Ugis Sarkans

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.

ORCID iD: 0000-0001-9227-8488

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

Sarkans team

The Functional Genomics 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 (now part of the Samples, Phenotypes and Ontologies 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

2015

ArrayExpress update--simplifying data submissions.
Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T, Megy K, Pilicheva E, Rustici G, Tikhonov A, Parkinson H, Petryszak R, Sarkans U, Brazma A.
Nucleic Acids Res Volume 43 (2015) p.d1113-6
DOI: 10.1093/nar/gku1057

2014

Updates to BioSamples database at European Bioinformatics Institute.
Faulconbridge A, Burdett T, Brandizi M, Gostev M, Pereira R, Vasant D, Sarkans U, Brazma A, Parkinson H.
Nucleic Acids Res Volume 42 (2014) p.d50-2
DOI: 10.1093/nar/gkt1081

Biomarkers in autism spectrum disorder: the old and the new.
Ruggeri B, Sarkans U, Schumann G, Persico AM.
Psychopharmacology (Berl) Volume 231 (2014) p.1201-1216
DOI: 10.1007/s00213-013-3290-7

2013

ArrayExpress update--trends in database growth and links to data analysis tools.
Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U.
Nucleic Acids Res Volume 41 (2013) p.d987-90
DOI: 10.1093/nar/gks1174

2012

The BioSample Database (BioSD) at the European Bioinformatics Institute.
Gostev M, Faulconbridge A, Brandizi M, Fernandez-Banet J, Sarkans U, Brazma A, Parkinson H.
Nucleic Acids Res Volume 40 (2012) p.d64-70
DOI: 10.1093/nar/gkr937

graph2tab, a library to convert experimental workflow graphs into tabular formats.
Brandizi M, Kurbatova N, Sarkans U, Rocca-Serra P.
Bioinformatics Volume 28 (2012) p.1665-1667
DOI: 10.1093/bioinformatics/bts258

2011

Human metabolic profiles are stably controlled by genetic and environmental variation.
Nicholson G, Rantalainen M, Maher AD, Li JV, Malmodin D, Ahmadi KR, Faber JH, Hallgrímsdóttir IB, Barrett A, Toft H, Krestyaninova M, Viksna J, Neogi SG, Dumas ME, Sarkans U, The Molpage Consortium, Silverman BW, Donnelly P, Nicholson JK, Allen M, Zondervan KT, Lindon JC, Spector TD, McCarthy MI, Holmes E, Baunsgaard D, Holmes CC.
Mol Syst Biol Volume 7 (2011) p.525
DOI: 10.1038/msb.2011.57

A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection.
Nicholson G, Rantalainen M, Li JV, Maher AD, Malmodin D, Ahmadi KR, Faber JH, Barrett A, Min JL, Rayner NW, Toft H, Krestyaninova M, Viksna J, Neogi SG, Dumas ME, Sarkans U, MolPAGE Consortium, Donnelly P, Illig T, Adamski J, Suhre K, Allen M, Zondervan KT, Spector TD, Nicholson JK, Lindon JC, Baunsgaard D, Holmes E, McCarthy MI, Holmes CC.
PLoS Genet Volume 7 (2011) p.e1002270
DOI: 10.1371/journal.pgen.1002270

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, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A.
Nucleic Acids Res Volume 39 (2011) p.d1002-4
DOI: 10.1093/nar/gkq1040

2009

A System for Information Management in BioMedical Studies--SIMBioMS.
Krestyaninova M, Zarins A, Viksna J, Kurbatova N, Rucevskis P, Neogi SG, Gostev M, Perheentupa T, Knuuttila J, Barrett A, Lappalainen I, Rung J, Podnieks K, Sarkans U, McCarthy MI, Brazma A.
Bioinformatics Volume 25 (2009) p.2768-2769
DOI: 10.1093/bioinformatics/btp420

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, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A.
Nucleic Acids Res Volume 37 (2009) p.d868-72
DOI: 10.1093/nar/gkn889

2008

Data storage and analysis in ArrayExpress and Expression Profiler.
Rustici G, Kapushesky M, Kolesnikov N, Parkinson H, Sarkans U, Brazma A.
Curr Protoc Bioinformatics Volume Chapter 7 (2008) p.unit 7.13
DOI: 10.1002/0471250953.bi0713s23

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, Mani R, Rayner T, Sharma A, William E, Sarkans U, Brazma A.
Nucleic Acids Res Volume 35 (2007) p.d747-50
DOI: 10.1093/nar/gkl995

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK Jr, Laursen K, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ Jr, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A.
Nat Biotechnol Volume 25 (2007) p.1127-1133
DOI: 10.1038/nbt1347

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 SG, Krestyaninova M, McCarthy MI, Brazma A, Sarkans U.
BMC Bioinformatics Volume 8 (2007) p.52
DOI: 10.1186/1471-2105-8-52

2006

Standards for systems biology.
Brazma A, Krestyaninova M, Sarkans U.
Nat Rev Genet Volume 7 (2006) p.593-605
DOI: 10.1038/nrg1922

Data storage and analysis in ArrayExpress.
Brazma A, Kapushesky M, Parkinson H, Sarkans U, Shojatalab M.
Methods Enzymol Volume 411 (2006) p.370-386
DOI: 10.1016/s0076-6879(06)11020-4

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ Jr, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A.
BMC Bioinformatics Volume 7 (2006) p.489
DOI: 10.1186/1471-2105-7-489

Wrestling with SUMO and bio-ontologies.
Stoeckert C, Ball C, Brazma A, Brinkman R, Causton H, Fan L, Fostel J, Fragoso G, Heiskanen M, Holstege F, Morrison N, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Sarkans U, Sherlock G, Stevens R, Taylor C, Taylor R, Whetzel P, White J.
Nat Biotechnol Volume 24 (2006) p.21-2; author reply 23
DOI: 10.1038/nbt0106-21a

2005

The ArrayExpress gene expression database: a software engineering and implementation perspective.
Sarkans U, Parkinson H, Lara GG, Oezcimen A, Sharma A, Abeygunawardena N, Contrino S, Holloway E, Rocca-Serra P, Mukherjee G, Shojatalab M, Kapushesky M, Sansone SA, Farne A, Rayner T, Brazma A.
Bioinformatics Volume 21 (2005) p.1495-1501
DOI: 10.1093/bioinformatics/bti157

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 GG, Holloway E, Kapushesky M, Lilja P, Mukherjee G, Oezcimen A, Rayner T, Rocca-Serra P, Sharma A, Sansone S, Brazma A.
Nucleic Acids Res Volume 33 (2005) p.d553-5
DOI: 10.1093/nar/gki056

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, Rayner T, Sharma A, Brazma A, Sarkans U, Shojatalab M.
Plant Physiol Volume 139 (2005) p.632-636
DOI: 10.1104/pp.105.063156

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, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R.
Nat Biotechnol Volume 22 (2004) p.177-183
DOI: 10.1038/nbt926

Expression Profiler: next generation--an online platform for analysis of microarray data.
Kapushesky M, Kemmeren P, Culhane AC, Durinck S, Ihmels J, Körner C, Kull M, Torrente A, Sarkans U, Vilo J, Brazma A.
Nucleic Acids Res Volume 32 (2004) p.w465-70
DOI: 10.1093/nar/gkh470

2003

Expression Profiler
Vilo J, Kapushesky M, Kemmeren P, Sarkans U, Brazma A.
Volume (2003) p.142
DOI: 10.1109/hicss.1994.323567

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, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Sansone SA.
C R Biol Volume 326 (2003) p.1075-1078
DOI: 10.1016/j.crvi.2003.09.026

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 GG, Oezcimen A, Rocca-Serra P, Sansone SA.
Nucleic Acids Res Volume 31 (2003) p.68-71
DOI: 10.1093/nar/gkg091

2002

Design and implementation of microarray gene expression markup language (MAGE-ML).
Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert CJ Jr, Brazma A.
Genome Biol Volume 3 (2002) p.research0046
DOI: 10.1186/gb-2002-3-9-research0046

Microarray data representation, annotation and storage.
Brazma A, Sarkans U, Robinson A, Vilo J, Vingron M, Hoheisel J, Fellenberg K.
Adv Biochem Eng Biotechnol Volume 77 (2002) p.113-139

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 CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M.
Nat Genet Volume 29 (2001) p.365-371
DOI: 10.1038/ng1201-365

Team members

Ahmed Ali
Marco Brandizi
Miroslaw Dylag
Mikhail Gostev
Nikolay Kolesnikov
Michael Maguire
Olga Melnichuk
Ekaterina Pilicheva
Andrew Tikhonov