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Items: 1 to 50 of 176

1.

Depletion of the chromatin looping proteins CTCF and cohesin causes chromatin compaction: insight into chromatin folding by polymer modelling.

Tark-Dame M, Jerabek H, Manders EM, van der Wateren IM, Heermann DW, van Driel R.

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].

2.

Robustness of DNA repair through collective rate control.

Verbruggen P, Heinemann T, Manders E, von Bornstaedt G, van Driel R, Höfer T.

PLoS Comput Biol. 2014 Jan 30;10(1):e1003438. doi: 10.1371/journal.pcbi.1003438. eCollection 2014 Jan.

3.

A role for MeCP2 in switching gene activity via chromatin unfolding and HP1γ displacement.

Brink MC, Piebes DG, de Groote ML, Luijsterburg MS, Casas-Delucchi CS, van Driel R, Rots MG, Cardoso MC, Verschure PJ.

PLoS One. 2013 Jul 23;8(7):e69347. doi: 10.1371/journal.pone.0069347. Print 2013.

4.

Rethinking the life sciences. To better serve society, biomedical research has to regain its trust and get organized to tackle larger projects.

Swierstra T, Vermeulen N, Braeckman J, van Driel R.

EMBO Rep. 2013 Apr;14(4):310-4. doi: 10.1038/embor.2013.30. Epub 2013 Mar 19. No abstract available.

5.

Anthropometry-corrected exposure modeling as a method to improve trunk posture assessment with a single inclinometer.

Van Driel R, Trask C, Johnson PW, Callaghan JP, Koehoorn M, Teschke K.

J Occup Environ Hyg. 2013;10(3):143-54. doi: 10.1080/15459624.2012.757479.

PMID:
23351120
6.

Nuclear Organization and Gene Expression: Visualization of Transcription and Higher Order Chromatin Structure.

van Driel R, Verschure PJ.

Mapping Protein/DNA Interactions by Cross-Linking [Internet]. Paris: Institut national de la santé et de la recherche médicale; 2001.

7.

Chromatin folding--from biology to polymer models and back.

Tark-Dame M, van Driel R, Heermann DW.

J Cell Sci. 2011 Mar 15;124(Pt 6):839-45. doi: 10.1242/jcs.077628.

8.

Stable S/MAR-based episomal vectors are regulated at the chromatin level.

Tessadori F, Zeng K, Manders E, Riool M, Jackson D, van Driel R.

Chromosome Res. 2010 Nov;18(7):757-75. doi: 10.1007/s10577-010-9165-4. Epub 2010 Nov 16.

9.

Transcribed DNA is preferentially located in the perichromatin region of mammalian cell nuclei.

Niedojadlo J, Perret-Vivancos C, Kalland KH, Cmarko D, Cremer T, van Driel R, Fakan S.

Exp Cell Res. 2011 Feb 15;317(4):433-44. doi: 10.1016/j.yexcr.2010.10.026. Epub 2010 Nov 5.

PMID:
21056558
10.

Photoreceptors CRYTOCHROME2 and phytochrome B control chromatin compaction in Arabidopsis.

van Zanten M, Tessadori F, McLoughlin F, Smith R, Millenaar FF, van Driel R, Voesenek LA, Peeters AJ, Fransz P.

Plant Physiol. 2010 Dec;154(4):1686-96. doi: 10.1104/pp.110.164616. Epub 2010 Oct 8.

11.

The role of DNA methylation, nucleosome occupancy and histone modifications in paramutation.

Haring M, Bader R, Louwers M, Schwabe A, van Driel R, Stam M.

Plant J. 2010 Aug;63(3):366-78. doi: 10.1111/j.1365-313X.2010.04245.x. Epub 2010 Apr 29.

12.

Stochastic and reversible assembly of a multiprotein DNA repair complex ensures accurate target site recognition and efficient repair.

Luijsterburg MS, von Bornstaedt G, Gourdin AM, Politi AZ, Moné MJ, Warmerdam DO, Goedhart J, Vermeulen W, van Driel R, Höfer T.

J Cell Biol. 2010 May 3;189(3):445-63. doi: 10.1083/jcb.200909175.

13.

Phytochrome B and histone deacetylase 6 control light-induced chromatin compaction in Arabidopsis thaliana.

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.

PLoS Genet. 2009 Sep;5(9):e1000638. doi: 10.1371/journal.pgen.1000638. Epub 2009 Sep 4.

14.

Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C).

Louwers M, Splinter E, van Driel R, de Laat W, Stam M.

Nat Protoc. 2009;4(8):1216-29. doi: 10.1038/nprot.2009.113. Epub 2009 Jul 30.

PMID:
19644461
15.

Heterochromatin protein 1 is recruited to various types of DNA damage.

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.

J Cell Biol. 2009 May 18;185(4):577-86. doi: 10.1083/jcb.200810035.

16.

Tissue- and expression level-specific chromatin looping at maize b1 epialleles.

Louwers M, Bader R, Haring M, van Driel R, de Laat W, Stam M.

Plant Cell. 2009 Mar;21(3):832-42. doi: 10.1105/tpc.108.064329. Epub 2009 Mar 31.

17.

Assembly of multiprotein complexes that control genome function.

Dinant C, Luijsterburg MS, Höfer T, von Bornstaedt G, Vermeulen W, Houtsmuller AB, van Driel R.

J Cell Biol. 2009 Apr 6;185(1):21-6. doi: 10.1083/jcb.200811080. Epub 2009 Mar 30. Review.

18.

Spatially confined folding of chromatin in the interphase nucleus.

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.

Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3812-7. doi: 10.1073/pnas.0809501106. Epub 2009 Feb 20.

19.

Spatial organization of nucleotide excision repair proteins after UV-induced DNA damage in the human cell nucleus.

Solimando L, Luijsterburg MS, Vecchio L, Vermeulen W, van Driel R, Fakan S.

J Cell Sci. 2009 Jan 1;122(Pt 1):83-91. doi: 10.1242/jcs.031062. Epub 2008 Dec 9.

20.

The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes.

Luijsterburg MS, White MF, van Driel R, Dame RT.

Crit Rev Biochem Mol Biol. 2008 Nov-Dec;43(6):393-418. doi: 10.1080/10409230802528488 . Review.

PMID:
19037758
21.

Structural analysis of interphase X-chromatin based on statistical shape theory.

Yang S, Illner D, Teller K, Solovei I, van Driel R, Joffe B, Cremer T, Eils R, Rohr K.

Biochim Biophys Acta. 2008 Nov;1783(11):2089-99. doi: 10.1016/j.bbamcr.2008.08.007. Epub 2008 Aug 30.

22.

Shape normalization of 3D cell nuclei using elastic spherical mapping.

Gladilin E, Goetze S, Mateos-Langerak J, VAN Driel R, Eils R, Rohr K.

J Microsc. 2008 Jul;231(Pt 1):105-14. doi: 10.1111/j.1365-2818.2008.02021.x.

23.

Intracellular manipulation of chromatin using magnetic nanoparticles.

Kanger JS, Subramaniam V, van Driel R.

Chromosome Res. 2008;16(3):511-22. doi: 10.1007/s10577-008-1239-1. Review.

PMID:
18461487
24.

Exploring the behavior of small eukaryotic gene networks.

Bruggeman FJ, Oancea I, van Driel R.

J Theor Biol. 2008 Jun 7;252(3):482-7. doi: 10.1016/j.jtbi.2008.02.024. Epub 2008 Feb 25.

PMID:
18433776
25.

Purification of a herpes-like virus from abalone (Haliotis spp.) with ganglioneuritis and detection by transmission electron microscopy.

Tan J, Lancaster M, Hyatt A, van Driel R, Wong F, Warner S.

J Virol Methods. 2008 May;149(2):338-41. doi: 10.1016/j.jviromet.2007.12.019.

PMID:
18374425
26.

Random loop model for long polymers.

Bohn M, Heermann DW, van Driel R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Nov;76(5 Pt 1):051805. Epub 2007 Nov 27.

PMID:
18233679
27.

Genetic and epidemiological characterization of Middle Point orbivirus, a novel virus isolated from sentinel cattle in northern Australia.

Cowled C, Melville L, Weir R, Walsh S, Hyatt A, Van Driel R, Davis S, Gubala A, Boyle D.

J Gen Virol. 2007 Dec;88(Pt 12):3413-22.

PMID:
18024911
28.

Chromatin is wonderful stuff.

van Driel R.

Semin Cell Dev Biol. 2007 Oct;18(5):649-50. Epub 2007 Oct 7. No abstract available.

PMID:
17964198
29.

The perichromatin region: a functional compartment in the nucleus that determines large-scale chromatin folding.

Fakan S, van Driel R.

Semin Cell Dev Biol. 2007 Oct;18(5):676-81. Epub 2007 Aug 25. Review.

PMID:
17920313
30.

Three-dimensional genome organization in interphase and its relation to genome function.

Goetze S, Mateos-Langerak J, van Driel R.

Semin Cell Dev Biol. 2007 Oct;18(5):707-14. Epub 2007 Aug 25. Review.

PMID:
17905616
31.

A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data.

Post LJ, Roos M, Marshall MS, van Driel R, Breit TM.

Bioinformatics. 2007 Nov 15;23(22):3080-7. Epub 2007 Sep 19.

PMID:
17881406
32.

Nuclear architecture: Is it important for genome function and can we prove it?

Mateos-Langerak J, Goetze S, Leonhardt H, Cremer T, van Driel R, Lanctôt C.

J Cell Biochem. 2007 Dec 1;102(5):1067-75. Review.

PMID:
17786936
33.

Domain-wide regulation of gene expression in the human genome.

Gierman HJ, Indemans MH, Koster J, Goetze S, Seppen J, Geerts D, van Driel R, Versteeg R.

Genome Res. 2007 Sep;17(9):1286-95. Epub 2007 Aug 10.

34.

Dynamic in vivo interaction of DDB2 E3 ubiquitin ligase with UV-damaged DNA is independent of damage-recognition protein XPC.

Luijsterburg MS, Goedhart J, Moser J, Kool H, Geverts B, Houtsmuller AB, Mullenders LH, Vermeulen W, van Driel R.

J Cell Sci. 2007 Aug 1;120(Pt 15):2706-16. Epub 2007 Jul 17.

35.

Light-regulated large-scale reorganization of chromatin during the floral transition in Arabidopsis.

Tessadori F, Schulkes RK, van Driel R, Fransz P.

Plant J. 2007 Jun;50(5):848-57. Epub 2007 Apr 23.

36.

Direct observation of nanomechanical properties of chromatin in living cells.

de Vries AH, Krenn BE, van Driel R, Subramaniam V, Kanger JS.

Nano Lett. 2007 May;7(5):1424-7. Epub 2007 Apr 24.

PMID:
17451276
37.

The three-dimensional structure of human interphase chromosomes is related to the transcriptome map.

Goetze S, Mateos-Langerak J, Gierman HJ, de Leeuw W, Giromus O, Indemans MH, Koster J, Ondrej V, Versteeg R, van Driel R.

Mol Cell Biol. 2007 Jun;27(12):4475-87. Epub 2007 Apr 9.

38.

Large-scale dissociation and sequential reassembly of pericentric heterochromatin in dedifferentiated Arabidopsis cells.

Tessadori F, Chupeau MC, Chupeau Y, Knip M, Germann S, van Driel R, Fransz P, Gaudin V.

J Cell Sci. 2007 Apr 1;120(Pt 7):1200-8.

39.

Pericentromeric heterochromatin domains are maintained without accumulation of HP1.

Mateos-Langerak J, Brink MC, Luijsterburg MS, van der Kraan I, van Driel R, Verschure PJ.

Mol Biol Cell. 2007 Apr;18(4):1464-71. Epub 2007 Feb 21.

40.

Recruitment of the nucleotide excision repair endonuclease XPG to sites of UV-induced dna damage depends on functional TFIIH.

Zotter A, Luijsterburg MS, Warmerdam DO, Ibrahim S, Nigg A, van Cappellen WA, Hoeijmakers JH, van Driel R, Vermeulen W, Houtsmuller AB.

Mol Cell Biol. 2006 Dec;26(23):8868-79. Epub 2006 Sep 25.

41.

Truncated HP1 lacking a functional chromodomain induces heterochromatinization upon in vivo targeting.

Brink MC, van der Velden Y, de Leeuw W, Mateos-Langerak J, Belmont AS, van Driel R, Verschure PJ.

Histochem Cell Biol. 2006 Jan;125(1-2):53-61. Epub 2005 Nov 10.

PMID:
16283356
42.

Mathematical modeling of nucleotide excision repair reveals efficiency of sequential assembly strategies.

Politi A, Moné MJ, Houtsmuller AB, Hoogstraten D, Vermeulen W, Heinrich R, van Driel R.

Mol Cell. 2005 Sep 2;19(5):679-90.

43.

Imaging in situ protein-DNA interactions in the cell nucleus using FRET-FLIM.

Cremazy FG, Manders EM, Bastiaens PI, Kramer G, Hager GL, van Munster EB, Verschure PJ, Gadella TJ Jr, van Driel R.

Exp Cell Res. 2005 Oct 1;309(2):390-6.

PMID:
16040027
44.

In vivo HP1 targeting causes large-scale chromatin condensation and enhanced histone lysine methylation.

Verschure PJ, van der Kraan I, de Leeuw W, van der Vlag J, Carpenter AE, Belmont AS, van Driel R.

Mol Cell Biol. 2005 Jun;25(11):4552-64.

45.

Micro magnetic tweezers for nanomanipulation inside live cells.

de Vries AH, Krenn BE, van Driel R, Kanger JS.

Biophys J. 2005 Mar;88(3):2137-44. Epub 2004 Nov 19.

46.

In vivo dynamics of chromatin-associated complex formation in mammalian nucleotide excision repair.

Moné MJ, Bernas T, Dinant C, Goedvree FA, Manders EM, Volker M, Houtsmuller AB, Hoeijmakers JH, Vermeulen W, van Driel R.

Proc Natl Acad Sci U S A. 2004 Nov 9;101(45):15933-7. Epub 2004 Nov 1.

47.

Where do we go in the nucleus?

Fakan S, van Driel R.

Biol Cell. 2004 Oct;96(8):553-4. No abstract available.

PMID:
15519690
48.

Nuclear architecture and genome functioning in plants and animals: what can we learn from both?

van Driel R, Fransz P.

Exp Cell Res. 2004 May 15;296(1):86-90. Review.

PMID:
15120998
49.

Cytogenetics as a tool to study gene regulation.

Tessadori F, van Driel R, Fransz P.

Trends Plant Sci. 2004 Mar;9(3):147-53. Review. No abstract available.

PMID:
15003238
50.

Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location.

Greil F, van der Kraan I, Delrow J, Smothers JF, de Wit E, Bussemaker HJ, van Driel R, Henikoff S, van Steensel B.

Genes Dev. 2003 Nov 15;17(22):2825-38.

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