European Bioinformatics Institute

Ugis Sarkans

Technical Team Leader, Functional genomics development

PhD in Computer Science, University of Latvia, 1998. Postdoctoral research at the University of Wales, Aberystwyth, 2000. At EMBL-EBI since 2000.

ugis [at] ebi.ac.uk

Tel:+44 (0)1223 494 603 / Fax:+44 (0)1223 494 468

Sarkans team

The Functional genomics software development team, led by Dr Ugis Sarkans, develops software for ArrayExpress and the EBI BioSamples database. ArrayExpress, one of EMBL-EBI's core resources, holds data from over a million microarray and sequencing assays. The BioSamples database centralises the handling of biological sample information from other EMBL-EBI resources, and holds data on more than 1.5 million samples. Together with the Functional genomics production team, the development team builds and maintains ArrayExpress and BioSamples infrastructures such as data management tools, user interfaces, programmatic interfaces, and a data annotation and submission system for ArrayExpress. The team collaborates on a number of European ‘multi-omics’ projects in a data-management capacity.

Publications

2012

Graph2tab, a library to convert experimental workflow graphs into tabular formats

BRANDIZI, M., KURBATOVA N., Sarkans U., and Rocca-Serra P.

Bioinformatics. Volume 28, Number 12, (2012), p.1665-1667

Analysis of Gene Expression Data from Non-Small Cell Lung Carcinoma Cell Lines Reveals Distinct Sub-Classes from Those Identified at the Phenotype Level

Dalby, A. R., EMAM I., and Franke R.

PLoS ONE. Volume 7, Number 11, (2012),

Gene Expression Atlas update - Value-added database of microarray and sequencing-based functional genomics experiments

KAPUSHESKY, M., ADAMUSIAK T., BURDETT T., CULHANE A., FARNE A., FILIPPOV A., HOLLOWAY E., KLEBANOV A., KRYVYCH N., KURBATOVA N., et al.

Nucleic Acids Research. Volume 40, Number D1, (2012), p.D1077-D1081

The BioSample Database (BioSD) at the European Bioinformatics Institute

GOSTEV, M., FAULCONBRIDGE A., BRANDIZI M., FERNANDEZ-BANET J., Sarkans U., BRAZMA A., and Parkinson H.

Nucleic Acids Research. Volume 40, Number D1, (2012), p.D64-D70

2011

Human metabolic profiles are stably controlled by genetic and environmental variation

Nicholson, G., Rantalainen M., Maher A. D., Li J. V., Malmodin D., Ahmadi K. R., Faber J. H., Hallgrímsdóttir I. B., Barrett A., Toft H., et al.

Molecular Systems Biology. Volume 7, (2011),

A genome-wide metabolic QTL analysis in europeans implicates two Loci shaped by recent positive selection

Nicholson, G., Rantalainen M., Li J. V., Maher A. D., Malmodin D., Ahmadi K. R., Faber J. H., Barrett A., Min J. L., Rayner N. W., et al.

PLoS Genetics. Volume 7, Number 9, (2011),

Arrayexpress update-An archive of microarray and high-throughput sequencing-based functional genomics experiments

Parkinson, H., Sarkans U., KOLESNIKOV N., ABEYGUNAWARDENA N., BURDETT T., DYLAG M., EMAM I., FARNE A., HASTINGS E., HOLLOWAY E., et al.

Nucleic Acids Research. Volume 39, Number SUPPL. 1, (2011), p.D1002-D1004

SAIL-a software system for sample and phenotype availability across biobanks and cohorts

GOSTEV, M., FERNANDEZ-BANET J., Rung J., Dietrich J., Prokopenko I., Ripatti S., McCarthy M. I., BRAZMA A., and KRESTYANINOVA M.

Bioinformatics. Volume 27, Number 4, (2011), p.589-591

2010

ISA software suite: Supporting standards-compliant experimental annotation and enabling curation at the community level

Rocca-Serra, P., BRANDIZI M., Maguire E., Sklyar N., TAYLOR C., Begley K., Field D., Harris S., Hide W., Hofmann O., et al.

Bioinformatics. Volume 26, Number 18, (2010), p.2354-2356

Modeling sample variables with an Experimental Factor Ontology

MALONE, J., HOLLOWAY E., ADAMUSIAK T., KAPUSHESKY M., Zheng J., KOLESNIKOV N., ZHUKOVA A., BRAZMA A., and Parkinson H.

Bioinformatics. Volume 26, Number 8, (2010), p.1112-1118

Public data archives for genomic structural variation

Church, D. M., LAPPALAINEN I., Sneddon T. P., HINTON J., MAGUIRE M., Lopez J., Garner J., Paschall J., Dicuccio M., Yaschenko E., et al.

Nature Genetics. Volume 42, Number 10, (2010), p.813-814

2009

Gene expression Atlas at the European Bioinformatics Institute

KAPUSHESKY, M., EMAM I., HOLLOWAY E., KURNOSOV P., ZORIN A., MALONE J., RUSTICI G., WILLIAMS E., Parkinson H., and BRAZMA A.

Nucleic Acids Research. Volume 38, Number SUPPL.1, (2009), p.D690-D698

Improvements to services at the European Nucleotide Archive

Leinonen, R., Akhtar R., Birney E., Bonfield J., Bower L., Corbett M., Cheng Y., Demiralp F., Faruque N., Goodgame N., et al.

Nucleic Acids Research. Volume 38, Number SUPPL.1, (2009), p.D39-D45

A system for information management in BioMedical studies - SIMBioMS

KRESTYANINOVA, M., Zarins A., Viksna J., KURBATOVA N., Rucevskis P., Neogi S. G., GOSTEV M., Perheentupa T., Knuuttila J., Barrett A., et al.

Bioinformatics. Volume 25, Number 20, (2009), p.2768-2769

ArrayExpress update - From an archive of functional genomics experiments to the atlas of gene expression

Parkinson, H., KAPUSHESKY M., KOLESNIKOV N., RUSTICI G., Shojatalab M., ABEYGUNAWARDENA N., Berube H., DYLAG M., EMAM I., FARNE A., et al.

Nucleic Acids Research. Volume 37, Number SUPPL. 1, (2009), p.D868-D872

2008

The first RSBI (ISA-TAB) workshop: "Can a simple format work for complex studies?"

Sansone, S. - A., Rocca-Serra P., BRANDIZI M., BRAZMA A., Field D., Fostel J., Garrow A. G., Gilbert J., Goodsaid F., Hardy N., et al.

OMICS A Journal of Integrative Biology. Volume 12, Number 2, (2008), p.143-149

Data storage and analysis in ArrayExpress and expression profiler

RUSTICI, G., KAPUSHESKY M., Kolesniko N., Parkinson H., Sarkans U., and BRAZMA A.

Current Protocols in Bioinformatics. Number SUPPL. 23, (2008), p.7.13.1-7.13.27

Data storage and analysis in ArrayExpress and Expression Profiler.

RUSTICI, G., KAPUSHESKY M., KOLESNIKOV N., Parkinson H., Sarkans U., and BRAZMA A.

Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]. Volume Chapter 7, (2008),

2007

The Functional Genomics Experiment model (FuGE): An extensible framework for standards in functional genomics

Jones, A. R., Miller M., Aebersold R., Apweiler R., Ball C. A., BRAZMA A., DeGreef J., Hardy N., Hermjakob H., Hubbard S. J., et al.

Nature Biotechnology. Volume 25, Number 10, (2007), p.1127-1133

PASSIM - An open source software system for managing information in biomedical studies

Viksna, J., Celms E., Opmanis M., Podnieks K., Rucevskis P., Zarins A., Barrett A., Neogi S. G., KRESTYANINOVA M., McCarthy M. I., et al.

BMC Bioinformatics. Volume 8, (2007),

ArrayExpress - A public database of microarray experiments and gene expression profiles

Parkinson, H., KAPUSHESKY M., Shojatalab M., ABEYGUNAWARDENA N., COULSON R., FARNE A., HOLLOWAY E., Kolesnykov N., Lilja P., Lukk M., et al.

Nucleic Acids Research. Volume 35, Number SUPPL. 1, (2007), p.D747-D750

2006

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

Rayner, T. F., Rocca-Serra P., Spellman P. T., Causton H. C., FARNE A., HOLLOWAY E., Irizarry R. A., Liu J., Maier D. S., Miller M., et al.

BMC Bioinformatics. Volume 7, (2006),

[20] Data Storage and Analysis in ArrayExpress

BRAZMA, A., KAPUSHESKY M., Parkinson H., Sarkans U., and Shojatalab M.

Methods in Enzymology. Volume 411, (2006), p.370-386

Standards for systems biology

BRAZMA, A., KRESTYANINOVA M., and Sarkans U.

Nature Reviews Genetics. Volume 7, Number 8, (2006), p.593-605

To the editor [2]

Stoeckert, C., Ball C., BRAZMA A., Brinkman R., Causton H., Fan L., Fostel J., Fragoso G., Heiskanen M., Holstege F., et al.

Nature Biotechnology. Volume 24, Number 1, (2006), p.21-22

2005

ArrayExpress - A public repository for microarray gene expression data at the EBI

Parkinson, H., Sarkans U., Shojatalab M., ABEYGUNAWARDENA N., Contrino S., COULSON R., FARNE A., Lara G. G., HOLLOWAY E., KAPUSHESKY M., et al.

Nucleic Acids Research. Volume 33, Number DATABASE ISS., (2005), p.D553-D555

The ArrayExpress gene expression database: A software engineering and implementation perspective

Sarkans, U., Parkinson H., Lara G. G., Oezcimen A., SHARMA A., ABEYGUNAWARDENA N., Contrino S., HOLLOWAY E., Rocca-Serra P., MUKHERJEE G., et al.

Bioinformatics. Volume 21, Number 8, (2005), p.1495-1501

Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for arabidopsis gene expression data to ArrayExpress

MUKHERJEE, G., ABEYGUNAWARDENA N., Parkinson H., Contrino S., Durinck S., FARNE A., HOLLOWAY E., Lilja P., Moreau Y., Oezcimen A., et al.

Plant Physiology. Volume 139, Number 2, (2005), p.632-636

2004

The HUPO PSI's Molecular Interaction format - A community standard for the representation of protein interaction data

Hermjakob, H., Montecchi-Palazzi L., Bader G., Wojcik J., Salwinski L., Ceol A., Moore S., Orchard S., Sarkans U., von Mering C., et al.

Nature Biotechnology. Volume 22, Number 2, (2004), p.177-183

Expression profiler: Next generation - An online platform for analysis of microarray data

KAPUSHESKY, M., Kemmeren P., Culhane A. C., Durinck S., Ihmels J., Körner C., Kull M., Torrente A., Sarkans U., Vilo J., et al.

Nucleic Acids Research. Volume 32, Number WEB SERVER ISS., (2004), p.W465-W470

2003

ArrayExpress: A public database of gene expression data at EBI

Rocca-Serra, P., BRAZMA A., Parkinson H., Sarkans U., Shojatalab M., Contrino S., Vilo J., ABEYGUNAWARDENA N., MUKHERJEE G., HOLLOWAY E., et al.

Comptes Rendus - Biologies. Volume 326, Number 10-11, (2003), p.1075-1078

ArrayExpress - A public repository for microarray gene expression data at the EBI

BRAZMA, A., Parkinson H., Sarkans U., Shojatalab M., Vilo J., ABEYGUNAWARDENA N., HOLLOWAY E., KAPUSHESKY M., Kemmeren P., Lara G. G., et al.

Nucleic Acids Research. Volume 31, Number 1, (2003), p.68-71

2002

Microarray data representation, annotation and storage.

BRAZMA, A., Sarkans U., Robinson A., Vilo J., Vingron M., Hoheisel J., and Fellenberg K.

Advances in biochemical engineering/biotechnology. Volume 77, (2002), p.113-139

Design and implementation of microarray gene expression markup language (MAGE-ML).

Spellman, P. T., Miller M., Stewart J., Troup C., Sarkans U., Chervitz S., Bernhart D., Sherlock G., Ball C., Lepage M., et al.

Genome biology. Volume 3, Number 9, (2002),

2001

Minimum information about a microarray experiment (MIAME) - Toward standards for microarray data

BRAZMA, A., Hingamp P., QUACKENBUSH J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C. A., Causton H. C., et al.

Nature Genetics. Volume 29, Number 4, (2001), p.365-371

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