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Nat Commun, 2023

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2023

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Nat Commun, 2022

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2022

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Nat Commun, 2022

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Canonical Wnt and TGF-β/BMP signaling enhance melanocyte regeneration and suppress invasiveness, migration, and proliferation of melanoma cells

Katkat E, Demirci Y, Heger G, Karagulle D, Papatheodorou I, Brazma A, Ozhan G.

2022

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Brain Regeneration Resembles Brain Cancer at Its Early Wound Healing Stage and Diverges From Cancer Later at Its Proliferation and Differentiation Stages.

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Front Cell Dev Biol, 2022

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The BioImage Archive - Building a Home for Life-Sciences Microscopy Data.

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J Mol Biol, 2022

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Nucleic Acids Res, 2022

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Nucleic Acids Res, 2022

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Single-Cell Analysis Reveals the Immune Characteristics of Myeloid Cells and Memory T Cells in Recovered COVID-19 Patients With Different Severities.

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Front Immunol, 2021

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The BioImage Archive - building a home for life-sciences microscopy data

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2021

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Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses.

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Sci Rep, 2021

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Nat Commun, 2021

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Nat Methods, 2021

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An integrated landscape of protein expression in human cancer.

Jarnuczak AF, Najgebauer H, Barzine M, Kundu DJ, Ghavidel F, Perez-Riverol Y, Papatheodorou I, Brazma A, Vizcaíno JA.

Sci Data, 2021

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User-friendly, scalable tools and workflows for single-cell RNA-seq analysis.

Moreno P, Huang N, Manning JR, Mohammed S, Solovyev A, Polanski K, Bacon W, Chazarra R, Talavera-López C, Doyle MA, Marnier G, Grüning B, Rasche H, George N, Fexova SK, Alibi M, Miao Z, Perez-Riverol Y, Haeussler M, Brazma A, Teichmann S, Meyer KB, Papatheodorou I.

Nat Methods, 2021

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Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.

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Nat Med, 2021

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Tumour gene expression signature in primary melanoma predicts long-term outcomes.

Garg M, Couturier DL, Nsengimana J, Fonseca NA, Wongchenko M, Yan Y, Lauss M, Jönsson GB, Newton-Bishop J, Parkinson C, Middleton MR, Bishop DT, McDonald S, Stefanos N, Tadross J, Vergara IA, Lo S, Newell F, Wilmott JS, Thompson JF, Long GV, Scolyer RA, Corrie P, Adams DJ, Brazma A, Rabbie R.

Nat Commun, 2021

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Meta-analysis reveals consistent immune response patterns in COVID-19 infected patients at single-cell resolution

Garg M, Li X, Moreno P, Papatheodorou I, Shu Y, Brazma A, Miao Z.

2021

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Transcriptomics data availability and reusability in the transition from microarray to next-generation sequencing

Rustici G, Williams E, Barzine M, Brazma A, Bumgarner R, Chierici M, Furlanello C, Greger L, Jurman G, Miller M, Ouellette BF, Quackenbush J, Reich M, Stoeckert CJ, Taylor RC, Trutane SC, Weller J, Wilhelm B, Winegarden N.

2021

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From ArrayExpress to BioStudies.

Sarkans U, Füllgrabe A, Ali A, Athar A, Behrangi E, Diaz N, Fexova S, George N, Iqbal H, Kurri S, Munoz J, Rada J, Papatheodorou I, Brazma A.

Nucleic Acids Res, 2021

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Urinary metabolic phenotyping for Alzheimer's disease.

Kurbatova N, Garg M, Whiley L, Chekmeneva E, Jiménez B, Gómez-Romero M, Pearce J, Kimhofer T, D'Hondt E, Soininen H, Kłoszewska I, Mecocci P, Tsolaki M, Vellas B, Aarsland D, Nevado-Holgado A, Liu B, Snowden S, Proitsi P, Ashton NJ, Hye A, Legido-Quigley C, Lewis MR, Nicholson JK, Holmes E, Brazma A, Lovestone S.

Sci Rep, 2020

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Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.

Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L, PCAWG Consortium.

Nat Commun, 2020

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Guidelines for reporting single-cell RNA-seq experiments.

Füllgrabe A, George N, Green M, Nejad P, Aronow B, Fexova SK, Fischer C, Freeberg MA, Huerta L, Morrison N, Scheuermann RH, Taylor D, Vasilevsky N, Clarke L, Gehlenborg N, Kent J, Marioni J, Teichmann S, Brazma A, Papatheodorou I.

Nat Biotechnol, 2020

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Transparency and reproducibility in artificial intelligence.

Haibe-Kains B, Adam GA, Hosny A, Khodakarami F, Massive Analysis Quality Control (MAQC) Society Board of Directors, Waldron L, Wang B, McIntosh C, Goldenberg A, Kundaje A, Greene CS, Broderick T, Hoffman MM, Leek JT, Korthauer K, Huber W, Brazma A, Pineau J, Tibshirani R, Hastie T, Ioannidis JPA, Quackenbush J, Aerts HJWL.

Nature, 2020

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Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.

Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L, PCAWG Consortium.

Nat Commun, 2020

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Using Deep Learning to Extrapolate Protein Expression Measurements.

Barzine MP, Freivalds K, Wright JC, Opmanis M, Rituma D, Ghavidel FZ, Jarnuczak AF, Celms E, Čerāns K, Jonassen I, Lace L, Vizcaíno JA, Choudhary JS, Brazma A, Viksna J.

Proteomics, 2020

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Sex differences in oncogenic mutational processes.

Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N, PCAWG Tumour Subtypes and Clinical Translation, Boutros PC, PCAWG Consortium.

Nat Commun, 2020

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Myocyte-Specific Upregulation of ACE2 in Cardiovascular Disease: Implications for SARS-CoV-2-Mediated Myocarditis.

Tucker NR, Chaffin M, Bedi KC, Papangeli I, Akkad AD, Arduini A, Hayat S, Eraslan G, Muus C, Bhattacharyya RP, Stegmann CM, Human Cell Atlas Lung Biological Network, Margulies KB, Ellinor PT, Human Cell Atlas Lung Biological Network Consortium Members.

Circulation, 2020

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Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci.

Cavadas B, Camacho R, Ferreira JC, Ferreira RM, Figueiredo C, Brazma A, Fonseca NA, Pereira L.

Microorganisms, 2020

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Putative cell type discovery from single-cell gene expression data.

Miao Z, Moreno P, Huang N, Papatheodorou I, Brazma A, Teichmann SA.

Nat Methods, 2020

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SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues.

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Cell, 2020

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Dysregulation at multiple points of the kynurenine pathway is a ubiquitous feature of renal cancer: implications for tumour immune evasion.

Hornigold N, Dunn KR, Craven RA, Zougman A, Trainor S, Shreeve R, Brown J, Sewell H, Shires M, Knowles M, Fukuwatari T, Maher ER, Burns J, Bhattarai S, Menon M, Brazma A, Scelo G, Feulner L, Riazalhosseini Y, Lathrop M, Harris A, Selby PJ, Banks RE, Vasudev NS.

Br J Cancer, 2020

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SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes.

Sungnak W, Huang N, Bécavin C, Berg M, Queen R, Litvinukova M, Talavera-López C, Maatz H, Reichart D, Sampaziotis F, Worlock KB, Yoshida M, Barnes JL, HCA Lung Biological Network.

Nat Med, 2020

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Tumour gene expression signature in primary melanoma predicts long-term outcomes: A prospective multicentre study

Garg M, Couturier D, Nsengimana J, Fonseca NA, Wongchenko M, Yan Y, Lauss M, Jönsson GB, Newton-Bishop J, Parkinson C, Middleton MR, Bishop T, Corrie P, Adams DJ, Brazma A, Rabbie R.

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Pan-cancer analysis of whole genomes.

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Nature, 2020

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Genomic basis for RNA alterations in cancer.

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Nature, 2020

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High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.

Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, Creighton CJ, PCAWG Consortium.

Nat Commun, 2020

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Expression Atlas update: from tissues to single cells.

Papatheodorou I, Moreno P, Manning J, Fuentes AM, George N, Fexova S, Fonseca NA, Füllgrabe A, Green M, Huang N, Huerta L, Iqbal H, Jianu M, Mohammed S, Zhao L, Jarnuczak AF, Jupp S, Marioni J, Meyer K, Petryszak R, Prada Medina CA, Talavera-López C, Teichmann S, Vizcaino JA, Brazma A.

Nucleic Acids Res, 2020

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Blood transcriptome profile induced by an efficacious vaccine formulated with salivary antigens from cattle ticks.

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NPJ Vaccines, 2019

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A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters.

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Cell, 2019

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An integrated landscape of protein expression in human cancer

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Dynamics of gene regulatory networks and their dependence on network topology and quantitative parameters - the case of phage λ.

Ruklisa D, Brazma A, Cerans K, Schlitt T, Viksna J.

BMC Bioinformatics, 2019

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The PRIDE database and related tools and resources in 2019: improving support for quantification data.

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ArrayExpress update - from bulk to single-cell expression data.

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Nucleic Acids Res, 2019

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A call for public archives for biological image data.

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Oncotarget, 2018

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A General Framework for Interrogation of mRNA Stability Programs Identifies RNA-Binding Proteins that Govern Cancer Transcriptomes.

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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 Res, 2018

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 Res, 2018

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 Res, 2018

doi:10.1093/nar/gkx965.

Germline determinants of the somatic mutation landscape in 2,642 cancer genomes

Waszak SM, Tiao G, Zhu B, Rausch T, Muyas F, Rodríguez-Martín B, Rabionet R, Yakneen S, Escaramis G, Li Y, Saini N, Roberts SA, Demidov GM, Pitkänen 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, Rätsch 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 JM, Vega FMDL, Easton DF, Estivill X, Korbel JO, on behalf of the PCAWG Germline Working group%, and the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network.

2017

doi:10.1101/208330.

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 H, Markowski J, Waszak S, Korbel J, Zhang Z, Brazma A, Rätsch G, Schwarz R, Stegle O, PCAWG Group 3.

2017

doi:10.1101/225441.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Thybert D, Roller M, Navarro FC, 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, Oosterhout CV, 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.

2017

doi:10.1101/158659.

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, 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.

2017

doi:10.1101/183889.

clustComp, a bioconductor package for the comparison of clustering results.

Torrente A, Brazma A.

Bioinformatics, 2017

doi:10.1093/bioinformatics/btx532.

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 Rep, 2017

doi:10.1016/j.celrep.2017.08.010.

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 AN, Rätsch G, Tan P, Göke J, on behalf of the PCAWG Transcriptome Working Group, and the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network.

2017

doi:10.1101/176487.

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.

Nat Methods, 2017

doi:10.1038/nmeth.4326.

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 CJ, on behalf of the PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network.

2017

doi:10.1101/099861.

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 Rep, 2017

doi:10.1016/j.celrep.2017.07.025.

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 AM, 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 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.

2017

doi:10.1101/146811.

Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer

Fonseca NA, He Y, Greger L, Brazma A, Zhang Z, PCAWG3.

2017

doi:10.1101/148684.

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, 2017

doi:10.1093/bioinformatics/btx143.

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.

Sci Rep, 2017

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 Med Inform Decis Mak, 2017

doi:10.1186/s12911-017-0424-6.

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.

Sci Rep, 2016

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, 2016

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.

Nat Commun, 2016

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.

Int J Cancer, 2016

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.

Mol Cell Endocrinol, 2016

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, 2016

doi:10.1093/bioinformatics/btv762.

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 Res, 2016

doi:10.1093/nar/gkv1045.

The BioStudies database.

McEntyre J, Sarkans U, Brazma A.

Mol Syst Biol, 2015

doi:10.15252/msb.20156658.

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.

Skelet Muscle, 2015

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, 2015

doi:10.1371/journal.pone.0137367.

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, 2015

doi:10.1186/1471-2164-16-s8-s2.

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, 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, 2015

doi:10.1126/science.1261877.

Cellular phenotype database: a repository for systems microscopy data.

Kirsanova C, Brazma A, Rustici G, Sarkans U.

Bioinformatics, 2015

doi:10.1093/bioinformatics/btv199.

ArrayExpress update--simplifying data submissions.

Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T, Megy K, Pilicheva E, Rustici G, Tikhonov A, Parkinson H, Petryszak R, Sarkans U, Brazma A.

Nucleic Acids Res, 2015

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.

Nat Commun, 2014

doi:10.1038/ncomms6135.

RNA-Seq gene profiling--a systematic empirical comparison.

Fonseca NA, Marioni J, Brazma A.

PLoS One, 2014

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, 2014

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 Biol, 2014

doi:10.4161/rna.29196.

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, 2014

doi:10.2337/db14-0385.

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 Res, 2014

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 Res, 2014

doi:10.1093/nar/gkt1081.

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.

Nat Biotechnol, 2013

doi:10.1038/nbt.2702.

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, 2013

doi:10.1038/nature12531.

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, 2013

doi:10.1016/j.cell.2013.07.007.

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 Biol, 2013

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 Syst Biol, 2013

doi:10.1186/1752-0509-7-52.

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.

J Pathol, 2013

doi:10.1002/path.4209.

A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.

Lahti L, Torrente A, Elo LL, Brazma A, Rung J.

Nucleic Acids Res, 2013

doi:10.1093/nar/gkt229.

Reuse of public genome-wide gene expression data.

Rung J, Brazma A.

Nat Rev Genet, 2013

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, 2013

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 Res, 2013

doi:10.1093/nar/gks1174.

Tools for mapping high-throughput sequencing data.

Fonseca NA, Rung J, Brazma A, Marioni JC.

Bioinformatics, 2012

doi:10.1093/bioinformatics/bts605.

An integrated encyclopedia of DNA elements in the human genome.

ENCODE Project Consortium.

Nature, 2012

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 Res, 2012

doi:10.1101/gr.142281.112.

MageComet--web application for harmonizing existing large-scale experiment descriptions.

Xue V, Burdett T, Lukk M, Taylor J, Brazma A, Parkinson H.

Bioinformatics, 2012

doi:10.1093/bioinformatics/bts148.

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, 2012

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 Res, 2012

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 Res, 2012

doi:10.1093/nar/gkr913.

Expression and Genetic Variation Databases for Cancer Research

Rung J, Brazma A.

2011

doi:10.1007/978-94-007-1567-7_5.

A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection.

Nicholson G, Rantalainen M, Li JV, Maher AD, Malmodin D, Ahmadi KR, Faber JH, Barrett A, Min JL, Rayner NW, Toft H, Krestyaninova M, Viksna J, Neogi SG, Dumas ME, Sarkans U, MolPAGE Consortium, Donnelly P, Illig T, Adamski J, Suhre K, Allen M, Zondervan KT, Spector TD, Nicholson JK, Lindon JC, Baunsgaard D, Holmes E, McCarthy MI, Holmes CC.

PLoS Genet, 2011

doi:10.1371/journal.pgen.1002270.

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.

Nat Genet, 2011

doi:10.1038/ng.906.

A user's guide to the encyclopedia of DNA elements (ENCODE).

ENCODE Project Consortium.

PLoS Biol, 2011

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, 2011

doi:10.1093/bioinformatics/btr012.

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, 2011

doi:10.2144/000113591.

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, 2011

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 Res, 2011

doi:10.1093/nar/gkq1040.

Large scale comparison of global gene expression patterns in human and mouse.

Zheng-Bradley X, Rung J, Parkinson H, Brazma A.

Genome Biol, 2010

doi:10.1186/gb-2010-11-12-r124.

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, 2010

doi:10.1093/bioinformatics/btq462.

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 Genet, 2010

doi:10.1371/journal.pgen.1000976.

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.

Nat Med, 2010

doi:10.1038/nm.2130.

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, 2010

doi:10.1038/nature08987.

A global map of human gene expression.

Lukk M, Kapushesky M, Nikkilä J, Parkinson H, Goncalves A, Huber W, Ukkonen E, Brazma A.

Nat Biotechnol, 2010

doi:10.1038/nbt0410-322.

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, 2010

doi:10.1093/bioinformatics/btq099.

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, 2010

doi:10.1186/1471-2105-11-112.

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 Res, 2010

doi:10.1093/nar/gkp936.

Probabilistic retrieval and visualization of biologically relevant microarray experiments

Caldas J, Gehlenborg N, Faisal A, Brazma A, Kaski S.

BMC Bioinformatics, 2009

doi:.

Visualization of large microarray experiments with space maps

Gehlenborg N, Brazma A.

BMC Bioinformatics, 2009

doi:.

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 Genet, 2009

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, 2009

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, 2009

doi:10.1093/bioinformatics/btp354.

Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges.

Brazma A.

ScientificWorldJournal, 2009

doi:10.1100/tsw.2009.57.

Probabilistic retrieval and visualization of biologically relevant microarray experiments.

Caldas J, Gehlenborg N, Faisal A, Brazma A, Kaski S.

Bioinformatics, 2009

doi:10.1093/bioinformatics/btp215.

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.

Mol Oncol, 2009

doi:10.1016/j.molonc.2008.11.003.

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 Biol, 2009

doi:10.1186/gb-2009-10-1-202.

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

Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A.

Nucleic Acids Res, 2009

doi:10.1093/nar/gkn889.

Proceedings of the 6th Asia-Pacific Bioinformatics Conference: Kyoto, Japan, 14-17 January 2008

Brazma A, Miyano S, Akutsu T.

2008

doi:10.1142/p544.

Data storage and analysis in ArrayExpress and Expression Profiler.

Rustici G, Kapushesky M, Kolesnikov N, Parkinson H, Sarkans U, Brazma A.

Curr Protoc Bioinformatics, 2008

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.

Nat Biotechnol, 2008

doi:10.1038/nbt.1411.

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, 2008

doi:10.1089/omi.2008.0019.

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.

Nat Biotechnol, 2008

doi:10.1038/nbt1391.

The BREW workshop series: a stimulating experience in PhD education.

Giegerich R, Brazma A, Jonassen I, Ukkonen E, Vingron M.

Brief Bioinform, 2008

doi:10.1093/bib/bbn002.

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 Res, 2008

doi:10.1093/nar/gkm797.

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.

Nat Biotechnol, 2007

doi:10.1038/nbt1347.

Current approaches to gene regulatory network modelling.

Schlitt T, Brazma A.

BMC Bioinformatics, 2007

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 Comput Biol, 2007

doi:10.1371/journal.pcbi.0030144.

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 Biol, 2007

doi:10.1186/gb-2007-8-5-r73.

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, 2007

doi:10.1186/1471-2105-8-52.

ArrayExpress--a public database of microarray experiments and gene expression profiles.

Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, Brazma A.

Nucleic Acids Res, 2007

doi:10.1093/nar/gkl995.

ArrayExpress service for reviewers/editors of DNA microarray papers.

Brazma A, Parkinson H, ArrayExpress team, EMBL-EBI.

Nat Biotechnol, 2006

doi:10.1038/nbt1106-1321.

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, 2006

doi:10.1186/1471-2105-7-489.

Data storage and analysis in ArrayExpress.

Brazma A, Kapushesky M, Parkinson H, Sarkans U, Shojatalab M.

Methods Enzymol, 2006

doi:10.1016/s0076-6879(06)11020-4.

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, 2006

doi:10.1089/omi.2006.10.205.

MGED standards: work in progress.

Ball CA, Brazma A.

OMICS, 2006

doi:10.1089/omi.2006.10.138.

Standards for systems biology.

Brazma A, Krestyaninova M, Sarkans U.

Nat Rev Genet, 2006

doi:10.1038/nrg1922.

Modelling in molecular biology: describing transcription regulatory networks at different scales.

Schlitt T, Brazma A.

Philos Trans R Soc Lond B Biol Sci, 2006

doi:10.1098/rstb.2005.1806.

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, 2006

doi:10.1038/440024a.

Wrestling with SUMO and bio-ontologies.

Stoeckert C, Ball C, Brazma A, Brinkman R, Causton H, Fan L, Fostel J, Fragoso G, Heiskanen M, Holstege F, Morrison N, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Sarkans U, Sherlock G, Stevens R, Taylor C, Taylor R, Whetzel P, White J.

Nat Biotechnol, 2006

doi:10.1038/nbt0106-21a.

ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression.

Blake J, Schwager C, Kapushesky M, Brazma A.

Bioinformatics, 2006

doi:10.1093/bioinformatics/btk022.

Reconstruction of gene regulatory networks under the finite state linear model.

Ruklisa D, Brazma A, Viksna J.

Genome Inform, 2005

doi:.

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

Mukherjee G, Abeygunawardena N, Parkinson H, Contrino S, Durinck S, Farne A, Holloway E, Lilja P, Moreau Y, Oezcimen A, Rayner T, Sharma A, Brazma A, Sarkans U, Shojatalab M.

Plant Physiol, 2005

doi:10.1104/pp.105.063156.

Fusing microarray experiments with multivariate regression.

Gilks WR, Tom BD, Brazma A.

Bioinformatics, 2005

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, 2005

doi:10.1093/bioinformatics/bti644.

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, 2005

doi:10.1093/bioinformatics/bti525.

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, 2005

doi:10.1093/bioinformatics/bti157.

Modelling gene networks at different organisational levels.

Schlitt T, Brazma A.

FEBS Lett, 2005

doi:10.1016/j.febslet.2005.01.073.

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

Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R, Farne A, Lara GG, Holloway E, Kapushesky M, Lilja P, Mukherjee G, Oezcimen A, Rayner T, Rocca-Serra P, Sharma A, Sansone S, Brazma A.

Nucleic Acids Res, 2005

doi:10.1093/nar/gki056.

An open letter on microarray data from the MGED Society.

Microarray Gene Expression Data Mged Society.

Microbiology (Reading), 2004

doi:10.1099/mic.0.27637-0.

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 Biol, 2004

doi:10.1371/journal.pbio.0020317.

Funding high-throughput data sharing.

Ball CA, Sherlock G, Brazma A.

Nat Biotechnol, 2004

doi:10.1038/nbt0904-1179.

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.

Environ Health Perspect, 2004

doi:10.1289/ehp.112-1277123.

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.

Nat Genet, 2004

doi:10.1038/ng1377.

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.

Cytogenet Genome Res, 2004

doi:10.1159/000078003.

Expression Profiler: next generation--an online platform for analysis of microarray data.

Kapushesky M, Kemmeren P, Culhane AC, Durinck S, Ihmels J, Körner C, Kull M, Torrente A, Sarkans U, Vilo J, Brazma A.

Nucleic Acids Res, 2004

doi:10.1093/nar/gkh470.

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.

Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R.

Nat Biotechnol, 2004

doi:10.1038/nbt926.

ArrayExpress: a public database of gene expression data at EBI.

Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S, Vilo J, Abeygunawardena N, Mukherjee G, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Sansone SA.

C R Biol, 2003

doi:10.1016/j.crvi.2003.09.026.

From gene networks to gene function.

Schlitt T, Palin K, Rung J, Dietmann S, Lappe M, Ukkonen E, Brazma A.

Genome Res, 2003

doi:10.1101/gr.1111403.

[Standardization of microarray experiment data].

Brazma A, Ikeo K, Tateno Y.

Tanpakushitsu Kakusan Koso, 2003

doi:.

Towards reconstruction of gene networks from expression data by supervised learning.

Soinov LA, Krestyaninova MA, Brazma A.

Genome Biol, 2003

doi:10.1186/gb-2003-4-1-r6.

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.

Mol Biol Cell, 2003

doi:10.1091/mbc.e02-08-0499.

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

Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA.

Nucleic Acids Res, 2003

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 Res, 2003

doi:10.1093/nar/gkg066.

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.

2002

doi:10.1007/3-540-45713-5.

Learning about gene regulatory networks from gene deletion experiments.

Schlitt T, Brazma A.

Comp Funct Genomics, 2002

doi:10.1002/cfg.220.

Building and analysing genome-wide gene disruption networks.

Rung J, Schlitt T, Brazma A, Freivalds K, Vilo J.

Bioinformatics, 2002

doi:10.1093/bioinformatics/18.suppl_2.s202.

Correlating gene promoters and expression in gene disruption experiments.

Palin K, Ukkonen E, Brazma A, Vilo J.

Bioinformatics, 2002

doi:10.1093/bioinformatics/18.suppl_2.s172.

The underlying principles of scientific publication.

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Bioinformatics, 2002

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Standards for microarray data.

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Science, 2002

doi:10.1126/science.298.5593.539b.

Microarray data representation, annotation and storage.

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

Adv Biochem Eng Biotechnol, 2002

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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 Biol, 2002

doi:10.1186/gb-2002-3-9-research0046.

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.

Mol Cell, 2002

doi:10.1016/s1097-2765(02)00531-2.

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

Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M.

Nat Genet, 2001

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