Genetics

Machine Learning for detection of viral sequences in human metagenomic datasets.

BACKGROUND: Detection of highly divergent or yet unknown viruses from metagenomics sequencing datasets is a major bioinformatics challenge. When human samples are sequenced, a large proportion of assembled contigs are classified as "unknown", as conventional methods find no similarity to known sequences. We wished to explore whether machine learning algorithms using Relative Synonymous Codon Usage...

SiRNA silencing efficacy prediction based on a deep architecture.

BACKGROUND: Small interfering RNA (siRNA) can be used to post-transcriptional gene regulation by knocking down targeted genes. In functional genomics, biomedical research and cancer therapeutics, siRNA design is a critical research topic. Various computational algorithms have been developed to select the most effective siRNA, whereas the efficacy prediction accuracy is not so satisfactory. Many ex...

Deep learning-based quantification of abdominal fat on magnetic resonance images.

Obesity is increasingly prevalent and associated with increased risk of developing type 2 diabetes, cardiovascular diseases, and cancer. Magnetic reso...

Data mining and machine learning approaches for the integration of genome-wide association and methylation data: methodology and main conclusions from GAW20.

BACKGROUND: Multiple layers of genetic and epigenetic variability are being simultaneously explored in an increasing number of health studies. We summ...

Serum vitamin D deficiency and vitamin D receptor gene polymorphism are associated with increased risk of cardiovascular disease in a Chinese rural population.

Several studies have reported a conflicting association between vitamin D deficiency, vitamin D receptor (VDR) polymorphism, and the risk of cardiovas...

HLBS-PopOmics: an online knowledge base to accelerate dissemination and implementation of research advances in population genomics to reduce the burden of heart, lung, blood, and sleep disorders.

Recent dramatic advances in multiomics research coupled with exponentially increasing volume, complexity, and interdisciplinary nature of publications...

Fuzzy entropy based on differential evolution for breast gland segmentation.

For the diagnosis and treatment of breast tumors, the automatic detection of glands is a crucial step. The true segmentation of the gland is directly ...

Universal method for robust detection of circadian state from gene expression.

Circadian clocks play a key role in regulating a vast array of biological processes, with significant implications for human health. Accurate assessme...

AluScanCNV2: An R package for copy number variation calling and cancer risk prediction with next-generation sequencing data.

The usage of next-generation sequencing (NGS) to detect copy number variation (CNV) is widely accepted in cancer research. Based on an AluScanCNV soft...

The key role of inoculated sludge in fast start-up of sequencing batch reactor for the domestication of aerobic granular sludge.

Two types of inoculated sludges, granular sludge that had been stored at -20°C and activated sludge, were investigated for the domestication of aerobi...

BERMP: a cross-species classifier for predicting mA sites by integrating a deep learning algorithm and a random forest approach.

N-methyladenosine (mA) is a prevalent RNA methylation modification involved in several biological processes. Hundreds or thousands of mA sites identif...

DES-Mutation: System for Exploring Links of Mutations and Diseases.

During cellular division DNA replicates and this process is the basis for passing genetic information to the next generation. However, the DNA copy pr...

RNA-seq analysis reveals different gene ontologies and pathways in rheumatoid arthritis and Kashin-Beck disease.

AIMS: To understand the pathogenesis of cartilage damage in Kashin-Beck disease (KBD) and rheumatoid arthritis (RA) which similar clinical symptoms.

Utilizing Deep Learning and Genome Wide Association Studies for Epistatic-Driven Preterm Birth Classification in African-American Women.

Genome-Wide Association Studies (GWAS) are used to identify statistically significant genetic variants in case-control studies. The main objective is ...

Machine learning identifies interacting genetic variants contributing to breast cancer risk: A case study in Finnish cases and controls.

We propose an effective machine learning approach to identify group of interacting single nucleotide polymorphisms (SNPs), which contribute most to th...

Novel symmetry-based gene-gene dissimilarity measures utilizing Gene Ontology: Application in gene clustering.

In recent years DNA microarray technology, leading to the generation of high-volume biological data, has gained significant attention. To analyze this...

Can Deep Learning Improve Genomic Prediction of Complex Human Traits?

The genetic analysis of complex traits does not escape the current excitement around artificial intelligence, including a renewed interest in "deep le...

An Efficient Feature Selection Strategy Based on Multiple Support Vector Machine Technology with Gene Expression Data.

The application of gene expression data to the diagnosis and classification of cancer has become a hot issue in the field of cancer classification. Ge...

Controlling Complexity of Cerebral Cortex Simulations-I: CxSystem, a Flexible Cortical Simulation Framework.

Simulation of the cerebral cortex requires a combination of extensive domain-specific knowledge and efficient software. However, when the complexity o...

Management practices associated with strongylid parasite prevalence on horse farms in rural counties of Kentucky.

Anthelmintic resistance among cyathostomin parasites is a wide-spread problem. The parasite control guidelines written by the American Association of ...