BACKGROUND: Gene expression plays a key intermediate role in linking molecular features at the DNA level and phenotype. However, owing to various limitations in experiments, the RNA-seq data are missing in many samples while there exist high-quality ...
MOTIVATION: Gene sets over-representation analysis (GSOA) is a common technique of enrichment analysis that measures the overlap between a gene set and selected instances (e.g. pathways). Despite its popularity, there is currently no established stan...
Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan
Oct 1, 2019
OBJECTIVE: To examine changes in the morphology and physiological functions of human proximal tubular epithelial cells (HK-2 cells) caused by total Dahuang (Radix Et Rhizoma Rhei Palmati) anthraquinones (TDA) and emodin.
The identification of transcription factor binding sites and cis-regulatory motifs is a frontier whereupon the rules governing protein-DNA binding are being revealed. Here, we developed a new method (DEep Sequence and Shape mOtif or DESSO) for cis-re...
Genome-wide association studies (GWAS) associate single nucleotide polymorphisms (SNPs) to complex phenotypes. Most human SNPs fall in non-coding regions and are likely regulatory SNPs, but linkage disequilibrium (LD) blocks make it difficult to dist...
Interactions between regulatory elements are of crucial importance for the understanding of transcriptional regulation and the interpretation of disease mechanisms. Hi-C technique has been developed for genome-wide detection of chromatin contacts. Ho...
Toxicological sciences : an official journal of the Society of Toxicology
May 1, 2019
The failure to predict kidney toxicity of new chemical entities early in the development process before they reach humans remains a critical issue. Here, we used primary human kidney cells and applied a systems biology approach that combines multidim...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2019
The cost of new drug development has been increasing, and repurposing known medications for new indications serves as an important way to hasten drug discovery. One promising approach to drug repositioning is to take advantage of machine learning (ML...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2019
In this chapter, we introduce the reader to a popular family of machine learning algorithms, called decision trees. We then review several approaches based on decision trees that have been developed for the inference of gene regulatory networks (GRNs...