AIMC Topic: Gene Expression Regulation
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GSOAP: a tool for visualization of gene set over-representation analysis.
Bioinformatics (Oxford, England)
May 1, 2020
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...
Artificial Intelligence Techniques to Computational Proteomics, Genomics, and Biological Sequence Analysis.
Current protein & peptide science
Jan 1, 2020
In vitro study of the nephrotoxicity of total Dahuang (Radix Et Rhizoma Rhei Palmati) anthraquinones and emodin in monolayer human proximal tubular epithelial cells cultured in a transwell chamber.
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.
Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework.
Nucleic acids research
Sep 5, 2019
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...
TAGOOS: genome-wide supervised learning of non-coding loci associated to complex phenotypes.
Nucleic acids research
Aug 22, 2019
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...
DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning.
Nucleic acids research
Jun 4, 2019
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...
A Systems Toxicology Approach for the Prediction of Kidney Toxicity and Its Mechanisms In Vitro.
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...
Using Drug Expression Profiles and Machine Learning Approach for Drug Repurposing.
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...
Unsupervised Gene Network Inference with Decision Trees and Random Forests.
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...
[Effects of ATP on expression of inflammatory factors in endothelial progenitor cells induced by LPS and the mechanisms].
Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences
Dec 28, 2018
To investigate the effects of adenosine triphosphate (ATP) on expression of inflammatory factors induced by lipopolysaccharide (LPS) in endothelial progenitor cells (EPCs), and to elucidate the possible mechanisms.
Methods: Mononuclear cells were is...
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