2023
- Parey E, Louis A, Montfort J, Bouchez O, Roques C, Iampietro C, Lluch J, Castinel A, Donnadieu C, Desvignes T, Floi Bucao C, Jouanno E, Wen M, Mejri S, Dirks R, Jansen H, Henkel C, Chen WJ, Zahm M, Cabau C, Klopp C, Thompson A, Robinson-Rechavi M, Braasch I, Lecointre G, Bobe J, Postlethwait JH, Berthelot C, Crollius HR, Guiguen Y. Genome structures resolve the early diversification of teleost fishes. Science 379(6632): 572-575. Free abstract
2022
- Cuello C, Stander EA, Jansen HJ, Dugé de Bernonville T, Oudin A, Birer-Williams C, Lanoue A, Giglioli-Guivarc’h N, Papon N, Dirks RP, Jensen MK, O’Connor SE, Besseau S, Courdavault V. An updated version of the Madagascar periwinkle genome. F1000Research 11-1541/v1. Free pdf
- Cuello C, Stander EA, Jansen HJ, Dugé de Bernonville T, Lanoue A, Giglioli-Guivarc’h N, Papon N, Dirks RP, Jensen MK, O’Connor SE, Besseau S, Courdavault V. Genome assembly of the medicinal plant Voacanga thouarsii. Genome Biol Evol: evac158. Free pdf
- Stander EA, Cuello C, Birer-Williams C, Kulagina N, Jansen H, Carqueijeiro I, Méteignier LV, Vergès V, Oudin A, Papon N, Dirks R, Jensen MK, O’Connor SE, Dugé de Bernonville T, Besseau S, Courdavault V. The Vinca minor genome highlights conserved evolutionary traits in monoterpene indole alkaloid synthesis. G3 (Bethesda): jkac268. Free pdf
- Azagi T, Dirks RP, Yebra-Pimentel ES, Schaap PJ, Koehorst JJ, Esser HJ, Sprong H. Assembly and comparison of Ca. Neoehrlichia mikurensis genomes. Microorganisms 10(6):1134. Free pdf
- Sueiro RA, Leiro JM, Blanco-Abad V, Raaijmakers J, de Bruijn I, Dirks RPH, Lamas J. Plant- and bacteria-derived compounds with anti-Philasterides dicentrarchi activity. Pathogens 11(2):267. Free pdf
2021
- Schneebauer G, Drechsel V, Dirks R, Faserl K, Sarg B, Pelster B. Expression of transport proteins in the rete mirabile of european silver and yellow eel. BMC Genomics 22(1):866. Free pdf
- Simon S, Breeschoten T, Jansen HJ, Dirks RP, Schranz ME, Ros VID. Genome and transcriptome analysis of the beet armyworm Spodoptera exigua reveals targets for pest control. G3 (Bethesda) 11(11):jkab311. Free pdf
- Kuhl H, Guiguen Y, Höhne C, Kreuz E, Du K, Klopp C, Lopez-Roques C, Yebra-Pimentel ES, Ciorpac M, Gessner J, Holostenco D, Kleiner W, Kohlmann K, Lamatsch DK, Prokopov D, Bestin A, Bonpunt E, Debeuf B, Haffray P, Morvezen R, Patrice P, Suciu R, Dirks R, Wuertz S, Kloas W, Schartl M, Stöck M. A 180 Myr-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes. Philos Trans R Soc Lond B Biol Sci 376(1832):20200089. Free pdf
- Jéhannet P, Palstra AP, Heinsbroek LTN, Kruijt L, Dirks RP, Swinkels W, Komen H. What goes wrong during early development of artificially reproduced European eel Anguilla anguilla? Clues from the larval transcriptome and gene expression patterns. Animals (Basel) 11(6):1710. Free pdf
- Byadgi O, Massimo M, Dirks RP, Pallavicini A, Bron JE, Ireland JH, Volpatti D, Galeotti M, Beraldo P. Innate immune-gene expression during experimental amyloodiniosis in European seabass (Dicentrarchus labrax). Vet Immunol Immunopathol 234:110217. Free abstract
- Piazzon MC, Mladineo I, Dirks RP, Santidrián Yebra-Pimentel E, Hrabar J, Sitjà-Bobadilla A. Ceratothoa oestroides infection in European sea bass: revealing a long misunderstood relationship. Front Immunol. 12:645607. Free pdf
- Liem M, Regensburg-Tuïnk T, Henkel C, Jansen H, Spaink H. Microbial diversity characterization of seawater in a pilot study using Oxford Nanopore Technologies long-read sequencing. BMC Res Notes 14(1):42. Free pdf
2020
- Palstra AP, Roque A, Kruijt L, Jéhannet P, Pérez-Sánchez J, Dirks RP. Physiological effects of water flow induced swimming exercise in seabream Sparus aurata. Front Physiol 11:610049. Free pdf
- Stander EA, Sepúlveda LJ, Dugé de Bernonville T, Carqueijeiro I, Koudounas K, Lemos Cruz P, Besseau S, Lanoue A, Papon N, Giglioli-Guivarc’h N, Dirks R, O’Connor SE, Atehortùa L, Oudin A, Courdavault V. Identifying genes involved in alkaloid biosynthesis in Vinca minor through transcriptomics and gene co-expression analysis. Biomolecules 10(12):1595. Free pdf
- Atre I, Mizrahi N, Yebra-Pimentel ES, Hausken K, Yom-Din S, Hurvitz A, Dirks R, Degani G, Levavi-Sivan B. Molecular characterization of two Russian sturgeon gonadotropin receptors: Cloning, expression analysis, and functional activity. Gen Comp Endocrinol 298:113557. Free abstract
- Byadgi O, Marroni F, Dirks R, Massimo M, Volpatti D, Galeotti M, Beraldo P. Transcriptome analysis of Amyloodinium ocellatum tomonts revealed basic Information on the major potential virulence factors. Genes (Basel) 11(11):1252. Free pdf
- Valle A, Leiro JM, Pereiro P, Figueras A, Novoa B, Dirks RPH, Lamas J. Interactions between the parasite Philasterides dicentrarchi and the immune system of the turbot Scophthalmus maximus. A transcriptomic analysis. Biology (Basel) 9(10):337. Free pdf
- Schneebauer G, Lindemann C, Drechsel V, Marohn L, Wysujack K, Santidrian E, Dirks R, Hanel R, Pelster B. Swimming under elevated hydrostatic pressure increases glycolytic activity in gas gland cells of the European eel. PLoS One 15(9):e0239627. Free pdf
- Syahputra, K, Kania, PW, Al-Jubury, A. Marnis, H, Mathiessen, H, Dirks, RP, Buchmann, K. Association between stress, metabolism, and growth in Ichthyophthirius multifiliis infected rainbow trout gills: Transcriptomic evidence. Aquaculture 526, 735384. Free abstract
- Yebra-Pimentel ES, Reis B, Gessner J, Wuertz S, Dirks RPH. Temperature training improves transcriptional homeostasis after heat shock in juvenile Atlantic sturgeon (Acipenser oxyrinchus). Fish Physiol Biochem 46(5):1653-1664. Free abstract
- Reddington K, Eccles D, O’Grady J, Drown DM, Hansen LH, Nielsen TK, Ducluzeau AL, Leggett RM, Heavens D, Peel N, Snutch TP, Bayega A, Oikonomopoulos S, Ragoussis I, Barry T, van der Helm E, Jolic D, Richardson H, Jansen H, Tyson JR, Jain M, Brown BL. Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function. Gigascience 9(6):giaa053. Free pdf
2019
- Yebra-Pimentel ES, Gebert M, Jansen HJ, Jong-Raadsen SA, Dirks RPH. Deep transcriptome analysis of the heat shock response in an Atlantic sturgeon (Acipenser oxyrinchus) cell line. Fish Shellfish Immunol 88:508-517. Free abstract
- Marnis H, Kania PW, Syahputra K, Zuo S, Dirks RP, Buchmann K. Transcriptomic analysis of Baltic cod (Gadus morhua) liver infected with Contracaecum osculatum third stage larvae indicates parasitic effects on growth and immune response. Fish Shellfish Immunol 93:965-976. Free abstract
- Rougeot J, Torraca V, Zakrzewska A, Kanwal Z, Jansen HJ, Sommer F, Spaink HP, Meijer AH. RNAseq profiling of leukocyte populations in zebrafish larvae reveals a cxcl11 chemokine gene as a marker of macrophage polarization during mycobacterial infection. Front Immunol 10:832. Free pdf
- Syahputra K, Kania PW, Al-Jubury A, Jafaar RM, Dirks RP, Buchmann K. Transcriptomic analysis of immunity in rainbow trout (Oncorhynchus mykiss) gills infected by Ichthyophthirius multifiliis. Fish Shellfish Immunol 86:486-496. Free abstract
- Fleming MS, Maugars G, Lafont AG, Rancon J, Fontaine R, Nourizadeh-Lillabadi R, Weltzien FA, Yebra-Pimentel ES, Dirks R, McCormick SD, Rousseau K, Martin P, Dufour S. Functional divergence of thyrotropin beta-subunit paralogs gives new insights into salmon smoltification metamorphosis. Sci Rep 9(1):4561. Free pdf
- Piazzon MC, Mladineo I, Naya-Català F, Dirks RP, Jong-Raadsen S, Vrbatović A, Hrabar J, Pérez-Sánchez J, Sitjà-Bobadilla A. Acting locally – affecting globally: RNA sequencing of gilthead sea bream with a mild Sparicotyle chrysophrii infection reveals effects on apoptosis, immune and hypoxia related genes. BMC Genomics 20(1):200. Free pdf
- Palstra AP, Mendez S, Dirks RP, Schaaf MJM. Cortisol acting through the glucocorticoid receptor is not involved in exercise-enhanced growth, but does affect the white skeletal muscle transcriptome in zebrafish (Danio rerio). Front Physiol 9:1889. Free pdf
2018
- Palstra AP, Kals J, Blanco Garcia A, Dirks RP, Poelman M. Immunomodulatory Effects of Dietary Seaweeds in LPS Challenged Atlantic Salmon Salmo salar as Determined by Deep RNA Sequencing of the Head Kidney Transcriptome. Front Physiol 9:625. Free pdf
2017
- Liem M, Jansen HJ, Dirks RP, Henkel CV, van Heusden GPH, Lemmers RJLF, Omer T, Shao S, Punt PJ, Spaink HP. De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing. Version 2. F1000Res 6:618. Free pdf
- Jain M, Tyson JR, Loose M, Ip CLC, Eccles DA, O’Grady J, Malla S, Leggett RM, Wallerman O, Jansen HJ, Zalunin V, Birney E, Brown BL, Snutch TP, Olsen HE; MinION Analysis and Reference Consortium. MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry. F1000Res 6:760. Free pdf
- Jansen HJ, Liem M, Jong-Raadsen SA, Dufour S, Weltzien FA, Swinkels W, Koelewijn A, Palstra AP, Pelster B, Spaink HP, Thillart GEVD, Dirks RP, Henkel CV. Rapid de novo assembly of the European eel genome from nanopore sequencing reads. Sci Rep 7(1):7213. Free pdf
- Schneebauer G, Dirks RP, Pelster B. Anguillicola crassus infection affects mRNA expression levels in gas gland tissue of European yellow and silver eel. PLoS One 12(8):e0183128. Free pdf
- De Meyer J, Maes GE, Dirks RP, Adriaens D. Differential gene expression in narrow- and broad-headed European glass eels (Anguilla anguilla) points to a transcriptomic link of head shape dimorphism with growth rate and chemotaxis. Mol Ecol 26(15):3943-3953. Free abstract
- Petit J, David L, Dirks R, Wiegertjes GF. Genomic and transcriptomic approaches to study immunology in cyprinids: What is next? Dev Comp Immunol 75:48-62. Review. Free pdf
2016
- Burgerhout E, Minegishi Y, Brittijn SA, de Wijze DL, Henkel CV, Jansen HJ, Spaink HP, Dirks RP, van den Thillart GEEJM. Changes in ovarian gene expression profiles and plasma hormone levels in maturing European eel (Anguilla anguilla); Biomarkers for broodstock selection. Gen Comp Endocrinol 225:185-196. Free abstract
- Pelster B, Schneebauer G, Dirks RP. Anguillicola crassus infection significantly affects the silvering related modifications in steady state mRNA levels in gas gland tissue of the European eel. Front Physiol 7:175. Free pdf
- Peñaranda DS, Morini M, Tveiten H, Vílchez MC, Gallego V, Dirks RP, van den Thillart GE, Pérez L, Asturiano JF. Temperature modulates testis steroidogenesis in European eel. Comp Biochem Physiol A Mol Integr Physiol 197:58-67. Free abstract
- Kolder IC, van der Plas-Duivesteijn SJ, Tan G, Wiegertjes GF, Forlenza M, Guler AT, Travin DY, Nakao M, Moritomo T, Irnazarow I, den Dunnen JT, Anvar SY, Jansen HJ, Dirks RP, Palmblad M, Lenhard B, Henkel CV, Spaink HP. A full-body transcriptome and proteome resource for the European common carp. BMC Genomics. 17(1):701. Free pdf
2015
- Palstra AP, Blok MC, Kals J, Blom E, Tuinhof-Koelma N, Dirks RP, Forlenza M, Blonk RJ. 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. Gen Comp Endocrinol 221:183-92. Free abstract
- Palstra AP, Fukaya K, Chiba H, Dirks RP, Planas JV, Ueda H. The olfactory transcriptome and progression of sexual maturation in homing chum salmon Oncorhynchus keta. PLoS One 10(9):e0137404. Free pdf
- Ip CLC, Loose M, Tyson JR, de Cesare M, Brown BL, Jain M, Leggett RM, Eccles DA, Zalunin V, Urban JM, Piazza P, Bowden RJ, Paten B, Mwaigwisya S, Batty EM, Simpson JT, Snutch TP, Birney E, Buck D, Goodwin S, Jansen HJ, O’Grady J, Olsen HE; MinION Analysis and Reference Consortium. MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000Res 4:1075. Free pdf
- Morini M, Pasquier J, Dirks R, van den Thillart G, Tomkiewicz J, Rousseau K, Dufour S, Lafont AG. Duplicated leptin receptors in two species of eel bring new insights into the evolution of the leptin system in vertebrates. PLoS One 10(5):e0126008. Free pdf
- Loman N, Goodwin S, Jansen H, Loose M. A disruptive sequencer meets disruptive publishing. F1000Res 4:1074. Free pdf
2014
- Rougeot J, Zakrzewska A, Kanwal Z, Jansen HJ, Spaink HP, Meijer AH. RNA sequencing of FACS-sorted immune cell populations from zebrafish infection models to identify cell specific responses to intracellular pathogens. Methods Mol Biol 1197:261-74. Free abstract
- Dirks RP, Burgerhout E, Brittijn SA, de Wijze DL, Ozupek H, Tuinhof-Koelma N, Minegishi Y, Jong-Raadsen SA, Spaink HP, van den Thillart GE. Identification of molecular markers in pectoral fin to predict artificial maturation of female European eels (Anguilla anguilla). Gen Comp Endocrinol 204:267-76. Free abstract
- Spaink HP, Jansen HJ, Dirks RP. Advances in genomics of bony fish. Brief Funct Genomics 13(2):144-56. Free pdf
2013
- Palstra AP, Beltran S, Burgerhout E, Brittijn SA, Magnoni LJ, Henkel CV, Jansen HJ, van den Thillart GE, Spaink HP, Planas JV. Deep RNA sequencing of the skeletal muscle transcriptome in swimming fish. PLoS One 8(1):e53171. Free pdf
- Ager-Wick E, Dirks RP, Burgerhout E, Nourizadeh-Lillabadi R, de Wijze DL, Spaink HP, van den Thillart GE, Tsukamoto K, Dufour S, Weltzien FA, Henkel CV. The pituitary gland of the European eel reveals massive expression of genes involved in the melanocortin system. PLoS One 8(10):e77396. Free pdf
- Palmblad M, Henkel CV, Dirks RP, Meijer AH, Deelder AM, Spaink HP. Parallel deep transcriptome and proteome analysis of zebrafish larvae. BMC Res Notes 6:428. Free pdf
- Vonk FJ, Casewell NR, Henkel CV, Heimberg AM, Jansen HJ, McCleary RJ, Kerkkamp HM, Vos RA, Guerreiro I, Calvete JJ, Wüster W, Woods AE, Logan JM, Harrison RA, Castoe TA, de Koning AP, Pollock DD, Yandell M, Calderon D, Renjifo C, Currier RB, Salgado D, Pla D, Sanz L, Hyder AS, Ribeiro JM, Arntzen JW, van den Thillart GE, Boetzer M, Pirovano W, Dirks RP, Spaink HP, Duboule D, McGlinn E, Kini RM, Richardson MK. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proc Natl Acad Sci U S A 110(51):20651-6. Free pdf
2012
- Henkel CV, Burgerhout E, de Wijze DL, Dirks RP, Minegishi Y, Jansen HJ, Spaink HP, Dufour S, Weltzien FA, Tsukamoto K, van den Thillart GE. Primitive duplicate Hox clusters in the European eel’s genome. PLoS One 7(2):e32231. Free pdf
- Henkel CV, Dirks RP, Jansen HJ, Forlenza M, Wiegertjes GF, Howe K, van den Thillart GE, Spaink HP. Comparison of the exomes of common carp (Cyprinus carpio) and zebrafish (Danio rerio). Zebrafish 9(2):59-67. Free pdf
- Minegishi Y, Henkel CV, Dirks RP, van den Thillart GE. Genomics in eels– towards aquaculture and biology. Mar Biotechnol (NY) 14(5):583-90. Free pdf
- Henkel CV, Dirks RP, de Wijze DL, Minegishi Y, Aoyama J, Jansen HJ, Turner B, Knudsen B, Bundgaard M, Hvam KL, Boetzer M, Pirovano W, Weltzien FA, Dufour S, Tsukamoto K, Spaink HP, van den Thillart GE. First draft genome sequence of the Japanese eel, Anguilla japonica. Gene 511(2):195-201. Free pdf
2011
- Zhang Y, Stupka E, Henkel CV, Jansen HJ, Spaink HP, Verbeek FJ. Identification of common carp innate immune genes with whole-genome sequencing and RNA-Seq data. J Integr Bioinform 8(2):169. Free pdf
- Ordas A, Hegedus Z, Henkel CV, Stockhammer OW, Butler D, Jansen HJ, Racz P, Mink M, Spaink HP, Meijer AH. Deep sequencing of the innate immune transcriptomic response of zebrafish embryos to Salmonella infection. Fish Shellfish Immunol 31(5):716-24. Free abstract
- Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Scaffolding pre- assembled contigs using SSPACE. Bioinformatics 27(4):578-9. Free pdf
