list of publications 2006 - 2016

Version 1


1: Tark-Dame M, Jerabek H, Manders EM, van der Wateren IM, Heermann DW, van Driel
R. Depletion of the chromatin looping proteins CTCF and cohesin causes chromatin 
compaction: insight into chromatin folding by polymer modelling. PLoS Comput
Biol. 2014 Oct 9;10(10):e1003877. doi: 10.1371/journal.pcbi.1003877. eCollection 
2014 Oct. Erratum in: PLoS Comput Biol. 2016 Jan;12(1):e1004716. van der Wateren,
Ingrid M [added]. PubMed PMID: 25299688; PubMed Central PMCID: PMC4191888.


2: Verbruggen P, Heinemann T, Manders E, von Bornstaedt G, van Driel R, Höfer T. 
Robustness of DNA repair through collective rate control. PLoS Comput Biol. 2014 
Jan 30;10(1):e1003438. doi: 10.1371/journal.pcbi.1003438. eCollection 2014 Jan.
PubMed PMID: 24499930; PubMed Central PMCID: PMC3907289.


3: Brink MC, Piebes DG, de Groote ML, Luijsterburg MS, Casas-Delucchi CS, van
Driel R, Rots MG, Cardoso MC, Verschure PJ. A role for MeCP2 in switching gene
activity via chromatin unfolding and HP1γ displacement. PLoS One. 2013 Jul
23;8(7):e69347. doi: 10.1371/journal.pone.0069347. Print 2013. PubMed PMID:
23935992; PubMed Central PMCID: PMC3720725.


4: Swierstra T, Vermeulen N, Braeckman J, van Driel R. Rethinking the life
sciences. To better serve society, biomedical research has to regain its trust
and get organized to tackle larger projects. EMBO Rep. 2013 Apr;14(4):310-4. doi:
10.1038/embor.2013.30. Epub 2013 Mar 19. PubMed PMID: 23507979; PubMed Central
PMCID: PMC3615664.


5: Van Driel R, Trask C, Johnson PW, Callaghan JP, Koehoorn M, Teschke K.
Anthropometry-corrected exposure modeling as a method to improve trunk posture
assessment with a single inclinometer. J Occup Environ Hyg. 2013;10(3):143-54.
doi: 10.1080/15459624.2012.757479. PubMed PMID: 23351120.


6: van Driel R, Verschure PJ. Nuclear Organization and Gene Expression:
Visualization of Transcription and Higher Order Chromatin Structure. Mapping
Protein/DNA Interactions by Cross-Linking [Internet]. Paris: Institut national de
la santé et de la recherche médicale; 2001. Available from
http://www.ncbi.nlm.nih.gov/books/NBK7101/
PubMed PMID: 21413360.


7: Tark-Dame M, van Driel R, Heermann DW. Chromatin folding--from biology to
polymer models and back. J Cell Sci. 2011 Mar 15;124(Pt 6):839-45. doi:
10.1242/jcs.077628. PubMed PMID: 21378305.


8: Tessadori F, Zeng K, Manders E, Riool M, Jackson D, van Driel R. Stable
S/MAR-based episomal vectors are regulated at the chromatin level. Chromosome
Res. 2010 Nov;18(7):757-75. doi: 10.1007/s10577-010-9165-4. Epub 2010 Nov 16.
PubMed PMID: 21080054; PubMed Central PMCID: PMC2996544.


9: Niedojadlo J, Perret-Vivancos C, Kalland KH, Cmarko D, Cremer T, van Driel R, 
Fakan S. Transcribed DNA is preferentially located in the perichromatin region of
mammalian cell nuclei. Exp Cell Res. 2011 Feb 15;317(4):433-44. doi:
10.1016/j.yexcr.2010.10.026. Epub 2010 Nov 5. PubMed PMID: 21056558.


10: van Zanten M, Tessadori F, McLoughlin F, Smith R, Millenaar FF, van Driel R, 
Voesenek LA, Peeters AJ, Fransz P. Photoreceptors CRYTOCHROME2 and phytochrome B 
control chromatin compaction in Arabidopsis. Plant Physiol. 2010
Dec;154(4):1686-96. doi: 10.1104/pp.110.164616. Epub 2010 Oct 8. PubMed PMID:
20935177; PubMed Central PMCID: PMC2996035.


11: Haring M, Bader R, Louwers M, Schwabe A, van Driel R, Stam M. The role of DNA
methylation, nucleosome occupancy and histone modifications in paramutation.
Plant J. 2010 Aug;63(3):366-78. doi: 10.1111/j.1365-313X.2010.04245.x. Epub 2010 
Apr 29. PubMed PMID: 20444233.


12: Luijsterburg MS, von Bornstaedt G, Gourdin AM, Politi AZ, Moné MJ, Warmerdam 
DO, Goedhart J, Vermeulen W, van Driel R, Höfer T. Stochastic and reversible
assembly of a multiprotein DNA repair complex ensures accurate target site
recognition and efficient repair. J Cell Biol. 2010 May 3;189(3):445-63. doi:
10.1083/jcb.200909175. PubMed PMID: 20439997; PubMed Central PMCID: PMC2867314.


13: Tessadori F, van Zanten M, Pavlova P, Clifton R, Pontvianne F, Snoek LB,
Millenaar FF, Schulkes RK, van Driel R, Voesenek LA, Spillane C, Pikaard CS,
Fransz P, Peeters AJ. Phytochrome B and histone deacetylase 6 control
light-induced chromatin compaction in Arabidopsis thaliana. PLoS Genet. 2009
Sep;5(9):e1000638. doi: 10.1371/journal.pgen.1000638. Epub 2009 Sep 4. PubMed
PMID: 19730687; PubMed Central PMCID: PMC2728481.


14: Louwers M, Splinter E, van Driel R, de Laat W, Stam M. Studying physical
chromatin interactions in plants using Chromosome Conformation Capture (3C). Nat 
Protoc. 2009;4(8):1216-29. doi: 10.1038/nprot.2009.113. Epub 2009 Jul 30. PubMed 
PMID: 19644461.


15: Louwers M, Bader R, Haring M, van Driel R, de Laat W, Stam M. Tissue- and
expression level-specific chromatin looping at maize b1 epialleles. Plant Cell.
2009 Mar;21(3):832-42. doi: 10.1105/tpc.108.064329. Epub 2009 Mar 31. PubMed
PMID: 19336692; PubMed Central PMCID: PMC2671708.


16: Luijsterburg MS, Dinant C, Lans H, Stap J, Wiernasz E, Lagerwerf S, Warmerdam
DO, Lindh M, Brink MC, Dobrucki JW, Aten JA, Fousteri MI, Jansen G, Dantuma NP,
Vermeulen W, Mullenders LH, Houtsmuller AB, Verschure PJ, van Driel R.
Heterochromatin protein 1 is recruited to various types of DNA damage. J Cell
Biol. 2009 May 18;185(4):577-86. doi: 10.1083/jcb.200810035. PubMed PMID:
19451271; PubMed Central PMCID: PMC2711568.


17: Dinant C, Luijsterburg MS, Höfer T, von Bornstaedt G, Vermeulen W,
Houtsmuller AB, van Driel R. Assembly of multiprotein complexes that control
genome function. J Cell Biol. 2009 Apr 6;185(1):21-6. doi: 10.1083/jcb.200811080.
Epub 2009 Mar 30. Review. PubMed PMID: 19332890; PubMed Central PMCID:
PMC2700518.


18: Mateos-Langerak J, Bohn M, de Leeuw W, Giromus O, Manders EM, Verschure PJ,
Indemans MH, Gierman HJ, Heermann DW, van Driel R, Goetze S. Spatially confined
folding of chromatin in the interphase nucleus. Proc Natl Acad Sci U S A. 2009
Mar 10;106(10):3812-7. doi: 10.1073/pnas.0809501106. Epub 2009 Feb 20. PubMed
PMID: 19234129; PubMed Central PMCID: PMC2656162.


19: Solimando L, Luijsterburg MS, Vecchio L, Vermeulen W, van Driel R, Fakan S.
Spatial organization of nucleotide excision repair proteins after UV-induced DNA 
damage in the human cell nucleus. J Cell Sci. 2009 Jan 1;122(Pt 1):83-91. doi:
10.1242/jcs.031062. Epub 2008 Dec 9. PubMed PMID: 19066286.


20: Luijsterburg MS, White MF, van Driel R, Dame RT. The major architects of
chromatin: architectural proteins in bacteria, archaea and eukaryotes. Crit Rev
Biochem Mol Biol. 2008 Nov-Dec;43(6):393-418. doi: 10.1080/10409230802528488 .
Review. PubMed PMID: 19037758.


21: Yang S, Illner D, Teller K, Solovei I, van Driel R, Joffe B, Cremer T, Eils
R, Rohr K. Structural analysis of interphase X-chromatin based on statistical
shape theory. Biochim Biophys Acta. 2008 Nov;1783(11):2089-99. doi:
10.1016/j.bbamcr.2008.08.007. Epub 2008 Aug 30. PubMed PMID: 18789978.


22: Gladilin E, Goetze S, Mateos-Langerak J, VAN Driel R, Eils R, Rohr K. Shape
normalization of 3D cell nuclei using elastic spherical mapping. J Microsc. 2008 
Jul;231(Pt 1):105-14. doi: 10.1111/j.1365-2818.2008.02021.x. PubMed PMID:
18638194.


23: Kanger JS, Subramaniam V, van Driel R. Intracellular manipulation of
chromatin using magnetic nanoparticles. Chromosome Res. 2008;16(3):511-22. doi:
10.1007/s10577-008-1239-1. Review. PubMed PMID: 18461487.


24: Bruggeman FJ, Oancea I, van Driel R. Exploring the behavior of small
eukaryotic gene networks. J Theor Biol. 2008 Jun 7;252(3):482-7. doi:
10.1016/j.jtbi.2008.02.024. Epub 2008 Feb 25. PubMed PMID: 18433776.


25: Tan J, Lancaster M, Hyatt A, van Driel R, Wong F, Warner S. Purification of a
herpes-like virus from abalone (Haliotis spp.) with ganglioneuritis and detection
by transmission electron microscopy. J Virol Methods. 2008 May;149(2):338-41.
doi: 10.1016/j.jviromet.2007.12.019. PubMed PMID: 18374425.


26: Bohn M, Heermann DW, van Driel R. Random loop model for long polymers. Phys
Rev E Stat Nonlin Soft Matter Phys. 2007 Nov;76(5 Pt 1):051805. Epub 2007 Nov 27.
PubMed PMID: 18233679.


27: Cowled C, Melville L, Weir R, Walsh S, Hyatt A, Van Driel R, Davis S, Gubala 
A, Boyle D. Genetic and epidemiological characterization of Middle Point
orbivirus, a novel virus isolated from sentinel cattle in northern Australia. J
Gen Virol. 2007 Dec;88(Pt 12):3413-22. PubMed PMID: 18024911.


28: van Driel R. Chromatin is wonderful stuff. Semin Cell Dev Biol. 2007
Oct;18(5):649-50. Epub 2007 Oct 7. PubMed PMID: 17964198.


29: Fakan S, van Driel R. The perichromatin region: a functional compartment in
the nucleus that determines large-scale chromatin folding. Semin Cell Dev Biol.
2007 Oct;18(5):676-81. Epub 2007 Aug 25. Review. PubMed PMID: 17920313.


30: Goetze S, Mateos-Langerak J, van Driel R. Three-dimensional genome
organization in interphase and its relation to genome function. Semin Cell Dev
Biol. 2007 Oct;18(5):707-14. Epub 2007 Aug 25. Review. PubMed PMID: 17905616.


31: Post LJ, Roos M, Marshall MS, van Driel R, Breit TM. A semantic web approach 
applied to integrative bioinformatics experimentation: a biological use case with
genomics data. Bioinformatics. 2007 Nov 15;23(22):3080-7. Epub 2007 Sep 19.
PubMed PMID: 17881406.


32: Mateos-Langerak J, Goetze S, Leonhardt H, Cremer T, van Driel R, Lanctôt C.
Nuclear architecture: Is it important for genome function and can we prove it? J 
Cell Biochem. 2007 Dec 1;102(5):1067-75. Review. PubMed PMID: 17786936.


33: Gierman HJ, Indemans MH, Koster J, Goetze S, Seppen J, Geerts D, van Driel R,
Versteeg R. Domain-wide regulation of gene expression in the human genome. Genome
Res. 2007 Sep;17(9):1286-95. Epub 2007 Aug 10. PubMed PMID: 17693573; PubMed
Central PMCID: PMC1950897.


34: Luijsterburg MS, Goedhart J, Moser J, Kool H, Geverts B, Houtsmuller AB,
Mullenders LH, Vermeulen W, van Driel R. Dynamic in vivo interaction of DDB2 E3
ubiquitin ligase with UV-damaged DNA is independent of damage-recognition protein
XPC. J Cell Sci. 2007 Aug 1;120(Pt 15):2706-16. Epub 2007 Jul 17. PubMed PMID:
17635991.


35: Tessadori F, Schulkes RK, van Driel R, Fransz P. Light-regulated large-scale 
reorganization of chromatin during the floral transition in Arabidopsis. Plant J.
2007 Jun;50(5):848-57. Epub 2007 Apr 23. PubMed PMID: 17470059.


36: de Vries AH, Krenn BE, van Driel R, Subramaniam V, Kanger JS. Direct
observation of nanomechanical properties of chromatin in living cells. Nano Lett.
2007 May;7(5):1424-7. Epub 2007 Apr 24. PubMed PMID: 17451276.


37: Goetze S, Mateos-Langerak J, Gierman HJ, de Leeuw W, Giromus O, Indemans MH, 
Koster J, Ondrej V, Versteeg R, van Driel R. The three-dimensional structure of
human interphase chromosomes is related to the transcriptome map. Mol Cell Biol. 
2007 Jun;27(12):4475-87. Epub 2007 Apr 9. PubMed PMID: 17420274; PubMed Central
PMCID: PMC1900058.


38: Tessadori F, Chupeau MC, Chupeau Y, Knip M, Germann S, van Driel R, Fransz P,
Gaudin V. Large-scale dissociation and sequential reassembly of pericentric
heterochromatin in dedifferentiated Arabidopsis cells. J Cell Sci. 2007 Apr
1;120(Pt 7):1200-8. PubMed PMID: 17376962.


39: Mateos-Langerak J, Brink MC, Luijsterburg MS, van der Kraan I, van Driel R,
Verschure PJ. Pericentromeric heterochromatin domains are maintained without
accumulation of HP1. Mol Biol Cell. 2007 Apr;18(4):1464-71. Epub 2007 Feb 21.
PubMed PMID: 17314413; PubMed Central PMCID: PMC1838966.


40: Zotter A, Luijsterburg MS, Warmerdam DO, Ibrahim S, Nigg A, van Cappellen WA,
Hoeijmakers JH, van Driel R, Vermeulen W, Houtsmuller AB. Recruitment of the
nucleotide excision repair endonuclease XPG to sites of UV-induced dna damage
depends on functional TFIIH. Mol Cell Biol. 2006 Dec;26(23):8868-79. Epub 2006
Sep 25. PubMed PMID: 17000769; PubMed Central PMCID: PMC1636808.


41: Brink MC, van der Velden Y, de Leeuw W, Mateos-Langerak J, Belmont AS, van
Driel R, Verschure PJ. Truncated HP1 lacking a functional chromodomain induces
heterochromatinization upon in vivo targeting. Histochem Cell Biol. 2006
Jan;125(1-2):53-61. Epub 2005 Nov 10. PubMed PMID: 16283356.