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author:("Wei, xuelong")
1.  Ensembl Genomes 2013: scaling up access to genome-wide data 
Nucleic Acids Research  2013;42(D1):D546-D552.
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.
doi:10.1093/nar/gkt979
PMCID: PMC3965094  PMID: 24163254
2.  N-(2-Methyl­phen­yl)-1,2-benzoselen­azol-3(2H)-one 
In the title Ebselen [systematic name: (2-phenyl-1,2-benzoisoselenazol-3-(2H)-one)] analogue, C14H11NOSe, the benzisoselenazolyl moiety (r.m.s. deviation = 0.0209 Å) is nearly perpendicular to the N-arenyl ring, making a dihedral angle of 78.15 (11)°. In the crystal, mol­ecules are linked by C—H⋯O and Se⋯O inter­actions into chains along the c-axis direction. The Se⋯O distance [2.733 (3) Å] is longer than that in Ebselen (2.571 (3) Å].
doi:10.1107/S1600536813024744
PMCID: PMC3790406  PMID: 24098225
3.  2,2′-(Diselane-1,2-di­yl)dinicotinamide N,N′-dimethyl­formamide disolvate 
The asymmetric unit of the title compound, C12H10N4O2Se2·2C3H7NO, contains two solvent mol­ecules and two half mol­ecules of the dinicotinamide, each of which sits on a center of symmetry passing through the middle of the Se—Se bond. In each mol­ecule, the two pyridyl groups and diseleno group are approximately coplanar (r.m.s. deviations from planarity for all non-H atoms = 0.011 and 0.008 Å in the two mol­ecules). Inter­molecular N—H⋯O hydrogen bonds stablilize the crystal packing.
doi:10.1107/S1600536810015047
PMCID: PMC2979017  PMID: 21579243
4.  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. Using flanking markers as anchors, QTLs originally reported on individual genetic maps have been systematically aligned to the rice sequence where they can be searched as standard genomic features. Researchers can determine whether a QTL co-localizes with other QTLs detected in independent experiments and can combine data from multiple studies to improve the resolution of a QTL position. Candidate genes falling within a QTL interval can be identified and their relationship to particular phenotypes can be inferred based on functional annotations provided by ontology terms. Mutations identified in functional genomics populations and association mapping panels can be aligned with QTL regions to facilitate fine mapping and validation of gene–phenotype associations. By assembling and integrating diverse types of data and information across species and levels of biological complexity, the QTL database enhances the potential to understand and utilize QTL information in biological research.
doi:10.1093/database/bap005
PMCID: PMC2790302  PMID: 20157478
5.  Gramene: a growing plant comparative genomics resource 
Nucleic Acids Research  2007;36(Database issue):D947-D953.
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 is an open-source project. All data and software are freely downloadable through the ftp site (ftp.gramene.org/pub/gramene) and available for use without restriction. Gramene's core data types include genome assembly and annotations, other DNA/mRNA sequences, genetic and physical maps/markers, genes, quantitative trait loci (QTLs), proteins, ontologies, literature and comparative mappings. Since our last NAR publication 2 years ago, we have updated these data types to include new datasets and new connections among them. Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose). We have significantly improved the web interface in order to provide a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions.
doi:10.1093/nar/gkm968
PMCID: PMC2238951  PMID: 17984077

Results 1-5 (5)