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RNA Biology & Applied Bioinformatics

Research publications RNA Biology & Applied Bioinformatics


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. Transcriptome 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.


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):e0145252 

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):e0147151.

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 Sept 8; 69-72


Locati M, Terpstra I, de Leeuw W, 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. NAR 2015 Aug 18;43(14):e89


A range finding protocol to support design for transcriptomics experimentation: examples of in-vitro and in-vivo murine UV exposure.

Authors: Bruning O, Rodenburg W, van Oostrum C, Jonker MJ, de Jong M, Dekker R, Rauwerda J, Ensink W, de Vries A, Breit TM

PLoS One. 2014 May 13;9(5):e97089

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Absence/presence calling in microarray-based CGH experiments with non-model organisms.

Authors: Jonker MJ, de Leeuw Wim, Marinković M, Wittink FRA, Rauwerda H, Bruning O, Ensink WA, Fluit AC, Boel ECH, de Jong M, Timo M. Breit

Nucleic Acids Res. 2014;42(11)

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Life spanning murine gene expression profiles in relation to chronological and pathological aging in multiple organs

Authors: 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

Aging Cell. 2013 Oct;12(5):901-9

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Aging on a different scale – chronological versus pathology-related aging.

Authors: Melis JPM, Jonker MJ, Vijg J, Hoeijmakers JHJ, Breit TM, van Steeg H

Aging (Albany NY). 2013 Oct;5(10):782-8

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Transcriptome analysis of a long-lived natural Drosophila variant: a prominent role of stress- and reproduction-genes in lifespan extension.

Authors: Doroszuk, A., Jonker, M.J., Pul, N., Breit, T.M. & Zwaan, B.J.

BMC Genomics. 2012 May 4;13:167

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RNA isolation for transcriptomics of human and mouse small skin biopsies

Authors: Bruning, O., Rodenburg, W, Radonic, Teodora, Zwinderman, A.H., Vries, A de, Breit, T.M. & Jong, H.M. de

BMC Res Notes. 2011 Oct 24;4:438

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Serious complications in gene-expression studies with stress perturbation: an example with UV-exposed p53-mutant mouse embryonic fibroblasts

Authors: Bruning O, Yuan X, Rodenburg W, Bruins W, van Oostrom CT, Rauwerda H, Wittink FRA, Jonker MJ, de Vries A, Breit TM.

Transcription. 2010 Nov;1(3):159-164

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Integrating Heterogeneous Sequence Information for Transcriptome-Wide Microarray Design; a Zebrafish example.

Authors: Rauwerda H, de Jong M, de Leeuw WC, Spaink HP, Breit TM


BMC Res Notes 2010 Jul 13;3:192



Operon structure of Staphylococcus aureus

Authors: ten Broeke-Smits NJ, Pronk TE, Jongerius I, Bruning O, Wittink FR, Breit TM, van Strijp JA, Fluit AC, Boel CH

Nucleic Acids Res. 2010 Jun;38(10):3263-74

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RNA isolation method for single embryo transcriptome analysis in zebrafish

Authors: de Jong M, Rauwerda H, Bruning O, Verkooijen J, Spaink HP, Breit TM

BMC Res Notes. 2010 Mar 16;3:73

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SigWinR; the SigWin-detector updated and ported to R

Authors: de Leeuw WC, Rauwerda H, Inda MA, Bruning O, Breit TM.

BMC Res Notes. 2009 Oct 6;2:205

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Using R in Taverna: RShell v1.2 

Authors: H Rauwerda, I Wassink, PBT Neerincx, PE van der Vet, TM Breit, JAM Leunissen and A Nijholt

BMC Res Notes 2009 Jul 16;2:138

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The 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

Authors: Bruning O, Bruins W, Jonker MJ, Zwart E, van der Hoeven T, Pennings JLA, Rauwerda H, de Vries A, Breit TM.

Mol Cell Biol. 2008 Mar;28(6):1974-87

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Salvaging Affymetrix probes after probe-level re-annotation

Authors: de Leeuw WC, Rauwerda H, Jonker MJ, Breit TM.

BMC Res Notes. 2008 Aug 19;1:66

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SigWin-detector: a Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences

Authors: Inda MA, van Batenburg MF, Roos M, Belloum AS, Vasunin D, Wibisono A, van Kampen AH, Breit TM.

BMC Res Notes. 2008 Aug 8;1:63

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Towards Design Space Exploration for Biological Systems

Authors: Pronk TE, Polstra S., Pimentel AD, Breit TM.

Journal of Computers, Vol 3, No 2 (2008), 1-9, Feb 2008

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The semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data

Authors: Post LJG, Roos M, Marshall MS, van Driel R, Breit TM

Bioinformatics. 2007 Nov 15;23(22):3080-7

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