Publications

2022

  1. 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

  1. 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

  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)

2016

  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
  2. 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)
  3. Mantikou E. Bruning O, Mastenbroek S, Repping S, Breit T, de Jong, M. Evaluation of RNA amplification protocols for human oocyte transcriptome analysis. Fertility and Sterility, Fertil Steril. 2016 Feb;105(2):511-519
  4. Mantikou E , Jonker MJ, Wong KM, van Montfoort APA, de Jong M, Breit TM, Repping S, Mastenbroek S, Factors affecting the gene expression of in-vitro cultured human preimplantation embryos. Human Reproduction 2016 Feb;31(2):298-311
  5. 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 Brief. 2016 Sep; 8: 69–72
  6. Feng Y, Jonker MJ, Moustakas I, Brul S, Ter Kuile BH. Dynamics of mutations during development of resistance by Pseudomonas aeruginosa against five antibiotics. Antimicrob Agents Chemother.2016 Jun 20;60(7):4229-36
  7. Fluit A, Jansen M, Bosch T, Jansen W, Schouls L, Jonker M, Boel C. rRNA Operon Copy Number Can Explain the Distinct Epidemiology of Hospital-Associated Methicillin-ResistantStaphylococcus aureus. Antimicrobial Agents and Chemotherapy. 2016 Dec; 60 (12): 7313–7320

2015

  1. Gamba P, Jonker MJ, Hamoen, LW A novel feedback loop that controls bimodal expression of genetic competence. Plos Genetics 2015 Jun 25;11
  2. Händel N, Ottea S, Jonker M, Brul S, ter Kuile BH. Factors That Affect Transfer of the IncI1 β-lactam Resistance Plasmid pESBL-283 between E. coli strains. Plos One 2015 Apr 1;10(4)
  3. 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. Nucleic Acids Res. 2015 Aug 18;43(14)
  4. 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)
  5. Kleijkers SHM, Eijssen LMT, Coonen E, Derhaag JG, Mantikou, Jonker MJ, Mastenbroek S, Repping S, Evers JLH, Dumoulin JCM, van Montfoort APA Differences in gene expression profiles between human preimplantation embryos cultured in two different IVF culture media. Human Reproduction 2015 Jul 22
  6. Mirabella R, Rauwerda H, Allmann SA, Spyropoulou E, Vries M, Boersma M, Breit TM; Haring M, Schuurink RC. WRKY40 and WRKY6 act downstream of the green leaf volatile E-2-hexenal in Arabidopsis. Plant Journal 2015 Aug 4.
  7. Gawehns, F., Ma, L., Bruning, O., Houterman, P.M., Boeren, S., Cornelissen, B.J., Rep, M. & Takken, F.L. The effector repertoire of determines the tomato xylem proteome composition following infection. Frontiers in Plant Science. 2015 Nov 4;6:967.

2014

  1. Tulinski P; Duim B; Wittink FR; Jonker MJ; Breit TM; van Putten JP; Wagenaar JA; Fluit AC. Staphylococcus aureus ST398 gene expression profiling during ex vivo colonization of porcine nasal epithelium. BMC genomics 2014, 15:915
  2. 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 Absence/presence calling in microarray-based CGH experiments with non-model organisms.Nucleic Acids Res. 2014;42(11)
  3. Aflitos, S., & the 150 Tomato Genome Consortium Exploring genetic variation in the tomato Solanum Lycopersicon clade by whole-genome sequencing. 2014 Plant J. 2014 Oct;80(1):136-48
  4. Schaap MM, Wackers PFK, Huijskens I, Jonker M, Hendriks G, Breit TM, van Steeg Water B,H, Luijten M A novel toxicogenomics-based approach to categorize (non-)genotoxic carcinogens. Archives of Toxicology 2014
  5. Melis JPM, Derks KWJ, Pronk T, Wackers P, Schaap MM, Zwart E, van IJcken WF Jonker M, Breit TM, Pothof J, van Steeg H, Luijten M In vivo murine hepatic microRNA and mRNA expression signatures predicting the (non-)genotoxic carcinogenic potential of chemicals. Archives of Toxicology 2014
  6. 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)
  7. van Dycke KCG, Nijman RN, Wackers PFK, Jonker MJ, Rodenburg W, van Oostrom CTN, Salvatori DCF, Breit TM, van Steeg H, Luijten M, van der Horst GTJ. A day and night difference in the response of the hepatic transcriptome to cyclophosphamide treatment.Arch Toxico. 2015 Feb;89(2):221-3

2013

  1. 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.
  2. de Knegt GJ, Bruning O, ten Kate MT, de Jong M, van Belkum A, Endtz H, Breit TM, Bakker-Woudenberg IAAJM, de Steenwinkel JEM. Rifampicin-induced transcriptome response in rifampicin-resistant Mycobacterium tuberculosis. Tuberculosis 2013 Jan;93(1):96-101.
  3. Surdova K, Gamba P, Claessen D, Siersma T, Jonker MJ, Errington J, Hamoen LW. The conserved DNA-binding protein WhiA is involved in cell division in Bacillus subtilis. Journal of Bacteriology 2013 Dec;195(24):5450-60.
  4. Sasidharan R, Mustroph A, Boonman A, Akman M, Ammerlaan AM, Breit T, Schranz ME, Voesenek LA, van Tienderen P.Root transcript profiling of two Rorippa (Brassicaceae) species reveals gene clusters associated with extreme submergence tolerance. Plant Physiol. 2013 Nov;163(3):1277-92.
  5. Melis JPM, Jonker MJ, Vijg J, Hoeijmakers JHJ, Breit TM, van Steeg H Aging on a different scale – chronological versus pathology-related aging. Aging 2013 Oct;5(10):782-8.

2012

  1. Chikhovskaya JV, Jonker MJ, Meissner A, Breit TM, Repping S, van Pelt AMM Human testis-derived embryonic stem cell-like cells are not pluripotent, but possess potential of mesenchymal progenitors. Human Reproduction 2012 Jan;27(1):210-21.
  2. Hackenberg C, Huege J, Engelhardt A, Wittink FRA, Laue , Matthijs HCP, Kopka J, Bauwe H. Low-carbon acclimation in carboxysome-less and photorespiratory mutants of the cyanobacterium Synechocystis sp. strain PCC 6803 Microbiology 2012 Feb;158(Pt 2):398-413.
  3. Röschmann K, van Kuijen A-M, Luiten S; Jonker M, Breit T, Fokkens W, Petersen A, van Drunen . M 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. Clin Exp Immunol. 2012 Mar;167(3):413-21.
  4. 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 2012May 4;13(1):167.
  5. Röschmann K; van Kuijen A-M; Jonker M; Breit T; Luiten S; Fokkens W; Petersen A Comparison of Timothy grass pollen extract- and single major allergen-induced gene expression and mediator release in airway epithelial cells: a meta-analysis Clinical & Experimental Allergy, 2012 Oct;42(10):1479-90.
  6. Schaap MM, Zwart EP, Wackers P, Huijskens I, van de Water B, Breit TM, van Steeg H, Jonker MJ, Luijten M Dissecting Modes of Action of Non-Genotoxic 1 Carcinogens in Primary Mouse Hepatocytes. Archives of Toxicology 2012 Nov;86(11):1717-27.
  7. Marinković M, de Leeuw WC, de Jong M, Kraak MHS, Admiraal W, Breit TM, Jonker MJ Combining next-generation sequencing and microarray technology into a transcriptomics approach for non-model organisms: example Chironomus riparius. Plos One 2012;7(10):e48096.
  8. Marinković M, de Bruijn K, Asselman M, Bogaert M, Jonker M, Kraak M. Response of the non-biting midge Chironomus riparius to multi-generation toxicant exposure Environmental Science & Technology 2012 Nov 6;46(21):12105-11.
  9. Marinković M, de Leeuw W, Ensink W, de Jong M, Breit TM, Admiraal W, Kraak M, Jonker M. Gene expression patterns and life cycle responses of toxicant exposed chironomids Environmental Science & Technology 2012 Nov 20;46(22):12679-86.

2011

  1. SETAC book; editors Gestel CAM, Jonker MJ, Kammenga JE, Laskowski R, Svendsen Mixture toxicity: linking approaches from ecology and human toxicology. SETAC press 280p ISBN 987-1-4398-3008-6
  2. Röschmann K, Luiten S, Jonker M, Breit TM, Fokkens W, Petersen A, van DrunenTimothy Grass pollen extract-induced gene expression and signaling pathways in airway epithelial cells. Clin Exp Allergy. 2011 Jun;41(6):830-41.
  3. Marinković M, Verweij R, Nummerdor G, Jonker M, Kraak M, Admiraal W. Life cycle responses of the midge Chironomus riparius to compounds with different modes of action Environmental Science & Technology 2011, 45, 1645–1651.
  4. Hakvoort TBM, Moerland PD, Frijters R, Sokolovi? A, Labruyère WT, Vermeulen JLM, Ver Loren van Themaat E, Breit TM, Wittink FRA, van Kampen A, Verhoeven AJ, Lamers WH, Sokolovi? M Interorgan coordination of the murine adaptive response to fasting. J Biol Chem. 2011 May 6;286(18):16332-43.
  5. Pennings JLA, Rodenburg W, Imholz S, Koster MPH, van Oostrom CTM, Breit TM, Schielen PCJI, de Vries A Gene expression profiling identifies new liver-derived potential biomarkers for Down Syndrome screening Plos One 2011 Apr 14;6(4):e18866.
  6. Melis JPM, Hoogervorst EM, van Oostrom CThM, Zwart E, Breit TM, Pennings JLA, de Vries A, van Steeg H Strong selection for the truncated ?N-p53 isoform in murine urinary bladder tumors. Oncogene 2011 Apr 14;30(15):1764-72.
  7. 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.
  8. de Bekker C, Bruning O, Breit TM, Wosten HAB Single cell transcriptomics of neighboring hyphae of Aspergillus niger Genome Biol. 2011 Aug 4;12(8):R71.
  9. Yuan X, Jonker MJ, de Wilde J, Verhoef A, Wittink FRA, van Benthem J, Bessems JG, Hakkert BC, Kuiper R, van Steeg H, Breit TM, Luijten M Finding maximal transcriptome differences between reprotoxic and non-reprotoxic phthalate responses in rat testis. Journal of Applied Toxicology 2011 31 (5); 421-430.
  10. Jonker MJ, Gerhardt A, Backhaus T, van Gestel CAM. Test Design, mixture characterization, and data evaluation. In Mixture toxicity: linking approaches from ecology and human toxicology eds Gestel CAM, Jonker MJ, Kammenga JE, Laskowski R, Svendsen, Chapter 4, p121-156.
  11. Belloum A, Inda MA, Vasunin D, Korkhov V, Zhao Z, Rauwerda H, Breit TM, Bubak M, and Hertzberger LO. Collaborative e-Science experiments and scientific workflows Internet Computing IEEE 2011,July-Aug; 15 (4): 39-47.

2010

  1. Jorg Brunner, Floyd R.A. Wittink, Martijs J. Jonker, Mark de Jong, Timo M. Breit, Marja L. Laine, Johannes J. de Soet and Wim Crielaard The core genome of the anaerobic oral pathogenic bacterium Porphyromonas gingivalis.BMC Microbiol. 2010 Sep 29;10:252.
  2. Stockhammer OW, Rauwerda H, Wittink F, Breit TM, Meijer AH, Spaink HP. Transcriptome analysis of Traf6 function in the innate immune response of zebrafish embryos. Molecular Immunology 2010 Nov-Dec;48(1-3):179-90.
  3. van de Water B, Huijskens I, Jonker M , Breit T, Vrieling, H Predictive Gene-expression Signatures of Non-Genotoxic Carcinogen Responses in Mouse Embryonic Stem Cells Drug metabolomics review 2010 aug;42Sup1; 54-55.
  4. K Boer, JA Gorter, PB Crino, M Nellist, FE Jansen, WGM Spliet, PC van Rijen, FRA Wittink, TM Breit, D Troost, WJ Wadman, E AronicaGene expression analysis of TSC-cortical tubers reveals higher expression levels for cell adhesion and inflammatory factors. Brain Pathol. 2010 Jul;20(4):704-19.
  5. Pouw N, Treffers-Westerlaken E, Kraan J, Wittink FRA, ten Hagen T, Verweij J, Debets R. Combination of IL-21 and IL-15 enhances tumour-specific cytotoxicity and cytokine production of TCR-transduced primary T cells. Cancer Immunol Immunother. 2010 Jun;59(6):921-31.
  6. 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.
  7. Swain S, Wren JF, Sturzenbaum SR, Kille P, Morgan AJ, Jager T, Jonker MJ, Hankard PK, Svendsen C, Owen J, Hedley BA, Blaxter M, Spurgeon DJ. Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans BMC Systems Biology 2010, 4:32.
  8. 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.
  9. 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
  10. 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.
  11. Wassink I, Ooms M, Neerincx P, van der Veer G, Rauwerda H, Leunissen JAM, Breit TM, Nijholt A, van der Vet P. e-BioFlow: Improving Practical Use of Workflow Systems in Bioinformatics ITBAM, Aug/Sept 2010, Bilbao. Lecture Notes in Computer Science, 2010, Volume 6266/2010, 1-15, DOI: 10.1007/978-3-642-15020-3_1

2009

  1. K Boer, PB Crino, M Nellist, JA Gorter,M Nellist, FE Jansen, WGM Spliet, PC van Rijen, FRA Wittink, TM Breit, D Troost, WJ Wadman, E AronicaGene expression analysis of TSC-cortical tubers reveals higher expression levels for cell adhesion and inflammatory factors. Epilepsia2009 Nov;50;357.
  2. 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. Finding transcriptomics biomarkers for in vivo identification 1 of (non-)genotoxic carcinogens using wild-type and Xpa/p53 mutant mouse models. Carcinogenesis 2009 Oct;30(10):1805-12.
  3. Hackenberg C, Engelhardt E, Matthijs HCP, Wittink F, Bauwe H, Kaplan A, Hagemann M Photorespiratory 2-phosphoglycolate metabolism and photoreduction of O2 cooperate in high light acclimation of Synechocystis sp. strain PCC 6803Planta. 2009 Sep;230(4):625-37.
  4. Oomes SJCM, Jonkers M, Wittink F, Hehenkamp JO,Breit, TM, Brul S.The effect of calcium on the transcriptome of sporulating B. subtilis cells. Int J Food Microbiol. 2009 Aug 15;133(3):234-42.
  5. 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. Persistent transcription-blocking DNA lesions trigger somatic growth attenuation associated with longevity. Nat Cell Biol. 2009 May;11(5):604-15.
  6. van Hooff SR, Koster J, Hulsen T, van Schaik BDC, Roos M, van Batenburg MF, Versteeg R, van Kampen AHC.The construction of genome-based transcriptional units. OMICS, 2009 Apr;13(2):105-14.
  7. Bosnacki D, Pronk TE, de Vink EP. In Silico Modelling and Analysis of Ribosome Kinetics and aa-tRNA Competition. Lecture Notes in Bioinformatics: Transactions on Computational System Biology XI. Priami C, Back R-J, Petre I (eds.) Springer Verlag. 2009, pages 69-89.
  8. 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.
  9. Pronk TE, During HJ, Schieving F, Werger MJA Diversity by Temporal Oscillations in Plant Communities with a Differential Timing of Reproduction In: Game Theory: Strategies, Equilibria, and Theorems. Ingrid N. Haugen and Anna S. Nilsen (editors). 2009 pp. 297-317.
  10. 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.
  11. PBT Neerincx, H Rauwerda, H Nie, MAM Groenen, TM Breit, JAM Leunissen OligoRAP – an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity. BMC Proc. 2009 Jul 16; 3 Suppl 4:S4.
  12. I. Wassink, K. Wolstencroft, M. Roos, P.B.T. Neerincx, P. van der Vet, H. Rauwerda, T. Breit Analysing scientific workflows: why workflows not only connect web services. Workshop on Scientific Workflows SWF2009.
  13. W. Fikkert, P. van der Vet, H. Rauwerda, T. Breit and A. Nijholt, Gestures to Intuitively Control Large Displays, in: Advances in Gesture-Based Human-Computer Interaction and Simulation, M. Sales Dias, S. Gibet, M. Wanderley (eds.), revised selected papers, pp. 199-205, Springer Berlin / Heidelberg, Lecture Notes in Computer Science.
  14. Rauwerda H, van der Vet P, Breit TM, Nijholt A. E-BioFlow: Different Perspectives on Scientific Workows. Communications in Computer and Information Science 2009.

2008

  1. Schumacher B, van der Pluijm I, Moorhouse MJ, Kosteas T, Robinson AR, Suh Y, Breit TM, van Steeg H, Niedernhofer LJ, van IJcken W, Bartke A, Spindler SR, Hoeijmakers JH, van der Horst GT, Garinis GA. Delayed and accelerated aging share common longevity assurance mechanisms. PLoS Genet. 2008 Aug 15;4(8):e1000161.
  2. Luppens SB, Kara D, Bandounas L, Jonker MJ, Wittink FR, Bruning O, Breit TM, Ten Cate JM, Crielaard W. Effect of Veillonella parvula on the antimicrobial resistance and gene expression of Streptococcus mutans grown in a dual-species biofilm. Oral Microbiol Immunol. 2008 Jun;23(3):183-189.
  3. Owen J, Hedley BA, Svendsen C, Wren J, Jonker MJ, Hankard PK, Lister LJ, Stürzenbaum SR, Morgan AJ, Spurgeon DJ, Blaxter ML, Kille P. Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus. BMC Genomics 2008 Jun 3;9:266.
  4. Svendsen C, Owen J , Kille P, Wren J, Jonker MJ, Headley BA , Morgan AJ, Blaxter ML, Stürzenbaum SR, Hankard PK, Lister LJ, Spurgeon DJ. Comparative Transcriptomic Responses to Chronic Cadmium, Fluoranthene, and Atrazine Exposure in Lumbricus rubellus. Environ. Sci. Technol. 2008 Jun 1;42(11):4208-4214.
  5. Vroling AB, Jonker MJ, Breit TM, Fokkens WJ, van Drunen CM. Comparison of expression profiles induced by dust mite in airway epithelia reveals a common pathway. Allergy 2008 Apr;63(4):461-467.
  6. 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.
  7. Smit van Dixhoorn MG, Munir R, Sussman G, Stad R, de Haan M, van der Hoeven T, Rauwerda H, Breit TM, Thallinger GG, Wadee AA. Gene expression profiling of suppressor mechanisms in tuberculosis. Mol Immunol. 2008 Mar;45(6):1573-1586.
  8. Vroling AB, Jonker MJ, Luiten S, Breit TM, Fokkens WJ, van Drunen CM. Primary nasal epithelium exposed to house dust mite extract shows activated expression in allergic individuals. Am J Respir Cell Mol Biol. 2008 Mar;38(3):293-299.
  9. Mirabella R, Rauwerda H, Struys EA, Jakobs C, Triantaphylidès C, Haring MA, Schuurink RC. The Arabidopsis her1 mutant implicates GABA in E-2-hexenal responsiveness. Plant J. 2008 Jan;53(2):197-213.
  10. Aronica E, de Boer J, Becker A, Redeker S, Spliet WG, van Rijen PC, Wittink F, Breit TM, Wadman WJ, Lopes da Silva FH, Troost D, Gorter JA. Gene expression profile analysis of epilepsy-associated gangliogliomas. Neuroscience. 2008;151(1):272-292.
  11. Baken KA, Pennings JLA, Jonker MJ, Schaap MM, de Vries A, van Steeg H, Breit TM, van Loveren H. Identification of overlap in gene expression profiles induced by model compounds offers opportunities for immunotoxicity screening. Toxicology and Applied Pharmacology 2008 Jan 1;226(1):46-59.
  12. 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.
  13. 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.
  14. D. Bosnacki, T.E. Pronk, E.P. de Vink, In Silico Modelling and Analysis of Ribosome Kinetics and aa-tRNA Competition, Proc. of COMPMOD 2008, Workshop on Computational Models for Cell Processes, satelite event of FM 2008, Turku, Finland, R.-J. Back and I. Petre (eds.), Turku Centre for Computer Science, pages 23-38, 2008.
  15. Wassink I, Rauwerda H, van der Vet P, Breit TM, Nijholt A. (2008) E-BioFlow: Different Perspectives on Scientific Workflows, Bioinformatics Research and Development, BIRD 2008, 07-09 Jul 2008, Vienna, Austria. pp. 243-257. Communications in Computer and Information Science 13 (XXI). Springer Verlag. ISSN 1865-0929 ISBN 978-3-540-70598-7.
  16. Pronk TE, Polstra S., Pimentel AD, Breit TM. Towards Design Space Exploration for Biological Systems. Journal of Computers 2008 3;1-9.

2007

  1. Banus S, Vandebriel RJ, Pennings JL, Gremmer ER, Wester PW, van Kranen HJ, Breit TM, Demant P, Mooi FR, Hoebee B, Kimman TG. Comparative gene expression profiling in two congenic mouse strains following Bordetella pertussis infection. BMC Microbiol. 2007 Oct 12;7:88.
  2. Bruins W, Jonker M, Bruning O, Pennings J, Schaap M, Hoogervorst E, Speksnijder E, van Steeg H, Breit TM, de Vries A. Delayed expression of Apoptotic and Cell Cycle processes in Carcinogen-Exposed Bladders of Mice lacking p53.S389A Phosphorylation. Carcinogenesis 2007 Aug;28(8):1814-1823.
  3. Banus HA, Pennings JLA, Vandebriel RJ, Wester PW, Breit TM, Mooi FR, Hoebee B, Kimman TG. Lung response to Bordetella pertussis infection in mice identified by gene-expression profiling. Immunogenetics 2007 Jul;59(7):555-564.
  4. Keijser BJF, ter Beek A, Rauwerda H, Schuren F, Montijn R, van der Spek H, Brul S. Analysis of temporal gene expression during Bacillus subtilis spore germination and outgrowth. J. Bacteriol. 2007 May;189(9):3624-3634.
  5. Gorter JA, van Vliet EA, Rauwerda H, Breit TM, Stad R, van Schaik L, Vreugdenhil E, Redeker S, Hendriksen E, Aronica E, Lopes da Silva FH, Wadman WJ. Dynamic changes of proteases and protease inhibitors revealed by microarray analysis in CA3 and entorhinal cortex during epileptogenesis in the rat Journal: Epilepsia 2007 48 Suppl 5:53-64.
  6. Kooter IM, Pennings J, Fokkens P, Leseman D, Boere J, Gerlofs M, Cassee F, Schalk JA, Orzechowski T, Schaap M, Breit TM, Dormans J, van Oostrom C, de Vries A, van Steeg H. Ozone induces clear cellular and molecular responses in the mouse lung independently of the transcription-coupled repair status. J Appl Physiol. 2007 Mar;102(3):1185-1192.
  7. Pronk TE, Pimentel AD, Roos M, Breit TM. Taking the example of computer systems engineering for the analysis of biological cell systems. BioSystems, 2007 Nov-Dec;90(3):623-635.
  8. van der Vet P, Kulyk O, Wassink I, Fikkert FW, Rauwerda H, van Dijk EMAG, van der Veer G, Breit TM, Nijholt A. Smart environments for collaborative design, implementation and interpretation of scientific experiments. In: Proc. Int. Workshop on AI for Human Computing (T. Huang, A. Nijholt, M. Pantic and A. Pentland, Eds.), Twentieth International Joint Conference on Artificial Intelligence, Hyderabad, India 2007, pp. 79-86
  9. 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.
  10. Rauwerda H., de Leeuw, WC, Adriaanse J, Bouwhuis M, van der Vet P, Breit TM. The role of e-BioLabs in a life sciences collaborative working environment. 2007 e-challenges, The Hague, the Netherlands. Published in Expanding the Knowledge Enconomy: Issues, Applications, Case Studies, vol. 4, P. Cunningham and M. Cunningham, Eds.: IOS, Amsterdam, 2007, pp. 866-873.
  11. Pronk TE, de Vink E. Bosnacki D, Breit TM. Stochastic modeling of codon bias with PRISM. Proceedings of the 3rd international workshop on Methods and Tools for Coordinating, Distributed and Mobile Systems MTCoord 2007, Paphos, June 4, 2007, I. Linden and C. Talcott (eds.), Computer Science Department, University of Cyprus, Nicosia, 2007, 15 pages.
  12. Korkhov V, Vasunin D, Wibisono A, Belloum A, Inda MA, Roos M, Breit TM. VLAM-G: Interactive dataflow driven workflow engine for Grid enabled resources. Scientific programming 2007 15(3); 173-188.
  13. Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Ogbuji C, Rees J, Stephens S, Wong G, Wu E, Zaccagnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH. Advancing Translational Research with the Semantic Web, BMC Bioinformatics, Vol. 8, suppl.2, 2007.
  14. Kashyap V, Cheung KH, Doherty D, Samwald M, Marshall MS, Luciano J, Stephens S, Herman I, Hookway R. An ontology based approach for data integration; An application in Biomedical Research. Book Chapter in Cardoso, J., Hepp, M., Lytras, M. (Eds.) "Real-world Applications of Semantic Web Technology and Ontologies", Springer 2007. Hardcover ISBN-10: 0-387-48530-9, ISBN-13: 978-0-387-48530-0
  15. Pronk TE, Polstra S, Pimentel AD, Breit TM. Evaluating the design of biological cells using a computer workbench. Proceedings of the IEEE 40th Annual Simulation Symposium (ANSS) 2007, pages 88-98.

2006 and before

  1. Baken KA, Pennings JLA, Breit TM, de Vries A, van Steeg H,d, van Loveren H, Gene expression profiling of bis(tri-n-butyltin)oxide (TBTO) induced immunotoxicity in mice and rats. Journal of Immunotoxicology 2006 Dec 1;3(4):227-244.
  2. Gorter JA, van Vliet EA, Aronica E, Breit TM, Rauwerda H, Lopes da Silva FH, Wadman WJ. Potential new anti-epileptogenic targets indicated by microarray analysis in a rat model for temporal lobe epilepsy. J Neurosci. 2006 Oct 25;26(43):11083-11110.
  3. Yang XX, Breit TM, Verschure PJ. Dysregulation of gene expression in Huntington's disease by epigenetic changes in chromatin structure. Journal of Neurology Neurosurgery and Psychiatry 2005 Oct;76: Suppl. 4 Abstract
  4. Versteeg R, van Schaik BD, van Batenburg MF, Roos M, Monajemi R, Caron H, Bussemaker HJ, van Kampen AH. The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. Genome Res. 2003 Sep;13(9):1998-2004.
  5. Inda MA, Belloum ASZ, Roos M, Vasunin D, de Laat C, Hertzberger LO, Breit TM. Interactive Workflows in a Virtual Laboratory for e-Bioscience: the SigWin-Detector Tool for Gene Expression Analysis. Proceedings of the second IEEE International Conference on e-Science and Grid Computing (e-Science 2006 Amsterdam), 2006 Dec. 19
  6. Marshall MS, Post L, Roos M, Breit TM. Using semantic web tools to integrate experimental measurement data on our own terms. Conference: International Workshop on Knowledge Systems in Bioinformatics (KSinBIT'06), On the Move to Meaningful Internet Systems Conference 2006 (OTM2006), Montpellier, France, 2006.
  7. Rauwerda H, Roos M, Hertzberger BO, Breit TM. The promise of a virtual lab in drug discovery. Drug Discov Today. 2006 Mar;11(5-6):228-236. Review.
  8. Katrenko S, Marshall MS, Roos M, P. Adriaans. Learning Biological Interactions from Medline Abstracts Conference: Learning Language in Logic (LLL05) Workshop, ICML05, Bonn, Germany, 2005.
  9. Roos M, Jansen MG, Marshall MS, Breit TM. Future application of ontologies in e-Bioscience. W3C Workshop on Semantic Web for Life Sciences 2004. Position paper.
  10. E. C. Kaletas, H. Afsarmanesh, T. M. Breit, and L. O. Hertzberger, "EXPRESSIVE - A Database for Micro-Array Gene Expression Studies", University of Amsterdam, Informatics Intitute, Amsterdam, Technical report CS-2001-02, 2001.