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List of works by Helen Parkinson

A global map of human gene expression

scientific article

A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction.

scientific article published on 12 October 2017

A mouse informatics platform for phenotypic and translational discovery.

scientific article

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

scientific article

A standard nomenclature for referencing and authentication of pluripotent stem cells

scientific article published in January 2018

A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog

scientific article published on 15 February 2018

A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog

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

scientific article

An atlas of genetic scores to predict multi-omic traits

scientific article published on 29 March 2023

Anatomy ontologies and potential users: bridging the gap

scientific article published on 09 August 2011

Annotare--a tool for annotating high-throughput biomedical investigations and resulting data

scientific article

Annotation of environmental OMICS data: application to the transcriptomics domain

scientific article

Applying the ARRIVE Guidelines to an In Vivo Database

scientific article

ArrayExpress service for reviewers/editors of DNA microarray papers

scientific article published in November 2006

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

scientific article

ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression

scientific article

ArrayExpress update--simplifying data submissions

scientific article

ArrayExpress update--trends in database growth and links to data analysis tools

scientific article (publication date: 2013)

ArrayExpress--a public repository for microarray gene expression data at the EBI

scientific article

ArrayExpress--a public repository for microarray gene expression data at the EBI

scientific article (publication date: 2003)

ArrayExpress: a public database of gene expression data at EBI.

scientific article

Author Correction: Leveraging European infrastructures to access 1 million human genomes by 2022

scientific article published on 01 November 2019

BioSamples database: an updated sample metadata hub

scientific article published on 01 January 2019

Building bridges between cellular and molecular structural biology

scientific article

CLO: The cell line ontology

scientific article

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

scientific article published on January 2006

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

scientific article

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

scientific article

Corrigendum: High-throughput discovery of novel developmental phenotypes.

scientific article published on 8 November 2017

Data standards for Omics data: the basis of data sharing and reuse

scientific article (publication date: 2011)

Data storage and analysis in ArrayExpress

scientific article

Data storage and analysis in ArrayExpress and Expression Profiler

scientific article

Desiderata for the development of next-generation electronic health record phenotype libraries

scientific article published on 01 September 2021

Development of FuGO: an ontology for functional genomics investigations

scientific article published on January 2006

Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).

scientific article published on January 2006

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

scientific article

Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium.

scientific article published on 26 June 2017

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

scientific article published on 07 March 2019

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

scientific article

Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.

scientific article

Features of a FAIR vocabulary ⬇️

Finding our way through phenotypes

scientific article

GA4GH: International policies and standards for data sharing across genomic research and healthcare

scientific article published on 10 November 2021

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments

scientific article

Gene Ontology Consortium: going forward

scientific article (publication date: 2015)

Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data

scientific article published on 13 May 2020

Gene expression atlas at the European bioinformatics institute

scientific article

Gramene 2016: comparative plant genomics and pathway resources

scientific article

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

scientific article published on 6 February 2018

High-throughput discovery of genetic determinants of circadian misalignment

scientific article published on 13 January 2020

High-throughput discovery of novel developmental phenotypes

scientific article published on 14 September 2016

Human and mouse essentiality screens as a resource for disease gene discovery

scientific article published on 31 January 2020

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

scientific article

Identification of genes required for eye development by high-throughput screening of mouse knockouts

scientific article published on 21 December 2018

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

scientific article published on 18 January 2018

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

scientific article (publication date: 20 March 2017)

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

scientific article

Identifying genetic determinants of inflammatory pain in mice using a large-scale gene-targeted screen

scientific article published on 13 September 2021

Importing ArrayExpress datasets into R/Bioconductor

scientific article published on 08 June 2009

Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer’s Disease Data

article

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

scientific article published on 23 December 2010

Leveraging European infrastructures to access 1 million human genomes by 2022

scientific article published on 27 August 2019

LifeTime and improving European healthcare through cell-based interceptive medicine

scientific article published on 07 September 2020

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

scientific article

MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB.

scientific article

MIAME/Plant - adding value to plant microarrray experiments

scientific article

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

scientific article published on 02 April 2012

Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop

scientific article (publication date: 25 December 2010)

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

scientific article (publication date: December 2001)

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)

scientific article

Modeling biomedical experimental processes with OBI

scientific article

Modeling sample variables with an Experimental Factor Ontology

scientific article

Mondo: Unifying diseases for the world, by the world

Mouse Phenotype Database Integration Consortium: integration [corrected] of mouse phenome data resources

scientific article

Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density

scientific article published on 28 December 2020

NCRI Informatics Initiative

article

Natural variation in a Drosophila clock gene and temperature compensation

scientific article published in December 1997

Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information

scientific article published on 4 April 2012

OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript

scientific article

Open Targets: a platform for therapeutic target identification and validation

scientific article

PDX Finder: A Portal for Patient-Derived tumor Xenograft Model Discovery

PDX Finder: A portal for patient-derived tumor xenograft model discovery

scientific article published on 01 January 2019

PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models.

scientific article published in November 2017

PhenoImageShare: an image annotation and query infrastructure

scientific article

Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress

scientific article (publication date: October 2005)

Pleiotropy data resource as a primer for investigating co-morbidities/multi-morbidities and their role in disease

scientific article published on 15 September 2021

Precision medicine: Look to the mice.

scientific article published on 23 July 2015

Prevalence of sexual dimorphism in mammalian phenotypic traits

scientific article

Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine

scientific article published on 17 March 2021

Rapid establishment of the European Bank for induced Pluripotent Stem Cells (EBiSC) - the Hot Start experience

scientific article

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

scientific article

Soft windowing application to improve analysis of high-throughput phenotyping data

scientific article published on 01 March 2020

Standards and ontologies for functional genomics 2.

scientific article published on January 2004

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

scientific article published on January 2003

Standards for microarray data

scientific article

Submission of microarray data to public repositories

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Ten Simple Rules for Selecting a Bio-ontology

scientific article

The ArrayExpress gene expression database: a software engineering and implementation perspective

scientific article published on 25 November 2004

The BioSample Database (BioSD) at the European Bioinformatics Institute

scientific article

The Deep Genome Project

scientific article published on 03 February 2020

The EMBL nucleotide sequence database.

scientific article

The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization

scientific article published on 22 February 2022

The European Bioinformatics Institute's data resources.

scientific article

The European Genome-phenome Archive in 2021

scientific article published on 01 January 2022

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

scientific article

The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation

scientific article published on 19 May 2018

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

scientific article

The MGED Ontology: a resource for semantics-based description of microarray experiments

scientific article published on 21 January 2006

The MGED ontology: a framework for describing functional genomics experiments

scientific article published on January 2003

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

scientific article

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

scientific article

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

scientific article published on 01 January 2019

The Ontology for Biomedical Investigations

scientific article

The SOFG Anatomy Entry List (SAEL): an annotation tool for functional genomics data

scientific article

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

scientific article

The cellular microscopy phenotype ontology

scientific article published on 18 May 2016

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

scientific article

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

scientific article

The underlying principles of scientific publication.

scientific article published in November 2002

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

scientific article

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

scientific article

Updates to BioSamples database at European Bioinformatics Institute

scientific article

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

scientific article published on 14 February 2018

Using ontologies to annotate microarray experiments

scientific article published on January 2006

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

scientific article published on April 2016

Workshop proceedings: GWAS summary statistics standards and sharing

scientific article published on 13 October 2021

Wrestling with SUMO and bio-ontologies

scientific article

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments

scientific article

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