Alvis Brazma

Alvis Brazma

Senior Team Leader, Functional Genomics

PhD in Computer Science, Moscow State University, 1987. Postdoctoral research at New Mexico State University, USA. At EMBL-EBI since 1997.

Dr Alvis Brazma oversees the development and services for several major resources, including ArrayExpress, the Gene Expression Atlas and the BioStudies Database. His main research interests concern integrative data analysis to reveal patterns of gene and protein expression in normal and diseased state. He has over 100 scientific publications and is a Principal Investigator on several large collaborative genomics and biomedical projects, including the kidney cancer project of the International Cancer Genome Consortium. Dr Brazma studied mathematics at the University of Latvia, Riga, before obtaining his PhD in computer science from the Moscow State University. He was a lecturer at the University of Latvia and a visiting Researcher at Helsinki University before joining EMBL-EBI in 1997. Dr Brazma was among the first scientists to use microarray data to study gene regulation. In 1999 he founded the Microarray Gene Expression Data society was instrumental in starting ArrayExpress, one of the major international repositories for functional genomics data.

ORCID iD: 0000-0001-5988-7409

Tel:+44 (0)1223 494 658 / Fax:+44 (0)1223 494 468

http://www.ebi.ac.uk/~brazma (personal homepage)

Research

Find out about research activity in the Brazma research group

Brazma team

Led by Dr Alvis Brazma, the Functional Genomics team focuses on providing bioinformatics services and conducting research in gene expression and high-throughput sequencing applications to functional genomics. The team participates in software development related to biomedical informatics and systems microscopy, and is responsible for the Gene Expression Atlas, which encompasses transcriptomics and proteomics. Together with the Sarkans and Petryszak teams, the Functional Genomics team works on the ArrayExpress Archive of Functional Genomics Data, Expression Atlas and the BioStudies Database. Students in the team focus on data analysis and developing new methods and algorithms, integration of data across multiple platforms and types of data. The team is a major contributor to EMBL-EBI's training in transcriptomics and the use of EMBL-EBI tools.

Publications

2016

Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.
Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E, Burdett T, Füllgrabe A, Fuentes AM, Jupp S, Koskinen S, Mannion O, Huerta L, Megy K, Snow C, Williams E, Barzine M, Hastings E, Weisser H, Wright J, Jaiswal P, Huber W, Choudhary J, Parkinson HE, Brazma A.
Nucleic acids research Volume 44 (2016) p.D746-52

2015

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.
Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D, Petryszak R, Mudge JM, Fonseca N, Brazma A, Guigo R, Harrow J.
BMC genomics Volume 16 Suppl 8 (2015) p.S2

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.
Leigh-Brown S, Goncalves A, Thybert D, Stefflova K, Watt S, Flicek P, Brazma A, Marioni JC, Odom DT.
PloS one Volume 10 (2015) p.e0137367

Cellular phenotype database: a repository for systems microscopy data.
Kirsanova C, Brazma A, Rustici G, Sarkans U.
Bioinformatics (Oxford, England) Volume 31 (2015) p.2736-2740

The BioStudies database.
McEntyre J, Sarkans U, Brazma A.
Molecular systems biology Volume 11 (2015) p.847

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.
Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J, GTEx Consortium, Geuvadis Consortium, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG.
Science (New York, N.Y.) Volume 348 (2015) p.666-669

A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging.
Su J, Ekman C, Oskolkov N, Lahti L, Ström K, Brazma A, Groop L, Rung J, Hansson O.
Skeletal muscle Volume 5 (2015) p.35

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 research Volume 43 (2015) p.D1113-6

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 research Volume 42 (2014) p.D50-2

Distinct developmental profile of lower-body adipose tissue defines resistance against obesity-associated metabolic complications.
Pinnick KE, Nicholson G, Manolopoulos KN, McQuaid SE, Valet P, Frayn KN, Denton N, Min JL, Zondervan KT, Fleckner J, MolPAGE Consortium, McCarthy MI, Holmes CC, Karpe F.
Diabetes Volume 63 (2014) p.3785-3797

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.
Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A.
Nucleic acids research Volume 42 (2014) p.D926-32

Variation in genomic landscape of clear cell renal cell carcinoma across Europe.
Scelo G, Riazalhosseini Y, Greger L, Letourneau L, Gonzàlez-Porta M, Wozniak MB, Bourgey M, Harnden P, Egevad L, Jackson SM, Karimzadeh M, Arseneault M, Lepage P, How-Kit A, Daunay A, Renault V, Blanché H, Tubacher E, Sehmoun J, Viksna J, Celms E, Opmanis M, Zarins A, Vasudev NS, Seywright M, Abedi-Ardekani B, Carreira C, Selby PJ, Cartledge JJ, Byrnes G, Zavadil J, Su J, Holcatova I, Brisuda A, Zaridze D, Moukeria A, Foretova L, Navratilova M, Mates D, Jinga V, Artemov A, Nedoluzhko A, Mazur A, Rastorguev S, Boulygina E, Heath S, Gut M, Bihoreau MT, Lechner D, Foglio M, Gut IG, Skryabin K, Prokhortchouk E, Cambon-Thomsen A, Rung J, Bourque G, Brennan P, Tost J, Banks RE, Brazma A, Lathrop GM.
Nature communications Volume 5 (2014) p.5135

Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress.
Marguerat S, Lawler K, Brazma A, Bähler J.
RNA biology Volume 11 (2014) p.702-714

Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants.
Greger L, Su J, Rung J, Ferreira PG, Geuvadis consortium, Lappalainen T, Dermitzakis ET, Brazma A.
PloS one Volume 9 (2014) p.e104567

RNA-Seq gene profiling--a systematic empirical comparison.
Fonseca NA, Marioni J, Brazma A.
PloS one Volume 9 (2014) p.e107026

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 research Volume 41 (2013) p.D987-90

Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing.
Majewski IJ, Mittempergher L, Davidson NM, Bosma A, Willems SM, Horlings HM, de Rink I, Greger L, Hooijer GK, Peters D, Nederlof PM, Hofland I, de Jong J, Wesseling J, Kluin RJ, Brugman W, Kerkhoven R, Nieboer F, Roepman P, Broeks A, Muley TR, Jassem J, Niklinski J, van Zandwijk N, Brazma A, Oshlack A, van den Heuvel M, Bernards R.
The Journal of pathology Volume 230 (2013) p.270-276

HSM - a hybrid system based approach for modelling intracellular networks.
Brazma A, Cerans K, Ruklisa D, Schlitt T, Viksna J.
Gene Volume 518 (2013) p.70-77

Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum.
Lawler K, Hammond-Kosack K, Brazma A, Coulson RM.
BMC systems biology Volume 7 (2013) p.52

Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.
Stefflova K, Thybert D, Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC, Flicek P, Odom DT.
Cell Volume 154 (2013) p.530-540

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.
't Hoen PA, Friedländer MR, Almlöf J, Sammeth M, Pulyakhina I, Anvar SY, Laros JF, Buermans HP, Karlberg O, Brännvall M, GEUVADIS Consortium, den Dunnen JT, van Ommen GJ, Gut IG, Guigó R, Estivill X, Syvänen AC, Dermitzakis ET, Lappalainen T.
Nature biotechnology Volume 31 (2013) p.1015-1022

A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.
Lahti L, Torrente A, Elo LL, Brazma A, Rung J.
Nucleic acids research Volume 41 (2013) p.e110

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.
Gonzàlez-Porta M, Frankish A, Rung J, Harrow J, Brazma A.
Genome biology Volume 14 (2013) p.R70

Reuse of public genome-wide gene expression data.
Rung J, Brazma A.
Nature reviews. Genetics Volume 14 (2013) p.89-99

Transcriptome and genome sequencing uncovers functional variation in humans.
Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM, Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET.
Nature Volume 501 (2013) p.506-511

2012

Tools for mapping high-throughput sequencing data.
Fonseca NA, Rung J, Brazma A, Marioni JC.
Bioinformatics (Oxford, England) Volume 28 (2012) p.3169-3177

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 research Volume 40 (2012) p.D64-70

An integrated encyclopedia of DNA elements in the human genome.
ENCODE Project Consortium.
Nature Volume 489 (2012) p.57-74

Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma.
Caldas J, Gehlenborg N, Kettunen E, Faisal A, Rönty M, Nicholson AG, Knuutila S, Brazma A, Kaski S.
Bioinformatics (Oxford, England) Volume 28 (2012) p.246-253

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.
Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E, Flicek P, Brazma A, Odom DT, Marioni JC.
Genome research Volume 22 (2012) p.2376-2384

Gene Expression Atlas update--a 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, Kurnosov P, Malone J, Melnichuk O, Petryszak R, Pultsin N, Rustici G, Tikhonov A, Travillian RS, Williams E, Zorin A, Parkinson H, Brazma A.
Nucleic acids research Volume 40 (2012) p.D1077-81

MageComet--web application for harmonizing existing large-scale experiment descriptions.
Xue V, Burdett T, Lukk M, Taylor J, Brazma A, Parkinson H.
Bioinformatics (Oxford, England) Volume 28 (2012) p.1402-1403

2011

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 MI, Brazma A, Krestyaninova M.
Bioinformatics (Oxford, England) Volume 27 (2011) p.589-591

A user's guide to the encyclopedia of DNA elements (ENCODE).
ENCODE Project Consortium.
PLoS biology Volume 9 (2011) p.e1001046

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 genetics Volume 7 (2011) p.e1002270

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 research Volume 39 (2011) p.D1002-4

A pipeline for RNA-seq data processing and quality assessment.
Goncalves A, Tikhonov A, Brazma A, Kapushesky M.
Bioinformatics (Oxford, England) Volume 27 (2011) p.867-869

Contributions of the EMERALD project to assessing and improving microarray data quality.
Beisvåg V, Kauffmann A, Malone J, Foy C, Salit M, Schimmel H, Bongcam-Rudloff E, Landegren U, Parkinson H, Huber W, Brazma A, Sandvik AK, Kuiper M.
BioTechniques Volume 50 (2011) p.27-31

Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes.
Kutter C, Brown GD, Gonçalves A, Wilson MD, Watt S, Brazma A, White RJ, Odom DT.
Nature genetics Volume 43 (2011) p.948-955

2010

Large scale comparison of global gene expression patterns in human and mouse.
Zheng-Bradley X, Rung J, Parkinson H, Brazma A.
Genome biology Volume 11 (2010) p.R124

A global map of human gene expression.
Lukk M, Kapushesky M, Nikkilä J, Parkinson H, Goncalves A, Huber W, Ukkonen E, Brazma A.
Nature biotechnology Volume 28 (2010) p.322-324

International network of cancer genome projects.
International Cancer Genome Consortium, Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabé RR, Bhan MK, Calvo F, Eerola I, Gerhard DS, Guttmacher A, Guyer M, Hemsley FM, Jennings JL, Kerr D, Klatt P, Kolar P, Kusada J, Lane DP, Laplace F, Youyong L, Nettekoven G, Ozenberger B, Peterson J, Rao TS, Remacle J, Schafer AJ, Shibata T, Stratton MR, Vockley JG, Watanabe K, Yang H, Yuen MM, Knoppers BM, Bobrow M, Cambon-Thomsen A, Dressler LG, Dyke SO, Joly Y, Kato K, Kennedy KL, Nicolás P, Parker MJ, Rial-Sebbag E, Romeo-Casabona CM, Shaw KM, Wallace S, Wiesner GL, Zeps N, Lichter P, Biankin AV, Chabannon C, Chin L, Clément B, de Alava E, Degos F, Ferguson ML, Geary P, Hayes DN, Hudson TJ, Johns AL, Kasprzyk A, Nakagawa H, Penny R, Piris MA, Sarin R, Scarpa A, Shibata T, van de Vijver M, Futreal PA, Aburatani H, Bayés M, Botwell DD, Campbell PJ, Estivill X, Gerhard DS, Grimmond SM, Gut I, Hirst M, López-Otín C, Majumder P, Marra M, McPherson JD, Nakagawa H, Ning Z, Puente XS, Ruan Y, Shibata T, Stratton MR, Stunnenberg HG, Swerdlow H, Velculescu VE, Wilson RK, Xue HH, Yang L, Spellman PT, Bader GD, Boutros PC, Campbell PJ, Flicek P, Getz G, Guigó R, Guo G, Haussler D, Heath S, Hubbard TJ, Jiang T, Jones SM, Li Q, López-Bigas N, Luo R, Muthuswamy L, Ouellette BF, Pearson JV, Puente XS, Quesada V, Raphael BJ, Sander C, Shibata T, Speed TP, Stein LD, Stuart JM, Teague JW, Totoki Y, Tsunoda T, Valencia A, Wheeler DA, Wu H, Zhao S, Zhou G, Stein LD, Guigó R, Hubbard TJ, Joly Y, Jones SM, Kasprzyk A, Lathrop M, López-Bigas N, Ouellette BF, Spellman PT, Teague JW, Thomas G, Valencia A, Yoshida T, Kennedy KL, Axton M, Dyke SO, Futreal PA, Gerhard DS, Gunter C, Guyer M, Hudson TJ, McPherson JD, Miller LJ, Ozenberger B, Shaw KM, Kasprzyk A, Stein LD, Zhang J, Haider SA, Wang J, Yung CK, Cros A, Cross A, Liang Y, Gnaneshan S, Guberman J, Hsu J, Bobrow M, Chalmers DR, Hasel KW, Joly Y, Kaan TS, Kennedy KL, Knoppers BM, Lowrance WW, Masui T, Nicolás P, Rial-Sebbag E, Rodriguez LL, Vergely C, Yoshida T, Grimmond SM, Biankin AV, Bowtell DD, Cloonan N, deFazio A, Eshleman JR, Etemadmoghadam D, Gardiner BB, Gardiner BA, Kench JG, Scarpa A, Sutherland RL, Tempero MA, Waddell NJ, Wilson PJ, McPherson JD, Gallinger S, Tsao MS, Shaw PA, Petersen GM, Mukhopadhyay D, Chin L, DePinho RA, Thayer S, Muthuswamy L, Shazand K, Beck T, Sam M, Timms L, Ballin V, Lu Y, Ji J, Zhang X, Chen F, Hu X, Zhou G, Yang Q, Tian G, Zhang L, Xing X, Li X, Zhu Z, Yu Y, Yu J, Yang H, Lathrop M, Tost J, Brennan P, Holcatova I, Zaridze D, Brazma A, Egevard L, Prokhortchouk E, Banks RE, Uhlén M, Cambon-Thomsen A, Viksna J, Ponten F, Skryabin K, Stratton MR, Futreal PA, Birney E, Borg A, Børresen-Dale AL, Caldas C, Foekens JA, Martin S, Reis-Filho JS, Richardson AL, Sotiriou C, Stunnenberg HG, Thoms G, van de Vijver M, van't Veer L, Calvo F, Birnbaum D, Blanche H, Boucher P, Boyault S, Chabannon C, Gut I, Masson-Jacquemier JD, Lathrop M, Pauporté I, Pivot X, Vincent-Salomon A, Tabone E, Theillet C, Thomas G, Tost J, Treilleux I, Calvo F, Bioulac-Sage P, Clément B, Decaens T, Degos F, Franco D, Gut I, Gut M, Heath S, Lathrop M, Samuel D, Thomas G, Zucman-Rossi J, Lichter P, Eils R, Brors B, Korbel JO, Korshunov A, Landgraf P, Lehrach H, Pfister S, Radlwimmer B, Reifenberger G, Taylor MD, von Kalle C, Majumder PP, Sarin R, Rao TS, Bhan MK, Scarpa A, Pederzoli P, Lawlor RA, Delledonne M, Bardelli A, Biankin AV, Grimmond SM, Gress T, Klimstra D, Zamboni G, Shibata T, Nakamura Y, Nakagawa H, Kusada J, Tsunoda T, Miyano S, Aburatani H, Kato K, Fujimoto A, Yoshida T, Campo E, López-Otín C, Estivill X, Guigó R, de Sanjosé S, Piris MA, Montserrat E, González-Díaz M, Puente XS, Jares P, Valencia A, Himmelbauer H, Himmelbaue H, Quesada V, Bea S, Stratton MR, Futreal PA, Campbell PJ, Vincent-Salomon A, Richardson AL, Reis-Filho JS, van de Vijver M, Thomas G, Masson-Jacquemier JD, Aparicio S, Borg A, Børresen-Dale AL, Caldas C, Foekens JA, Stunnenberg HG, van't Veer L, Easton DF, Spellman PT, Martin S, Barker AD, Chin L, Collins FS, Compton CC, Ferguson ML, Gerhard DS, Getz G, Gunter C, Guttmacher A, Guyer M, Hayes DN, Lander ES, Ozenberger B, Penny R, Peterson J, Sander C, Shaw KM, Speed TP, Spellman PT, Vockley JG, Wheeler DA, Wilson RK, Hudson TJ, Chin L, Knoppers BM, Lander ES, Lichter P, Stein LD, Stratton MR, Anderson W, Barker AD, Bell C, Bobrow M, Burke W, Collins FS, Compton CC, DePinho RA, Easton DF, Futreal PA, Gerhard DS, Green AR, Guyer M, Hamilton SR, Hubbard TJ, Kallioniemi OP, Kennedy KL, Ley TJ, Liu ET, Lu Y, Majumder P, Marra M, Ozenberger B, Peterson J, Schafer AJ, Spellman PT, Stunnenberg HG, Wainwright BJ, Wilson RK, Yang H.
Nature Volume 464 (2010) p.993-998

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, Brazma A.
Nucleic acids research Volume 38 (2010) p.D690-8

The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays.
Vainshtein Y, Sanchez M, Brazma A, Hentze MW, Dandekar T, Muckenthaler MU.
BMC bioinformatics Volume 11 (2010) p.112

A CD8+ T cell transcription signature predicts prognosis in autoimmune disease.
McKinney EF, Lyons PA, Carr EJ, Hollis JL, Jayne DR, Willcocks LC, Koukoulaki M, Brazma A, Jovanovic V, Kemeny DM, Pollard AJ, Macary PA, Chaudhry AN, Smith KG.
Nature medicine Volume 16 (2010) p.586-91, 1p following 591

Annotare--a tool for annotating high-throughput biomedical investigations and resulting data.
Shankar R, Parkinson H, Burdett T, Hastings E, Liu J, Miller M, Srinivasa R, White J, Brazma A, Sherlock G, Stoeckert CJ, Ball CA.
Bioinformatics (Oxford, England) Volume 26 (2010) p.2470-2471

Modeling sample variables with an Experimental Factor Ontology.
Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H.
Bioinformatics (Oxford, England) Volume 26 (2010) p.1112-1118

Use of genome-wide expression data to mine the "Gray Zone" of GWA studies leads to novel candidate obesity genes.
Naukkarinen J, Surakka I, Pietiläinen KH, Rissanen A, Salomaa V, Ripatti S, Yki-Järvinen H, van Duijn CM, Wichmann HE, Kaprio J, Taskinen MR, Peltonen L, ENGAGE Consortium.
PLoS genetics Volume 6 (2010) p.e1000976

2009

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 research Volume 37 (2009) p.D868-72

Probabilistic retrieval and visualization of biologically relevant microarray experiments.
Caldas J, Gehlenborg N, Faisal A, Brazma A, Kaski S.
Bioinformatics (Oxford, England) Volume 25 (2009) p.i145-53

Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges.
Brazma A.
TheScientificWorldJournal Volume 9 (2009) p.420-423

Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008).
Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, Goldbeter A, Hace N, Henney A, Hood L, Iyengar R, Jackson V, Kallioniemi O, Klingmüller U, Kolar P, Kolch W, Kyriakopoulou C, Laplace F, Lehrach H, Marcus F, Matrisian L, Nolan G, Pelkmans L, Potti A, Sander C, Seljak M, Singer D, Sorger P, Stunnenberg H, Superti-Furga G, Uhlen M, Vidal M, Weinstein J, Wigle D, Williams M, Wolkenhauer O, Zhivotovsky B, Zinovyev A, Zupan B.
Molecular oncology Volume 3 (2009) p.9-17

Importing ArrayExpress datasets into R/Bioconductor.
Kauffmann A, Rayner TF, Parkinson H, Kapushesky M, Lukk M, Brazma A, Huber W.
Bioinformatics (Oxford, England) Volume 25 (2009) p.2092-2094

Importing ArrayExpress datasets into R/Bioconductor.
Kauffmann A, Rayner TF, Parkinson H, Kapushesky M, Lukk M, Brazma A, Huber W.
Bioinformatics (Oxford, England) Volume 25 (2009) p.2092-2094

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 (Oxford, England) Volume 25 (2009) p.2768-2769

Integrating sequence, evolution and functional genomics in regulatory genomics.
Vingron M, Brazma A, Coulson R, van Helden J, Manke T, Palin K, Sand O, Ukkonen E.
Genome biology Volume 10 (2009) p.202

The fission yeast homeodomain protein Yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback.
Aligianni S, Lackner DH, Klier S, Rustici G, Wilhelm BT, Marguerat S, Codlin S, Brazma A, de Bruin RA, Bähler J.
PLoS genetics Volume 5 (2009) p.e1000626

2008

The BREW workshop series: a stimulating experience in PhD education.
Giegerich R, Brazma A, Jonassen I, Ukkonen E, Vingron M.
Briefings in bioinformatics Volume 9 (2008) p.250-253

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).
Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F, Dauga D, Davidson DR, Gimenez G, Goo YA, Grimmond S, Henrich T, Herrmann BG, Johnson MH, Korb M, Mills JC, Oudes AJ, Parkinson HE, Pascal LE, Pollet N, Quackenbush J, Ramialison M, Ringwald M, Salgado D, Sansone SA, Sherlock G, Stoeckert CJ, Swedlow J, Taylor RC, Walashek L, Warford A, Wilkinson DG, Zhou Y, Zon LI, Liu AY, True LD.
Nature biotechnology Volume 26 (2008) p.305-312

Data storage and analysis in ArrayExpress and Expression Profiler.
Rustici G, Kapushesky M, Kolesnikov N, Parkinson H, Sarkans U, Brazma A.
Current protocols in bioinformatics Volume Chapter 7 (2008) p.Unit 7.13

The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".
Sansone SA, Rocca-Serra P, Brandizi M, Brazma A, Field D, Fostel J, Garrow AG, Gilbert J, Goodsaid F, Hardy N, Jones P, Lister A, Miller M, Morrison N, Rayner T, Sklyar N, Taylor C, Tong W, Warner G, Wiemann S, Members of the RSBI Working Group.
Omics : a journal of integrative biology Volume 12 (2008) p.143-149

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S.
Nature biotechnology Volume 26 (2008) p.889-896

4DXpress: a database for cross-species expression pattern comparisons.
Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T.
Nucleic acids research Volume 36 (2008) p.D847-53

2007

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

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, Laursen K, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A.
Nature biotechnology Volume 25 (2007) p.1127-1133

Prediction of gene expression in embryonic structures of Drosophila melanogaster.
Samsonova AA, Niranjan M, Russell S, Brazma A.
PLoS computational biology Volume 3 (2007) p.e144

Current approaches to gene regulatory network modelling.
Schlitt T, Brazma A.
BMC bioinformatics Volume 8 Suppl 6 (2007) p.S9

Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study.
Rustici G, van Bakel H, Lackner DH, Holstege FC, Wijmenga C, Bähler J, Brazma A.
Genome biology Volume 8 (2007) p.R73

2006

MGED standards: work in progress.
Ball CA, Brazma A.
Omics : a journal of integrative biology Volume 10 (2006) p.138-144

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, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A.
BMC bioinformatics Volume 7 (2006) p.489

Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).
Deutsch EW, Ball CA, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen J, Davidson D, Eichner LJ, Goo YA, Grimmond S, Henrich T, Johnson MH, Korb M, Mills JC, Oudes A, Parkinson HE, Pascal LE, Quackenbush J, Ramialison M, Ringwald M, Sansone SA, Sherlock G, Stoeckert CJ, Swedlow J, Taylor RC, Walashek L, Zhou Y, Liu AY, True LD.
Omics : a journal of integrative biology Volume 10 (2006) p.205-208

ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression.
Blake J, Schwager C, Kapushesky M, Brazma A.
Bioinformatics (Oxford, England) Volume 22 (2006) p.765-767

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.
Nature biotechnology Volume 24 (2006) p.21-2; author reply 23

Modelling in molecular biology: describing transcription regulatory networks at different scales.
Schlitt T, Brazma A.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 361 (2006) p.483-494

Data storage and analysis in ArrayExpress.
Brazma A, Kapushesky M, Parkinson H, Sarkans U, Shojatalab M.
Methods in enzymology Volume 411 (2006) p.370-386

ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression.
Blake J, Schwager C, Kapushesky M, Brazma A.
Bioinformatics (Oxford, England) Volume 22 (2006) p.765-767

Top-down standards will not serve systems biology.
Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N.
Nature Volume 440 (2006) p.24

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.
Nature biotechnology Volume 24 (2006) p.21-2; author reply 23

Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).
Deutsch EW, Ball CA, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen J, Davidson D, Eichner LJ, Goo YA, Grimmond S, Henrich T, Johnson MH, Korb M, Mills JC, Oudes A, Parkinson HE, Pascal LE, Quackenbush J, Ramialison M, Ringwald M, Sansone SA, Sherlock G, Stoeckert CJ, Swedlow J, Taylor RC, Walashek L, Zhou Y, Liu AY, True LD.
Omics : a journal of integrative biology Volume 10 (2006) p.205-208

ArrayExpress service for reviewers/editors of DNA microarray papers.
Brazma A, Parkinson H, ArrayExpress team, EMBL-EBI.
Nature biotechnology Volume 24 (2006) p.1321-1322

Standards for systems biology.
Brazma A, Krestyaninova M, Sarkans U.
Nature reviews. Genetics Volume 7 (2006) p.593-605

2005

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 physiology Volume 139 (2005) p.632-636

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.
Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, Huber W.
Bioinformatics (Oxford, England) Volume 21 (2005) p.3439-3440

A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings.
Torrente A, Kapushesky M, Brazma A.
Bioinformatics (Oxford, England) Volume 21 (2005) p.3993-3999

Fusing microarray experiments with multivariate regression.
Gilks WR, Tom BD, Brazma A.
Bioinformatics (Oxford, England) Volume 21 Suppl 2 (2005) p.ii137-43

Modelling gene networks at different organisational levels.
Schlitt T, Brazma A.
FEBS letters Volume 579 (2005) p.1859-1866

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 (Oxford, England) Volume 21 (2005) p.1495-1501

Reconstruction of gene regulatory networks under the finite state linear model.
Ruklisa D, Brazma A, Viksna J.
Genome informatics. International Conference on Genome Informatics Volume 16 (2005) p.225-236

2004

Funding high-throughput data sharing.
Ball CA, Sherlock G, Brazma A.
Nature biotechnology Volume 22 (2004) p.1179-1183

Submission of microarray data to public repositories.
Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N.
PLoS biology Volume 2 (2004) p.E317

An open letter on microarray data from the MGED Society.
Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Icahn C, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N, Microarray Gene Expression Data (MGED) Society.
Microbiology (Reading, England) Volume 150 (2004) p.3522-3524

Periodic gene expression program of the fission yeast cell cycle.
Rustici G, Mata J, Kivinen K, Lió P, Penkett CJ, Burns G, Hayles J, Brazma A, Nurse P, Bähler J.
Nature genetics Volume 36 (2004) p.809-817

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.
Nature biotechnology Volume 22 (2004) p.177-183

Standards for microarray data: an open letter.
Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N, MGED Society.
Environmental health perspectives Volume 112 (2004) p.A666-7

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 research Volume 32 (2004) p.W465-70

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, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Sansone SA.
Comptes rendus biologies Volume 326 (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 GG, Oezcimen A, Rocca-Serra P, Sansone SA.
Nucleic acids research Volume 31 (2003) p.68-71

From gene networks to gene function.
Schlitt T, Palin K, Rung J, Dietmann S, Lappe M, Ukkonen E, Brazma A.
Genome research Volume 13 (2003) p.2568-2576

Towards reconstruction of gene networks from expression data by supervised learning.
Soinov LA, Krestyaninova MA, Brazma A.
Genome biology Volume 4 (2003) p.R6

[Standardization of microarray experiment data].
Brazma A, Ikeo K, Tateno Y.
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme Volume 48 (2003) p.280-285

The European Bioinformatics Institute's data resources.
Brooksbank C, Camon E, Harris MA, Magrane M, Martin MJ, Mulder N, O'Donovan C, Parkinson H, Tuli MA, Apweiler R, Birney E, Brazma A, Henrick K, Lopez R, Stoesser G, Stoehr P, Cameron G.
Nucleic acids research Volume 31 (2003) p.43-50

Global transcriptional responses of fission yeast to environmental stress.
Chen D, Toone WM, Mata J, Lyne R, Burns G, Kivinen K, Brazma A, Jones N, Bähler J.
Molecular biology of the cell Volume 14 (2003) p.214-229

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, Brazma A.
Genome biology Volume 3 (2002) p.RESEARCH0046

Standards for microarray data.
Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, Brazma A, Quackenbush J, Microarray Gene Expression Data (MGED) Society.
Science (New York, N.Y.) Volume 298 (2002) p.539

Correlating gene promoters and expression in gene disruption experiments.
Palin K, Ukkonen E, Brazma A, Vilo J.
Bioinformatics (Oxford, England) Volume 18 Suppl 2 (2002) p.S172-80

Microarray data representation, annotation and storage.
Brazma A, Sarkans U, Robinson A, Vilo J, Vingron M, Hoheisel J, Fellenberg K.
Advances in biochemical engineering/biotechnology Volume 77 (2002) p.113-139

Protein interaction verification and functional annotation by integrated analysis of genome-scale data.
Kemmeren P, van Berkum NL, Vilo J, Bijma T, Donders R, Brazma A, Holstege FC.
Molecular cell Volume 9 (2002) p.1133-1143

Learning about gene regulatory networks from gene deletion experiments.
Schlitt T, Brazma A.
Comparative and functional genomics Volume 3 (2002) p.499-503

The underlying principles of scientific publication.
Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, Brazma A, Quackenbush J, Microarray Gene Expression Data.
Bioinformatics (Oxford, England) Volume 18 (2002) p.1409

1991

Inductive synthesis of dot expressions
Brāzma A.
Lecture notes in computer science Volume 502 (1991) p.156-212