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Differences in gene expression profiles between human preimplantation embryos cultured in two different IVF culture media†.

Kleijkers SH, Eijssen LM, Coonen E, Derhaag JG, Mantikou E, Jonker MJ, Mastenbroek S, Repping S, Evers JL, Dumoulin JC, van Montfoort AP.

Hum Reprod. 2015 Oct;30(10):2303-11. doi: 10.1093/humrep/dev179. Epub 2015 Jul 22.


A Novel Feedback Loop That Controls Bimodal Expression of Genetic Competence.

Gamba P, Jonker MJ, Hamoen LW.

PLoS Genet. 2015 Jun 25;11(6):e1005047. doi: 10.1371/journal.pgen.1005047. eCollection 2015 Jun.


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 May 27;6(3):51-5. doi: 10.1080/21541264.2015.1064195.


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.


Expectations and Outcomes of Reserve Network Performance following Re-zoning of the Great Barrier Reef Marine Park.

Emslie MJ, Logan M, Williamson DH, Ayling AM, MacNeil MA, Ceccarelli D, Cheal AJ, Evans RD, Johns KA, Jonker MJ, Miller IR, Osborne K, Russ GR, Sweatman HP.

Curr Biol. 2015 Apr 20;25(8):983-92. doi: 10.1016/j.cub.2015.01.073. Epub 2015 Mar 26.


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. 2014 Oct 2. [Epub ahead of print]


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.


The conserved DNA-binding protein WhiA is involved in cell division in Bacillus subtilis.

Surdova K, Gamba P, Claessen D, Siersma T, Jonker MJ, Errington J, Hamoen LW.

J Bacteriol. 2013 Dec;195(24):5450-60. doi: 10.1128/JB.00507-13. Epub 2013 Oct 4.


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 PF, Robinson J, van der Horst GT, Dollé ME, Vijg J, Breit TM, Hoeijmakers JH, van Steeg H.

Aging Cell. 2013 Oct;12(5):901-9. doi: 10.1111/acel.12118. Epub 2013 Jul 14.


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.


Response of the nonbiting midge Chironomus riparius to multigeneration toxicant exposure.

Marinković M, de Bruijn K, Asselman M, Bogaert M, Jonker MJ, Kraak MH, Admiraal W.

Environ Sci Technol. 2012 Nov 6;46(21):12105-11. doi: 10.1021/es300421r. Epub 2012 Oct 19.


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.

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