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Thoughts from SNP-SIG 2012: future challenges in the annotation of genetic variations.

Chapter 15: Disease Gene Prioritization

Disease-causing aberrations in the normal function of a gene define that gene as a disease gene. Proving a causal link between a gene and a disease experimentally is expensive and time-consuming. Comprehensive prioritization of candidate genes prior …

A large-scale evaluation of computational protein function prediction

Collective judgment predicts disease-associated single nucleotide variants

BACKGROUND: In recent years the number of human genetic variants deposited into the publicly available databases has been increasing exponentially. The latest version of dbSNP, for example, contains ~50 million validated Single Nucleotide Variants …

Homology-based inference sets the bar high for protein function prediction

Mercury resistance and mercuric reductase activities and expression among chemotrophic thermophilic Aquificae

Mercury (Hg) resistance (mer) by the reduction of mercuric to elemental Hg is broadly distributed among the Bacteria and Archaea and plays an important role in Hg detoxification and biogeochemical cycling. MerA is the protein subunit of the …

Comparative genomic and physiological analysis provides insights into the role ofAcidobacteriain organic carbon utilization in Arctic tundra soils

Acidobacteria are among the most abundant bacterial phyla found in terrestrial ecosystems, but relatively little is known about their diversity, distribution and most critically, their function. Understanding the functional activities encoded in …

TrAnsFuSE refines the search for protein function: oxidoreductases

Non-equilibrium catalysis of electron transfer reactions (i.e. redox) regulates the flux of key elements found in biological macromolecules. The enzymes responsible, oxidoreductases, contain specific transition metals in poorly sequence-conserved …

Bioinformatics for personal genome interpretation

An international consortium released the first draft sequence of the human genome 10 years ago. Although the analysis of this data has suggested the genetic underpinnings of many diseases, we have not yet been able to fully quantify the relationship …

Disease-related mutations predicted to impact protein function

BACKGROUND: Non-synonymous single nucleotide polymorphisms (nsSNPs) alter the protein sequence and can cause disease. The impact has been described by reliable experiments for relatively few mutations. Here, we study predictions for functional impact …