Mathematical biosciences and engineering : MBE
Sep 30, 2019
Copy number variations (CNVs) play an important role in many types of cancer. With the rapid development of next generation sequencing (NGS) techniques, many methods for detecting CNVs of a single sample have emerged: (i) require genome-wide data of ...
ATAC-seq has been widely adopted to identify accessible chromatin regions across the genome. However, current data analysis still utilizes approaches initially designed for ChIP-seq or DNase-seq, without considering the transposase digested DNA fragm...
MOTIVATION: Computational identification of promoters is notoriously difficult as human genes often have unique promoter sequences that provide regulation of transcription and interaction with transcription initiation complex. While there are many at...
The associations between diseases/traits and copy number variants (CNVs) have not been systematically investigated in genome-wide association studies (GWASs), primarily due to a lack of robust and accurate tools for CNV genotyping. Herein, we propose...
Identifying genomic locations of natural selection from sequence data is an ongoing challenge in population genetics. Current methods utilizing information combined from several summary statistics typically assume no correlation of summary statistics...
Journal of bioinformatics and computational biology
Oct 1, 2018
Multifunctional genes are important genes because of their essential roles in human cells. Studying and analyzing multifunctional genes can help understand disease mechanisms and drug discovery. We propose a computational method for scoring gene mult...
MOTIVATION: Identifying molecular mechanisms that drive cancers from early to late stages is highly important to develop new preventive and therapeutic strategies. Standard machine learning algorithms could be used to discriminate early- and late-sta...
The human genome is now investigated through high-throughput functional assays, and through the generation of population genomic data. These advances support the identification of functional genetic variants and the prediction of traits (e.g. deleter...