Rare disease variant curation from literature: assessing gaps with creatine transport deficiency in focus.

Background: Approximately 4-8% of the world suffers from a rare disease. Rare diseases are often difficult to diagnose, and many do not have approved therapies. Genetic sequencing has the potential to shorten the current diagnostic process, increase mechanistic understanding, and facilitate research on therapeutic approaches but is limited by the difficulty of novel variant pathogenicity interpretation and the communication of known causative variants.

AVIA 3.0: interactive portal for genomic variant and sample level analysis.

Summary: The Annotation, Visualization and Impact Analysis (AVIA) is a web application combining multiple features to annotate and visualize genomic variant data. Users can investigate functional significance of their genetic alterations across samples, genes and pathways. Version 3.

Assessment of Coagulation Homeostasis in Blunt, Penetrating, and Thermal Trauma: Guidance for a Multicenter Systems Biology Approach.

Introduction: Provisioning care for traumatically injured patients makes conducting research very proximal to injury difficult. These studies also inherently have regulatory barriers to overcome. Here we outline a protocol for acute-phase enrollment of traumatically injured patients into a prospective observational clinical trial with precise and comprehensive sample acquisition in support of a systems biology approach to a research study.

AVIA v2.0: annotation, visualization and impact analysis of genomic variants and genes.

Unlabelled: As sequencing becomes cheaper and more widely available, there is a greater need to quickly and effectively analyze large-scale genomic data. While the functionality of AVIA v1.0, whose implementation was based on ANNOVAR, was comparable with other annotation web servers, AVIA v2.

Knowledge and theme discovery across very large biological data sets using distributed queries: a prototype combining unstructured and structured data.

As the discipline of biomedical science continues to apply new technologies capable of producing unprecedented volumes of noisy and complex biological data, it has become evident that available methods for deriving meaningful information from such data are simply not keeping pace. In order to achieve useful results, researchers require methods that consolidate, store and query combinations of structured and unstructured data sets efficiently and effectively. As we move towards personalized medicine, the need to combine unstructured data, such as medical literature, with large amounts of highly structured and high-throughput data such as human variation or expression data from very large cohorts, is especially urgent.

Guanine holes are prominent targets for mutation in cancer and inherited disease.

Single base substitutions constitute the most frequent type of human gene mutation and are a leading cause of cancer and inherited disease. These alterations occur non-randomly in DNA, being strongly influenced by the local nucleotide sequence context. However, the molecular mechanisms underlying such sequence context-dependent mutagenesis are not fully understood.

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools.

The non-B DB, available at http://nonb.abcc.ncifcrf.

Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes.

Although the capability of DNA to form a variety of non-canonical (non-B) structures has long been recognized, the overall significance of these alternate conformations in biology has only recently become accepted en masse. In order to provide access to genome-wide locations of these classes of predicted structures, we have developed non-B DB, a database integrating annotations and analysis of non-B DNA-forming sequence motifs. The database provides the most complete list of alternative DNA structure predictions available, including Z-DNA motifs, quadruplex-forming motifs, inverted repeats, mirror repeats and direct repeats and their associated subsets of cruciforms, triplex and slipped structures, respectively.