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Gene Expression Regulation

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[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
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...

DeepMirTar: a deep-learning approach for predicting human miRNA targets.

Bioinformatics (Oxford, England)
MOTIVATION: MicroRNAs (miRNAs) are small non-coding RNAs that function in RNA silencing and post-transcriptional regulation of gene expression by targeting messenger RNAs (mRNAs). Because the underlying mechanisms associated with miRNA binding to mRN...

[Application of machine learning in the CRISPR/Cas9 system].

Yi chuan = Hereditas
The third generation of the CRISPR/Cas9-mediated genome fixed-point editing technology has been widely used in the field of gene editing and gene expression regulation. How to improve the on-target efficiency and specificity of this system, as well a...

DeFine: deep convolutional neural networks accurately quantify intensities of transcription factor-DNA binding and facilitate evaluation of functional non-coding variants.

Nucleic acids research
The complex system of gene expression is regulated by the cell type-specific binding of transcription factors (TFs) to regulatory elements. Identifying variants that disrupt TF binding and lead to human diseases remains a great challenge. To address ...

L1000FWD: fireworks visualization of drug-induced transcriptomic signatures.

Bioinformatics (Oxford, England)
MOTIVATION: As part of the NIH Library of Integrated Network-based Cellular Signatures program, hundreds of thousands of transcriptomic signatures were generated with the L1000 technology, profiling the response of human cell lines to over 20 000 sma...

Semi-supervised network inference using simulated gene expression dynamics.

Bioinformatics (Oxford, England)
MOTIVATION: Inferring the structure of gene regulatory networks from high-throughput datasets remains an important and unsolved problem. Current methods are hampered by problems such as noise, low sample size, and incomplete characterizations of regu...

Extreme learning machines for reverse engineering of gene regulatory networks from expression time series.

Bioinformatics (Oxford, England)
MOTIVATION: The reconstruction of gene regulatory networks (GRNs) from genes profiles has a growing interest in bioinformatics for understanding the complex regulatory mechanisms in cellular systems. GRNs explicitly represent the cause-effect of regu...

Evaluation of luteinizing hormone regulation of maturation and apoptosis, expression of LHR and FSHR in cumulus-oocyte complexes in Lanzhou fat-tailed sheep.

Polish journal of veterinary sciences
The present study aimed to assess LH effects on in vitro maturation (IVM) and apoptosis and also to explore the gene expressions of LHR and FSHR in cumulus-oocyte complexes (COCs) of the sheep. COCs were in vitro matured 24h in the IVM medium supplem...

Using neural networks for reducing the dimensions of single-cell RNA-Seq data.

Nucleic acids research
While only recently developed, the ability to profile expression data in single cells (scRNA-Seq) has already led to several important studies and findings. However, this technology has also raised several new computational challenges. These include ...