Publications

Beuningen N van, Alkema S, Hijlkema N, Ulfhake, B, Frias R, Ritskes-Hoitinga M, & Alkema W. The 3Ranker: An AI-based algorithm for finding non-animal alternative methods. Altern Lab Anim, 51. 2023. PMID: 37864460

Alkema W, Boekhorst J, Eijlander RT, Schnittger S, De Gruyter F, Lukovac S, Schilling K, Kortman GAM. Charting host-microbe co-metabolism in skin aging and application to metagenomics data. PLoS One. 2021 Nov 10;16(11):e0258960. doi: 10.1371/journal.pone.0258960. PMID: 34758050

Ritskes-Hoitinga M, Alkema W. The Use of Artificial Intelligence for the Fast and Effective Identification of Three Rs-based Literature. Altern Lab Anim. 2021 Jul;49(4):133-136. doi: 10.1177/02611929211048447. PMID: 34581190

Van Luijk JAKR, Popa M, Swinkels J, Menon JML, Alkema W, Roeleveld N, Hoffmann SE, Schlünssen V, Mandrioli D, Ritskes-Hoitinga M, Scheepers PTJ. Establishing a health-based recommended occupational exposure limit for nitrous oxide using experimental animal data – A systematic review protocol. Environ Res. 2019 Nov;178:108711. doi: 10.1016/j.envres.2019.108711. Epub 2019 Sep 7. PMID: 31520819

Willems E, Alkema W, Keizer-Garritsen J, Suppers A, van der Flier M, Philipsen RHLA, van den Heuvel LP, Volokhina E, van der Molen RG, Herberg JA, Levin M, Wright VJ, Ahout IML, Ferwerda G, Emonts M, Boeddha NP, Rivero-Calle I, Torres FM, Wessels HJCT, de Groot R, van Gool AJ, Gloerich J, de Jonge MI. Biosynthetic homeostasis and resilience of the complement system in health and infectious disease. EBioMedicine. 2019 Jul;45:303-313. doi: 10.1016/j.ebiom.2019.06.008. Epub 2019 Jun 29. PMID: 31262714

Alkema W, Boekhorst J, Wels M, van Hijum SA. Microbial bioinformatics for food safety and production. Brief Bioinform. 2016 Mar;17(2):283-92. doi: 10.1093/bib/bbv034. Epub 2015 Jun 16. PMID: 26082168

Fleuren WW, Toonen EJ, Verhoeven S, Frijters R, Hulsen T, Rullmann T, van Schaik R, de Vlieg J, Alkema W. Identification of new biomarker candidates for glucocorticoid induced insulin resistance using literature mining. BioData Min. 2013 Feb 4;6(1):2. doi: 10.1186/1756-0381-6-2. PMID: 23379763

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. Molecular pathway profiling of T lymphocyte signal transduction pathways; Th1 and Th2 genomic fingerprints are defined by TCR and CD28-mediated signaling. BMC Immunol. 2012 Mar 14;13:12. doi: 10.1186/1471-2172-13-12. PMID: 22413885

Fleuren WW, Alkema W. Application of text mining in the biomedical domain. Methods. 2015 Mar;74:97-106. doi: 10.1016/j.ymeth.2015.01.015. Epub 2015 Jan 30. PMID: 25641519

Fleuren WW, Linssen MM, Toonen EJ, van der Zon GC, Guigas B, de Vlieg J, Dokter WH, Ouwens DM, Alkema W. Prednisolone induces the Wnt signalling pathway in 3T3-L1 adipocytes. Arch Physiol Biochem. 2013 May;119(2):52-64. doi: 10.3109/13813455.2013.774022. Epub 2013 Mar 19. PMID: 23506355

Frijters R, van Vugt M, Smeets R, van Schaik R, de Vlieg J, Alkema W. Literature mining for the discovery of hidden connections between drugs, genes and diseases. PLoS Comput Biol. 2010;6(9):e1000943. Published 2010 Sep 23. doi:10.1371/journal.pcbi.1000943 May 1;26(9):1629- 39. doi: 10.1091/mbc.E14-07-1197. Epub 2015 Mar 4. PMID: 25739453