ZF-screens BV (ZFS)
Leiden, The Netherlands

Contact
Dr. Ron P. Dirks
dirks@zfscreens.com
Phone: +31 71 3322270

Address
ZF-screens BV
J.H. Oortweg 19
2333 CH Leiden (The Netherlands)

Group description
ZF-screens BV is a spin-off company from Leiden University. The team (~7 people) includes a managing director, controller, lab manager/bioinformatician, senior researchers, lab technician and PhD student. Its core business is centered around (1) using the latest sequencing technology for de novo genome assembly and transcriptome profiling, (2) using CRISPR/Cas9 technology for targeted gene mutagenesis in zebrafish and (3) using fish larvae for high-throughput in vivo drug, compound and toxicity screens. ZF-screens has organized and hosted Eel genome symposia and Genomics and Bioinformatics Workshops.

Main lines of research
– ZF-screens is co-owner of an Illumina HiSeq2500 sequencer and has been actively involved in the early access programs of Oxford Nanopore sequencers. The company has multiple years of experience with de novo vertebrate genome assembly (e.g. European and Japanese eel) and gene expression profiling based on RNAseq analysis. Its technologies include state-of-the-art genomics tools and CRISPR/Cas9 gene targeting technology. ZF-screens has developed a robotic high-throughput compound screening platform based on zebrafish larvae.
– ZF-screens has participated in multiple (inter)national research projects, including FP6, FP7 and Horizon2020 projects and Marie Curie ITN projects. Research has been focused at artificial reproduction of aquacultured fish species, de novo assembly of fish genome sequences, and development of in vivo pharmacological and toxicological screening models based on zebrafish larvae.

Links
– Portal ZF-screens: http://www.zfscreens.com/
– Marie-Curie ITN project FishForPharma: www.fishforpharma.com
– Marie-Curie ITN project IMPRESS: http://www.impress-itn.eu/
– Horizon2020 project ParaFishControl: http://www.parafishcontrol.eu/
– IMI project PreDict-TB: http://www.predict-tb.eu/

Relevant publications
1. E. Burgerhout; Y. Minegishi; S.A. Brittijn; D.L. de Wijze; C.V. Henkel; H.J. Jansen; H.P. Spaink; R.P. Dirks; G.E. van den Thillart. Changes in ovarian gene expression profiles and plasma hormone levels in maturing European eel (Anguilla anguilla); Biomarkers for broodstock selection. General and Comparative Endocrinology 225: 185-196. 2016.
2. A.P. Palstra; K. Fukaya; H. Chiba; R.P. Dirks; J.V. Planas; H. Ueda. The olfactory transcriptome and progression of sexual maturation in homing chum salmon Oncorhynchus keta. PLoS One 10: e0137404. 2015.
3. A.P. Palstra; M.C. Blok; J. Kals; E. Blom; N. Tuinhof-Koelma; R.P. Dirks; M. Forlenza; R.J. Blonk. In- and outdoor reproduction of first generation common sole Solea solea under a natural photothermal regime: Temporal progression of sexual maturation assessed by monitoring plasma steroids and gonadotropin mRNA expression. General and Comparative Endocrinology 221: 183-192. 2015.
4. R.P. Dirks; E. Burgerhout; S.A. Brittijn; D.L. de Wijze; H. Ozupek; N. Tuinhof-Koelma; Y. Minegishi; S.A. Jong-Raadsen; H.P. Spaink; G.E. van den Thillart. Identification of molecular markers in pectoral fin to predict artificial maturation of female European eels (Anguilla anguilla). General and Comparative Endocrinology 204: 267-276. 2014.
5. H.P.Spaink; H.J. Jansen; R.P. Dirks. Advances in genomics of bony fish. Briefings in Functional Genomics 13: 144-156. 2014.
6. F.J. Vonk; N.R. Casewell; C.V. Henkel; A.M. Heimberg; H.J. Jansen; R.J. McCleary; H.M. Kerkkamp; R.A. Vos; I. Guerreiro; J.J. Calvete; W. Wüster; A.E. Woods; J.M. Logan; R.A. Harrison; T.A. Castoe; A.P. de Koning; D.D. Pollock; M. Yandell; D. Calderon; C. Renjifo; R.B. Currier; D. Salgado; D. Pla; L. Sanz; A.S. Hyder; J.M. Ribeiro; J.W. Arntzen; G.E. van den Thillart; M. Boetzer; W. Pirovano; R.P. Dirks; H.P. Spaink; D. Duboule; E. McGlinn; R.M. Kini; M.K. Richardson MK. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proceeding of the National Academy of Sciences of the USA 110: 20651-20656. 2013.
7. E. Ager-Wick; R.P. Dirks; E. Burgerhout; R. Nourizadeh-Lillabadi; D.L. de Wijze; H.P. Spaink; G.E. van den Thillart; K. Tsukamoto; S. Dufour; F.A. Weltzien; C.V. Henkel. The pituitary gland of the European eel reveals massive expression of genes involved in the melanocortin system. PLoS One 8: e77396. 2013.
8. E. Burgerhout; S.A. Brittijn; C. Tudorache; D.L. de Wijze; R.P. Dirks; G.E. van den Thillart. Male European eels are highly efficient long distance swimmers: effects of endurance swimming on maturation. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 166: 522-527. 2013.
9. H.P. Spaink; C. Cui; M.I. Wiweger; H.J. Jansen; W.J. Veneman; R. Marín-Juez; J. de Sonneville; A. Ordas; V. Torraca; W. van der Ent; W.P. Leenders; A.H. Meijer; B.E. Snaar-Jagalska; R.P. Dirks. Robotic injection of zebrafish embryos for high-throughput screening in disease models. Methods 62: 246-254. 2013.
10. C.V. Henkel; R.P. Dirks; D.L. de Wijze; Y. Minegishi; J. Aoyama; H.J. Jansen; B. Turner; B. Knudsen; M. Bundgaard; K.L. Hvam; M. Boetzer; W. Pirovano; F.A. Weltzien; S. Dufour; K. Tsukamoto; H.P. Spaink; G.E. van den Thillart GE. First draft genome sequence of the Japanese eel, Anguilla japonica. Gene 511: 195-201. 2012.
11. C.V. Henkel; R.P. Dirks; H.J. Jansen; M. Forlenza; G.F. Wiegertjes; K. Howe; G.E. van den Thillart; H.P. Spaink. Comparison of the exomes of common carp (Cyprinus carpio) and zebrafish (Danio rerio). Zebrafish 9: 59-67. 2012.
12. Y. Minegishi; R.P. Dirks; D.L. de Wijze; S.A. Brittijn; E. Burgerhout; H.P. Spaink; G.E. van den Thillart. Quantitative bioassays for measuring biologically functional gonadotropins based on eel gonadotropic receptors. General and Comparative Endocrinology 178: 145-152. 2012.
13. Y. Minegishi; C.V. Henkel; R.P. Dirks; G.E. van den Thillart. Genomics in eels–towards aquaculture and biology. Marine Biotechnology (NY) 14: 583-590. 2012.
14. C.V. Henkel; E. Burgerhout; D.L. de Wijze; R.P. Dirks; Y. Minegishi; H.J. Jansen; H.P. Spaink; S. Dufour; F.A. Weltzien; K. Tsukamoto; G.E. van den Thillart. Primitive duplicate Hox clusters in the European eel’s genome. PLoS One 7: e32231. 2012.
15. E. Burgerhout; S.A. Brittijn; T. Kurwie; P. Decker; R.P. Dirks; A.P. Palstra; H.P. Spaink; G.E. van den Thillart. First artificial hybrid of the eel species Anguilla australis and Anguilla anguilla. BMC Developmental Biology 11:16. 2011.