Publications

Publications

2018

The PRIDE database and related tools and resources in 2019: improving support for quantification data.
Perez-Riverol Y, Csordas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu DJ, Inuganti A, Griss J, Mayer G, Eisenacher M, Pérez E, Uszkoreit J, Pfeuffer J, Sachsenberg T, Yilmaz S, Tiwary S, Cox J, Audain E, Walzer M, Jarnuczak AF, Ternent T, Brazma A, Vizcaíno JA. Nucleic acids research (2018) DOI: 10.1093/nar/gky1106
A call for public archives for biological image data.
Ellenberg J, Swedlow JR, Barlow M, Cook CE, Sarkans U, Patwardhan A, Brazma A, Birney E. Nature methods Volume 15 (2018) p.849-854 DOI: 10.1038/s41592-018-0195-8
Publisher Correction: Image Data Resource: a bioimage data integration and publication platform.
Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Carazo Salas RE, Swedlow JR. Nature methods Volume 15 (2018) p.984 DOI: 10.1038/s41592-018-0169-x
ArrayExpress update - from bulk to single-cell expression data.
Athar A, Füllgrabe A, George N, Iqbal H, Huerta L, Ali A, Snow C, Fonseca NA, Petryszak R, Papatheodorou I, Sarkans U, Brazma A. Nucleic acids research (2018) DOI: 10.1093/nar/gky964
An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures.
Collord G, Tarpey P, Kurbatova N, Martincorena I, Moran S, Castro M, Nagy T, Bignell G, Maura F, Young MD, Berna J, Tubio JMC, McMurran CE, Young AMH, Sanders M, Noorani I, Price SJ, Watts C, Leipnitz E, Kirsch M, Schackert G, Pearson D, Devadass A, Ram Z, Collins VP, Allinson K, Jenkinson MD, Zakaria R, Syed K, Hanemann CO, Dunn J, McDermott MW, Kirollos RW, Vassiliou GS, Esteller M, Behjati S, Brazma A, Santarius T, McDermott U. Scientific reports Volume 8 (2018) p.13537 DOI: 10.1038/s41598-018-31659-0
Aberration hubs in protein interaction networks highlight actionable targets in cancer.
Karimzadeh M, Jandaghi P, Papadakis AI, Trainor S, Rung J, Gonzàlez-Porta M, Scelo G, Vasudev NS, Brazma A, Huang S, Banks RE, Lathrop M, Najafabadi HS, Riazalhosseini Y. Oncotarget Volume 9 (2018) p.25166-25180 DOI: 10.18632/oncotarget.25382
A General Framework for Interrogation of mRNA Stability Programs Identifies RNA-Binding Proteins that Govern Cancer Transcriptomes.
Perron G, Jandaghi P, Solanki S, Safisamghabadi M, Storoz C, Karimzadeh M, Papadakis AI, Arseneault M, Scelo G, Banks RE, Tost J, Lathrop M, Tanguay S, Brazma A, Huang S, Brimo F, Najafabadi HS, Riazalhosseini Y. Cell reports Volume 23 (2018) p.1639-1650 DOI: 10.1016/j.celrep.2018.04.031
Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.
Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin AA, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Nachtweide S, Quail MA, Sisu C, Stanke M, Stefflova K, Van Oosterhout C, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams DJ, Brazma A, Gerstein M, Paten B, Pham S, Keane TM, Odom DT, Flicek P. Genome research Volume 28 (2018) p.448-459 DOI: 10.1101/gr.234096.117
Expression Atlas: gene and protein expression across multiple studies and organisms.
Papatheodorou I, Fonseca NA, Keays M, Tang YA, Barrera E, Bazant W, Burke M, Füllgrabe A, Fuentes AM, George N, Huerta L, Koskinen S, Mohammed S, Geniza M, Preece J, Jaiswal P, Jarnuczak AF, Huber W, Stegle O, Vizcaino JA, Brazma A, Petryszak R. Nucleic acids research Volume 46 (2018) p.D246-D251 DOI: 10.1093/nar/gkx1158
The BioStudies database-one stop shop for all data supporting a life sciences study.
Sarkans U, Gostev M, Athar A, Behrangi E, Melnichuk O, Ali A, Minguet J, Rada JC, Snow C, Tikhonov A, Brazma A, McEntyre J. Nucleic acids research Volume 46 (2018) p.D1266-D1270 DOI: 10.1093/nar/gkx965
Evaluation of Protein-Ligand Docking by Cyscore.
Cao Y, Dai W, Miao Z. Methods in molecular biology (Clifton, N.J.) Volume 1762 (2018) p.233-243 DOI: 10.1007/978-1-4939-7756-7_12

2017

clustComp, a bioconductor package for the comparison of clustering results.
Torrente A, Brazma A. Bioinformatics (Oxford, England) Volume 33 (2017) p.4001-4003 DOI: 10.1093/bioinformatics/btx532
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Assessing the Gene Regulatory Landscape in 1,188 Human Tumors
Calabrese C, Lehmann K, Urban L, Liu F, Erkek S, Fonseca N, Kahles A, Kilpinen-Barrett LH, Markowski J, Waszak S, Korbel J, Zhang Z, Brazma A, Raetsch G, Schwarz R, Stegle O, PCAWG-3. Preprint DOI: 10.1101/225441
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Germline determinants of the somatic mutation landscape in 2,642 cancer genomes
Waszak SM, Tiao G, Zhu B, Rausch T, Muyas F, Rodriguez-Martin B, Rabionet R, Yakneen S, Escaramis G, Li Y, Saini N, Roberts SA, Demidov GM, Pitkanen E, Delaneau O, Heredia-Genestar JM, Weischenfeldt J, Shringarpure SS, Chen J, Nakagawa H, Alexandrov LB, Drechsel O, Dursi LJ, Segre AV, Garrison E, Erkek S, Habermann N, Urban L, Khurana E, Cafferkey A, Hayashi S, Imoto S, Aaltonen LA, Alvarez EG, Baez-Ortega A, Bailey M, Bosio M, Bruzos AL, Buchhalter I, Bustamante CD, Calabrese C, DiBiase A, Gerstein M, Holik AZ, Hua X, Huang K, Letunic I, Klimczak LJ, Koster R, Kumar S, McLellan M, Mashl J, Mirabello L, Newhouse S, Prasad A, Raetsch G, Schlesner M, Schwarz R, Sharma P, Shmaya T, Sidiropoulos N, Song L, Susak H, Tanskanen T, Tojo M, Wedge DC, Wright M, Wu Y, Ye K, Yellapantula VD, Zamora J, Butte AJ, Getz G, Simpson J, Ding L, Marques-Bonet T, Navarro A, Brazma A, Campbell P, Chanock SJ, Chatterjee N, Stegle O, Siebert R, Ossowski S, Harismendy O, Gordenin DA, Tubio JMC, De La Vega FM, Easton DF, Estivill X, Korbel J, PCAWG Germline Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Net. Preprint DOI: 10.1101/208330
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Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types
PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Fonseca NA, He Y, Kahles A, Lehmann K, Liu F, Shiraishi Y, Soulette CM, Urban L, Demircioğlu D, Greger L, Li S, Liu D, Perry MD, Xiang L, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, PCAWG Transcriptome Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network. Preprint DOI: 10.1101/183889
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A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters
Demircioğlu D, Kindermans M, Nandi T, Cukuroglu E, Calabrese C, Fonseca NA, Kahles A, Lehmann K, Stegle O, Brazma A, Brooks A, Rätsch G, Tan P, Göke J, PCAWG Transcriptome Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network. Preprint DOI: 10.1101/176487
Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.
Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS. Cell reports Volume 20 (2017) p.2201-2214 DOI: 10.1016/j.celrep.2017.08.010
Impact of Alternative Splicing on the Human Proteome.
Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO. Cell reports Volume 20 (2017) p.1229-1241 DOI: 10.1016/j.celrep.2017.07.025
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Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin A, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Quail MA, Sisu C, Stanke M, Stefflova K, Van Oosterhout C, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams D, Brazma A, Gerstein M, Paten B, Pham S, Keane T, Odom DT, Flicek P. Preprint DOI: 10.1101/158659
The RNASeq-er API-a gateway to systematically updated analysis of public RNA-seq data.
Petryszak R, Fonseca NA, Füllgrabe A, Huerta L, Keays M, Tang YA, Brazma A. Bioinformatics (Oxford, England) Volume 33 (2017) p.2218-2220 DOI: 10.1093/bioinformatics/btx143
The Image Data Resource: A Bioimage Data Integration and Publication Platform.
Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Salas REC, Swedlow JR. Nature methods Volume 14 (2017) p.775-781 DOI: 10.1038/nmeth.4326
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Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer
Fonseca NA, He Y, Greger L, Brazma A, Zhang Z, - PCAWG-3. Preprint DOI: 10.1101/148684
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An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures
Collord G, Tarpey P, Kurbatova N, Martincorena I, Moran S, Castro M, Nagy T, Bignell G, Maura F, Berna J, Tubio JM, McMurran CE, Young AMH, Young MD, Noorani I, Price SJ, Watts C, Leipnitz E, Kirsch M, Schackert G, Pearson D, Devadass A, Ram Z, Collins VP, Allinson K, Jenkinson M, Zakaria R, Syed K, Hanemann CO, Dunn J, McDermott M, Kirollos R, Vassiliou GS, Esteller M, Behjati S, Brazma A, Santarius T, McDermott U. Preprint DOI: 10.1101/146811
Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma.
Arseneault M, Monlong J, Vasudev NS, Laskar RS, Safisamghabadi M, Harnden P, Egevad L, Nourbehesht N, Panichnantakul P, Holcatova I, Brisuda A, Janout V, Kollarova H, Foretova L, Navratilova M, Mates D, Jinga V, Zaridze D, Mukeria A, Jandaghi P, Brennan P, Brazma A, Tost J, Scelo G, Banks RE, Lathrop M, Bourque G, Riazalhosseini Y. Scientific reports Volume 7 (2017) p.44876 DOI: 10.1038/srep44876
Orchestrating differential data access for translational research: a pilot implementation.
Brandizi M, Melnichuk O, Bild R, Kohlmayer F, Rodriguez-Castro B, Spengler H, Kuhn KA, Kuchinke W, Ohmann C, Mustonen T, Linden M, Nyrönen T, Lappalainen I, Brazma A, Sarkans U. BMC medical informatics and decision making Volume 17 (2017) p.30 DOI: 10.1186/s12911-017-0424-6
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Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, Creighton C. Preprint DOI: 10.1101/099861

2016

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Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing.
Ferreira PG, Oti M, Barann M, Wieland T, Ezquina S, Friedländer MR, Rivas MA, Esteve-Codina A, GEUVADIS Consortium, Rosenstiel P, Strom TM, Lappalainen T, Guigó R, Sammeth M. Scientific reports Volume 6 (2016) p.32406 DOI: 10.1038/srep32406
Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression.
Torrente A, Lukk M, Xue V, Parkinson H, Rung J, Brazma A. PloS one Volume 11 (2016) p.e0157484 DOI: 10.1371/journal.pone.0157484
Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.
Wright JC, Mudge J, Weisser H, Barzine MP, Gonzalez JM, Brazma A, Choudhary JS, Harrow J. Nature communications Volume 7 (2016) p.11778 DOI: 10.1038/ncomms11778
Subtype-specific micro-RNA expression signatures in breast cancer progression.
Haakensen VD, Nygaard V, Greger L, Aure MR, Fromm B, Bukholm IR, Lüders T, Chin SF, Git A, Caldas C, Kristensen VN, Brazma A, Børresen-Dale AL, Hovig E, Helland Å. International journal of cancer Volume 139 (2016) p.1117-1128 DOI: 10.1002/ijc.30142
HMGB1 binds to the rs7903146 locus in TCF7L2 in human pancreatic islets.
Zhou Y, Oskolkov N, Shcherbina L, Ratti J, Kock KH, Su J, Martin B, Oskolkova MZ, Göransson O, Bacon J, Li W, Bucciarelli S, Cilio C, Brazma A, Thatcher B, Rung J, Wierup N, Renström E, Groop L, Hansson O. Molecular and cellular endocrinology Volume 430 (2016) p.138-145 DOI: 10.1016/j.mce.2016.01.027
Modelling-based experiment retrieval: a case study with gene expression clustering.
Blomstedt P, Dutta R, Seth S, Brazma A, Kaski S. Bioinformatics (Oxford, England) Volume 32 (2016) p.1388-1394 DOI: 10.1093/bioinformatics/btv762

2015

The BioStudies database.
McEntyre J, Sarkans U, Brazma A. Molecular systems biology Volume 11 (2015) p.847 DOI: 10.15252/msb.20156658
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 DOI: 10.1093/nar/gkv1045
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 DOI: 10.1186/s13395-015-0059-1
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 DOI: 10.1371/journal.pone.0137367
PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data.
Kurbatova N, Mason JC, Morgan H, Meehan TF, Karp NA. PloS one Volume 10 (2015) p.e0131274 DOI: 10.1371/journal.pone.0131274
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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 DOI: 10.1186/1471-2164-16-S8-S2
Applying the ARRIVE Guidelines to an In Vivo Database.
Karp NA, Meehan TF, Morgan H, Mason JC, Blake A, Kurbatova N, Smedley D, Jacobsen J, Mott RF, Iyer V, Matthews P, Melvin DG, Wells S, Flenniken AM, Masuya H, Wakana S, White JK, Lloyd KC, Reynolds CL, Paylor R, West DB, Svenson KL, Chesler EJ, de Angelis MH, Tocchini-Valentini GP, Sorg T, Herault Y, Parkinson H, Mallon AM, Brown SD. PLoS biology Volume 13 (2015) p.e1002151 DOI: 10.1371/journal.pbio.1002151
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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 DOI: 10.1126/science.1261877
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 DOI: 10.1093/bioinformatics/btv199

2014

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 DOI: 10.1093/nar/gku1057
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 DOI: 10.1038/ncomms6135
RNA-Seq gene profiling--a systematic empirical comparison.
Fonseca NA, Marioni J, Brazma A. PloS one Volume 9 (2014) p.e107026 DOI: 10.1371/journal.pone.0107026
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 DOI: 10.1371/journal.pone.0104567
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 DOI: 10.4161/rna.29196
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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 DOI: 10.2337/db14-0385

2013

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 DOI: 10.1093/nar/gkt1270
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 DOI: 10.1093/nar/gkt1081
The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.
Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, Blake A, Chen CK, Easty R, Di Fenza A, Fiegel T, Grifiths M, Horne A, Karp NA, Kurbatova N, Mason JC, Matthews P, Oakley DJ, Qazi A, Regnart J, Retha A, Santos LA, Sneddon DJ, Warren J, Westerberg H, Wilson RJ, Melvin DG, Smedley D, Brown SD, Flicek P, Skarnes WC, Mallon AM, Parkinson H. Nucleic acids research Volume 42 (2014) p.D802-9 DOI: 10.1093/nar/gkt977
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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 DOI: 10.1038/nature12531
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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 DOI: 10.1038/nbt.2702
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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 DOI: 10.1016/j.cell.2013.07.007
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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 DOI: 10.1002/path.4209
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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 DOI: 10.1186/gb-2013-14-7-r70
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 DOI: 10.1186/1752-0509-7-52
IsoCleft Finder - a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities.
Kurbatova N, Chartier M, Zylber MI, Najmanovich R. F1000Research Volume 2 (2013) p.117 DOI: 10.12688/f1000research.2-117.v2
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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 DOI: 10.1093/nar/gkt229

2012

Reuse of public genome-wide gene expression data.
Rung J, Brazma A. Nature reviews. Genetics Volume 14 (2013) p.89-99 DOI: 10.1038/nrg3394
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 DOI: 10.1016/j.gene.2012.11.084
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 DOI: 10.1093/nar/gks1174
Tools for mapping high-throughput sequencing data.
Fonseca NA, Rung J, Brazma A, Marioni JC. Bioinformatics (Oxford, England) Volume 28 (2012) p.3169-3177 DOI: 10.1093/bioinformatics/bts605
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An integrated encyclopedia of DNA elements in the human genome.
ENCODE Project Consortium. Nature Volume 489 (2012) p.57-74 DOI: 10.1038/nature11247
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 DOI: 10.1101/gr.142281.112
graph2tab, a library to convert experimental workflow graphs into tabular formats.
Brandizi M, Kurbatova N, Sarkans U, Rocca-Serra P. Bioinformatics (Oxford, England) Volume 28 (2012) p.1665-1667 DOI: 10.1093/bioinformatics/bts258
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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 DOI: 10.1093/bioinformatics/bts148
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Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs.
Roux J, Gonzàlez-Porta M, Robinson-Rechavi M. Nucleic acids research Volume 40 (2012) p.5890-5900 DOI: 10.1093/nar/gks279

2011

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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 DOI: 10.1093/bioinformatics/btr634
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 DOI: 10.1093/nar/gkr937
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 DOI: 10.1093/nar/gkr913
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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 DOI: 10.1371/journal.pgen.1002270
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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 DOI: 10.1038/ng.906
ontoCAT: an R package for ontology traversal and search.
Kurbatova N, Adamusiak T, Kurnosov P, Swertz MA, Kapushesky M. Bioinformatics (Oxford, England) Volume 27 (2011) p.2468-2470 DOI: 10.1093/bioinformatics/btr375
OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript.
Adamusiak T, Burdett T, Kurbatova N, Joeri van der Velde K, Abeygunawardena N, Antonakaki D, Kapushesky M, Parkinson H, Swertz MA. BMC bioinformatics Volume 12 (2011) p.218 DOI: 10.1186/1471-2105-12-218
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A user's guide to the encyclopedia of DNA elements (ENCODE).
ENCODE Project Consortium. PLoS biology Volume 9 (2011) p.e1001046 DOI: 10.1371/journal.pbio.1001046
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 DOI: 10.1093/bioinformatics/btr012
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Expression and Genetic Variation Databases for Cancer Research
Rung J, Brazma A. Cancer Systems Biology, Bioinformatics and Medicine: Research and Clinical Applications Springer Netherlands DOI: 10.1007/978-94-007-1567-7_5
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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 DOI: 10.2144/000113591

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 DOI: 10.1186/gb-2010-11-12-r124
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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 DOI: 10.1093/bioinformatics/btq693
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 DOI: 10.1093/nar/gkq1040
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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 DOI: 10.1093/bioinformatics/btq462
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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 DOI: 10.1371/journal.pgen.1000976
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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 DOI: 10.1038/nm.2130
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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 DOI: 10.1038/nbt0410-322
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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, 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, 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, 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 DOI: 10.1038/nature08987
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 DOI: 10.1093/bioinformatics/btq099
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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 DOI: 10.1186/1471-2105-11-112

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, Brazma A. Nucleic acids research Volume 38 (2010) p.D690-8 DOI: 10.1093/nar/gkp936
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Probabilistic retrieval and visualization of biologically relevant microarray experiments.
Caldas J, Gehlenborg N, Faisal A, Brazma A, Kaski S. BMC bioinformatics Volume 10 (2009) p.P1-P1 DOI: 10.1186/1471-2105-10-S13-P1
Visualization of large microarray experiments with space maps.
Gehlenborg N, Brazma A. BMC bioinformatics Volume 10 (2009) p.O7-O7 DOI: 10.1186/1471-2105-10-S13-O7
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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 DOI: 10.1371/journal.pgen.1000626
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 DOI: 10.1093/bioinformatics/btp420
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 DOI: 10.1093/bioinformatics/btp354
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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 DOI: 10.1093/bioinformatics/btp215
Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges.
Brazma A. TheScientificWorldJournal Volume 9 (2009) p.420-423 DOI: 10.1100/tsw.2009.57
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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 DOI: 10.1186/gb-2009-10-1-202

2008

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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 DOI: 10.1016/j.molonc.2008.11.003
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 DOI: 10.1093/nar/gkn889
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 DOI: 10.1002/0471250953.bi0713s23
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 DOI: 10.1038/nbt.1411
Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.
Najmanovich R, Kurbatova N, Thornton J. Bioinformatics (Oxford, England) Volume 24 (2008) p.i105-11 DOI: 10.1093/bioinformatics/btn263
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 DOI: 10.1089/omi.2008.0019
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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 DOI: 10.1038/nbt1391
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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 DOI: 10.1093/bib/bbn002
Proceedings of the 6th Asia-Pacific Bioinformatics Conference: Kyoto, Japan, 14-17 January 2008
Brazma A, Miyano S, Akutsu T. DOI: 10.1142/p544

2007

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 DOI: 10.1093/nar/gkm797
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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 DOI: 10.1038/nbt1347
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Current approaches to gene regulatory network modelling.
Schlitt T, Brazma A. BMC bioinformatics Volume 8 Suppl 6 (2007) p.S9 DOI: 10.1186/1471-2105-8-S6-S9
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 DOI: 10.1371/journal.pcbi.0030144
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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
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 DOI: 10.1186/gb-2007-8-5-r73

2006

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 research Volume 35 (2007) p.D747-50 DOI: 10.1093/nar/gkl995
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 DOI: 10.1186/1471-2105-7-489
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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 DOI: 10.1038/nbt1106-1321
Standards for systems biology.
Brazma A, Krestyaninova M, Sarkans U. Nature reviews. Genetics Volume 7 (2006) p.593-605 DOI: 10.1038/nrg1922
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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 DOI: 10.1038/440024a
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 DOI: 10.1098/rstb.2005.1806
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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 DOI: 10.1089/omi.2006.10.205
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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 DOI: 10.1038/nbt0106-21a
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MGED standards: work in progress.
Ball CA, Brazma A. Omics : a journal of integrative biology Volume 10 (2006) p.138-144 DOI: 10.1089/omi.2006.10.138
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 DOI: 10.1016/s0076-6879(06)11020-4

2005

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 DOI: 10.1093/bioinformatics/btk022
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 DOI: 10.1104/pp.105.063156
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Fusing microarray experiments with multivariate regression.
Gilks WR, Tom BD, Brazma A. Bioinformatics (Oxford, England) Volume 21 Suppl 2 (2005) p.ii137-43 DOI: 10.1093/bioinformatics/bti1123
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 DOI: 10.1093/bioinformatics/bti644
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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 DOI: 10.1093/bioinformatics/bti525
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Modelling gene networks at different organisational levels.
Schlitt T, Brazma A. FEBS letters Volume 579 (2005) p.1859-1866 DOI: 10.1016/j.febslet.2005.01.073
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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
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 research Volume 33 (2005) p.D553-5 DOI: 10.1093/nar/gki056

2004

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 DOI: 10.1093/bioinformatics/bti157
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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 DOI: 10.1099/mic.0.27637-0
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Funding high-throughput data sharing.
Ball CA, Sherlock G, Brazma A. Nature biotechnology Volume 22 (2004) p.1179-1183 DOI: 10.1038/nbt0904-1179
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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 DOI: 10.1371/journal.pbio.0020317
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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 DOI: 10.1289/ehp.112-1277123
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 DOI: 10.1093/nar/gkh470
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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 DOI: 10.1038/ng1377
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 DOI: 10.1038/nbt926
Report on the thirteenth international workshop on the identification and functional, evolutionary and expression analysis of transcribed sequences: comparative and functional genomics workshop.
Brazma A, Freeman T, Gardiner K, Weissman S, Werner T, Korn B. Cytogenetic and genome research Volume 105 (2004) p.11-17 DOI: 10.1159/000078003

2003

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 DOI: 10.1101/gr.1111403
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 DOI: 10.1016/j.crvi.2003.09.026
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[Standardization of microarray experiment data].
Brazma A, Ikeo K, Tateno Y. Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme Volume 48 (2003) p.280-285
Towards reconstruction of gene networks from expression data by supervised learning.
Soinov LA, Krestyaninova MA, Brazma A. Genome biology Volume 4 (2003) p.R6 DOI: 10.1186/gb-2003-4-1-r6
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 DOI: 10.1093/nar/gkg091
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 DOI: 10.1093/nar/gkg066
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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 DOI: 10.1091/mbc.E02-08-0499

2002

*
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 DOI: 10.1093/bioinformatics/18.11.1409
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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 DOI: 10.1126/science.298.5593.539b
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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 DOI: 10.1186/gb-2002-3-9-research0046
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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 DOI: 10.1016/s1097-2765(02)00531-2
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Chip technology
Hoheisel J, Brazma A, Büssow K, Cantor CR, Christians FC, Chui G, Diaz R, Drmanac R, Drmanac S, Eickhoff H, Fellenberg K, Hannenhalli S, Hoheisel J, Hou A, Hubbell E, Jin H, Jin P, Jurinke C, Konthur Z, Köster H, Kwon S, Lacy S, Lehrach H, Lipshutz R, Little D, Lueking A, McGall GH, Moeur B, Nordhoff E, Nyarsik L, Pevzner PA, Robinson A, Sarkans U, Shafto J, Sohail M, Southern EM, Swanson D, Ukrainczyk T, van den Boom D, Vilo J, Vingron M, Walter G, Xu C. DOI: 10.1007/3-540-45713-5
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Correlating gene promoters and expression in gene disruption experiments.
Palin K, Ukkonen E, Brazma A, Vilo J. Bioinformatics Volume 18 Suppl 2 (2002) p.S172-80 DOI: 10.1093/bioinformatics/18.suppl_2.s172
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
Learning about gene regulatory networks from gene deletion experiments.
Schlitt T, Brazma A. Comparative and functional genomics Volume 3 (2002) p.499-503 DOI: 10.1002/cfg.220
Building and analysing genome-wide gene disruption networks.
Rung J, Schlitt T, Brazma A, Freivalds K, Vilo J. Bioinformatics (Oxford, England) Volume 18 Suppl 2 (2002) p.S202-10 DOI: 10.1093/bioinformatics/18.suppl_2.s202

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. Nature genetics Volume 29 (2001) p.365-371 DOI: 10.1038/ng1201-365
Gene expression data analysis.
Brazma A, Vilo J. Microbes and infection Volume 3 (2001) p.823-829 DOI: 10.1016/s1286-4579(01)01440-x
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On the importance of standardisation in life sciences.
Brazma A. Bioinformatics (Oxford, England) Volume 17 (2001) p.113-114 DOI: 10.1093/bioinformatics/17.2.113

2000

Gene expression data analysis.
Brazma A, Vilo J. FEBS letters Volume 480 (2000) p.17-24 DOI: 10.1016/s0014-5793(00)01772-5
One-stop shop for microarray data.
Brazma A, Robinson A, Cameron G, Ashburner M. Nature Volume 403 (2000) p.699-700 DOI: 10.1038/35001676
Mining for putative regulatory elements in the yeast genome using gene expression data.
Vilo J, Brazma A, Jonassen I, Robinson A, Ukkonen E. Proceedings. International Conference on Intelligent Systems for Molecular Biology Volume 8 (2000) p.384-394

1998

Predicting gene regulatory elements in silico on a genomic scale.
Brazma A, Jonassen I, Vilo J, Ukkonen E. Genome research Volume 8 (1998) p.1202-1215 DOI: 10.1101/gr.8.11.1202
Pattern discovery in biosequences
Brāzma A, Jonassen I, Vilo J, Ukkonen E. Lecture notes in computer science Volume 1433 (1998) p.257-270 DOI: 10.1007/bfb0054081
Approaches to the automatic discovery of patterns in biosequences.
Brazma A, Jonassen I, Eidhammer I, Gilbert D. Journal of computational biology : a journal of computational molecular cell biology Volume 5 (1998) p.279-305 DOI: 10.1089/cmb.1998.5.279