Research Topics
| Ugis SarkansSummaryAffiliation: Wellcome Trust Genome Campus Country: UK Publications
| Collaborators
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Detail Information
Publications
PASSIM--an open source software system for managing information in biomedical studiesJuris Viksna
Institute of Mathematics and Computer Science, Riga, University of Latvia, Latvia
BMC Bioinformatics 8:52. 2007..There is a clear need for lightweight open source systems for patient and sample information management...
The ArrayExpress gene expression database: a software engineering and implementation perspectiveUgis Sarkans
EMBL Outstation Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Bioinformatics 21:1495-501. 2005..Our experience will be both relevant and useful for most bioinformaticians involved in developing information systems for a wide range of high-throughput technologies...- ArrayExpress: a public database of gene expression data at EBIPhilippe Rocca-Serra
EMBL Outstation-Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
C R Biol 326:1075-8. 2003..Data retrieval is performed through a dedicated web interface. Relevant results may be exported to ExpressionProfiler, the EBI based expression analysis tool available online (http://www.ebi.ac.uk/arrayexpress)... - ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experimentsHelen Parkinson
Functional Genomics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
Nucleic Acids Res 39:D1002-4. 2011..Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy... - Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpressGaurab Mukherjee
EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Plant Physiol 139:632-6. 2005..The AtMIAMExpress submission tool is available at http://www.ebi.ac.uk/at-miamexpress/. The software is open source and is available from http://sourceforge.net/projects/miamexpress/. For information, contact miamexpress@ebi.ac.uk... - ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expressionHelen Parkinson
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
Nucleic Acids Res 37:D868-72. 2009..In this update, we describe the ArrayExpress developments over the last two years... - ArrayExpress--a public repository for microarray gene expression data at the EBIAlvis Brazma
European Bioinformatics Institute, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
Nucleic Acids Res 31:68-71. 2003..With an increasing number of organisations adopting MAGE-ML standard, the volume of submissions to ArrayExpress is increasing rapidly. The database can be accessed at http://www.ebi.ac.uk/arrayexpress... 
Data storage and analysis in ArrayExpress and Expression ProfilerGabriella Rustici
European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
Curr Protoc Bioinformatics . 2008....- ArrayExpress update--trends in database growth and links to data analysis toolsGabriella Rustici
Functional Genomics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
Nucleic Acids Res 41:D987-90. 2013..Additionally, R objects, for microarray data, and binary alignment format files, for sequencing data, have been generated for a significant proportion of ArrayExpress data... - A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TABTim F Rayner
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
BMC Bioinformatics 7:489. 2006..However, the complexity of the MAGE-ML format has made its use impractical for laboratories lacking dedicated bioinformatics support... - The BioSample Database (BioSD) at the European Bioinformatics InstituteMikhail Gostev
EMBL EBI, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
Nucleic Acids Res 40:D64-70. 2012..A simple tab-delimited format facilitates submissions of sample information to the database, initially via email to biosamples@ebi.ac.uk... - Data storage and analysis in ArrayExpressAlvis Brazma
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Methods Enzymol 411:370-86. 2006..This chapter describes all major ArrayExpress components from the user perspective: how to submit to, retrieve from, and analyze data in ArrayExpress... - Microarray data representation, annotation and storageAlvis Brazma
EMBL Outstation Hinxton, European Bioinformatics Institute, Cambridge, UK
Adv Biochem Eng Biotechnol 77:113-39. 2002..We describe two data models--a simpler one called ArrayExpressB and the complete model ArrayExpressC, and discuss some implementation issues. For latest developments see http: wwwebi.ac.uk/arrayexpress.. - The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction dataHenning Hermjakob
European Bioinformatics Institute, EBI Hinxton, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Nat Biotechnol 22:177-83. 2004.... - A System for Information Management in BioMedical Studies--SIMBioMSMaria Krestyaninova
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101SD, UK
Bioinformatics 25:2768-9. 2009..Protocols for transferring data to durable archives at the European Bioinformatics Institute have been implemented. AVAILABILITY: The source code, documentation and initialization scripts are available at http://simbioms.org... - graph2tab, a library to convert experimental workflow graphs into tabular formatsMarco Brandizi
European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
Bioinformatics 28:1665-7. 2012..The problem of converting the graph of an experimental workflow into a table-based representation occurs in many such formats and is not easy to solve... - Standards for systems biologyAlvis Brazma
European Bioinformatics Institute, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
Nat Rev Genet 7:593-605. 2006..Why are some standards more successful than others, what are the prerequisites for a standard to succeed and what are the possible pitfalls?.. - Expression Profiler: next generation--an online platform for analysis of microarray dataMisha Kapushesky
European Bioinformatics Institute, United Kingdom
Nucleic Acids Res 32:W465-70. 2004..EP:NG is an open-source project, encouraging broad distribution and further extensions from the scientific community... - Wrestling with SUMO and bio-ontologiesChristian Stoeckert
Nat Biotechnol 24:21-2; author reply 23. 2006 - The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomicsAndrew R Jones
School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
Nat Biotechnol 25:1127-33. 2007..Such advances are important for transparent data management and mining in functional genomics and systems biology... - Design and implementation of microarray gene expression markup language (MAGE-ML)Paul T Spellman
Department of Cell and Molecular Biology, University of California at Berkeley, Berkeley, CA 94720 3206, USA
Genome Biol 3:RESEARCH0046. 2002..Only when data can be easily exchanged will the entire biological community be able to derive the full benefit from such microarray studies...