (NCS) influences gene expression by impacting the translation initiation rate. The NCS optimization problem is to find an NCS that maximizes gene expression. The problem is important in genetic engineering. However, current...
Gene expression is inherently dynamic, due to complex regulation and stochastic biochemical events. However, the effects of these dynamics on cell phenotypes can be difficult to determine. Researchers have historically been limited to passive observa...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 25, 2023
Learning representations from data is a fundamental step for machine learning. High-quality and robust drug representations can broaden the understanding of pharmacology, and improve the modeling of multiple drug-related prediction tasks, which furth...
Computer methods and programs in biomedicine
Dec 2, 2023
BACKGROUND: In Diffuse Large B-Cell Lymphoma (DLBCL), several methodologies are emerging to derive novel biomarkers to be incorporated in the risk assessment. We realized a pipeline that relies on autoencoders (AE) and Explainable Artificial Intellig...
Deep learning methods have recently become the state of the art in a variety of regulatory genomic tasks, including the prediction of gene expression from genomic DNA. As such, these methods promise to serve as important tools in interpreting the ful...
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