2020

1. Dekker RJ, Ensink WA, van Leeuwen S, Rauwerda J, Breit TM Overhauling a faulty control in the CDC-recommended SARS-CoV-2 RT-PCR test panel. 2020 bioRxiv 2020.06.12.147819; doi: https://doi.org/10.1101/2020.06.12.147819
2. Breit TM, Rauwerda J, Pagano JFB, Ensink WA, Nehrdich U, Spaink HP, Dekker RJ Immunoglobulin switch-like recombination regions implicated in the formation of extrachromosomal circular 45S rDNA involved in the maternal-specific translation system of zebrafish. 2020 bioRxiv 2020.01.31.928739
3. Pagano JFB  Discovery of a dedicated, maternal-specific translation system in early zebrafish embryogenesis. 2020 PhD thesis University of Amsterdam
4. Swarge B, Abhyankar W, Jonker MJ, Hoefsloot H, Kramer G, Setlow P, Brul S, Koning de S. Integrative analysis of proteome and transcriptome dynamics during Bacillus subtilis spore revival. mSphere. 2020 Aug 5;5(4):e00463-20. doi: 10.1128/mSphere.00463-20.PMID: 3275933
5. van der Kloet FM, Buurmans J, Jonker MJ, Smilde AK, Westerhuis JA. Increased comparability between RNA-Seq and microarray data by utilization of gene sets. PLoS Comput Biol. 2020 Sep 30;16(9): e1008295. doi: 10.1371/journal.pcbi.1008295. eCollection 2020 Sep
6. Kemp V, Laconi A, Cocciolo G, Berends A, Breit TM, Verheije, MH. MiRNA repertoire and host immune factor regulation upon avian coronavirus infection in eggs, Arch Virol. 2020 Apr;165(4):835-843890.

2019

1. Breit TM, Pagano JFB, van der Jagt PL, Mittring E, Ensink WA, van Olst M, van Leeuwen S, de Leeuw W, Nehrdich U, Spaink HP, Rauwerda J, Dekker RJ New observations on non-coding RNAs involved in the dual translation system in zebrafish development 2019 bioRxiv 869651; doi: https://doi.org/10.1101/869651
2. Pagano JFB, Dekker RJ, Ensink WA, van Olst M, Bos A, van Leeuwen S, de Leeuw WC, Nehrdich U, Spaink HP, Rauwerda J, Jonker MJ, Breit TM An alternative spliceosome defined by distinct snRNAs in early zebrafish embryogenesis 2019 bioRxiv 858944; doi: https://doi.org/10.1101/858944
3. Pagano JFB, Locati MD, Ensink WA, van Olst M, van Leeuwen S, de Leeuw WC, Nehrdich U, Spaink H, Rauwerda J, Jonker MJ, Dekker RJ, Breit TM Maternal- and Somatic-type snoRNA Expression and Processing in Zebrafish Development 2019 bioRxiv 858936; doi: https://doi.org/10.1101/858936
4. Hoeksema M, Jonker MJ, Brul S, Ter Kuile BH.Effects of a previously selected antibiotic resistance on mutations acquired during development of a second resistance in Escherichia coli.BMC Genomics. 2019 Apr 11;20(1):284. doi: 10.1186/s12864-019-5648-7
5. Opperhuizen AL, Foppen E, Jonker MJ, Wackers P, van Faassen M, van Weeghel M, van Kerkhof L, Fliers E, Kalsbeek A. Effects of Light-at-Night on the Rat Liver - A Role for the Autonomic Nervous System. Front Neurosci. 2019 Jun 20;13:647.
6. Gray DA, Dugar G, Gamba P, Strahl H, Jonker MJ, Hamoen LW Extreme slow growth as alternative strategy to survive deep starvation in bacteria Nat Commun. 2019 Feb 21;10(1):890. 

2018

1. Bohorquez LC, Surdova K, Jonker MJ, Hamoen LW. The conserved DNA binding protein WhiA influences chromosome segregation in Bacillus subtilis. J Bacteriol. 2018 Jan 29. 
2. Hammoudi V, Fokkens L, Beerens B, Vlachakis G, Chatterjee S, Arroyo-Mateos M, Wackers PFK, Jonker MJ, van den Burg HA. The Arabidopsis SUMO E3 ligase SIZ1 mediates the temperature dependent trade-off between plant immunity and growth. PLoS Genet. 2018 Jan 22;14(1):
3. Locati MD, Pagano JFB, Abdullah F, Ensink WA, van Olst M, van Leeuwen S, Nehrdich U, Spaink HP, Rauwerda H, Jonker MJ, Dekker RJ, Breit T. Identifying small RNAs derived from maternal- and somatic-type rRNAs in Zebrafish Development. Genome. 2018 Feb 9
4. Smits MAJ, Wong KM, Mantikou E, Korver CM, Jongejan A, Breit TM, Goddijn M, Mastenbroek S, Repping S. Age-related gene expression profiles of immature human oocytes Molecular Human Reproduction Mol Hum Reprod. 2018 Oct 1;24(10):469-477
5. Hoeksema M, Jonker MJ, Bel K, Brul S, Ter Kuile BH. Genome rearrangements in Escherichia coli during de novo acquisition of resistance to a single antibiotic or two antibiotics successively. BMC Genomics. 2018 Dec 27;19(1):973

2017

1. Hammoudi V, Vlachakis G, de Jonge R, Breit TM, van den Burg HA Genetic characterization of T-DNA insertions in the genome of the Arabidopsis thaliana sumo1/2 knock-down line. Plant Signaling & Behavior.2017 Mar 4;12(3):e1293216.
2. Locati MD, Pagano JFB, Ensink WA, van Olst M, van Leeuwen S, Nehrdich U, Zhu K, Spaink HP, Girard G, Rauwerda H, Jonker MJ, Dekker RJ, and Breit TM Linking Maternal and Somatic 5S rRNA types with Different Sequence-Specific Non-LTR Retrotransposons. RNA. 2017 Apr;23(4):446-456
3. Rauwerda H, Pagano JFP, de Leeuw WC, Ensink W, Nehrdich U, de Jong M, Jonker M, Spaink H, Breit TM ranscriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos. BMC Genomics. 2017 Apr 11;18(1):287
4. Locati, M, Pagano, JFB, Girard, G, Ensink, W, van Olst, M, van Leeuwen, S, Nehrdich, U, Spaink, H, Rauwerda, H, Jonker, M, Dekker, R, Breit, TM, Expression of Distinct Maternal and Somatic 5.8S, 18S, and 28S rRNA Types during Zebrafish Development. RNA.2017 Aug;23(8):1188-1199.
5. van Hagen M, Piebes DGE, de Leeuw WC, Vuist IM, van Roon-Mom WMC, Moerland PD Verschure PJ maternal snoRNA The dynamics of early-state transcriptional changes and aggregate formation in a Huntington’s disease cell model. BMC Genomics . 2017 May 12;18(1):373.
6. Gao Y, Wenzel M, Jonker MJ, Hamoen LW. Free SepF interferes with recruitment of late cell division proteins. Sci Rep. 2017 Dec 5;7(1):16928 
7. Smith RL, Tan JME, Jonker MJ, Jongejan A, Buissink T, Veldhuijzen S, van Kampen AHC, Brul S, van der Spek H. Beyond the polymerase-γ theory: Production of ROS as a mode of NRTI-induced mitochondrial toxicity. PLoS One. 2017 Nov 2;12(11)