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Gene Expression Regulation

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Multi-task learning for the simultaneous reconstruction of the human and mouse gene regulatory networks.

Scientific reports
The reconstruction of Gene Regulatory Networks (GRNs) from gene expression data, supported by machine learning approaches, has received increasing attention in recent years. The task at hand is to identify regulatory links between genes in a network....

Development of a quantitative systems pharmacology model of chronic kidney disease: metabolic bone disorder.

American journal of physiology. Renal physiology
Chronic kidney disease mineral bone disorder (CKD-MBD) is a virtually universal complication of kidney diseases, starting early in the course of disease and resulting in devastating clinical consequences ranging from bone fragility to accelerated ath...

Machine-learning-driven biomarker discovery for the discrimination between allergic and irritant contact dermatitis.

Proceedings of the National Academy of Sciences of the United States of America
Contact dermatitis tremendously impacts the quality of life of suffering patients. Currently, diagnostic regimes rely on allergy testing, exposure specification, and follow-up visits; however, distinguishing the clinical phenotype of irritant and all...

Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure.

Nature communications
Understanding the genetic regulatory code governing gene expression is an important challenge in molecular biology. However, how individual coding and non-coding regions of the gene regulatory structure interact and contribute to mRNA expression leve...

Extraction of the molecular level biomedical event trigger based on gene ontology using radial belief neural network techniques.

Bio Systems
Detection of molecular level biomedical event extraction plays a vital role in creating and visualizing the applications related to natural language processing. Cystic Fibrosis is an inherited genetic and debilitating pathology involving the respirat...

Recognized trophoblast-like cells conversion from human embryonic stem cells by BMP4 based on convolutional neural network.

Reproductive toxicology (Elmsford, N.Y.)
The use of models of stem cell differentiation to trophoblastic cells provides an effective perspective for understanding the early molecular events in the establishment and maintenance of human pregnancy. In combination with the newly developed deep...

Identification of contributing genes of Huntington's disease by machine learning.

BMC medical genomics
BACKGROUND: Huntington's disease (HD) is an inherited disorder caused by the polyglutamine (poly-Q) mutations of the HTT gene results in neurodegeneration characterized by chorea, loss of coordination, cognitive decline. However, HD pathogenesis is s...

Deep learning approach for predicting functional Z-DNA regions using omics data.

Scientific reports
Computational methods to predict Z-DNA regions are in high demand to understand the functional role of Z-DNA. The previous state-of-the-art method Z-Hunt is based on statistical mechanical and energy considerations about B- to Z-DNA transition using ...

Identification of early liver toxicity gene biomarkers using comparative supervised machine learning.

Scientific reports
Screening agrochemicals and pharmaceuticals for potential liver toxicity is required for regulatory approval and is an expensive and time-consuming process. The identification and utilization of early exposure gene signatures and robust predictive mo...