Genomes and Genes
Affiliation: Centre for Ecology and Hydrology
- Laying the foundation for a Genomic Rosetta Stone: creating information hubs through the use of consensus identifiersBart Van Brabant
Laboratory of Microbiology, Ghent University, Ghent, Belgium
OMICS 12:123-7. 2008....
- The Genomic Standards ConsortiumDawn Field
Centre for Ecology and Hydrology, Maclean Building, Crowmarsh Gifford, Wallingford, Oxfordshire, United Kingdom
PLoS Biol 9:e1001088. 2011....
- The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated toolsAndreas Wilke
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
BMC Bioinformatics 13:141. 2012..Sequence similarity search results encoded in an open, exchangeable format have the potential to limit the needs for computational reanalysis of these data sets. A prerequisite for sharing of similarity results is a common reference...
- A call for an international network of genomic observatories (GOs)Neil Davies
Biodiversity Institute, Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK
Gigascience 1:5. 2012..The foundational layer of biodiversity-genetic variation-would thus be mainstreamed into Earth Observation systems enabling predictive modelling of biodiversity dynamics and resultant impacts on ecosystem services...
- Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic datasetPeter E Larsen
Argonne National Laboratory, 9700, S, Cass Ave, Argonne, Illinois, USA
Microb Inform Exp 1:4. 2011..abstract:..
- Meeting report: the fourth Genomic Standards Consortium (GSC) workshopDawn Field
NERC Centre for Ecology and Hydrology, Mansfield Road, Oxford, OX1 3SR United Kingdom
OMICS 12:101-8. 2008..g., compliant with MIGS/MIMS), but also be extended to include a variety of data processing and calculations. Further information about the Genomic Standards Consortium and its range of activities can be found at http://gensc.org...
- Meeting report: the fifth Genomic Standards Consortium (GSC) workshopDawn Field
NERC Center for Ecology and Hydrology, Oxford, United Kingdom
OMICS 12:109-13. 2008..Further information about the GSC and its range of activities can be found at http://gensc.org...
- Foreword to the special issue on the Fifth Genomic Standards consortium workshopDawn Field
NERC Centre for Ecology and Hydrology, Mansfield Rd, Oxford OX1 3SR, United Kingdom
OMICS 12:99. 2008
- The positive role of the ecological community in the genomic revolutionDawn Field
Molecular Evolution and Bioinformatics Section, Oxford Centre for Ecology and Hydrology, Oxford, UK
Microb Ecol 53:507-11. 2007..These integrative bioinformatics and data management initiatives underscore the increasingly important role ecologists have to play in the genomic (metagenomic) revolution...
- How do we compare hundreds of bacterial genomes?Dawn Field
Oxford Centre for Ecology and Hydrology, Oxford OX1 3SR, UK
Curr Opin Microbiol 9:499-504. 2006..The benefits of large-scale comparative genomic analyses are driving the community to think about how to manage our public collections of genomes in novel ways...
- The minimum information about a genome sequence (MIGS) specificationDawn Field
Natural Environmental Research Council Centre for Ecology and Hydrology, Oxford OX1 3SR, UK
Nat Biotechnol 26:541-7. 2008..As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases...
- Bioinformatics and data management support for environmental genomicsDawn Field
Environmental Genomics Thematic Programme Data Center, Oxford Centre for Ecology and Hydrology, Oxford, United Kingdom
PLoS Biol 3:e297. 2005
- Meeting report: eGenomics: Cataloguing our Complete Genome Collection IIDawn Field
Molecular Evolution and Bioinformatics Section, Oxford Centre for Ecology and Hydrology, Oxford, United Kingdom
OMICS 10:100-4. 2006..The workshop proceedings and outcomes are set to help guide the development of the GSC's Minimal Information about a Genome Sequence (MIGS) specification...
- Cataloguing our current genome collectionDawn Field
Molecular Evolution and Bioinformatics Section, Oxford Centre for Ecology and Hydrology, Mansfield Road, Oxford UK OX1 3SR
Microbiology 151:1016-9. 2005
- Open software for biologists: from famine to feastDawn Field
NERC Environmental Bioinformatics Centre, Oxford, UK
Nat Biotechnol 24:801-3. 2006..Developing and deploying specialized computing systems for specific research communities is achievable, cost effective and has wide-ranging benefits...
- Databases and software for the comparison of prokaryotic genomesDawn Field
Oxford Centre for Ecology and Hydrology, Mansfield Road, Oxford OX1 3SR, UK
Microbiology 151:2125-32. 2005..This article reviews progress towards the development of computational tools and databases for organizing and extracting biological meaning from the comparison of large collections of genomes...
- Handlebar: a flexible, web-based inventory manager for handling barcoded samplesTim Booth
NERC Centre for Ecology and Hydrology, Oxford, UK
Biotechniques 42:300, 302. 2007
- Toward interoperable bioscience dataSusanna Assunta Sansone
Oxford e Research Centre, University of Oxford, Oxford, UK
Nat Genet 44:121-6. 2012..Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision...
- Large-scale comparative genomic ranking of taxonomically restricted genes (TRGs) in bacterial and archaeal genomesGareth A Wilson
Centre for Ecology and Hydrology CEH Oxford, Oxford, United Kindgom
PLoS ONE 2:e324. 2007..This lack of homology confounds attempts to establish the likelihood that a hypothetical gene is expressed and, if so, to determine the putative function of the protein...
- EBI metagenomics--a new resource for the analysis and archiving of metagenomic dataSarah Hunter
European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK, Oxford e Research Centre, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK and NERC Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
Nucleic Acids Res 42:D600-6. 2014....
- Simulating social-ecological systems: the Island Digital Ecosystem Avatars (IDEA) consortiumNeil Davies
Gump South Pacific Research Station, University of California Berkeley, Moorea, BP 244 98728 French Polynesia Biodiversity Institute, Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford, OX1 3PS UK Berkeley Institute for Data Science, 190 Doe Library, University of California, Berkeley, CA 94720 USA
Gigascience 5:14. 2016..As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions. ..
- High rates of recombination in otitis media isolates of non-typeable Haemophilus influenzaeAlison J Cody
Molecular Infectious Diseases Group, Department of Paediatrics, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
Infect Genet Evol 3:57-66. 2003..These findings provide a population based foundation for a better understanding of the role of NTHi LPS as a virulence factor and its potential as a candidate vaccine...
- The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?"Susanna Assunta Sansone
EMBL EBI The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
OMICS 12:143-9. 2008..This article is part of the special issue of OMICS on the activities of the Genomics Standards Consortium (GSC)...
- Using the genome to understand pathogenicityDawn Field
Oxford Centre for Ecology an Hydrology, UK
Methods Mol Biol 266:261-87. 2004....
- Concept of sample in OMICS technologyNorman Morrison
School of Computer Science, University of Manchester, United Kingdom
OMICS 10:127-37. 2006....
- Annotation of environmental OMICS data: application to the transcriptomics domainNorman Morrison
School of Computer Science, University of Manchester, Manchester, United Kingdom
OMICS 10:172-8. 2006..Finally, we make an open call to the community for participation in the Env Community and its future activities...
- Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotationSamuel V Angiuoli
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
OMICS 12:137-41. 2008..In addition, there is no central repository to store and disseminate procedures and protocols for genome annotation. We highlight the importance of SOPs for genome annotation and endorse an online repository of SOPs...
- PlantTribes: a gene and gene family resource for comparative genomics in plantsP Kerr Wall
Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
Nucleic Acids Res 36:D970-6. 2008..All data and analyses are accessible through a flexible interface allowing users to explore the classification, to place query sequences within the classification, and to download results for further study...
- Defining linkages between the GSC and NSF's LTER program: how the Ecological Metadata Language (EML) relates to GCDML and other outcomesInigo San Gil
Department of Biology, LTER Network Office, University of New Mexico, Albuquerque, New Mexico 87131, USA
OMICS 12:151-6. 2008..All these action items have been accepted by the LTER contingent, and further collaboration between the GSC and LTER is expected...
- Habitat-Lite: a GSC case study based on free text terms for environmental metadataLynette Hirschman
Information Technology Center, The MITRE Corporation, Bedford, Massachusetts 01730, USA
OMICS 12:129-36. 2008..We invite the community's feedback on its further development to provide a minimum list of terms to capture high-level habitat information and to provide classification bins needed for future studies...
- A standard MIGS/MIMS compliant XML Schema: toward the development of the Genomic Contextual Data Markup Language (GCDML)Renzo Kottmann
Microbial Genomics Group, Max Planck Institute for Marine Microbiology and Jacobs University Bremen, 28359 Bremen, Germany
OMICS 12:115-21. 2008..GCDML is freely available, and can be downloaded, along with documentation, from the GSC Web site (http://gensc.org)...
- The plasmid genome databaseLars Mølbak
Danish Veterinary Institute, Bulowsvej 27, DK 1790 Copenhagen V, Denmark
Microbiology 149:3043-5. 2003
- Public repositories need serious fundingBela Tiwari
Nature 439:912. 2006
- Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USASandra Orchard
EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
Proteomics 6:4439-43. 2006....
- Toward a standards-compliant genomic and metagenomic publication recordGeorge M Garrity
Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
OMICS 12:157-60. 2008....
- Working together to put molecules on the mapDawn Field
Nature 453:978. 2008
- Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI projectChris F Taylor
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
Nat Biotechnol 26:889-96. 2008
- Development of FuGO: an ontology for functional genomics investigationsPatricia L Whetzel
Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
OMICS 10:199-204. 2006....