Ultrasound-dependent kinetics of bone mineralization.

Bone Mineral Density (BMD) is an important parameter in the development of orthopedic fracture-healing methods. A recent article (Inoue, S., et al.

Haplosaurus computes protein haplotypes for use in precision drug design.

Selecting the most appropriate protein sequences is critical for precision drug design. Here we describe Haplosaurus, a bioinformatic tool for computation of protein haplotypes. Haplosaurus computes protein haplotypes from pre-existing chromosomally-phased genomic variation data.

Comparison of different statistical approaches for urinary peptide biomarker detection in the context of coronary artery disease.

Background: When combined with a clinical outcome variable, the size, complexity and nature of mass-spectrometry proteomics data impose great statistical challenges in the discovery of potential disease-associated biomarkers. The purpose of this study was thus to evaluate the effectiveness of different statistical methods applied for urinary proteomic biomarker discovery and different methods of classifier modelling in respect of the diagnosis of coronary artery disease in 197 study subjects and the prognostication of acute coronary syndromes in 368 study subjects.

Results: Computing the discovery sub-cohorts comprising [Formula: see text] of the study subjects based on the Wilcoxon rank sum test, t-score, cat-score, binary discriminant analysis and random forests provided largely different numbers (ranging from 2 to 398) of potential peptide biomarkers.

Ensembl comparative genomics resources.

Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses.

The BioMart community portal: an innovative alternative to large, centralized data repositories.

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide.

Community-driven development for computational biology at Sprints, Hackathons and Codefests.

Background: Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches.

BioJS: an open source standard for biological visualisation - its status in 2014.

BioJS is a community-based standard and repository of functional components to represent biological information on the web. The development of BioJS has been prompted by the growing need for bioinformatics visualisation tools to be easily shared, reused and discovered. Its modular architecture makes it easy for users to find a specific functionality without needing to know how it has been built, while components can be extended or created for implementing new functionality.

PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants.

PICARA is an analytical pipeline designed to systematically summarize observed SNP/trait associations identified by genome wide association studies (GWAS) and to identify candidate genes involved in the regulation of complex trait variation. The pipeline provides probabilistic inference about a priori candidate genes using integrated information derived from genome-wide association signals, gene homology, and curated gene sets embedded in pathway descriptions. In this paper, we demonstrate the performance of PICARA using data for flowering time variation in maize - a key trait for geographical and seasonal adaption of plants.

GrameneMart: the BioMart data portal for the Gramene project.

Gramene is a well-established resource for plant comparative genome analysis. Data are generated through automated and curated analyses and made available through web interfaces such as GrameneMart. The Gramene project was an early adopter of the BioMart software, which remains an integral and well-used component of the Gramene website.

BioMart Central Portal: an open database network for the biological community.

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each.

Gramene database in 2010: updates and extensions.

Now in its 10th year, the Gramene database (http://www.gramene.org) has grown from its primary focus on rice, the first fully-sequenced grass genome, to become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice.

Gramene QTL database: development, content and applications.

Gramene is a comparative information resource for plants that integrates data across diverse data domains. In this article, we describe the development of a quantitative trait loci (QTL) database and illustrate how it can be used to facilitate both the forward and reverse genetics research. The QTL database contains the largest online collection of rice QTL data in the world.

Gramene: a growing plant comparative genomics resource.

Gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species.

Gramene: a bird's eye view of cereal genomes.

Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind's most important source of calories and contribute tens of billions of dollars annually to the world economy (FAO 1999, http://www.fao.org; USDA 1997, http://www.

The Ensembl Web site: mechanics of a genome browser.

The Ensembl Web site (http://www.ensembl.org/) is the principal user interface to the data of the Ensembl project, and currently serves >500,000 pages (approximately 2.

EnsMart: a generic system for fast and flexible access to biological data.

The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools.