Ugis Sarkans

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc PASSIM--an open source software system for managing information in biomedical studies
    Juris Viksna
    Institute of Mathematics and Computer Science, Riga, University of Latvia, Latvia
    BMC Bioinformatics 8:52. 2007
  2. ncbi request reprint The ArrayExpress gene expression database: a software engineering and implementation perspective
    Ugis Sarkans
    EMBL Outstation Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 21:1495-501. 2005
  3. ncbi request reprint ArrayExpress: a public database of gene expression data at EBI
    Philippe 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
  4. pmc Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress
    Gaurab Mukherjee
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Plant Physiol 139:632-6. 2005
  5. pmc ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments
    Helen Parkinson
    Functional Genomics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 39:D1002-4. 2011
  6. pmc ArrayExpress update--trends in database growth and links to data analysis tools
    Gabriella Rustici
    Functional Genomics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 41:D987-90. 2013
  7. pmc ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression
    Helen Parkinson
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 37:D868-72. 2009
  8. pmc ArrayExpress--a public repository for microarray gene expression data at the EBI
    Alvis Brazma
    European Bioinformatics Institute, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 31:68-71. 2003
  9. pmc Updates to BioSamples database at European Bioinformatics Institute
    Adam Faulconbridge
    European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 42:D50-2. 2014
  10. doi request reprint Data storage and analysis in ArrayExpress and Expression Profiler
    Gabriella Rustici
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    Curr Protoc Bioinformatics . 2008

Detail Information

Publications22

  1. pmc PASSIM--an open source software system for managing information in biomedical studies
    Juris 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...
  2. ncbi request reprint The ArrayExpress gene expression database: a software engineering and implementation perspective
    Ugis 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...
  3. ncbi request reprint ArrayExpress: a public database of gene expression data at EBI
    Philippe 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)...
  4. pmc Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress
    Gaurab 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...
  5. pmc ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments
    Helen 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...
  6. pmc ArrayExpress update--trends in database growth and links to data analysis tools
    Gabriella 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...
  7. pmc ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression
    Helen 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...
  8. pmc ArrayExpress--a public repository for microarray gene expression data at the EBI
    Alvis 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...
  9. pmc Updates to BioSamples database at European Bioinformatics Institute
    Adam Faulconbridge
    European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 42:D50-2. 2014
    ....
  10. doi request reprint Data storage and analysis in ArrayExpress and Expression Profiler
    Gabriella Rustici
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    Curr Protoc Bioinformatics . 2008
    ....
  11. pmc A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
    Tim 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...
  12. pmc graph2tab, a library to convert experimental workflow graphs into tabular formats
    Marco 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...
  13. pmc The BioSample Database (BioSD) at the European Bioinformatics Institute
    Mikhail 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...
  14. ncbi request reprint Data storage and analysis in ArrayExpress
    Alvis 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...
  15. ncbi request reprint Microarray data representation, annotation and storage
    Alvis 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..
  16. ncbi request reprint The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data
    Henning Hermjakob
    European Bioinformatics Institute, EBI Hinxton, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Biotechnol 22:177-83. 2004
    ....
  17. pmc A System for Information Management in BioMedical Studies--SIMBioMS
    Maria 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...
  18. ncbi request reprint Standards for systems biology
    Alvis 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?..
  19. pmc Expression Profiler: next generation--an online platform for analysis of microarray data
    Misha 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...
  20. ncbi request reprint Wrestling with SUMO and bio-ontologies
    Christian Stoeckert
    Nat Biotechnol 24:21-2; author reply 23. 2006
  21. ncbi request reprint The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics
    Andrew 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...
  22. pmc 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...