Toxicological sciences : an official journal of the Society of Toxicology
37707797
The aryl hydrocarbon receptor (AhR) is an inducible transcription factor whose ligands include the potent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Ligand-activated AhR binds to DNA at dioxin response elements (DREs) conta...
Enhancers control gene expression and have crucial roles in development and homeostasis. However, the targeted de novo design of enhancers with tissue-specific activities has remained challenging. Here we combine deep learning and transfer learning t...
Medical & biological engineering & computing
38635004
A tissue sample is a valuable resource for understanding a patient's symptoms and health status in relation to tumor growth. Recent research seeks to establish a connection between tissue-specific tumor samples and genetic markers (genes). This break...
As vast histological archives are digitised, there is a pressing need to be able to associate specific tissue substructures and incident pathology to disease outcomes without arduous annotation. Here, we learn self-supervised representations using a ...
BACKGROUND: Cell free DNA (cfDNA)-based assays hold great potential in detecting early cancer signals yet determining the tissue-of-origin (TOO) for cancer signals remains a challenging task. Here, we investigated the contribution of a methylation at...
BACKGROUND: A number of deep learning models have been developed to predict epigenetic features such as chromatin accessibility from DNA sequence. Model evaluations commonly report performance genome-wide; however, cis regulatory elements (CREs), whi...
Pathogenic variants underlying Mendelian diseases often disrupt the normal physiology of a few tissues and organs. However, variant effect prediction tools that aim to identify pathogenic variants are typically oblivious to tissue contexts. Here we r...
In the context of multi-omics data analytics for various diseases, transcriptome-wide association studies leveraging genetically predicted gene expression hold promise for identifying novel regions linked to complex traits. However, existing methods ...
Species-specific differences in protein translation can affect the design of protein-based drugs. Consequently, efficient expression of recombinant proteins often requires codon optimization. Publicly available optimization tools do not always result...
BACKGROUND: Single-cell multi-omics technologies, particularly single-cell RNA sequencing (scRNA-seq), have revolutionized our understanding of cellular heterogeneity and development by providing insights into gene expression at the single-cell level...