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The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory .EMBL-EBI is listed in the Registry of Research Data Repositories re3data.org. Wikipedia.


Villar D.,University of Cambridge | Flicek P.,European Bioinformatics Institute | Odom D.T.,University of Cambridge
Nature Reviews Genetics | Year: 2014

Differences in transcription factor binding can contribute to organismal evolution by altering downstream gene expression programmes. Genome-wide studies in Drosophila melanogaster and mammals have revealed common quantitative and combinatorial properties of in vivo DNA binding, as well as marked differences in the rate and mechanisms of evolution of transcription factor binding in metazoans. Here, we review the recently discovered rapid 're-wiring' of in vivo transcription factor binding between related metazoan species and summarize general principles underlying the observed patterns of evolution. We then consider what might explain the differences in genome evolution between metazoan phyla and outline the conceptual and technological challenges facing this research field. © 2014 Macmillan Publishers Limited. Source


Galperin M.Y.,U.S. National Center for Biotechnology Information | Fernandez-Suarez X.M.,European Bioinformatics Institute
Nucleic Acids Research | Year: 2012

The 19th annual Database Issue of Nucleic Acids Research features descriptions of 92 new online databases covering various areas of molecular biology and 100 papers describing recent updates to the databases previously described in NAR and other journals. The highlights of this issue include, among others, a description of neXtProt, a knowledgebase on human proteins; a detailed explanation of the principles behind the NCBI Taxonomy Database; NCBI and EBI papers on the recently launched BioSample databases that store sample information for a variety of database resources; descriptions of the recent developments in the Gene Ontology and UniProt Gene Ontology Annotation projects; updates on Pfam, SMART and InterPro domain databases; update papers on KEGG and TAIR, two universally acclaimed databases that face an uncertain future; and a separate section with 10 wiki-based databases, introduced in an accompanying editorial. The NAR online Molecular Biology Database Collection, available at http://www.oxfordjournals.org/nar/database/a/, has been updated and now lists 1380 databases. Brief machine-readable descriptions of the databases featured in this issue, according to the BioDBcore standards, will be provided at the http://biosharing.org/biodbcore web site. The full content of the Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/). Source


Orchard S.,European Bioinformatics Institute
Proteomics | Year: 2012

Molecular interaction databases are playing an ever more important role in our understanding of the biology of the cell. An increasing number of resources exist to provide these data and many of these have adopted the controlled vocabularies and agreed-upon standardised data formats produced by the Molecular Interaction workgroup of the Human Proteome Organization Proteomics Standards Initiative (HUPO PSI-MI). Use of these standards allows each resource to establish PSI Common QUery InterfaCe (PSICQUIC) service, making data from multiple resources available to the user in response to a single query. This cooperation between databases has been taken a stage further, with the establishment of the International Molecular Exchange (IMEx) consortium which aims to maximise the curation power of numerous data resources, and provide the user with a non-redundant, consistently annotated set of interaction data. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source


Clarke L.,European Bioinformatics Institute
Nature methods | Year: 2012

The 1000 Genomes Project was launched as one of the largest distributed data collection and analysis projects ever undertaken in biology. In addition to the primary scientific goals of creating both a deep catalog of human genetic variation and extensive methods to accurately discover and characterize variation using new sequencing technologies, the project makes all of its data publicly available. Members of the project data coordination center have developed and deployed several tools to enable widespread data access. Source


Orchard S.,European Bioinformatics Institute
Biochimica et Biophysica Acta - Proteins and Proteomics | Year: 2014

Significant advances have been made over the past ten years to standardize the data emerging from the proteomic workflows adopted by laboratories all over the world. Differences in workflows, instrumentation, analysis software and reporting methods initially resulted in very disparate data being generated by many of these research groups, making data storage and comparison challenging. As the data standards proposed by the HUPO-PSI have increasingly been adopted, and tools and databases implementing these data formats have become more readily available, data generated by these complex experimental procedures is now becoming easier to manipulate, to visualize and to analyse. Public domain databases now exist to collate the information generated by experimentalists and to make the generation of specific protein expression maps, and monitoring of changes in protein expression levels in response to external stimuli a real possibility. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. © 2013 Elsevier B.V. Source

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