AIMC Topic: Databases, Genetic

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Predicting Zoonotic Risk of Influenza A Viruses from Host Tropism Protein Signature Using Random Forest.

International journal of molecular sciences
Influenza A viruses remain a significant health problem, especially when a novel subtype emerges from the avian population to cause severe outbreaks in humans. Zoonotic viruses arise from the animal population as a result of mutations and reassortmen...

A disease similarity matrix based on the uniqueness of shared genes.

BMC medical genomics
BACKGROUND: Complex diseases involve many genes, and these genes are often associated with several different illnesses. Disease similarity measurement can be based on shared genotype or phenotype. Quantifying relationships between genes can reveal pr...

Geminivirus data warehouse: a database enriched with machine learning approaches.

BMC bioinformatics
BACKGROUND: The Geminiviridae family encompasses a group of single-stranded DNA viruses with twinned and quasi-isometric virions, which infect a wide range of dicotyledonous and monocotyledonous plants and are responsible for significant economic los...

Novelty Indicator for Enhanced Prioritization of Predicted Gene Ontology Annotations.

IEEE/ACM transactions on computational biology and bioinformatics
Biomolecular controlled annotations have become pivotal in computational biology, because they allow scientists to analyze large amounts of biological data to better understand test results, and to infer new knowledge. Yet, biomolecular annotation da...

An improved method for identification of small non-coding RNAs in bacteria using support vector machine.

Scientific reports
Bacterial small non-coding RNAs (sRNAs) are not translated into proteins, but act as functional RNAs. They are involved in diverse biological processes like virulence, stress response and quorum sensing. Several high-throughput techniques have enable...

Multiple-Swarm Ensembles: Improving the Predictive Power and Robustness of Predictive Models and Its Use in Computational Biology.

IEEE/ACM transactions on computational biology and bioinformatics
Machine learning is an integral part of computational biology, and has already shown its use in various applications, such as prognostic tests. In the last few years in the non-biological machine learning community, ensembling techniques have shown t...

Optimization of Gene Set Annotations Using Robust Trace-Norm Multitask Learning.

IEEE/ACM transactions on computational biology and bioinformatics
Gene set enrichment (GSE) is a useful tool for analyzing and interpreting large molecular datasets generated by modern biomedical science. The accuracy and reproducibility of GSE analysis are heavily affected by the quality and integrity of gene sets...

Identification of transcription factors that may reprogram lung adenocarcinoma.

Artificial intelligence in medicine
BACKGROUND: Lung adenocarcinoma is one of most threatening disease to human health. Although many efforts have been devoted to its genetic study, few researches have been focused on the transcription factors which regulate tumor initiation and progre...

SILVA, RDP, Greengenes, NCBI and OTT - how do these taxonomies compare?

BMC genomics
BACKGROUND: A key step in microbiome sequencing analysis is read assignment to taxonomic units. This is often performed using one of four taxonomic classifications, namely SILVA, RDP, Greengenes or NCBI. It is unclear how similar these are and how to...