Genetics

CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments.

BACKGROUND: Gene ontology (GO) enrichment is commonly used for inferring biological meaning from systems biology experiments. However, determining differential GO and pathway enrichment between DNA-binding experiments or using the GO structure to classify experiments has received little attention.

GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.

Cellular processes involve large numbers of RNA molecules. The functions of these RNA molecules and their binding to molecular machines are highly dependent on their 3D structures. One of the key challenges in RNA structure prediction and modeling is predicting the spatial arrangement of the various structural elements of RNA. As RNA folding is generally hierarchical, methods involving coarse-grai...

DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool.

There are currently 151 plants with draft genomes available but levels of functional annotation for putative protein products are low. Therefore, accu...

SAMSVM: A tool for misalignment filtration of SAM-format sequences with support vector machine.

Sequence alignment/map (SAM) formatted sequences [Li H, Handsaker B, Wysoker A et al., Bioinformatics 25(16):2078-2079, 2009.] have taken on a main ro...

PPDB: A Tool for Investigation of Plants Physiology Based on Gene Ontology.

Representing the way forward, from functional genomics and its ontology to functional understanding and physiological model, in a computationally trac...

Genomic signatures for paclitaxel and gemcitabine resistance in breast cancer derived by machine learning.

Increasingly, the effectiveness of adjuvant chemotherapy agents for breast cancer has been related to changes in the genomic profile of tumors. We inv...

Superiority of artificial neural networks for a genetic classification procedure.

The correct classification of individuals is extremely important for the preservation of genetic variability and for maximization of yield in breeding...

Development of molecular approach based on PCR assay for detection of histamine producing bacteria.

Histamine fish poisoning becomes highly concern not only in public health but also economic aspect. Histamine is produced from histidine in fish muscl...

OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization.

MOTIVATION: Exome sequencing has become a de facto standard method for Mendelian disease gene discovery in recent years, yet identifying disease-causi...

Effects of bovine subclinical mastitis caused by Corynebacterium spp. on somatic cell count, milk yield and composition by comparing contralateral quarters.

Subclinical mastitis caused by Corynebacterium spp. (as a group and at the species level) was investigated by evaluating contralateral (healthy and in...

Knowledge-based analysis of genetic associations of rheumatoid arthritis to inform studies searching for pleiotropic genes: a literature review and network analysis.

INTRODUCTION: Pleiotropy describes the genetic effect of a single gene on multiple phenotypic traits. Gene variants directly affect the normal process...

Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data.

Cell signaling underlies transcription/epigenetic control of a vast majority of cell-fate decisions. A key goal in cell signaling studies is to identi...

Application of the multifactor dimensionality reduction method in evaluation of the roles of multiple genes/enzymes in multidrug-resistant acquisition in Pseudomonas aeruginosa strains.

Multidrug-resistant Pseudomonas aeruginosa (MDRPA) infections are major threats to healthcare-associated infection control and the intrinsic molecular...

A Comparative Study on Multifactor Dimensionality Reduction Methods for Detecting Gene-Gene Interactions with the Survival Phenotype.

Genome-wide association studies (GWAS) have extensively analyzed single SNP effects on a wide variety of common and complex diseases and found many ge...

Rediscovery of Good-Turing estimators via Bayesian nonparametrics.

The problem of estimating discovery probabilities originated in the context of statistical ecology, and in recent years it has become popular due to i...

Learning the Structure of Biomedical Relationships from Unstructured Text.

The published biomedical research literature encompasses most of our understanding of how drugs interact with gene products to produce physiological r...

Model-Based Multifactor Dimensionality Reduction for Rare Variant Association Analysis.

Genome-wide association studies have revealed a vast amount of common loci associated to human complex diseases. Still, a large proportion of heritabi...

Multivariate Quantitative Multifactor Dimensionality Reduction for Detecting Gene-Gene Interactions.

OBJECTIVES: To determine gene-gene interactions and missing heritability of complex diseases is a challenging topic in genome-wide association studies...

Prediction of MicroRNA-Disease Associations Based on Social Network Analysis Methods.

MicroRNAs constitute an important class of noncoding, single-stranded, ~22 nucleotide long RNA molecules encoded by endogenous genes. They play an imp...

A mutation profile for top-k patient search exploiting Gene-Ontology and orthogonal non-negative matrix factorization.

MOTIVATION: As the quantity of genomic mutation data increases, the likelihood of finding patients with similar genomic profiles, for various disease ...