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S3QL: a distributed domain specific language for controlled semantic integration of life sciences data.
Deus HF, Correa MC, Stanislaus R, Miragaia M, Maass W, de Lencastre H, Fox R, Almeida JS. Deus HF, et al. BMC Bioinformatics. 2011 Jul 14;12:285. doi: 10.1186/1471-2105-12-285. BMC Bioinformatics. 2011. PMID: 21756325 Free PMC article.
Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.
Cole C, Krampis K, Karagiannis K, Almeida JS, Faison WJ, Motwani M, Wan Q, Golikov A, Pan Y, Simonyan V, Mazumder R. Cole C, et al. BMC Bioinformatics. 2014 Jan 27;15:28. doi: 10.1186/1471-2105-15-28. BMC Bioinformatics. 2014. PMID: 24467687 Free PMC article.
DASMiner: discovering and integrating data from DAS sources.
Veiga DF, Deus HF, Akdemir C, Vasconcelos AT, Almeida JS. Veiga DF, et al. BMC Syst Biol. 2009 Nov 17;3:109. doi: 10.1186/1752-0509-3-109. BMC Syst Biol. 2009. PMID: 19919683 Free PMC article.
RPPAML/RIMS: a metadata format and an information management system for reverse phase protein arrays.
Stanislaus R, Carey M, Deus HF, Coombes K, Hennessy BT, Mills GB, Almeida JS. Stanislaus R, et al. BMC Bioinformatics. 2008 Dec 22;9:555. doi: 10.1186/1471-2105-9-555. BMC Bioinformatics. 2008. PMID: 19102773 Free PMC article.
An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis.
Stanislaus R, Arthur JM, Rajagopalan B, Moerschell R, McGlothlen B, Almeida JS. Stanislaus R, et al. BMC Bioinformatics. 2008 Jan 7;9:4. doi: 10.1186/1471-2105-9-4. BMC Bioinformatics. 2008. PMID: 18179696 Free PMC article.
Automated smoother for the numerical decoupling of dynamics models.
Vilela M, Borges CC, Vinga S, Vasconcelos AT, Santos H, Voit EO, Almeida JS. Vilela M, et al. BMC Bioinformatics. 2007 Aug 21;8:305. doi: 10.1186/1471-2105-8-305. BMC Bioinformatics. 2007. PMID: 17711581 Free PMC article.
Parameter optimization in S-system models.
Vilela M, Chou IC, Vinga S, Vasconcelos AT, Voit EO, Almeida JS. Vilela M, et al. BMC Syst Biol. 2008 Apr 16;2:35. doi: 10.1186/1752-0509-2-35. BMC Syst Biol. 2008. PMID: 18416837 Free PMC article.
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