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Alvis Brazma
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An integrated encyclopedia of DNA elements in the human genome
ENCODE Project Consortium
Nature 489 (7414), 57, 2012
170462012
The PRIDE database and related tools and resources in 2019: improving support for quantification data
Y Perez-Riverol, A Csordas, J Bai, M Bernal-Llinares, S Hewapathirana, ...
Nucleic acids research 47 (D1), D442-D450, 2019
64212019
Minimum information about a microarray experiment (MIAME)—toward standards for microarray data
A Brazma, P Hingamp, J Quackenbush, G Sherlock, P Spellman, ...
Nature genetics 29 (4), 365-371, 2001
49492001
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
Y Perez-Riverol, J Bai, C Bandla, D García-Seisdedos, S Hewapathirana, ...
Nucleic acids research 50 (D1), D543-D552, 2022
37742022
SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues
CGK Ziegler, SJ Allon, SK Nyquist, IM Mbano, VN Miao, CN Tzouanas, ...
Cell 181 (5), 1016-1035. e19, 2020
24252020
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
S Durinck, Y Moreau, A Kasprzyk, S Davis, B De Moor, A Brazma, ...
Bioinformatics 21 (16), 3439-3440, 2005
22122005
Transcriptome and genome sequencing uncovers functional variation in humans
T Lappalainen, M Sammeth, MR Friedländer, PAC ‘t Hoen, J Monlong, ...
Nature 501 (7468), 506-511, 2013
20952013
Pan-cancer analysis of whole genomes
Nature 578 (7793), 82-93, 2020
1884*2020
ArrayExpress—a public repository for microarray gene expression data at the EBI
A Brazma, H Parkinson, U Sarkans, M Shojatalab, J Vilo, ...
Nucleic acids research 31 (1), 68-71, 2003
11362003
Gene expression data analysis
A Brazma, J Vilo
FEBS letters 480 (1), 17-24, 2000
9322000
Global transcriptional responses of fission yeast to environmental stress
D Chen, WM Toone, J Mata, R Lyne, G Burns, K Kivinen, A Brazma, ...
Molecular biology of the cell 14 (1), 214-229, 2003
9262003
ArrayExpress update—simplifying data submissions
N Kolesnikov, E Hastings, M Keays, O Melnichuk, YA Tang, E Williams, ...
Nucleic acids research 43 (D1), D1113-D1116, 2015
8212015
ArrayExpress—a public database of microarray experiments and gene expression profiles
H Parkinson, M Kapushesky, M Shojatalab, N Abeygunawardena, ...
Nucleic acids research 35 (suppl_1), D747-D750, 2007
8172007
The HUPO PSI's molecular interaction format—a community standard for the representation of protein interaction data
H Hermjakob, L Montecchi-Palazzi, G Bader, J Wojcik, L Salwinski, ...
Nature biotechnology 22 (2), 177-183, 2004
7592004
A user's guide to the encyclopedia of DNA elements (ENCODE)
RM Myers, J Stamatoyannopoulos, M Snyder, I Dunham, RC Hardison, ...
PLoS biology 9 (4), 2011
6772011
Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants
R Petryszak, M Keays, YA Tang, NA Fonseca, E Barrera, T Burdett, ...
Nucleic acids research 44 (D1), D746-D752, 2016
6432016
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
CF Taylor, D Field, SA Sansone, J Aerts, R Apweiler, M Ashburner, ...
Nature biotechnology 26 (8), 889-896, 2008
6242008
Periodic gene expression program of the fission yeast cell cycle
G Rustici, J Mata, K Kivinen, P Lió, CJ Penkett, G Burns, J Hayles, ...
Nature genetics 36 (8), 809-817, 2004
6062004
Design and implementation of microarray gene expression markup language (MAGE-ML)
PT Spellman, M Miller, J Stewart, C Troup, U Sarkans, S Chervitz, ...
Genome biology 3, 1-9, 2002
5982002
Modeling sample variables with an Experimental Factor Ontology
J Malone, E Holloway, T Adamusiak, M Kapushesky, J Zheng, ...
Bioinformatics 26 (8), 1112-1118, 2010
5742010
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