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High-throughput screening of a large collection of non-conventional yeasts reveals their potential for aroma formation in food fermentation.

Gamero A, Quintilla R, Groenewald M, Alkema W, Boekhout T, Hazelwood L.

Food Microbiol. 2016 Dec;60:147-59. doi: 10.1016/ Epub 2016 Jul 25.


Microbial bioinformatics for food safety and production.

Alkema W, Boekhorst J, Wels M, van Hijum SA.

Brief Bioinform. 2016 Mar;17(2):283-92. doi: 10.1093/bib/bbv034. Epub 2015 Jun 16.


Homer3 regulates the establishment of neutrophil polarity.

Wu J, Pipathsouk A, Keizer-Gunnink A, Fusetti F, Alkema W, Liu S, Altschuler S, Wu L, Kortholt A, Weiner OD.

Mol Biol Cell. 2015 May 1;26(9):1629-39. doi: 10.1091/mbc.E14-07-1197. Epub 2015 Mar 4.


Clustering analyses in peptidomics revealed that peptide profiles of infant formulae are descriptive.

Lambers TT, Gloerich J, van Hoffen E, Alkema W, Hondmann DH, van Tol EA.

Food Sci Nutr. 2015 Jan;3(1):81-90. doi: 10.1002/fsn3.196. Epub 2014 Dec 30.


Application of text mining in the biomedical domain.

Fleuren WW, Alkema W.

Methods. 2015 Mar;74:97-106. doi: 10.1016/j.ymeth.2015.01.015. Epub 2015 Jan 30. Review.


Fermentation-induced variation in heat and oxidative stress phenotypes of Lactococcus lactis MG1363 reveals transcriptome signatures for robustness.

Dijkstra AR, Alkema W, Starrenburg MJ, Hugenholtz J, van Hijum SA, Bron PA.

Microb Cell Fact. 2014 Nov 4;13:148. doi: 10.1186/s12934-014-0148-6.


Diversity in robustness of Lactococcus lactis strains during heat stress, oxidative stress, and spray drying stress.

Dijkstra AR, Setyawati MC, Bayjanov JR, Alkema W, van Hijum SA, Bron PA, Hugenholtz J.

Appl Environ Microbiol. 2014 Jan;80(2):603-11. doi: 10.1128/AEM.03434-13. Epub 2013 Nov 8.


Prednisolone induces the Wnt signalling pathway in 3T3-L1 adipocytes.

Fleuren WW, Linssen MM, Toonen EJ, van der Zon GC, Guigas B, de Vlieg J, Dokter WH, Ouwens DM, Alkema W.

Arch Physiol Biochem. 2013 May;119(2):52-64. doi: 10.3109/13813455.2013.774022. Epub 2013 Mar 19.


Identification of new biomarker candidates for glucocorticoid induced insulin resistance using literature mining.

Fleuren WW, Toonen EJ, Verhoeven S, Frijters R, Hulsen T, Rullmann T, van Schaik R, de Vlieg J, Alkema W.

BioData Min. 2013 Feb 4;6(1):2. doi: 10.1186/1756-0381-6-2.


Assessing the metabolic effects of prednisolone in healthy volunteers using urine metabolic profiling.

Ellero-Simatos S, Szymańska E, Rullmann T, Dokter WH, Ramaker R, Berger R, van Iersel TM, Smilde AK, Hankemeier T, Alkema W.

Genome Med. 2012 Nov 30;4(11):94. doi: 10.1186/gm395. eCollection 2012.


Org 214007-0: a novel non-steroidal selective glucocorticoid receptor modulator with full anti-inflammatory properties and improved therapeutic index.

van Lierop MJ, Alkema W, Laskewitz AJ, Dijkema R, van der Maaden HM, Smit MJ, Plate R, Conti PG, Jans CG, Timmers CM, van Boeckel CA, Lusher SJ, McGuire R, van Schaik RC, de Vlieg J, Smeets RL, Hofstra CL, Boots AM, van Duin M, Ingelse BA, Schoonen WG, Grefhorst A, van Dijk TH, Kuipers F, Dokter WH.

PLoS One. 2012;7(11):e48385. doi: 10.1371/journal.pone.0048385. Epub 2012 Nov 12.


Molecular pathway profiling of T lymphocyte signal transduction pathways; Th1 and Th2 genomic fingerprints are defined by TCR and CD28-mediated signaling.

Smeets RL, Fleuren WW, He X, Vink PM, Wijnands F, Gorecka M, Klop H, Bauerschmidt S, Garritsen A, Koenen HJ, Joosten I, Boots AM, Alkema W.

BMC Immunol. 2012 Mar 14;13:12. doi: 10.1186/1471-2172-13-12.


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.

BMC Bioinformatics. 2011 Aug 10;12:332. doi: 10.1186/1471-2105-12-332.


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.

Cell Signal. 2011 Nov;23(11):1708-15. doi: 10.1016/j.cellsig.2011.06.002. Epub 2011 Jun 13.


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.

Pharmacogenomics. 2011 Jul;12(7):985-98. doi: 10.2217/pgs.11.34. Epub 2011 Jun 2.


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.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W450-4. doi: 10.1093/nar/gkr310. Epub 2011 May 27.


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.

PLoS Comput Biol. 2010 Sep 23;6(9). pii: e1000943. doi: 10.1371/journal.pcbi.1000943.


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.

BMC Genomics. 2010 Jun 5;11:359. doi: 10.1186/1471-2164-11-359.


Mutation of Residue βF71 of Escherichia coli Penicillin Acylase Results in Enhanced Enantioselectivity and Improved Catalytic Properties.

Shapovalova IV, Alkema WB, Jamskova OV, de Vries E, Guranda DT, Janssen DB, Svedas DB.

Acta Naturae. 2009 Oct;1(3):94-8.


BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams.

Hulsen T, de Vlieg J, Alkema W.

BMC Genomics. 2008 Oct 16;9:488. doi: 10.1186/1471-2164-9-488.

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