Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
DNA accessibility has been a powerful tool in locating active regulatory elements in a cell type, but dissecting the combinatorial logic within these regulatory elements has been a continued challenge in the field. Deep learning models have been show...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
Genome-wide DNA methylomes have contributed greatly to tumor detection and subclassification. However, interpreting the biological impact of the DNA methylome at the individual gene level remains a challenge. MethylationToActivity (M2A) is a pipeline...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
Deep neural networks have demonstrated improved performance at predicting sequence specificities of DNA- and RNA-binding proteins. However, it remains unclear why they perform better than previous methods that rely on k-mers and position weight matri...
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...
DNA-protein interaction is one of the most crucial interactions in the biological system, which decides the fate of many processes such as transcription, regulation and splicing of genes. In this study, we trained our models on a training dataset of ...
We present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predi...
MOTIVATION: Histone modifications are epigenetic markers that impact gene expression by altering the chromatin structure or recruiting histone modifiers. Their accurate identification is key to unraveling the mechanisms by which they regulate gene ex...
We present a benchmark study of autonomous, chemical agents exhibiting associative learning of an environmental feature. Associative learning systems have been widely studied in cognitive science and artificial intelligence but are most commonly impl...
Information processing functions are essential for organisms to perceive and react to their complex environment, and for humans to analyze and rationalize them. While our brain is extraordinary at processing complex information, winner-take-all, as a...
In this paper, an intelligent dynamic perturbation orthogonal chirp division multiplexing (OCDM) encryption scheme based on cellular neural network and biological genetic encoding for seven-core optical fiber is proposed for the first time to our kno...