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The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.
Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO, Jansen RC, Parkinson H. Swertz MA, et al. BMC Bioinformatics. 2010 Dec 21;11 Suppl 12(Suppl 12):S12. doi: 10.1186/1471-2105-11-S12-S12. BMC Bioinformatics. 2010. PMID: 21210979 Free PMC article.
Molgenis-impute: imputation pipeline in a box.
Kanterakis A, Deelen P, van Dijk F, Byelas H, Dijkstra M, Swertz MA. Kanterakis A, et al. BMC Res Notes. 2015 Aug 19;8:359. doi: 10.1186/s13104-015-1309-3. BMC Res Notes. 2015. PMID: 26286716 Free PMC article.
XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments.
Swertz MA, Velde KJ, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R, Dijkstra M, Schofield P, Schughart K, Hancock JM, Smedley D, Wolstencroft K, Goble C, de Brock EO, Jones AR, Parkinson HE; Coordination of Mouse Informatics Resources (CASIMIR); Genotype-To-Phenotype (GEN2PHEN) Consortiums, Jansen RC. Swertz MA, et al. Genome Biol. 2010;11(3):R27. doi: 10.1186/gb-2010-11-3-r27. Epub 2010 Mar 9. Genome Biol. 2010. PMID: 20214801 Free PMC article.
System-wide molecular evidence for phenotypic buffering in Arabidopsis.
Fu J, Keurentjes JJ, Bouwmeester H, America T, Verstappen FW, Ward JL, Beale MH, de Vos RC, Dijkstra M, Scheltema RA, Johannes F, Koornneef M, Vreugdenhil D, Breitling R, Jansen RC. Fu J, et al. Nat Genet. 2009 Feb;41(2):166-7. doi: 10.1038/ng.308. Epub 2009 Jan 25. Nat Genet. 2009. PMID: 19169256
Comparative analysis of the human hepatic and adipose tissue transcriptomes during LPS-induced inflammation leads to the identification of differential biological pathways and candidate biomarkers.
Szalowska E, Dijkstra M, Elferink MG, Weening D, de Vries M, Bruinenberg M, Hoek A, Roelofsen H, Groothuis GM, Vonk RJ. Szalowska E, et al. BMC Med Genomics. 2011 Oct 6;4:71. doi: 10.1186/1755-8794-4-71. BMC Med Genomics. 2011. PMID: 21978410 Free PMC article.
Optimal analysis of complex protein mass spectra.
Dijkstra M, Jansen RC. Dijkstra M, et al. Proteomics. 2009 Aug;9(15):3869-76. doi: 10.1002/pmic.200701064. Proteomics. 2009. PMID: 19639597
The Genome of the Netherlands: design, and project goals.
Boomsma DI, Wijmenga C, Slagboom EP, Swertz MA, Karssen LC, Abdellaoui A, Ye K, Guryev V, Vermaat M, van Dijk F, Francioli LC, Hottenga JJ, Laros JF, Li Q, Li Y, Cao H, Chen R, Du Y, Li N, Cao S, van Setten J, Menelaou A, Pulit SL, Hehir-Kwa JY, Beekman M, Elbers CC, Byelas H, de Craen AJ, Deelen P, Dijkstra M, den Dunnen JT, de Knijff P, Houwing-Duistermaat J, Koval V, Estrada K, Hofman A, Kanterakis A, Enckevort Dv, Mai H, Kattenberg M, van Leeuwen EM, Neerincx PB, Oostra B, Rivadeneira F, Suchiman EH, Uitterlinden AG, Willemsen G, Wolffenbuttel BH, Wang J, de Bakker PI, van Ommen GJ, van Duijn CM. Boomsma DI, et al. Eur J Hum Genet. 2014 Feb;22(2):221-7. doi: 10.1038/ejhg.2013.118. Epub 2013 May 29. Eur J Hum Genet. 2014. PMID: 23714750 Free PMC article.
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