U
Ugis Sarkans
Researcher at European Bioinformatics Institute
Publications - 57
Citations - 11586
Ugis Sarkans is an academic researcher from European Bioinformatics Institute. The author has contributed to research in topics: Microarray databases & Minimum information about a microarray experiment. The author has an hindex of 27, co-authored 53 publications receiving 10668 citations. Previous affiliations of Ugis Sarkans include Wellcome Trust & University of Dundee.
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Journal ArticleDOI
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
Alvis Brazma,Pascal Hingamp,John Quackenbush,Gavin Sherlock,Paul T. Spellman,Chris Stoeckert,John Aach,Wilhelm Ansorge,Catherine A. Ball,Helen C. Causton,Terry Gaasterland,Patrick Glenisson,Frank C. P. Holstege,Irene F. Kim,Victor Markowitz,John C. Matese,Helen Parkinson,Alan J. Robinson,Ugis Sarkans,Steffen Schulze-Kremer,Jason E. Stewart,Ronald C. Taylor,Jaak Vilo,Martin Vingron +23 more
TL;DR: The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools.
Journal ArticleDOI
ArrayExpress—a public repository for microarray gene expression data at the EBI
Helen Parkinson,Ugis Sarkans,Mohammadreza Shojatalab,Niran Abeygunawardena,Sergio Contrino,Richard M.R. Coulson,Anna Farne,Gonzalo Garcia Lara,Ele Holloway,Misha Kapushesky,P. Lilja,Gaurab Mukherjee,Ahmet Oezcimen,Tim F. Rayner,Philippe Rocca-Serra,Anjan Sharma,Susanna-Assunta Sansone,Alvis Brazma +17 more
TL;DR: ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Informa-tion About a Microarray Experiment) requirements and stores well-annotated raw and normalized data.
Journal ArticleDOI
ArrayExpress update—simplifying data submissions
Nikolay Kolesnikov,Emma Hastings,Maria Keays,Olga Melnichuk,Y. Amy Tang,Eleanor Williams,Miroslaw Dylag,Natalja Kurbatova,Marco Brandizi,Tony Burdett,Karyn Megy,Ekaterina Pilicheva,Gabriella Rustici,Andrew Tikhonov,Helen Parkinson,Robert Petryszak,Ugis Sarkans,Alvis Brazma +17 more
TL;DR: The main development over the last two years has been the release of a new data submission tool Annotare, which has reduced the average submission time almost 3-fold and will become the only submission route into ArrayExpress, alongside MAGE-TAB format-based pipelines in the near future.
Journal ArticleDOI
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
Henning Hermjakob,Luisa Montecchi-Palazzi,Gary D. Bader,Jérôme Wojcik,Lukasz Salwinski,Arnaud Ceol,Susan Moore,Sandra Orchard,Ugis Sarkans,Christian von Mering,Bernd Roechert,Sylvain Poux,Eva Jung,Henning Mersch,Paul J. Kersey,Michael Lappe,Yixue Li,Rong Zeng,Debashis Rana,Macha Nikolski,Holger Husi,Christine Brun,K. Shanker,Seth G. N. Grant,Chris Sander,Peer Bork,Weimin Zhu,Akhilesh Pandey,Alvis Brazma,Bernard Jacq,Marc Vidal,David James Sherman,Pierre Legrain,Gianni Cesareni,Ioannis Xenarios,David Eisenberg,Boris Steipe,Christopher W. V. Hogue,Rolf Apweiler +38 more
TL;DR: This work proposes a community standard data model for the representation and exchange of protein interaction data, jointly developed by members of the Proteomics Standards Initiative (PSI) and the Human Proteome Organization (HUPO).
Journal ArticleDOI
ArrayExpress—a public database of microarray experiments and gene expression profiles
Helen Parkinson,Misha Kapushesky,Mohammadreza Shojatalab,Niran Abeygunawardena,Richard M.R. Coulson,Anna Farne,Ele Holloway,Nikolay Kolesnykov,P. Lilja,Margus Lukk,Roby Mani,Tim F. Rayner,Anjan Sharma,E. William,Ugis Sarkans,Alvis Brazma +15 more
TL;DR: The ArrayExpress Repository and Data Warehouse is a database of gene expression profiles selected from the repository and consistently re-annotated, which contains data from >50 000 hybridizations and >1 500000 individual expression profiles.