The liver is the primary site for the metabolism and detoxification of many compounds, including pharmaceuticals. Consequently, it is also the primary location for many adverse reactions. As the liver is not readily accessible for sampling in humans;...
Computer methods and programs in biomedicine
37453366
BACKGROUND AND OBJECTIVE: Prostate cancer is one of the most prevalent forms of cancer in men worldwide. Traditional screening strategies such as serum PSA levels, which are not necessarily cancer-specific, or digital rectal exams, which are often in...
The accurate prediction of patients with complex diseases, such as Alzheimer's disease (AD), as well as disease stages, including early- and late-stage cancer, is challenging owing to substantial variability among patients and limited availability of...
When analyzing data from in situ RNA detection technologies, cell segmentation is an essential step in identifying cell boundaries, assigning RNA reads to cells, and studying the gene expression and morphological features of cells. We developed a dee...
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...
Inferring gene expressions from histopathological images has long been a fascinating yet challenging task, primarily due to the substantial disparities between the two modality. Existing strategies using local or global features of histological image...
Differential analysis of bulk RNA-seq data often suffers from lack of good controls. Here, we present a generative model that replaces controls, trained solely on healthy tissues. The unsupervised model learns a low-dimensional representation and can...
mRNA levels of all genes in a genome is a critical piece of information defining the overall state of the cell in a given environmental condition. Being able to reconstruct such condition-specific expression in fungal genomes is particularly importan...
Owing to the nondeterministic and nonlinear nature of gene expression, the steady-state intracellular protein abundance of a clonal population forms a distribution. The characteristics of this distribution, including expression strength and noise, ar...
Computer methods and programs in biomedicine
38091844
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...