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BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams.
Hulsen T, de Vlieg J, Alkema W. Hulsen T, et al. Among authors: alkema w. BMC Genomics. 2008 Oct 16;9:488. doi: 10.1186/1471-2164-9-488. BMC Genomics. 2008. PMID: 18925949 Free PMC article.
Prednisolone-induced differential gene expression in mouse liver carrying wild type or a dimerization-defective glucocorticoid receptor.
Frijters R, Fleuren W, Toonen EJ, Tuckermann JP, Reichardt HM, van der Maaden H, van Elsas A, van Lierop MJ, Dokter W, de Vlieg J, Alkema W. Frijters R, et al. Among authors: alkema w. BMC Genomics. 2010 Jun 5;11:359. doi: 10.1186/1471-2164-11-359. BMC Genomics. 2010. PMID: 20525385 Free PMC article.
PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood.
Hulsen T, Groenen PM, de Vlieg J, Alkema W. Hulsen T, et al. Among authors: alkema w. Nucleic Acids Res. 2009 Jan;37(Database issue):D731-7. doi: 10.1093/nar/gkn645. Epub 2008 Oct 2. Nucleic Acids Res. 2009. PMID: 18832367 Free PMC article.
Literature-based compound profiling: application to toxicogenomics.
Frijters R, Verhoeven S, Alkema W, van Schaik R, Polman J. Frijters R, et al. Among authors: alkema w. Pharmacogenomics. 2007 Nov;8(11):1521-34. doi: 10.2217/14622416.8.11.1521. Pharmacogenomics. 2007. PMID: 18034617
CoPub: a literature-based keyword enrichment tool for microarray data analysis.
Frijters R, Heupers B, van Beek P, Bouwhuis M, van Schaik R, de Vlieg J, Polman J, Alkema W. Frijters R, et al. Among authors: alkema w. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W406-10. doi: 10.1093/nar/gkn215. Epub 2008 Apr 28. Nucleic Acids Res. 2008. PMID: 18442992 Free PMC article.
ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs.
Sanders MP, Fleuren WW, Verhoeven S, van den Beld S, Alkema W, de Vlieg J, Klomp JP. Sanders MP, et al. Among authors: alkema w. BMC Bioinformatics. 2011 Aug 10;12:332. doi: 10.1186/1471-2105-12-332. BMC Bioinformatics. 2011. PMID: 21831265 Free PMC article.
Literature mining for the discovery of hidden connections between drugs, genes and diseases.
Frijters R, van Vugt M, Smeets R, van Schaik R, de Vlieg J, Alkema W. Frijters R, et al. Among authors: alkema w. PLoS Comput Biol. 2010 Sep 23;6(9):e1000943. doi: 10.1371/journal.pcbi.1000943. PLoS Comput Biol. 2010. PMID: 20885778 Free PMC article.
CoPub update: CoPub 5.0 a text mining system to answer biological questions.
Fleuren WW, Verhoeven S, Frijters R, Heupers B, Polman J, van Schaik R, de Vlieg J, Alkema W. Fleuren WW, et al. Among authors: alkema w. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W450-4. doi: 10.1093/nar/gkr310. Epub 2011 May 27. Nucleic Acids Res. 2011. PMID: 21622961 Free PMC article.
Prednisolone-induced beta cell dysfunction is associated with impaired endoplasmic reticulum homeostasis in INS-1E cells.
Linssen MM, van Raalte DH, Toonen EJ, Alkema W, van der Zon GC, Dokter WH, Diamant M, Guigas B, Ouwens DM. Linssen MM, et al. Among authors: alkema w. Cell Signal. 2011 Nov;23(11):1708-15. doi: 10.1016/j.cellsig.2011.06.002. Epub 2011 Jun 13. Cell Signal. 2011. PMID: 21689745
Prednisolone-induced changes in gene-expression profiles in healthy volunteers.
Toonen EJ, Fleuren WW, Nässander U, van Lierop MJ, Bauerschmidt S, Dokter WH, Alkema W. Toonen EJ, et al. Among authors: alkema w. Pharmacogenomics. 2011 Jul;12(7):985-98. doi: 10.2217/pgs.11.34. Epub 2011 Jun 2. Pharmacogenomics. 2011. PMID: 21635145 Clinical Trial.
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