Publications
2022
Han Rauwerda; Johanna F.B. Pagano; Wim C. de Leeuw; Wim Ensink; Marina van Olst; Ulrike Nehrdich; Martijs J. Jonker; Herman P. Spaink; Timo M Breit. Cellular Factors Involved in Transcriptome Dynamics in Early Zebrafish Embryogenesis. BioRxiv 2022 doi.org/10.1101/2022.09.29.510050
2021
Hammoudi V, Beerens B, Jonker MJ, Helderman TA, Vlachakis G, Giesbers M, Kwaaitaal M, van den Burg HA. The protein modifier SUMO is critical for integrity of the Arabidopsis shoot apex at warm ambient temperatures.J Exp Bot. 2021 Jun 9:erab262. doi: 10.1093/jxb/erab262.
2020
Breit TM, Rauwerda H, 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; doi: https://doi.org/10.1101/2020.01.31.928739
Pagano JFB. Discovery of a dedicated, maternal-specific translation system in early zebrafish embryogenesis. 2020 PhD thesis University of Amsterdam
Dekker RJ, Ensink WA, van Leeuwen S, Rauwerda H, 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
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
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
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):835-843. doi: 10.1007/s00705-020-0452
2019
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. doi: 10.1038/s41467-019-08719-8.
Opperhuizen A-L, 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., 20 June 2019 https://doi.org/10.3389/fnins.2019.00647
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
Pagano JFB, Locati MD, Ensink WA, van Olst M, van Leeuwen S, de Leeuw WC, Nehrdich U, Spaink HP, Rauwerda H, 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
Pagano JFB, Dekker RJ, Ensink WA, van Olst M, Bos A, van Leeuwen S, de Leeuw WC, Nehrdich U, Spaink HP, Rauwerda H, 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
Breit TM, Pagano JFB, van der Jagt PL, Mittring E, Ensink WA, van Olst M, van Leeuwen S, de Leeuw WC, Nehrdich U, Spaink HP, Rauwerda H, Dekker RJ. New observations on non-coding RNAs involved in the dual translation system in zebrafish development 2019 bioRxiv 869651; doi: https://doi.org/10.1101/86965
2018
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. pii: JB.00633-17. doi: 10.1128/JB.00633-17. (IF 3.1)
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):e1007157. doi: 10.1371/journal.pgen.1007157. (IF 6.1)
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. doi: 10.1139/gen-2017-0202
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. (IF 3,5)
2017
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
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
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.
Rauwerda J. Transcriptome dynamics in early zebrafish embryogenesis. 2017 PhD thesis University of Amsterdam
Locati M. Distinct maternal and somatic rRNA types in zebrafish development. 2017 PhD thesis University of Amsterdam
2016
Pagano JF, Rauwerda H; de Leeuw WC, Wackers P, de Jong M, Ensink W, Dekker R, Nehrdich U, Spaink H, Jonker M, Breit, TM Transcriptome data on maternal RNA of 24 individual zebrafish eggs from five sibling mothers. Data in Brief. 2016 Sep; 8: 69-72
Bruning O, Rodenburg W, Wackers PF, van Oostrom C, Jonker MJ, Dekker RJ, Rauwerda H, Ensink WA, de Vries A, Breit TM. Confounding Factors in the Transcriptome Analysis of an In-Vivo Exposure Experiment. PLoS One. 2016 Jan 20;11(1)
Rauwerda H, Wackers P, Pagano JF, de Jong M, Ensink W, Dekker R, Nehrdich U, Spaink H, Jonker M, Breit TM. Mother-Specific Signature in the Maternal Transcriptome Composition of Mature, Unfertilized Zebrafish Eggs. PLoS One. 2016 Jan 22;11(1)
2015
Locati M, Terpstra I, de Leeuw WC, Kuzak, M, Rauwerda H, Ensink W, van Leeuwen S, Nehrdich U, Spaink H, Jonker M, Breit TM, Dekker R, Improving small RNA-seq by using a Synthetic Spike-in Set for Size-Range Quality Control together with a Set for Data Normalization. Nucleic Acids Res. 2015 Aug 18;43(14)
Bruning O, Rauwerda H, Dekker RJ, de Leeuw WC, Wackers PFK, Ensink WA, Jonker MJ, Breit TM. Valuable lessons-learned in transcriptomics experimentation. Transcription 2015 May 27;6(3)
Bruning O. Improving design, execution and analysis of transcriptomics experimentation. 2015 PhD thesis University of Amsterdam
2014
Jonker MJ, de Leeuw WC, Marinković M, Wittink FRA, Rauwerda H, Bruning O, Ensink WA, Fluit AC, Boel ECH, de Jong M, Timo M. Breit Absence/presence calling in microarray-based CGH experiments with non-model organisms. Nucleic Acids Res. 2014;42(11)
Bruning O, Rodenburg W, van Oostrum C, Jonker MJ, de Jong M, Dekker R, Rauwerda J, Ensink W, de Vries A, Breit TM A range finding protocol to support design for transcriptomics experimentation: examples of in-vitro and in-vivo murine UV exposure. Plos One 2014 May 13;9(5)
2013
Melis JP, Jonker MJ, Vijg J, Hoeijmakers JH, Breit TM, van Steeg H. Aging on a different scale - chronological versus pathology-related aging. Aging 2013 Oct;5(10):782-8.
Jonker MJ, Melis JPM, Kuiper RV, van der Hoeven TV, Robinson J, van der Horst GTJ, Breit TM, Vijg J, Dolle M, Hoeijmakers JHJ, van Steeg H Lifelong murine gene expression profiles in relation to chronological and biological aging in multiple organs. Aging Cell. 2013 Oct;12(5):901-9.
2012
Doroszuk A, Jonker MJ, Pul N, Breit TM, Zwaan B. Transcriptome analysis of a long-lived natural Drosophila variant: a prominent role of stress- and reproduction-genes in lifespan extension. BMC Genomics 2012 May 4;13(1):167.
Marinković M. Gene expression in toxicant-exposed chironomids. 2012 PhD thesis University of Amsterdam
2011
Bruning O, Rodenburg W, Radonic T, Aeilko, Zwinderman AH, de Vries A, Breit TM, de Jong M RNA isolation for transcriptomics of Human and Mouse small skin biopsies BMC Research Notes 2011 Oct 24;4(1):438.
2010
Bruning O, Yuan X, Rodenburg W, Bruins W, van Oostrom CT, Rauwerda H, Wittink FRA, Jonker MJ, de Vries A, Breit TM. Serious complications in gene-expression studies with stress perturbation: an example with UV-exposed p53-mutant mouse embryonic fibroblasts. Transcription 2010 Nov-Dec:1; 3; 159-164
Rauwerda H, de Jong M, de Leeuw WC, Spaink HP, Breit TM Integrating Heterogeneous Sequence Information for Transcriptome-Wide Microarray Design; a Zebrafish example. BMC Res Notes 2010 Jul 13;3:192
Smits NJP, Pronk TE, Bruning O, Wittink FRA, Breit TM, van Strijp JAG, Fluit AC, Boel CHE Operon structure of Staphylococcus aureus. Nucleic Acids Res. 2010 Jun; 38(10):3263-74
de Jong M, Rauwerda H, Bruning O, Verkooijen J, Spaink HP, Breit TM RNA isolation method for single embryo transcriptome analysis in zebrafish, BMC Research Notes, 2010 Mar 16;3(1):73.
2009
de Leeuw WC, Rauwerda H, Inda MA, Bruning O, Breit TM. SigWinR; the SigWin-detector updated and ported to R. BMC Res Notes 2009 Oct 6;2(1):205.
H Rauwerda, I Wassink, PBT Neerincx, PE van der Vet, TM Breit, JAM Leunissen and A Nijholt Using R in Taverna: RShell v1.2 BMC Res Notes 2009 Jul 16;2:138.
2008
de Leeuw WC, Rauwerda H, Jonker MJ, Breit TM. Salvaging Affymetrix probes after probe-level re-annotation. BMC Res Notes 2008 Aug 19;1:66-71
Inda MA, van Batenburg MF, Roos M, Belloum AS, Vasunin D, Wibisono A, van Kampen AH, Breit TM. SigWin-detector: a Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences. BMC Res. Notes 2008 Aug 8;1:63-73.
Bruning O, Bruins W, Jonker MJ, Zwart E, van der Hoeven T, Pennings JLA, Rauwerda H, de Vries A, Breit TM. Absence of Ser389 phosphorylation in p53 affects the basal gene-expression level of many p53-dependent genes and alters the biphasic response to UV exposure in MEFs. Mol Cell Biol. 2008 Mar;28(6):1974-1987
Pronk TE, Polstra S., Pimentel AD, Breit TM. Towards Design Space Exploration for Biological Systems. Journal of Computers 2008 3;1-9.
2007
Post LJG, Roos M, Marshall MS, van Driel R, Breit TM. The semantic web Approach applied to integrative bioinformatics experimentation: a biological use case with genomics data. Bioinformatics 2007 Nov 15;23(22):3080-3087.