Current Bioinformatics - Volume 7, Issue 3, 2012

Healthcare has played a main role in the Semantic Web (SW) field given the knowledge representation possibilities that SW is capable of addressing. Nowadays there are a large number of ontologies which can be used for several domains of healthcare (genetics, proteins, cellular components, anatomy, and specific diseases among others). However, in some cases, the definition and population of these ontologies Read More

Recent proteomics studies of clinical samples have generated substantial interest. Aided by advances in analytical chemistry and bioinformatics, clinical proteomics has become a driving force behind molecular biomarker development. However, it is still difficult to manage and interpret large amounts of clinical proteomics data due to data integration challenges. The lack of practical metadata representation standards has pre Read More

The Linked Data initiative offers a straight method to publish structured data in the World Wide Web and link it to other data, resulting in a world wide network of semantically codified data known as the Linked Open Data cloud. The size of the Linked Open Data cloud, i.e. the amount of data published using Linked Data principles, is growing exponentially, including life sciences data. However, key information for biological rese Read More

Semantic Web technologies offer the potential to revolutionize management of health care data by increasing interoperability and reusability while reducing the need for redundant data collection and storage. From 1998 through 2010, Cleveland Clinic sponsored a project designed to explore and develop this potential. The product of this effort, SemanticDB, is a suite of software tools and knowledge resources built to facilitate Read More

Semantic Web languages and technologies can be used for the annotation, classification, and organization of knowledge assets and digital artifacts based on biomedical ontologies. In this paper, we present a semantic wiki, named DartWiki, to build ontology-based digital encyclopedia for the biomedicine domain. DartWiki provides a Web-based interface for accessing knowledge artifacts in both per-artifact and per-concept m Read More

We propose a new filter based feature selection algorithm for classification based on DNA microarray gene expression data. It utilizes null space of covariance matrix for feature selection. The algorithm can perform bulk reduction of features (genes) while maintaining the quality information in the reduced subset of features for discriminative purpose. Thus, it can be used as a pre-processing step for other feature selection algo Read More

The aim of this work is to establish a universal method of searching for similarities between sequences in an ndimensional sequence space. The presented idea extends out of the original Dot-Matrix and semihomology methods with a possibility of making analyses in an n-dimensional sequence space and indicates the method of similarity evaluation. The main novelty of the implemented dotPicker program is to allow f Read More

Codon usage, codon context, rare codons, nucleotide repetition and mRNA destabilizing sequences are but a few of the many factors that influence the efficiency of protein synthesis. Therefore, gene redesign for heterologous expression is a multi-objective optimization problem and the factors that need to be considered are often conflicting. Evolutionary approaches have already been shown to be able to evolve a sequence un Read More

microRNA (miRNA) target prediction plays an important role in studying the post-transcriptional regulation by miRNAs. Numerous target prediction tools have been utilized in several research approaches for in silico analysis.This type of analysis provides the initial step for further experimental validation in biological systems in order to complete the target validation.In this review, we summarize the computational tools based on Read More

Maize (Zea mays ssp. mays L.) is an important crop as well as an important model organism for fundamental research into the inheritance and functions of genes, the mechanistic relation between cytological crossovers and recombination, and the origin of the nucleolus. AR2/ERF is a large family of transcription factors in plant, encoding transcriptional regulators with a variety of functions involved in the developmental and Read More

Throughout endless experimental work, short records of dynamic molecular data are generated from time to time. Biomechanics data mining and knowledge discovery have become an important study area to turn the abundance of generated raw data into pieces of information. In data mining, researchers often encounter challenging issues and constraints, ranging from nature of the collected microarray data and devel Read More