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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. Haibe-Kains B, et al. Among authors: brazma a. Nature. 2020 Oct;586(7829):E14-E16. doi: 10.1038/s41586-020-2766-y. Epub 2020 Oct 14. Nature. 2020. PMID: 33057217 Free PMC article.
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. Quackenbush J, et al. Among authors: brazma a. Nature. 2006 Mar 2;440(7080):24. doi: 10.1038/440024a. Nature. 2006. PMID: 16511469 No abstract available.
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. Sansone SA, et al. Among authors: brazma a. OMICS. 2008 Jun;12(2):143-9. doi: 10.1089/omi.2008.0019. OMICS. 2008. PMID: 18447634
Importing ArrayExpress datasets into R/Bioconductor.
Kauffmann A, Rayner TF, Parkinson H, Kapushesky M, Lukk M, Brazma A, Huber W. Kauffmann A, et al. Among authors: brazma a. Bioinformatics. 2009 Aug 15;25(16):2092-4. doi: 10.1093/bioinformatics/btp354. Epub 2009 Jun 8. Bioinformatics. 2009. PMID: 19505942 Free PMC article.
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. Brazma A, et al. Nucleic Acids Res. 2003 Jan 1;31(1):68-71. doi: 10.1093/nar/gkg091. Nucleic Acids Res. 2003. PMID: 12519949 Free PMC article.
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. Rocca-Serra P, et al. Among authors: brazma a. C R Biol. 2003 Oct-Nov;326(10-11):1075-8. doi: 10.1016/j.crvi.2003.09.026. C R Biol. 2003. PMID: 14744115 Free article.
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. Ball CA, et al. Among authors: brazma a. PLoS Biol. 2004 Sep;2(9):E317. doi: 10.1371/journal.pbio.0020317. Epub 2004 Aug 31. PLoS Biol. 2004. PMID: 15340489 Free PMC article.
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. Ball C, et al. Among authors: brazma a. Environ Health Perspect. 2004 Aug;112(12):A666-7. doi: 10.1289/ehp.112-1277123. Environ Health Perspect. 2004. PMID: 15345376 Free PMC article. No abstract available.
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. Sarkans U, et al. Among authors: brazma a. Bioinformatics. 2005 Apr 15;21(8):1495-501. doi: 10.1093/bioinformatics/bti157. Epub 2004 Nov 25. Bioinformatics. 2005. PMID: 15564302
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK Jr, Laursen K, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ Jr, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A. Jones AR, et al. Among authors: brazma a. Nat Biotechnol. 2007 Oct;25(10):1127-33. doi: 10.1038/nbt1347. Nat Biotechnol. 2007. PMID: 17921998
226 results