T
Tomasz Adamusiak
Researcher at European Bioinformatics Institute
Publications - 16
Citations - 1668
Tomasz Adamusiak is an academic researcher from European Bioinformatics Institute. The author has contributed to research in topics: Ontology (information science) & Experimental factor ontology. The author has an hindex of 8, co-authored 14 publications receiving 1572 citations. Previous affiliations of Tomasz Adamusiak include University of Cambridge & University of Pennsylvania.
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Journal ArticleDOI
Modeling sample variables with an Experimental Factor Ontology
James Malone,Ele Holloway,Tomasz Adamusiak,Misha Kapushesky,Jie Zheng,Nikolay Kolesnikov,Anna Zhukova,Alvis Brazma,Helen Parkinson +8 more
TL;DR: The application of reference ontologies to data is a key problem, and this work presents guidelines on how community ontologies can be presented in an application ontology in a data-driven way.
Journal ArticleDOI
ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression
Helen Parkinson,Misha Kapushesky,Nikolay Kolesnikov,Gabriella Rustici,Mohammadreza Shojatalab,Niran Abeygunawardena,Hugo Bérubé,Miroslaw Dylag,Ibrahim Emam,Anna Farne,Ele Holloway,Margus Lukk,James Malone,Roby Mani,Ekaterina Pilicheva,Tim F. Rayner,Faisal I. Rezwan,Anjan Sharma,Eleanor Williams,Xiangqun Zheng Bradley,Tomasz Adamusiak,Marco Brandizi,Tony Burdett,Richard M.R. Coulson,Maria Krestyaninova,Pavel Kurnosov,Eamonn Maguire,Sudeshna Guha Neogi,Philippe Rocca-Serra,Susanna-Assunta Sansone,Nataliya Sklyar,Mengyao Zhao,Ugis Sarkans,Alvis Brazma +33 more
TL;DR: This update describes the ArrayExpress developments over the last two years and describes the new summary database and meta-analytical tool of ranked gene expression across multiple experiments and different biological conditions.
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ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments
Helen Parkinson,Ugis Sarkans,Nikolay Kolesnikov,Niran Abeygunawardena,Tony Burdett,Miroslaw Dylag,Ibrahim Emam,Anna Farne,Emma Hastings,Ele Holloway,Natalja Kurbatova,Margus Lukk,James Malone,Roby Mani,Ekaterina Pilicheva,Gabriella Rustici,Anjan Sharma,Eleanor Williams,Tomasz Adamusiak,Marco Brandizi,Nataliya Sklyar,Alvis Brazma +21 more
TL;DR: The ArrayExpress Archive is one of the three international public repositories of functional genomics data supporting publications and provides queries based on technology and sample attributes such as disease, cell types and anatomy.
Journal ArticleDOI
Gene Expression Atlas update—a value-added database of microarray and sequencing-based functional genomics experiments
Misha Kapushesky,Tomasz Adamusiak,Tony Burdett,Aedín C. Culhane,Anna Farne,Alexey Filippov,Ele Holloway,Andrey Klebanov,Nataliya Kryvych,Natalja Kurbatova,Pavel Kurnosov,James Malone,Olga Melnichuk,Robert Petryszak,Nikolay Pultsin,Gabriella Rustici,Andrew Tikhonov,Ravensara S. Travillian,Eleanor Williams,Andrey Zorin,Helen Parkinson,Alvis Brazma +21 more
TL;DR: The Gene Expression Atlas is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions.
Journal ArticleDOI
The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button
Morris A. Swertz,Martijn Dijkstra,Martijn Dijkstra,Tomasz Adamusiak,K. Joeri van der Velde,Alexandros Kanterakis,Erik T. Roos,Joris Lops,Gudmundur A. Thorisson,Danny Arends,George Byelas,Juha Muilu,Anthony J. Brookes,Engbert O. de Brock,Ritsert C. Jansen,Helen Parkinson +15 more
TL;DR: The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools.