Genome-wide association analyses have uncovered multiple genomic regions associated with T2D, but identification of the causal variants at these remains a challenge. There is growing interest in the potential of deep learning models - which predict e...
BACKGROUND: The three-dimensional (3D) structure of chromatins plays significant roles during cell differentiation and development. Hi-C and other 3C-based technologies allow us to look deep into the chromatin architectures. Many studies have suggest...
A gene is considered essential if loss of function results in loss of viability, fitness or in disease. This concept is well established for coding genes; however, non-coding regions are thought less likely to be determinants of critical functions. H...
Despite the importance of sperm DNA to human reproduction, currently no method exists to assess individual sperm DNA quality prior to clinical selection. Traditionally, skilled clinicians select sperm based on a variety of morphological and motility ...
MOTIVATION: Quantitative detection of histone modifications has emerged in the recent years as a major means for understanding such biological processes as chromosome packaging, transcriptional activation, and DNA damage. However, high-throughput exp...
Due to the large numbers of transcription factors (TFs) and cell types, querying binding profiles of all valid TF/cell type pairs is not experimentally feasible. To address this issue, we developed a convolutional-recurrent neural network model, call...
Enhancer is a DNA sequence of a genome that controls transcription of downstream target genes. Enhancers are known to be associated with certain epigenetic signatures. Machine learning tools, such as CSI-ANN, ChromHMM, and RFECS, were developed for p...
We present machine learning models of human genome three-dimensional structure that combine one dimensional (linear) sequence specificity, epigenomic information, and transcription factor binding profiles, with the polymer-based biophysical simulatio...
BACKGROUND: A large fraction of human and mouse autosomal genes are subject to random monoallelic expression (MAE), an epigenetic mechanism characterized by allele-specific gene expression that varies between clonal cell lineages. MAE is highly cell-...
BACKGROUND: DNA inside eukaryotic cells wraps around histones to form the 11nm chromatin fiber that can further fold into higher-order DNA loops, which may depend on the binding of architectural factors. Predicting how the DNA will fold given a distr...