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Age-related gene expression profiles of immature human oocytes.

Smits MAJ, Wong KM, Mantikou E, Korver CM, Jongejan A, Breit TM, Goddijn M, Mastenbroek S, Repping S.

Mol Hum Reprod. 2018 Oct 1;24(10):469-477. doi: 10.1093/molehr/gay036.


Identifying small RNAs derived from maternal- and somatic-type rRNAs in zebrafish development.

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 TM.

Genome. 2018 May;61(5):371-378. doi: 10.1139/gen-2017-0202. Epub 2018 Feb 9.


Expression of distinct maternal and somatic 5.8S, 18S, and 28S rRNA types during zebrafish development.

Locati MD, Pagano JFB, Girard G, Ensink WA, van Olst M, van Leeuwen S, Nehrdich U, Spaink HP, Rauwerda H, Jonker MJ, Dekker RJ, Breit TM.

RNA. 2017 Aug;23(8):1188-1199. doi: 10.1261/rna.061515.117. Epub 2017 May 12.


Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos.

Rauwerda H, Pagano JF, de Leeuw WC, Ensink W, Nehrdich U, de Jong M, Jonker M, Spaink HP, Breit TM.

BMC Genomics. 2017 Apr 11;18(1):287. doi: 10.1186/s12864-017-3672-z.


Genetic characterization of T-DNA insertions in the genome of the Arabidopsis thaliana sumo1/2 knock-down line.

Hammoudi V, Vlachakis G, de Jonge R, Breit TM, van den Burg HA.

Plant Signal Behav. 2017 Mar 4;12(3):e1293216. doi: 10.1080/15592324.2017.1293216.


Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons.

Locati MD, Pagano JF, Ensink WA, van Olst M, van Leeuwen S, Nehrdich U, Zhu K, Spaink HP, Girard G, Rauwerda H, Jonker MJ, Dekker RJ, Breit TM.

RNA. 2017 Apr;23(4):446-456. doi: 10.1261/rna.059642.116. Epub 2016 Dec 21.


Transcriptome data on maternal RNA of 24 individual zebrafish eggs from five sibling mothers.

Pagano JF, Rauwerda H, de Leeuw WC, Wackers P, de Jong M, Ensink W, Dekker R, Nehrdich U, Spaink HP, Jonker M, Breit TM.

Data Brief. 2016 Apr 26;8:69-72. doi: 10.1016/j.dib.2016.04.045. eCollection 2016 Sep.


Mother-Specific Signature in the Maternal Transcriptome Composition of Mature, Unfertilized Zebrafish Eggs.

Rauwerda H, Wackers P, Pagano JF, de Jong M, Ensink W, Dekker R, Nehrdich U, Spaink HP, Jonker M, Breit TM.

PLoS One. 2016 Jan 22;11(1):e0147151. doi: 10.1371/journal.pone.0147151. eCollection 2016.


Confounding Factors in the Transcriptome Analysis of an In-Vivo Exposure Experiment.

Bruning O, Rodenburg W, Wackers PF, van Oostrom C, Jonker MJ, Dekker RJ, Rauwerda H, Ensink WA, de Vries A, Breit TM.

PLoS One. 2016 Jan 20;11(1):e0145252. doi: 10.1371/journal.pone.0145252. eCollection 2016.


Factors affecting the gene expression of in vitro cultured human preimplantation embryos.

Mantikou E, Jonker MJ, Wong KM, van Montfoort AP, de Jong M, Breit TM, Repping S, Mastenbroek S.

Hum Reprod. 2016 Feb;31(2):298-311. doi: 10.1093/humrep/dev306. Epub 2015 Dec 17.


Evaluation of ribonucleic acid amplification protocols for human oocyte transcriptome analysis.

Mantikou E, Bruning O, Mastenbroek S, Repping S, Breit TM, de Jong M.

Fertil Steril. 2016 Feb;105(2):511-9.e4. doi: 10.1016/j.fertnstert.2015.10.025. Epub 2015 Nov 18.


WRKY40 and WRKY6 act downstream of the green leaf volatile E-2-hexenal in Arabidopsis.

Mirabella R, Rauwerda H, Allmann S, Scala A, Spyropoulou EA, de Vries M, Boersma MR, Breit TM, Haring MA, Schuurink RC.

Plant J. 2015 Sep;83(6):1082-96. doi: 10.1111/tpj.12953.


Valuable lessons-learned in transcriptomics experimentation.

Bruning O, Rauwerda H, Dekker RJ, de Leeuw WC, Wackers PF, Ensink WA, Jonker MJ, Breit TM.

Transcription. 2015;6(3):51-5. doi: 10.1080/21541264.2015.1064195. Review.


Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization.

Locati MD, Terpstra I, de Leeuw WC, Kuzak M, Rauwerda H, Ensink WA, van Leeuwen S, Nehrdich U, Spaink HP, Jonker MJ, Breit TM, Dekker RJ.

Nucleic Acids Res. 2015 Aug 18;43(14):e89. doi: 10.1093/nar/gkv303. Epub 2015 Apr 13.


Staphylococcus aureus ST398 gene expression profiling during ex vivo colonization of porcine nasal epithelium.

Tulinski P, Duim B, Wittink FR, Jonker MJ, Breit TM, van Putten JP, Wagenaar JA, Fluit AC.

BMC Genomics. 2014 Oct 20;15:915. doi: 10.1186/1471-2164-15-915.


A novel toxicogenomics-based approach to categorize (non-)genotoxic carcinogens.

Schaap MM, Wackers PF, Zwart EP, Huijskens I, Jonker MJ, Hendriks G, Breit TM, van Steeg H, van de Water B, Luijten M.

Arch Toxicol. 2015 Dec;89(12):2413-27. doi: 10.1007/s00204-014-1368-6. Epub 2014 Oct 2.


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

Bruning O, Rodenburg W, van Oostrom CT, Jonker MJ, de Jong M, Dekker RJ, Rauwerda H, Ensink WA, de Vries A, Breit TM.

PLoS One. 2014 May 13;9(5):e97089. doi: 10.1371/journal.pone.0097089. eCollection 2014.


A day and night difference in the response of the hepatic transcriptome to cyclophosphamide treatment.

Van Dycke KC, Nijman RM, Wackers PF, Jonker MJ, Rodenburg W, van Oostrom CT, Salvatori DC, Breit TM, van Steeg H, Luijten M, van der Horst GT.

Arch Toxicol. 2015 Feb;89(2):221-31. doi: 10.1007/s00204-014-1257-z. Epub 2014 May 13.


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

Jonker MJ, de Leeuw WC, Marinković M, Wittink FR, Rauwerda H, Bruning O, Ensink WA, Fluit AC, Boel CH, Jong Md, Breit TM.

Nucleic Acids Res. 2014 Jun;42(11):e94. doi: 10.1093/nar/gku343. Epub 2014 Apr 25.


In vivo murine hepatic microRNA and mRNA expression signatures predicting the (non-)genotoxic carcinogenic potential of chemicals.

Melis JP, Derks KW, Pronk TE, Wackers P, Schaap MM, Zwart E, van Ijcken WF, Jonker MJ, Breit TM, Pothof J, van Steeg H, Luijten M.

Arch Toxicol. 2014 Apr;88(4):1023-34. doi: 10.1007/s00204-013-1189-z. Epub 2014 Jan 5.


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

Melis JP, Jonker MJ, Vijg J, Hoeijmakers JH, Breit TM, van Steeg H.

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


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

Jonker MJ, Melis JP, Kuiper RV, van der Hoeven TV, Wackers PFK, Robinson J, van der Horst GT, Dollé ME, Vijg J, Breit TM, Hoeijmakers JH, van Steeg H.

Aging Cell. 2013 Oct;12(5):901-909. doi: 10.1111/acel.12118. Epub 2013 Jul 14.


Rifampicin-induced transcriptome response in rifampicin-resistant Mycobacterium tuberculosis.

de Knegt GJ, Bruning O, ten Kate MT, de Jong M, van Belkum A, Endtz HP, Breit TM, Bakker-Woudenberg IA, de Steenwinkel JE.

Tuberculosis (Edinb). 2013 Jan;93(1):96-101. doi: 10.1016/ Epub 2012 Nov 22.


Combining next-generation sequencing and microarray technology into a transcriptomics approach for the non-model organism Chironomus riparius.

Marinković M, de Leeuw WC, de Jong M, Kraak MH, Admiraal W, Breit TM, Jonker MJ.

PLoS One. 2012;7(10):e48096. doi: 10.1371/journal.pone.0048096. Epub 2012 Oct 25.


Gene expression patterns and life cycle responses of toxicant-exposed chironomids.

Marinković M, de Leeuw WC, Ensink WA, de Jong M, Breit TM, Admiraal W, Kraak MH, Jonker MJ.

Environ Sci Technol. 2012 Nov 20;46(22):12679-86. doi: 10.1021/es3033617. Epub 2012 Nov 9.


Comparison of Timothy grass pollen extract- and single major allergen-induced gene expression and mediator release in airway epithelial cells: a meta-analysis.

Röschmann KI, van Kuijen AM, Luiten S, Jonker MJ, Breit TM, Fokkens WJ, Petersen A, van Drunen CM.

Clin Exp Allergy. 2012 Oct;42(10):1479-90. doi: 10.1111/j.1365-2222.2012.04033.x.


Dissecting modes of action of non-genotoxic carcinogens in primary mouse hepatocytes.

Schaap MM, Zwart EP, Wackers PF, Huijskens I, van de Water B, Breit TM, van Steeg H, Jonker MJ, Luijten M.

Arch Toxicol. 2012 Nov;86(11):1717-27. doi: 10.1007/s00204-012-0883-6. Epub 2012 Jun 19.


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

Doroszuk A, Jonker MJ, Pul N, Breit TM, Zwaan BJ.

BMC Genomics. 2012 May 4;13:167. doi: 10.1186/1471-2164-13-167.


Purified Timothy grass pollen major allergen Phl p 1 may contribute to the modulation of allergic responses through a pleiotropic induction of cytokines and chemokines from airway epithelial cells.

Röschmann KI, van Kuijen AM, Luiten S, Jonker MJ, Breit TM, Fokkens WJ, Petersen A, van Drunen CM.

Clin Exp Immunol. 2012 Mar;167(3):413-21. doi: 10.1111/j.1365-2249.2011.04522.x.


Human testis-derived embryonic stem cell-like cells are not pluripotent, but possess potential of mesenchymal progenitors.

Chikhovskaya JV, Jonker MJ, Meissner A, Breit TM, Repping S, van Pelt AM.

Hum Reprod. 2012 Jan;27(1):210-21. doi: 10.1093/humrep/der383. Epub 2011 Nov 15.


RNA isolation for transcriptomics of human and mouse small skin biopsies.

Bruning O, Rodenburg W, Radonic T, Zwinderman AH, de Vries A, Breit TM, de Jong M.

BMC Res Notes. 2011 Oct 24;4:438. doi: 10.1186/1756-0500-4-438.


Single cell transcriptomics of neighboring hyphae of Aspergillus niger.

de Bekker C, Bruning O, Jonker MJ, Breit TM, Wösten HA.

Genome Biol. 2011 Aug 4;12(8):R71. doi: 10.1186/gb-2011-12-8-r71.


Gene expression profiling in a mouse model identifies fetal liver- and placenta-derived potential biomarkers for Down Syndrome screening.

Pennings JL, Rodenburg W, Imholz S, Koster MP, van Oostrom CT, Breit TM, Schielen PC, de Vries A.

PLoS One. 2011 Apr 14;6(4):e18866. doi: 10.1371/journal.pone.0018866.


Timothy grass pollen extract-induced gene expression and signalling pathways in airway epithelial cells.

Röschmann KI, Luiten S, Jonker MJ, Breit TM, Fokkens WJ, Petersen A, van Drunen CM.

Clin Exp Allergy. 2011 Jun;41(6):830-41. doi: 10.1111/j.1365-2222.2011.03713.x. Epub 2011 Apr 8.


Interorgan coordination of the murine adaptive response to fasting.

Hakvoort TB, Moerland PD, Frijters R, Sokolović A, Labruyère WT, Vermeulen JL, Ver Loren van Themaat E, Breit TM, Wittink FR, van Kampen AH, Verhoeven AJ, Lamers WH, Sokolović M.

J Biol Chem. 2011 May 6;286(18):16332-43. doi: 10.1074/jbc.M110.216986. Epub 2011 Mar 10.


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

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

Transcription. 2010 Nov;1(3):159-164. Epub 2010 Aug 30.


Genotoxic exposure: novel cause of selection for a functional ΔN-p53 isoform.

Melis JP, Hoogervorst EM, van Oostrom CT, Zwart E, Breit TM, Pennings JL, de Vries A, van Steeg H.

Oncogene. 2011 Apr 14;30(15):1764-72. doi: 10.1038/onc.2010.552. Epub 2010 Dec 13.


Finding maximal transcriptome differences between reprotoxic and non-reprotoxic phthalate responses in rat testis.

Yuan X, Jonker MJ, de Wilde J, Verhoef A, Wittink FR, van Benthem J, Bessems JG, Hakkert BC, Kuiper RV, van Steeg H, Breit TM, Luijten M.

J Appl Toxicol. 2011 Jul;31(5):421-30. doi: 10.1002/jat.1601. Epub 2010 Nov 9.


The core genome of the anaerobic oral pathogenic bacterium Porphyromonas gingivalis.

Brunner J, Wittink FR, Jonker MJ, de Jong M, Breit TM, Laine ML, de Soet JJ, Crielaard W.

BMC Microbiol. 2010 Sep 29;10:252. doi: 10.1186/1471-2180-10-252.


Transcriptome analysis of Traf6 function in the innate immune response of zebrafish embryos.

Stockhammer OW, Rauwerda H, Wittink FR, Breit TM, Meijer AH, Spaink HP.

Mol Immunol. 2010 Nov-Dec;48(1-3):179-90. doi: 10.1016/j.molimm.2010.08.011. Epub 2010 Sep 18.


Integrating heterogeneous sequence information for transcriptome-wide microarray design; a Zebrafish example.

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

BMC Res Notes. 2010 Jul 13;3:192. doi: 10.1186/1756-0500-3-192.


RNA isolation method for single embryo transcriptome analysis in zebrafish.

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

BMC Res Notes. 2010 Mar 16;3:73. doi: 10.1186/1756-0500-3-73.


Operon structure of Staphylococcus aureus.

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. doi: 10.1093/nar/gkq058. Epub 2010 Feb 11.


Gene expression analysis of tuberous sclerosis complex cortical tubers reveals increased expression of adhesion and inflammatory factors.

Boer K, Crino PB, Gorter JA, Nellist M, Jansen FE, Spliet WG, van Rijen PC, Wittink FR, Breit TM, Troost D, Wadman WJ, Aronica E.

Brain Pathol. 2010 Jul;20(4):704-19. doi: 10.1111/j.1750-3639.2009.00341.x. Epub 2009 Oct 8.


SigWinR; the SigWin-detector updated and ported to R.

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

BMC Res Notes. 2009 Oct 6;2:205. doi: 10.1186/1756-0500-2-205.


Finding transcriptomics biomarkers for in vivo identification of (non-)genotoxic carcinogens using wild-type and Xpa/p53 mutant mouse models.

Jonker MJ, Bruning O, van Iterson M, Schaap MM, van der Hoeven TV, Vrieling H, Beems RB, de Vries A, van Steeg H, Breit TM, Luijten M.

Carcinogenesis. 2009 Oct;30(10):1805-12. doi: 10.1093/carcin/bgp190. Epub 2009 Aug 20.


OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity.

Neerincx PB, Rauwerda H, Nie H, Groenen MA, Breit TM, Leunissen JA.

BMC Proc. 2009 Jul 16;3 Suppl 4:S4. doi: 10.1186/1753-6561-3-S4-S4.


Using R in Taverna: RShell v1.2.

Wassink I, Rauwerda H, Neerincx PB, van der Vet PE, Breit TM, Leunissen JA, Nijholt A.

BMC Res Notes. 2009 Jul 16;2:138. doi: 10.1186/1756-0500-2-138.


The effect of calcium on the transcriptome of sporulating B. subtilis cells.

Oomes SJ, Jonker MJ, Wittink FR, Hehenkamp JO, Breit TM, Brul S.

Int J Food Microbiol. 2009 Aug 15;133(3):234-42. doi: 10.1016/j.ijfoodmicro.2009.05.019. Epub 2009 May 22.


Persistent transcription-blocking DNA lesions trigger somatic growth attenuation associated with longevity.

Garinis GA, Uittenboogaard LM, Stachelscheid H, Fousteri M, van Ijcken W, Breit TM, van Steeg H, Mullenders LH, van der Horst GT, Brüning JC, Niessen CM, Hoeijmakers JH, Schumacher B.

Nat Cell Biol. 2009 May;11(5):604-15. doi: 10.1038/ncb1866. Epub 2009 Apr 12.

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