Papers by Arnaud Kerhornou
Bioinformatics, 2007
Summary: Here we present a computational protocol to analyze the promoter regions of a given set ... more Summary: Here we present a computational protocol to analyze the promoter regions of a given set of co-expressed genes, and its implementation through the use of Web services technologies. This protocol aims to cluster a set of co-regulated genes in subsets of genes showing similar configurations of transcription factor binding sites. All the steps of this protocol have been developed as web services that are compliant with BioMoby specifications. Availability: {http://genome.imim.es/cgi-bin/moby/GeneClustering_DataSubmission.cgi} Contact: arnaud.kerhornou@crg.es Supplementary information: Supplementary data are available at {http://genome.imim.es/webservices/}
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Nucleic Acids Research
Rhea (https://www.rhea-db.org) is an expert-curated knowledgebase of biochemical reactions based ... more Rhea (https://www.rhea-db.org) is an expert-curated knowledgebase of biochemical reactions based on the chemical ontology ChEBI (Chemical Entities of Biological Interest) (https://www.ebi.ac.uk/chebi). In this paper, we describe a number of key developments in Rhea since our last report in the database issue of Nucleic Acids Research in 2019. These include improved reaction coverage in Rhea, the adoption of Rhea as the reference vocabulary for enzyme annotation in the UniProt knowledgebase UniProtKB (https://www.uniprot.org), the development of a new Rhea website, and the designation of Rhea as an ELIXIR Core Data Resource. We hope that these and other developments will enhance the utility of Rhea as a reference resource to study and engineer enzymes and the metabolic systems in which they function.
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The Plant Genome, 2015
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Nucleic Acids Research, 2014
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Nucleic acids research, Jan 17, 2015
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data ... more Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of inclu...
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Nucleic acids research, Jan 8, 2015
Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in cro... more Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway br...
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ABSTRACT
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Nucleic acids research, Jan 20, 2015
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified ... more The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one m...
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This workshop will demonstrate Gramene’s genome browser and, associated annotation and visualizat... more This workshop will demonstrate Gramene’s genome browser and, associated annotation and visualization resources--including variation, phylogenetic trees and comparative maps (www.gramene.org). Release 40 hosts interlinked browsers for 28 complete reference plant genomes, each displaying community annotation, whole genome alignments, and additional analyses. Annotated protein coding genes are subjected to InterPro domain prediction, Gene Ontology assignment, and cross-referencing to third party databases such as RefSeq. SNP and structural diversity data, available for nine reference genomes, is visualized in the context of gene annotation and each variant site is classified with respect to its predicted consequence on transcript structure (e.g. Missense variant). For most studies users can drill-down to individual genotypes of each strain accession within the study’s diversity panel. Evolutionary histories of protein-coding genes are provided in phylogenetic gene trees using a method ...
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Plant and Cell Physiology, 2014
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Science, 2005
Theileria annulata and T. parva are closely related protozoan parasites that cause lymphoprolifer... more Theileria annulata and T. parva are closely related protozoan parasites that cause lymphoproliferative diseases of cattle. We sequenced the genome of T. annulata and compared it with that of T. parva to understand the mechanisms underlying transformation and tropism. Despite high conservation of gene sequences and synteny, the analysis reveals unequally expanded gene families and species-specific genes. We also identify divergent families of putative secreted polypeptides that may reduce immune recognition, candidate regulators of host-cell transformation, and a Theileria-specific protein domain [frequently associated in Theileria (FAINT)] present in a large number of secreted proteins.
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PLoS ONE, 2014
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Nucleic Acids Research, 2014
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International Journal for Parasitology, 2005
Centralisation of tools for analysis of genomic data is paramount in ensuring that research is al... more Centralisation of tools for analysis of genomic data is paramount in ensuring that research is always carried out on the latest currently available data. As such, World Wide Web sites providing a range of online analyses and displays of data can play a crucial role in guaranteeing consistency of in silico work. In this respect, the protozoan parasite research community is served by several resources, either focussing on data and tools for one species or taking a broader view and providing tools for analysis of data from many species, thereby facilitating comparative studies. In this paper, we give a broad overview of the online resources available. We then focus on the GeneDB project, detailing the features and tools currently available through it. Finally, we discuss data curation and its importance in keeping genomic data 'relevant' to the research community.
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Web services have become a key technology for bioinformatics, since life science databases are gl... more Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.
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Briefings in Bioinformatics, 2008
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Abstract The social amoebae are exceptional in their ability to alternate between unicellular and... more Abstract The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts.
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Papers by Arnaud Kerhornou