H Parkinson

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
    Danielle Welter
    European Bioinformatics Institute EMBL EBI, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK, Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA and Division of Policy, Communication and Education, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Nucleic Acids Res 42:D1001-6. 2014
  2. pmc MageComet--web application for harmonizing existing large-scale experiment descriptions
    Vincent Xue
    Department of Computer Science, Hunter College, City University of New York, NY 10065, USA
    Bioinformatics 28:1402-3. 2012
  3. pmc MIAME/Plant - adding value to plant microarrray experiments
    Philip Zimmermann
    Swiss Federal Institute of Technology ETH Zurich, ETH Center, CH 8092 Zurich, Switzerland
    Plant Methods 2:1. 2006
  4. pmc Anatomy ontologies and potential users: bridging the gap
    Ravensara S Travillian
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    J Biomed Semantics 2:S3. 2011
  5. pmc Modeling biomedical experimental processes with OBI
    Ryan R Brinkman
    British Columbia Cancer Agency, Vancouver, Canada
    J Biomed Semantics 1:S7. 2010
  6. pmc Large scale comparison of global gene expression patterns in human and mouse
    Xiangqun Zheng-Bradley
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
    Genome Biol 11:R124. 2010
  7. pmc XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments
    Morris A Swertz
    Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
    Genome Biol 11:R27. 2010
  8. pmc OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript
    Tomasz Adamusiak
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 12:218. 2011
  9. pmc The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button
    Morris A Swertz
    Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen and Department of Genetics, University Medical Center Groningen, P O Box 30001, 9700 RB Groningen, The Netherlands
    BMC Bioinformatics 11:S12. 2010
  10. pmc ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments
    Helen Parkinson
    Functional Genomics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 39:D1002-4. 2011

Collaborators

  • Marco Brandizi
  • M Vingron
  • James Malone
  • Gabriella Rustici
  • J Quackenbush
  • Ugis Sarkans
  • M A Tuli
  • S Schulze-Kremer
  • Anna Farne
  • T Gaasterland
  • J Vilo
  • Alvis Brazma
  • Tomasz Adamusiak
  • G Stoesser
  • GAVIN J contact SHERLOCK
  • Morris A Swertz
  • Tony Burdett
  • Danielle Welter
  • Vincent Xue
  • Ravensara S Travillian
  • Paul Schofield
  • Martijn Dijkstra
  • Danny Arends
  • Xiangqun Zheng-Bradley
  • Engbert O de Brock
  • Ryan R Brinkman
  • Ritsert C Jansen
  • Philip Zimmermann
  • Jacqueline Macarthur
  • Peggy Hall
  • Paul Flicek
  • Joannella Morales
  • Heather Junkins
  • Alan Klemm
  • Teri Manolio
  • Lucia Hindorff
  • Margus Lukk
  • Julie Taylor
  • John Hancock
  • Michael Gruenberger
  • Ann Marie Mallon
  • Jennifer M Fostel
  • Bruno M Tesson
  • Joeri K van der Velde
  • Susanna Assunta Sansone
  • Phillip Lord
  • Erik T Roos
  • Yongqun He
  • Christian J Stoeckert
  • Dirk Derom
  • Jessica A Turner
  • Rudi Alberts
  • Johan Rung
  • Andrew R Jones
  • Jie Zheng
  • Carole Goble
  • Alexandros Kanterakis
  • Gonzalo Vera
  • Philippe Rocca-Serra
  • Richard A Scheltema
  • K Joeri van der Velde
  • Klaus Schughart
  • Melanie Courtot
  • Alan Ruttenberg
  • George Byelas
  • Bjoern Peters
  • Damian Smedley
  • Gudmundur A Thorisson
  • Anthony J Brookes
  • John M Hancock
  • Katy Wolstencroft
  • Larisa N Soldatova
  • Joris Lops
  • Juha Muilu
  • David Craigon
  • Wilhelm Gruissem
  • Beatrice Schildknecht
  • Margarita Garcia-Hernandez
  • Lars Hennig
  • Sean May
  • Ulrich Wagner
  • Seung Rhee
  • Gaurab Mukherjee

Detail Information

Publications15

  1. pmc The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
    Danielle Welter
    European Bioinformatics Institute EMBL EBI, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK, Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA and Division of Policy, Communication and Education, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Nucleic Acids Res 42:D1001-6. 2014
    ..This article presents a number of recent improvements to the Catalog, including novel ways for users to interact with the Catalog and changes to the curation infrastructure...
  2. pmc MageComet--web application for harmonizing existing large-scale experiment descriptions
    Vincent Xue
    Department of Computer Science, Hunter College, City University of New York, NY 10065, USA
    Bioinformatics 28:1402-3. 2012
    ..Curation of such experiments, however, is an expert activity which involves repetitive manipulation of text. Existing tools for automated curation are few, which bottleneck the analysis pipeline...
  3. pmc MIAME/Plant - adding value to plant microarrray experiments
    Philip Zimmermann
    Swiss Federal Institute of Technology ETH Zurich, ETH Center, CH 8092 Zurich, Switzerland
    Plant Methods 2:1. 2006
    ..The power and value of systematic annotation of microarray data is convincingly demonstrated by data warehouses such as Genevestigator(R) or NASCArrays, and better experimental annotation will make these applications even more powerful...
  4. pmc Anatomy ontologies and potential users: bridging the gap
    Ravensara S Travillian
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    J Biomed Semantics 2:S3. 2011
    ..To evaluate how well current anatomical ontologies fit the way real-world users apply anatomy terms in their data annotations...
  5. pmc Modeling biomedical experimental processes with OBI
    Ryan R Brinkman
    British Columbia Cancer Agency, Vancouver, Canada
    J Biomed Semantics 1:S7. 2010
    ..AVAILABILITY : OBI is available at http://purl.obolibrary.org/obo/obi/2009-11-02/obi.owl...
  6. pmc Large scale comparison of global gene expression patterns in human and mouse
    Xiangqun Zheng-Bradley
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
    Genome Biol 11:R124. 2010
    ....
  7. pmc XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments
    Morris A Swertz
    Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
    Genome Biol 11:R27. 2010
    ..Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans...
  8. pmc OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript
    Tomasz Adamusiak
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 12:218. 2011
    ..This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups...
  9. pmc The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button
    Morris A Swertz
    Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen and Department of Genetics, University Medical Center Groningen, P O Box 30001, 9700 RB Groningen, The Netherlands
    BMC Bioinformatics 11:S12. 2010
    ..We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed...
  10. pmc ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments
    Helen Parkinson
    Functional Genomics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 39:D1002-4. 2011
    ..Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy...
  11. pmc ArrayExpress--a public repository for microarray gene expression data at the EBI
    H Parkinson
    European Bioinformatics Institute, EMBL EBI Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 33:D553-5. 2005
    ..Data can be visualized and analysed using Expression Profiler, the integrated data analysis tool. ArrayExpress is available at http://www.ebi.ac.uk/arrayexpress...
  12. pmc ArrayExpress--a public database of microarray experiments and gene expression profiles
    H Parkinson
    European Bioinformatics Institute, EMBL EBI Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 35:D747-50. 2007
    ..ArrayExpress supports community standards, including MIAME, MAGE-ML and more recently the proposal for a spreadsheet based data exchange format: MAGE-TAB. Availability: www.ebi.ac.uk/arrayexpress...
  13. pmc The EMBL nucleotide sequence database
    G Stoesser
    EMBL Outstation The European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 29:17-21. 2001
    ..For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT...
  14. ncbi request reprint Minimum information about a microarray experiment (MIAME)-toward standards for microarray data
    A Brazma
    European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nat Genet 29:365-71. 2001
    ..With respect to MIAME, we concentrate on defining the content and structure of the necessary information rather than the technical format for capturing it...