Massively parallel reporter assay (MPRA) is a high-throughput method that enables the study of the regulatory activities of tens of thousands of DNA oligonucleotides in a single experiment. While MPRA experiments have grown in popularity, their small...
American journal of medical genetics. Part A
36484420
The field of clinical genetics and genomics continues to evolve. In the past few decades, milestones like the initial sequencing of the human genome, dramatic changes in sequencing technologies, and the introduction of artificial intelligence, have u...
BACKGROUND: Structural variation (SV), which ranges from 50 bp to [Formula: see text] 3 Mb in size, is an important type of genetic variations. Deletion is a type of SV in which a part of a chromosome or a sequence of DNA is lost during DNA replicati...
Interpretation of noncoding genomic variants is one of the most important challenges in human genetics. Machine learning methods have emerged recently as a powerful tool to solve this problem. State-of-the-art approaches allow prediction of transcrip...
Structural variants (SVs) are a major driver of genetic diversity and disease in the human genome and their discovery is imperative to advances in precision medicine. Existing SV callers rely on hand-engineered features and heuristics to model SVs, w...
MOTIVATION: Efficient tapping into genomic information from a single microscopic image of an intact DNA molecule is an outstanding challenge and its solution will open new frontiers in molecular diagnostics. Here, a new computational method for optic...
Large-scale population variant data is often used to filter and aid interpretation of variant calls in a single sample. These approaches do not incorporate population information directly into the process of variant calling, and are often limited to ...
MOTIVATION: Enhancers are vital cis-regulatory elements that regulate gene expression. Enhancer RNAs (eRNAs), a type of long noncoding RNAs, are transcribed from enhancer regions in the genome. The tissue-specific expression of eRNAs is crucial in th...
Silencers are noncoding DNA sequence fragments located on the genome that suppress gene expression. The variation of silencers in specific cells is closely related to gene expression and cancer development. Computational approaches that exclusively r...
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...