ZFIN ID: ZDB-PERS-970422-1
Verbeek, Fons J.
Email: fverbeek@liacs.nl
URL: http://bio-imaging.liacs.nl
Address: Imaging & BioInformatics Leiden Institute of Advanced Computer Science: LIACS Leiden University Niels Bohrweg 1 Leiden, 2333 Netherlands
Phone: 31-71-5276934
Fax: 31-71-5276985

Construction of a 3D digital atlas of the zebrafish embryo.
Image processing, Analysis and 3D reconstruction from serial sections.

Hu, W., van Steijn, L., Li, C., Verbeek, F.J., Cao, L., Merks, R.M.H., Spaink, H.P. (2021) A Novel Function of TLR2 and MyD88 in the Regulation of Leukocyte Cell Migration Behavior During Wounding in Zebrafish Larvae. Frontiers in cell and developmental biology. 9:624571
van Wijk, R.C., Hu, W., Dijkema, S.M., van den Berg, D.J., Liu, J., Bahi, R., Verbeek, F.J., Simonsson, U.S.H., Spaink, H.P., van der Graaf, P.H., Krekels, E.H.J. (2020) Anti-tuberculosis effect of isoniazid scales accurately from zebrafish to humans. British journal of pharmacology. 177(24):5518-5533
van Steijn, L., Verbeek, F.J., Spaink, H.P., Merks, R.M.H. (2019) Predicting Metabolism from Gene Expression in an Improved Whole-Genome Metabolic Network Model of Danio rerio. Zebrafish. 16(4):348-362
Guo, Y., Xiong, Z., Verbeek, F.J. (2018) An efficient and robust hybrid method for segmentation of zebrafish objects from bright-field microscope images. Machine vision and applications. 29:1211-1225
Tang, X., van der Zwaan, D.M., Zammit, A., Rietveld, K.F.D., Verbeek, F.J. (2017) Fast Post-Processing Pipeline for Optical Projection Tomography. IEEE Transactions on Nanobioscience. 16:367-374
Guo, Y., Veneman, W.J., Spaink, H.P., Verbeek, F.J. (2017) Three-dimensional reconstruction and measurements of zebrafish larvae from high-throughput axial-view in vivo imaging.. Biomedical Optics Express. 8:2611-2634
Benard, E.L., Racz, P.I., Rougeot, J., Nezhinsky, A.E., Verbeek, F.J., Spaink, H.P., Meijer, A.H. (2015) Macrophage-Expressed Perforins Mpeg1 and Mpeg1.2 Have an Anti-Bacterial Function in Zebrafish. Journal of Innate Immunity. 7(2):136-52
Laroche, F.J., Tulotta, C., Lamers, G.E., Meijer, A.H., Yang, P., Verbeek, F.J., Blaise, M., Stougaard, J., and Spaink, H.P. (2013) The embryonic expression patterns of zebrafish genes encoding LysM-domains. Gene expression patterns : GEP. 13(7):212-24
Carvalho, R.V., Kleijn, J., Meijer, A.H., and Verbeek, F.J. (2012) Modeling innate immune response to early mycobacterium infection. Computational and Mathematical Methods in Medicine. 2012:790482
Bertens, L.M., Slob, J., and Verbeek, F.J. (2011) A generic organ based ontology system, applied to vertebrate heart anatomy, development and physiology. Journal of integrative bioinformatics. 8(2):167
Stoop, E.J., Schipper, T., Rosendahl Huber, S.K., Nezhinsky, A.E., Verbeek, F.J., Gurcha, S.S., Besra, G.S., Vandenbroucke-Grauls, C.M., Bitter, W., and van der Sar, A.M. (2011) Zebrafish embryo screen for mycobacterial genes involved in the initiation of granuloma formation reveals a newly identified ESX-1 component. Disease models & mechanisms. 4(4):526-36
Belmamoune, M., Potikanond, D., and Verbeek, F.J. (2010) Mining and analysing spatio-temporal patterns of gene expression in an integrative database framework. Journal of integrative bioinformatics. 7(3):128
Brittijn, S.A., Duivesteijn, S.J., Belmamoune, M., Bertens, L.F., Bitter, W., Debruijn, J.D., Champagne, D.L., Cuppen, E., Flik, G., Vandenbroucke-Grauls, C.M., Janssen, R.A., de Jong, I.M., de Kloet, E.R., Kros, A., Meijer, A.H., Metz, J.R., van der Sar, A.M., Schaaf, M.J., Schulte-Merker, S., Spaink, H.P., Tak, P.P., Verbeek, F.J., Vervoordeldonk, M.J., Vonk, F.J., Witte, F., Yuan, H., and Richardson, M.K. (2009) Zebrafish development and regeneration: new tools for biomedical research. The International journal of developmental biology. 53(5-6):835-850
Belmamoune, M., and Verbeek, F.J. (2008) Data integration for spatio-temporal patterns of gene expression of zebrafish development: the GEMS database. Journal of integrative bioinformatics. 5(2):151-9
Belmamoune, M., and Verbeek, F.J. (2007) Developmental Anatomy Ontology of Zebrafish: an Integrative semantic framework. Journal of integrative bioinformatics. 4(3):65
Zhang, Y., Woltering, J.M., and Verbeek, F.J. (2007) Screen of MicroRNA Targets in Zebrafish Using Heterogeneous Data Sources: A Case Study for Dre-miR-10 and Dre-miR-196. International Journal of Mathematical Physical and Engineering Sciences. 2(1):10-17
Welten, M.C.M., de Haan, S.B., ven den Boogert, N., Noordermeer, J.N., Lamers, G.E.M., Spaink, H.P., Meijer, A.H., and Verbeek, F.J. (2006) ZebraFISH: Fluorescent In Situ Hybridization Protocol and Three-Dimensional Imaging of Gene Expression Patterns. Zebrafish. 3(4):465-476
Kabli, S., Alia, A., Spaink, H.P., Verbeek, F.J., and De Groot, H.J.M. (2006) Magnetic Resonance Microscopy of the Adult Zebrafish. Zebrafish. 3(4):431-439
Diks, S.H., Bink, R.J., van de Water, S., Joore, J., van Rooijen, C., Verbeek, F.J., den Hertog, J., Peppelenbosch, M.P., and Zivkovic, D. (2006) The novel gene asb11: a regulator of the size of the neural progenitor compartment. The Journal of cell biology. 174(4):581-592
Corredor-Adamez, M., Welten, M.C., Spaink, H.P., Jeffery, J.E., Schoon, R.T., de Bakker, M.A., Bagowski, C.P., Meijer, A.H., Verbeek, F.J., and Richardson, M.K. (2005) Genomic annotation and transcriptome analysis of the zebrafish (Danio rerio) hox complex with description of a novel member, hoxb13a. Evolution & development. 7(5):362-375
Meijer, A.H., Verbeek, F.J., Salas-Vidal, E., Corredor-Adámez, M., Bussman, J., van der Sar, A.M., Otto, G.W., Geisler, R., and Spaink, H.P. (2005) Transcriptome profiling of adult zebrafish at the late stage of chronic tuberculosis due to Mycobacterium marinum infection. Molecular immunology. 42(10):1185-1203