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The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our resources include evidenced-based gene sets for all supported species; large-scale whole genome multiple species alignments across vertebrates and clade-specific alignments for eutherian(More)
Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms and farm animals. Over the past year we have increased the number of species that we support to 77 and expanded our genome browser with a new scrollable overview and improved(More)
Ensembl (http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model organisms. This year we released updated annotation (gene models, comparative genomics, regulatory regions and variation) on the new human assembly, GRCh38, although we continue to(More)
Model organisms are becoming increasingly important for the study of complex diseases such as type 1 diabetes (T1D). The non-obese diabetic (NOD) mouse is an experimental model for T1D having been bred to develop the disease spontaneously in a process that is similar to humans. Genetic analysis of the NOD mouse has identified around 50 disease loci, which(More)
A comparison of chain-of-states based methods for finding minimum energy pathways (MEPs) is presented. In each method, a set of images along an initial pathway between two local minima is relaxed to find a MEP. We compare the nudged elastic band (NEB), doubly nudged elastic band, string, and simplified string methods, each with a set of commonly used(More)
We present a method for optimizing transition state theory dividing surfaces with support vector machines. The resulting dividing surfaces require no a priori information or intuition about reaction mechanisms. To generate optimal dividing surfaces, we apply a cycle of machine-learning and refinement of the surface by molecular dynamics sampling. We(More)
Based on molecular grand canonical ensemble density functional theory, we present a theoretical description of how reaction barriers and enthalpies change as atoms in the system are subjected to alchemical transformations, from one element into another. The change in the energy barrier for the umbrella inversion of ammonia is calculated along an alchemical(More)
The Vertebrate Genome Annotation (VEGA) database (http://vega.sanger.ac.uk), initially designed as a community resource for browsing manual annotation of the human genome project, now contains five reference genomes (human, mouse, zebrafish, pig and rat). Its introduction pages have been redesigned to enable the user to easily navigate between whole genomes(More)
A generalized solid-state nudged elastic band (G-SSNEB) method is presented for determining reaction pathways of solid-solid transformations involving both atomic and unit-cell degrees of freedom. We combine atomic and cell degrees of freedom into a unified description of the crystal structure so that calculated reaction paths are insensitive to the choice(More)
New experimental techniques in epigenomics allow researchers to assay a diversity of highly dynamic features such as histone marks, DNA modifications or chromatin structure. The study of their fluctuations should provide insights into gene expression regulation, cell differentiation and disease. The Ensembl project collects and maintains the Ensembl(More)