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Page 1
Tools for mapping high-throughput sequencing data.
Fonseca NA, Rung J, Brazma A, Marioni JC. Fonseca NA, et al. Among authors: brazma a. Bioinformatics. 2012 Dec 15;28(24):3169-77. doi: 10.1093/bioinformatics/bts605. Epub 2012 Oct 11. Bioinformatics. 2012. PMID: 23060614
Building and analysing genome-wide gene disruption networks.
Rung J, Schlitt T, Brazma A, Freivalds K, Vilo J. Rung J, et al. Among authors: brazma a. Bioinformatics. 2002;18 Suppl 2:S202-10. doi: 10.1093/bioinformatics/18.suppl_2.s202. Bioinformatics. 2002. PMID: 12386004
From gene networks to gene function.
Schlitt T, Palin K, Rung J, Dietmann S, Lappe M, Ukkonen E, Brazma A. Schlitt T, et al. Among authors: brazma a. Genome Res. 2003 Dec;13(12):2568-76. doi: 10.1101/gr.1111403. Genome Res. 2003. PMID: 14656964 Free PMC article.
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
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 Jr, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A. Rayner TF, et al. Among authors: brazma a. BMC Bioinformatics. 2006 Nov 6;7:489. doi: 10.1186/1471-2105-7-489. BMC Bioinformatics. 2006. PMID: 17087822 Free PMC article.
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.
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. Krestyaninova M, et al. Among authors: brazma a. Bioinformatics. 2009 Oct 15;25(20):2768-9. doi: 10.1093/bioinformatics/btp420. Epub 2009 Jul 24. Bioinformatics. 2009. PMID: 19633095 Free PMC article.
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. Malone J, et al. Among authors: brazma a. Bioinformatics. 2010 Apr 15;26(8):1112-8. doi: 10.1093/bioinformatics/btq099. Epub 2010 Mar 3. Bioinformatics. 2010. PMID: 20200009 Free PMC article.
228 results