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RNA Biology & Applied Bioinformatics

Publications RNA Biology & Applied Bioinformatics

2017

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. doi: 10.1080/15592324.2017.1293216.

van Hagen M, Piebes DGE, de Leeuw WC, Vuist IM, van Roon-Mom WMC, Moerland PD Verschure PJ. 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.

Fluit, A. C., Jansen, M. D., Bosch, T., Jansen, W. T. M., Schouls, L., Jonker, M. J., & Boel, C. H. E. (2016). rRNA Operon Copy Number Can Explain the Distinct Epidemiology of Hospital-Associated Methicillin-Resistant Staphylococcus aureus. Antimicrobial Agents and Chemotherapy, 60(12), 7313–7320. http://doi.org/10.1128/AAC.01613-16

2016

Mantikou E. Bruning O, Mastenbroek S, Repping S, Breit T, de Jong, M Evaluation of RNA amplification protocols for human oocyte transcriptome analysis. Fertil Steril. 2016 Feb;105(2):511-519

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

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 July 60(7):4229-4236                                     

2015

Gamba P, Jonker MJ, Hamoen, LW. A novel feedback loop that controls bimodal expression of genetic competence. Plos Genetics 2015 Jun 25;11(6):e1005047.

Gawehns, F., Ma, L., Bruning, O., Houterman, P.M., Boeren, S., Cornelissen, B.J., Rep, M. & Takken, F.L. (2015). The effector repertoire of determines the tomato xylem proteome composition following infection. Frontiers in Plant Science, 6, 967. doi: 10.3389/fpls.2015.00967

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 April

Book Chapters

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

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

 

2014

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

Authors: 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

Arch Toxicol. 2014 Apr;88(4):1023-34

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

Authors: 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.

Arch Toxicol. 2014 May 13

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Exploring genetic variation in the tomato Solanum Lycopersicon clade by whole-genome sequencing.

Authors: Sander Peters & the 150 Tomato Genome Consortium

Plant J. 2014 Oct;80(1):136-148

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

Authors: Schaap MM, Wackers PFK, Huijskens I, Jonker M, Hendriks G, Breit TM, van Steeg Water B,H, Luijten M.

Archives of Toxicol. 2014 Oct 2

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

Authors: Tulinski P; Duim B; Wittink FR; Jonker MJ; Breit TM; van Putten JP; Wagenaar JA; Fluit AC. BMC genomics 2014, 15:915

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2013

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

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

J Bacteriol. 2013 Dec;195(24):5450-60

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Root transcript profiling of two Rorippa (Brassicaceae) species reveals gene clusters associated with extreme submergence tolerance.

Authors: Sasidharan R, Mustroph A, Boonman A, Akman M, Ammerlaan AM, Breit T, Schranz ME, Voesenek LA, van Tienderen P.

Plant Physiol. 2013 Nov;163(3):1277-92

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

Authors: de Knegt GJ, Bruning O, ten Kate MT, de Jong M, van Belkum A, Endtz H, Breit TM, Bakker-Woudenberg IAAJM, de Steenwinkel JEM.

Tuberculosis 2013 Jan;93(1):96-101.

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2012

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

Authors: Chikhovskaya, J.V., Jonker, M.J., Meissner, A., Breit, T.M., Repping, S. & Pelt, A.M.M. van

Hum Reprod. 2012 Jan;27(1):210-21

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Low-carbon acclimation in carboxysome less and photorespiratory mutants of the cyanobacterium Synechocystis sp. strain PCC 6803.

Authors: Hackenberg, C., Huege, J., Engelhardt, A., Wittink, F., Laue, M., Matthijs, H.C.P., Kopka, J., Bauwe, H. & Hagemann, M.

Microbiology, 2012 Feb;158(Pt 2):398-413

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Combining Next-Generation Sequencing and Microarray Technology into a Transcriptomics Approach for the Non-Model Organism Chironomus riparius.

Authors: Marinkovic, M., Leeuw, W.C. de, Jong, M. de, Kraak, M.H., Admiraal, W., Breit, T.M. & Jonker, M.J.

PLoS One, 2012;7(10):e48096

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Gene Expression Patterns and Life Cycle Responses of Toxicant-Exposed Chironomids.

Authors: Marinkovic, M., Leeuw, W.C. de, Ensink, W.A., Jong, M. de, Breit, T.M., Admiraal, W., Kraak, M.H. & Jonker, M.J.

Environ Sci Technol. 2012 Nov 20;46(22):12679-86

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Response of the Nonbiting Midge Chironomus riparius to Multigeneration Toxicant Exposure.

Authors: Marinkovic, M., Bruijn, K. de, Asselman, M., Bogaert, M., Jonker, M.J., Kraak, M.H. & Admiraal, W

Environ Sci Technol. 2012 Nov 6;46(21):12105-11

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

Authors: Roschmann, K.I., Kuijen, A.M. van, Luiten, S., Jonker, M.J., Breit, T.M., Fokkens, W.J., Petersen, A. & Drunen, C.M. van

Clin Exp Allergy. 2012 Oct;42(10):1479-90

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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.

Authors: Röschmann, K.I.L., Kuijen, A.M. van, Luiten, S., Jonker, M.J., Breit, T.M., Fokkens, W.J., Petersen, A. & Drunen, C.M. van

Clinical and experimental immunology, 167(3), 413-421.

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

Authors: Schaap, M.M., Zwart, E.P., Wackers, P.F., Huijskens, I., Water, B. van de, Breit, T.M., Steeg, H. van, Jonker, M.J. & Luijten, M.

Arch Toxicol. 2012 Nov;86(11):1717-27

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2011

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

Authors: Yuan, X., Jonker, M.J., Wilde, J. de, Verhoef, A., Wittink, F.R.A., Benthem, J. van, Bessems, J.G., Hakkert, B.C., Kuiper, R.V., Steeg, H. van, Breit, T.M. & Luijten, M.

J Appl Toxicol. 2011 Jul;31(5):421-30

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

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

Clin Exp Allergy. 2011 Jun;41(6):830-41

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Life cycle responses of the midge Chironomus riparius to compounds with different modes of action

Authors: Marinković M, Verweij R, Nummerdor G, Jonker M, Kraak M, Admiraal W.

Environmental Science & Technology 2011, 45, 1645–1651

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Interorgan coordination of the murine adaptive response to fasting

Authors: Hakvoort TBM, Moerland PD, Frijters R, Sokolović A, Labruyère WT, Vermeulen JLM, Ver Loren van Themaat E, Breit TM, Wittink FRA, van Kampen A, Verhoeven AJ, Lamers WH, Sokolović M

J Biol Chem. 2011 May 6;286(18):16332-43

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

Authors: 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.

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

Authors: 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

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Single cell transcriptomics of neighboring hyphae of Aspergillus niger

Authors: de Bekker C, Bruning O, Jonker MJ, Breit TM, Wosten HA.

Genome Biol. 2011 Aug 4;12(8):R71

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Collaborative e-Science experiments and scientific workflows

Authors: Belloum A, Inda MA, Vasunin D, Korkhov V, Zhao Z, Rauwerda H, Breit TM, Bubak M, and Hertzberger LO.

Internet Computing IEEE 2011, July-Aug; 15 (4): 39-47

2010

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

Authors: 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

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The core genome of the anaerobic oral pathogenic bacterium Porphyromonas gingivalis

Authors: 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

BMC Microbiol. 2010 Sep 29;10:252

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

Authors:  Stockhammer OW, Rauwerda H, Wittink F, Breit TM, Meijer AH, Spaink HP.

Mol Immunol. 2010 Nov-Dec;48(1-3):179-90

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Predictive Gene-expression Signatures of Non-Genotoxic Carcinogen Responses in Mouse Embryonic Stem Cells

Authors:  van de Water B, Huijskens I, Jonker M , Breit T, Vrieling, H

Drug metabolomics review 2010 aug;42Sup1; 54-55

 

e-BioFlow: Improving Practical Use of Workflow Systems in Bioinformatics ITBAM

Authors:  Wassink I, Ooms M, Neerincx P, van der Veer G, Rauwerda H, Leunissen JAM, Breit TM, Nijholt A, van der Vet P.

Bilbao. Lecture Notes in Computer Science, 2010, Volume 6266/2010, 1-15

 

Combination of IL-21 and IL-15 enhances tumour-specific cytotoxicity and cytokine production of TCR-transduced primary T cells

Authors: Pouw N, Treffers-Westerlaken E, Kraan J, Wittink F, ten Hagen T, Verweij J, Debets R.

Cancer Immunol Immunother. 2010 Jun;59(6):921-31.

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Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans

Authors: Swain S, Wren JF, Stürzenbaum SR, Kille P, Morgan AJ, Jager T, Jonker MJ, Hankard PK, Svendsen C, Owen J, Hedley BA, Blaxter M, Spurgeon DJ

BMC Syst Biol. 2010 Mar 23;4:32

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2009

Finding transcriptomics biomarkers for in vivo identification 1 of (non-)genotoxic carcinogens using wild-type and Xpa/p53 mutant mouse models

Authors: 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

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In Silico Modelling and Analysis of Ribosome Kinetics and aa-tRNA Competition.

Authors: Bosnacki D, Pronk TE, de Vink EP

Lecture Notes in Bioinformatics: Transactions on Computational System Biology XI. Priami C, Back R-J, Petre I (eds.) Springer Verlag. 2009, pages 69-89.

 

Analysing scientific workflows: why workflows not only connect web services. 

Authors: I. Wassink, K. Wolstencroft, M. Roos, P.B.T. Neerincx, P. van der Vet, H. Rauwerda, T. Breit

Workshop on Scientific Workflows SWF

 

Gestures to Intuitively Control Large Displays, in: Advances in Gesture-Based Human-Computer Interaction and Simulation.

Authors: W. Fikkert, P. van der Vet, H. Rauwerda, T. Breit and A. Nijholt

M. revised selected papers, pp. 199-205, Springer Berlin / Heidelberg, Lecture Notes in Computer Science.

 

E-BioFlow: Different Perspectives on Scientific Workows

Authors: Wassink I, Rauwerda H, van der Vet P, Breit TM, Nijholt A.

Communications in Computer and Information Science 2009. 

 

Photorespiratory 2-phosphoglycolate metabolism and photoreduction of O2 cooperate in high light acclimation of Synechocystis sp. strain PCC 6803

Authors: Hackenberg C, Engelhardt E, Matthijs HCP, Wittink F, Bauwe H, Kaplan A, Hagemann M

Planta. 2009 Sep;230(4):625-37

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

Authors: Oomes SJCM, Jonkers M, Wittink F, Hehenkamp JO, Breit TM, Brul S.

Int J Food Microbiol. 2009 Aug 15;133(3):234-42

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

Authors: 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

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The construction of genome-based transcriptional units

Authors: van Hooff SR, Koster J, Hulsen T, van Schaik BDC, Roos M, van Batenburg MF, Versteeg R, van Kampen AHC

OMICS, 2009 Apr;13(2):105-114

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Diversity by Temporal Oscillations in Plant Communities with a Differential Timing of Reproduction

Authors: Pronk TE, During HJ, Schieving F, Werger MJA

In: Game Theory: Strategies, Equilibria, and Theorems. Ingrid N. Haugen and Anna S. Nilsen (editors) 2009 pp. 297-317

 

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

Authors: PBT Neerincx, H Rauwerda, H Nie, MAM Groenen, TM Breit, JAM Leunissen

BMC Proc. 2009 Jul 16;3 Suppl 4:S4

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2008

Delayed and accelerated aging share common longevity assurance mechanisms

Authors: 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

PLoS Genet. 2008 Aug 15;4(8):e1000161

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In Silico Modelling and Analysis of Ribosome Kinetics and aa-tRNA Competition

Authors: D. Bosnacki, T.E. Pronk, E.P. de Vink

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 

 

Effect of Veillonella parvula on the antimicrobial resistance and gene expression of Streptococcus mutans grown in a dual-species biofilm

Authors: Luppens SB, Kara D, Bandounas L, Jonker MJ, Wittink F, Bruning O, Breit TM, ten Cate JM, Crielaard W.

Oral Microbiol Immunol. 2008 Jun;23(3):183-9

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Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus

Authors: Owen J, Hedley BA, Svendsen C, Wren J, Jonker MJ, Hankard PK, Lister LJ, Stürzenbaum SR, Morgan AJ, Spurgeon DJ, Blaxter ML, Kille P.

BMC Genomics. 2008 Jun 3;9:266

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Comparative Transcriptomic Responses to Chronic Cadmium, Fluoranthene, and Atrazine Exposure in Lumbricus rubellus

Authors: Svendsen C, Owen J , Kille P, Wren J, Jonker MJ, Headley BA , Morgan AJ, Blaxter ML, Stürzenbaum SR, Hankard PK, Lister LJ, Spurgeon DJ.

Environ. Sci. Technol. 2008 Jun 1;42(11):4208-4214

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Comparison of expression profiles induced by dust mite in airway epithelia reveals a common pathway

Authors: Vroling AB, Jonker MJ, Breit TM, Fokkens WJ, van Drunen CM.

Allergy 2008 Apr;63(4):461-467

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Gene Expression Profiling Of Suppressor Mechanisms In Tuberculosis

Authors: Smit van Dixhoorn MGA, Munir R, Stad R, de Haan M, van der Hoeven T, Rauwerda H, Breit TM, Thallinger GG, Wadee AA.

Mol Immunol. 2008 Mar;45(6):1573-86

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Primary nasal epithelium exposed to house dust mite extract shows activated expression in allergic individuals

Authors: Vroling AB, Jonker MJ, Luiten S, Breit TM, Fokkens WJ, van Drunen CM.

Am J Respir Cell Mol Biol. 2008 Mar;38(3):293-9

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The Arabidopsis her1 mutant implicates GABA in E-2-hexenal responsiveness

Authors: Mirabella R, Rauwerda H, Struys EA, Jakobs C, Triantaphylidès C, Haring MA, Schuurink RC.

Plant J. 2008 Jan;53(2):197-213

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Gene expression profile analysis of epilepsy-associated gangliogliomas

Authors: Aronica E, Boer K, Becker A, Redeker S, Spliet WGM, van Rijen PC, Wittink F, Breit TM, Wadman WJ, Gorter JA.

Neuroscience. 2008 Jan 2;151(1):272-92

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Overlapping gene expression profiles of model compounds provide opportunities for immunotoxicity screening

Authors: Baken KA, Pennings JL, Jonker MJ, Schaap MM, de Vries A, van Steeg H, Breit TM, van Loveren H.

Toxicol Appl Pharmacol. 2008 Jan 1;226(1):46-59

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E-BioFlow: Different Perspectives on Scientific Workflows

Authors: Wassink I, Rauwerda H, van der Vet P, Breit TM, Nijholt A.

Bioinformatics Research and Development, BIRD 2008, Vienna, Austria. Communications in Computer and Information Science 13 (XXI). Springer Verlag. ISSN 1865-0929 ISBN 978-3-540-70598-7 07-09 Jul 2008 pp. 243-257

2007

Comparative gene expression profiling in two congenic mouse strains following Bordetella pertussis infection

Authors: Banus S, Vandebriel RJ, Pennings JL, Gremmer ER, Wester PW, van Kranen HJ, Breit TM, Demant P, Mooi FR, Hoebee B, Kimman TG

BMC microbiology 2007 Oct 12;7:88

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Smart environments for collaborative design, implementation and interpretation of scientific experiments.

Authors: van der Vet P, Kulyk O, Wassink I, Fikkert FW, Rauwerda H, van Dijk EMAG, van der Veer G, Breit TM, Nijholt A.

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

 

Stochastic modeling of codon bias with PRISM

Authors: Pronk TE, de Vink E. Bosnacki D, Breit TM.

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.

 

Evaluating the design of biological cells using a computer workbench.

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

Proceedings of the IEEE 40th Annual Simulation Symposium (ANSS) 2007, pages 88-98.

 

Delayed expression of Apoptotic and Cell Cycle processes in Carcinogen-Exposed Bladders of Mice lacking p53.S389A Phosphorylation

Authors: Bruins W, Jonker MJ, Bruning O, Pennings J, Schaap M, Hoogervorst E, Speksnijder E, van Steeg H, Breit TM, de Vries A

Carcinogenesis. 2007 Aug;28(8):1814-23.

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Lung response to Bordetella pertussis infection in mice identified by gene-expression profiling

Authors: Banus HA, Pennings JLA, Vandebriel RJ, Wester PW, Breit TM, Mooi FR, Hoebee B, Kimman TG

Immunogenetics. 2007 Jul;59(7):555-64

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Analysis of temporal gene expression during Bacillus subtilis spore germination and outgrowth

Authors: Keijser BJF, ter Beek A, Rauwerda H, Schuren F, Montijn R, van der Spek H, Brul S

J. Bacteriol. 2007, May;189(9):3624-3634

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Dynamic changes of proteases and protease inhibitors revealed by microarray analysis in CA3 and entorhinal cortex during epileptogenesis in the rat

Authors: 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

Epilepsia 2007 48 Suppl 5:53-64

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Ozone induces clear cellular and molecular responses in the mouse lung independently of the transcription-coupled repair status

Authors: 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

J Appl Physiol. 2007, Mar;102(3):1185-92

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Taking the example of computer systems engineering for the analysis of biological cell systems

Authors: Pronk TE, Pimentel AD, Roos M, Breit TM

Biosystems. 2007 Nov-Dec;90(3):623-35

 

The role of e-BioLabs in a life sciences collaborative working environment

Authors: Rauwerda H, de Leeuw WC, Adriaanse J, Bouwhuis M, van der Vet P, Breit TM

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

 

VLAM-G: Interactive dataflow driven workflow engine for Grid enabled resources

Authors: Korkhov V, Vasunin D, Wibisono A, Belloum A, Inda MA, Roos M, Breit TM

Scientific programming 2007 15(3); 173-188

 

Advancing Translational Research with the Semantic Web

Authors: 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

BMC Bioinformatics. 2007 May 9;8 Suppl 3:S2

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An ontology based approach for data integration; An application in Biomedical Research

Authors: Kashyap V, Cheung KH, Doherty D, Samwald M, Marshall MS, Luciano J, Stephens S, Herman I, Hookway R. 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

2006

Gene expression profiling of bis(tri-n-butyltin)oxide (TBTO) induced immunotoxicity in mice and rats

Authors: Baken KA, Pennings JLA, Breit TM, de Vries A, van Steeg H, van Loveren H

Journal of Immunotoxicology 2006 Dec 1;3(4):227-244

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Interactive Workflows in a Virtual Laboratory for e-Bioscience: the SigWin-Detector Tool for Gene Expression Analysis. 

Authors: Inda MA, Belloum ASZ, Roos M, Vasunin D, de Laat C, Hertzberger LO, Breit TM.

Proceedings of the second IEEE International Conference on e-Science and Grid Computing (e-Science 2006 Amsterdam), 2006 Dec. 19

 

Using semantic web tools to integrate experimental measurement data on our own terms. 

Authors: Marshall MS, Post L, Roos M, Breit TM.

Conference: International Workshop on Knowledge Systems in Bioinformatics (KSinBIT'06), On the Move to Meaningful Internet Systems Conference 2006 (OTM2006), Montpellier, France, 2006. 

 

Potential new anti-epileptogenic targets indicated by microarray analysis in a rat model for temporal lobe epilepsy

Authors: Gorter JA, van Vliet EA, Aronica E, Breit TM, Rauwerda H, Lopes da Silva FH, Wadman WJ

J Neurosci. 2006, Oct 25;26(43):11083-11110

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The promise of a virtual lab in drug discovery

Authors: Rauwerda H, Roos M, Hertzberger LO, Breit TM

Drug Discov Today. 2006 Mar;11(5-6):228-36

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2005

Dysregulation of gene expression in Huntington's disease by epigenetic changes in chromatin structure.

Authors: Yang XX, Breit TM, Verschure PJ.

Journal of Neurology Neurosurgery and Psychiatry 2005 Oct;76:

 

Learning Biological Interactions from Medline Abstracts Conference: Learning Language in Logic (LLL05)

Authors: Katrenko S, Marshall MS, Roos M, P. Adriaans

Workshop, ICML05, Bonn, Germany

2004

The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes.

Authors: Versteeg R, van Schaik BD, van Batenburg MF, Roos M, Monajemi R, Caron H, Bussemaker HJ, van Kampen AH

Genome Res. 2003 Sep;13(9):1998-2004.

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Future application of ontologies in e-Bioscience 

Authors: Roos M, Jansen MG, Marshall MS, Breit TM

W3C Workshop on Semantic Web for Life Sciences

 

 

 2001

EXPRESSIVE - A Database for Micro-Array Gene Expression Studies

Authors: E. C. Kaletas, H. Afsarmanesh, T. M. Breit, and L. O. Hertzberger

University of Amsterdam, Informatics Intitute, Technical report CS-2001-02, 2001.