Helen Parkinson

Helen Parkinson

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Erratum: Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts.

Commun Biol 2019 7;2:97. Epub 2019 Mar 7.

Department of Ophthalmology & Vision Science, School of Medicine, U.C. Davis, Sacramento, CA, 95817, USA.

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http://dx.doi.org/10.1038/s42003-019-0349-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6405960PMC
March 2019

Harmonising phenomics information for a better interoperability in the rare disease field.

Eur J Med Genet 2018 Nov 7;61(11):706-714. Epub 2018 Feb 7.

INSERM, US14 - Orphanet, Plateforme Maladies Rares, 75014 Paris, France. Electronic address:

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http://dx.doi.org/10.1016/j.ejmg.2018.01.013DOI Listing
November 2018

Using OWL reasoning to support the generation of novel gene sets for enrichment analysis.

J Biomed Semantics 2018 02 14;9(1):10. Epub 2018 Feb 14.

Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, -4070, Basel, CH, Switzerland.

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http://dx.doi.org/10.1186/s13326-018-0175-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813370PMC
February 2018

Identification of genetic elements in metabolism by high-throughput mouse phenotyping.

Nat Commun 2018 01 18;9(1):288. Epub 2018 Jan 18.

German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.

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http://dx.doi.org/10.1038/s41467-017-01995-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5773596PMC
January 2018

Comparison, alignment, and synchronization of cell line information between CLO and EFO.

BMC Bioinformatics 2017 12 21;18(Suppl 17):557. Epub 2017 Dec 21.

Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1186/s12859-017-1979-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5763470PMC
December 2017

The cellular microscopy phenotype ontology.

J Biomed Semantics 2016 18;7:28. Epub 2016 May 18.

European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton Cambridge, CB10 1SD UK.

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http://dx.doi.org/10.1186/s13326-016-0074-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4870745PMC
November 2017

Corrigendum: High-throughput discovery of novel developmental phenotypes.

Nature 2017 11 8;551(7680):398. Epub 2017 Nov 8.

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http://dx.doi.org/10.1038/nature24643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5849394PMC
November 2017

Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression.

PLoS One 2016 20;11(6):e0157484. Epub 2016 Jun 20.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0157484PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4913919PMC
July 2017

The human-induced pluripotent stem cell initiative-data resources for cellular genetics.

Nucleic Acids Res 2017 01 12;45(D1):D691-D697. Epub 2016 Oct 12.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

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http://dx.doi.org/10.1093/nar/gkw928DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210631PMC
January 2017

Reporting phenotypes in mouse models when considering body size as a potential confounder.

J Biomed Semantics 2016 9;7. Epub 2016 Feb 9.

Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire UK.

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http://dx.doi.org/10.1186/s13326-016-0050-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748495PMC
October 2016

Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation.

J Biomed Semantics 2016 23;7. Epub 2016 Mar 23.

European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK ; Centre for Therapeutic Target Validation, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK.

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http://dx.doi.org/10.1186/s13326-016-0051-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804633PMC
October 2016

Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates.

J Biomed Semantics 2016 1;7:17. Epub 2016 Apr 1.

European Bioinformatics Institute (EMBL-EBI),European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1186/s13326-016-0055-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4818523PMC
October 2016

High-throughput discovery of novel developmental phenotypes.

Nature 2016 09 14;537(7621):508-514. Epub 2016 Sep 14.

The Jackson Laboratory, Bar Harbor, Maine 04609, USA.

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http://dx.doi.org/10.1038/nature19356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5295821PMC
September 2016

PhenoImageShare: an image annotation and query infrastructure.

J Biomed Semantics 2016 Jun 7;7:35. Epub 2016 Jun 7.

European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.

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http://dx.doi.org/10.1186/s13326-016-0072-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896029PMC
June 2016

Ten Simple Rules for Selecting a Bio-ontology.

PLoS Comput Biol 2016 Feb 11;12(2):e1004743. Epub 2016 Feb 11.

European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1004743DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4750991PMC
February 2016

Tools and data services registry: a community effort to document bioinformatics resources.

Nucleic Acids Res 2016 Jan 3;44(D1):D38-47. Epub 2015 Nov 3.

Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.

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http://dx.doi.org/10.1093/nar/gkv1116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702812PMC
January 2016

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.

Am J Hum Genet 2015 Jul 25;97(1):111-24. Epub 2015 Jun 25.

Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany; Berlin Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Institute of Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2015.05.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4572507PMC
July 2015

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.

Nucleic Acids Res 2015 Jan 27;43(Database issue):D1071-8. Epub 2014 Oct 27.

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA

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http://nar.oxfordjournals.org/content/43/D1/D1071.full.pdf
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gku1011
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http://dx.doi.org/10.1093/nar/gku1011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383880PMC
January 2015

ArrayExpress update--simplifying data submissions.

Nucleic Acids Res 2015 Jan 31;43(Database issue):D1113-6. Epub 2014 Oct 31.

European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK

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http://dx.doi.org/10.1093/nar/gku1057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383899PMC
January 2015

Finding our way through phenotypes.

PLoS Biol 2015 Jan 6;13(1):e1002033. Epub 2015 Jan 6.

Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1002033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285398PMC
January 2015

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.

J Biomed Semantics 2014 2;5:25. Epub 2014 Jun 2.

School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.

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http://dx.doi.org/10.1186/2041-1480-5-25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4098953PMC
July 2014

Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records.

Stand Genomic Sci 2014 Jun 29;9(3):1275-7. Epub 2014 Jan 29.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

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http://dx.doi.org/10.4056/sigs.4851102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4149001PMC
June 2014

The EBI RDF platform: linked open data for the life sciences.

Bioinformatics 2014 May 11;30(9):1338-9. Epub 2014 Jan 11.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneve, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btt765DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998127PMC
May 2014

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.

Nucleic Acids Res 2014 Jan 4;42(Database issue):D802-9. Epub 2013 Nov 4.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK and Mouse Informatics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gkt977DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964955PMC
January 2014

Updates to BioSamples database at European Bioinformatics Institute.

Nucleic Acids Res 2014 Jan 21;42(Database issue):D50-2. Epub 2013 Nov 21.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkt1081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965081PMC
January 2014

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations.

Nucleic Acids Res 2014 Jan 6;42(Database issue):D1001-6. Epub 2013 Dec 6.

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.

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http://nar.oxfordjournals.org/content/42/D1/D1001.full.pdf
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkt1229
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http://dx.doi.org/10.1093/nar/gkt1229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965119PMC
January 2014

Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans.

Mamm Genome 2012 Oct 19;23(9-10):641-52. Epub 2012 Sep 19.

Mammalian Genetics Unit, Medical Research Council Harwell, Harwell, Oxfordshire OX11 0RD, UK.

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http://dx.doi.org/10.1007/s00335-012-9428-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4106044PMC
October 2012

MageComet--web application for harmonizing existing large-scale experiment descriptions.

Bioinformatics 2012 May 2;28(10):1402-3. Epub 2012 Apr 2.

Department of Computer Science, Hunter College, City University of New York, NY 10065, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3348561PMC
May 2012

The BioSample Database (BioSD) at the European Bioinformatics Institute.

Nucleic Acids Res 2012 Jan 16;40(Database issue):D64-70. Epub 2011 Nov 16.

EMBL-EBI, the European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkr937DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245134PMC
January 2012

Anatomy ontologies and potential users: bridging the gap.

J Biomed Semantics 2011 Aug 9;2 Suppl 4:S3. Epub 2011 Aug 9.

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.

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http://dx.doi.org/10.1186/2041-1480-2-S4-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3194170PMC
August 2011

Large scale comparison of global gene expression patterns in human and mouse.

Genome Biol 2010 23;11(12):R124. Epub 2010 Dec 23.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1186/gb-2010-11-12-r124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3046484PMC
June 2011

Contributions of the EMERALD project to assessing and improving microarray data quality.

Biotechniques 2011 Jan;50(1):27-31

Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.

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https://www.future-science.com/doi/10.2144/000113591
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http://dx.doi.org/10.2144/000113591DOI Listing
January 2011

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.

BMC Bioinformatics 2010 Dec 21;11 Suppl 12:S12. Epub 2010 Dec 21.

Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Department of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands.

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http://www.biomedcentral.com/content/pdf/1471-2105-11-S12-S1
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http://www.biomedcentral.com/1471-2105/11/S12/S12
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http://dx.doi.org/10.1186/1471-2105-11-S12-S12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040526PMC
December 2010

Standards and ontologies for functional genomics: towards unified ontologies for biology and biomedicine.

Comp Funct Genomics 2003 ;4(1):116-20

European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1002/cfg.249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447377PMC
June 2010

The MGED ontology: a framework for describing functional genomics experiments.

Comp Funct Genomics 2003 ;4(1):127-32

Department of Genetics and Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1002/cfg.234DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447379PMC
June 2010

Standards and ontologies for functional genomics 2.

Comp Funct Genomics 2004 ;5(8):618-22

European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1002/cfg.448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447478PMC
June 2010

Modeling sample variables with an Experimental Factor Ontology.

Bioinformatics 2010 Apr 3;26(8):1112-8. Epub 2010 Mar 3.

Microarray Informatics Team, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.

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http://dx.doi.org/10.1093/bioinformatics/btq099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853691PMC
April 2010

Gene expression atlas at the European bioinformatics institute.

Nucleic Acids Res 2010 Jan 11;38(Database issue):D690-8. Epub 2009 Nov 11.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkp936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808905PMC
January 2010

Importing ArrayExpress datasets into R/Bioconductor.

Bioinformatics 2009 Aug 8;25(16):2092-4. Epub 2009 Jun 8.

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btp354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723004PMC
August 2009

Data storage and analysis in ArrayExpress and Expression Profiler.

Curr Protoc Bioinformatics 2008 Sep;Chapter 7:Unit 7.13

European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1002/0471250953.bi0713s23DOI Listing
September 2008

Cancer informatics in the U.K.: the NCRI informatics initiative.

Cancer Inform 2007 Feb 26;2:389-94. Epub 2007 Feb 26.

NCRI Informatics Initiative, London, U.K.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675486PMC
February 2007

Using ontologies to annotate microarray experiments.

Methods Enzymol 2006 ;411:325-39

Department of Genetics, Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.

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http://dx.doi.org/10.1016/S0076-6879(06)11017-4DOI Listing
December 2006

Data storage and analysis in ArrayExpress.

Methods Enzymol 2006 ;411:370-86

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1016/S0076-6879(06)11020-4DOI Listing
December 2006

ArrayExpress service for reviewers/editors of DNA microarray papers.

Nat Biotechnol 2006 Nov;24(11):1321-2

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http://dx.doi.org/10.1038/nbt1106-1321DOI Listing
November 2006

NCRI informatics initiative.

Nat Biotechnol 2005 Oct;23(10):1212

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http://dx.doi.org/10.1038/nbt1005-1212DOI Listing
October 2005