S
Simon Jupp
Researcher at European Bioinformatics Institute
Publications - 73
Citations - 3070
Simon Jupp is an academic researcher from European Bioinformatics Institute. The author has contributed to research in topics: Ontology (information science) & Semantic Web. The author has an hindex of 22, co-authored 70 publications receiving 2081 citations. Previous affiliations of Simon Jupp include University of Manchester & Wellcome Trust.
Papers
More filters
Journal ArticleDOI
Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants
Robert Petryszak,Maria Keays,Y. Amy Tang,Nuno A. Fonseca,Elisabet Barrera,Tony Burdett,Anja Füllgrabe,Alfonso Muñoz-Pomer Fuentes,Simon Jupp,Satu Koskinen,Oliver Mannion,Laura Huerta,Karyn Megy,Catherine Snow,Eleanor Williams,Mitra Barzine,Emma Hastings,Hendrik Weisser,James C. Wright,Pankaj Jaiswal,Wolfgang Huber,Jyoti S. Choudhary,Helen Parkinson,Alvis Brazma +23 more
TL;DR: The first proteomics study in human tissues is now displayed alongside transcriptomics data in the same tissues, and novel analyses and visualisations include: ‘enrichment’ in each differential comparison of GO terms, Reactome, Plant Reactome pathways and InterPro domains.
Journal ArticleDOI
Expression Atlas update: from tissues to single cells
Irene Papatheodorou,Pablo Moreno,Jonathan R. Manning,Alfonso Muñoz-Pomer Fuentes,Nancy George,Silvie Fexova,Nuno A. Fonseca,Anja Füllgrabe,Matthew Green,Ni Huang,Ni Huang,Laura Huerta,Haider Iqbal,Monica Jianu,Suhaib Mohammed,Lingyun Zhao,Andrew F. Jarnuczak,Simon Jupp,John C. Marioni,John C. Marioni,John C. Marioni,Kerstin B. Meyer,Robert Petryszak,Cesar Augusto Prada Medina,Carlos Talavera-López,Sarah A. Teichmann,Juan Antonio Vizcaíno,Alvis Brazma +27 more
TL;DR: Expression Atlas is extended with a new added-value service to display gene expression in single cells with the increased availability of single cell RNA-Seq datasets in the public archives.
Journal ArticleDOI
Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments
Robert Petryszak,Tony Burdett,Benedetto Fiorelli,Nuno A. Fonseca,Mar Gonzàlez-Porta,Emma Hastings,Wolfgang Huber,Simon Jupp,Maria Keays,Nataliya Kryvych,Julie A. McMurry,John C. Marioni,James Malone,Karyn Megy,Gabriella Rustici,Y. Amy Tang,Jan Taubert,Eleanor Williams,Oliver Mannion,Helen Parkinson,Alvis Brazma +20 more
TL;DR: The new version of Expression Atlas introduces the concept of ‘baseline’ expression, i.e. gene and splice variant abundance levels in healthy or untreated conditions, such as tissues or cell types, in order to maximize the biological value provided to the user.
Journal ArticleDOI
The EBI RDF Platform: Linked Open Data for the Life Sciences
Simon Jupp,James Malone,Jerven Bolleman,Marco Brandizi,Mark Davies,Leyla Garcia,Anna Gaulton,Sebastien Gehant,Camille Laibe,Nicole Redaschi,Sarala M. Wimalaratne,Maria Jesus Martin,Nicolas Le Novère,Helen Parkinson,Ewan Birney,Andrew M. Jenkinson +15 more
TL;DR: The EBI RDF platform has been developed to meet an increasing demand to coordinate RDF activities across the institute and provides a new entry point to querying and exploring integrated resources available at the EBI.
Journal ArticleDOI
Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics.
Maya Ghoussaini,Edward Mountjoy,Miguel Carmona,Gareth Peat,Ellen M. Schmidt,Andrew Hercules,Luca Fumis,Alfredo Miranda,Denise Carvalho-Silva,Annalisa Buniello,Tony Burdett,James D. Hayhurst,Jarrod Baker,Javier Ferrer,Asier Gonzalez-Uriarte,Simon Jupp,Mohd Anisul Karim,Gautier Koscielny,Sandra Machlitt-Northen,Cinzia Malangone,Zoë May Pendlington,Paola Roncaglia,Daniel Suveges,Daniel Wright,Olga Vrousgou,Eliseo Papa,Helen Parkinson,Jacqueline A. L. MacArthur,John A. Todd,Jeffrey C. Barrett,Jeremy Schwartzentruber,David G. Hulcoop,David Ochoa,Ellen M. McDonagh,Ellen M. McDonagh,Ian Dunham,Ian Dunham +36 more
TL;DR: Open Targets Genetics offers tools that enable users to prioritise causal variants and genes at disease-associated loci and access systematic cross-disease and disease-molecular trait colocalization analysis across 92 cell types and tissues including the eQTL Catalogue.