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Items: 13

1.

Spatial partitioning of the regulatory landscape of the X-inactivation centre.

Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum NL, Meisig J, Sedat J, Gribnau J, Barillot E, Blüthgen N, Dekker J, Heard E.

Nature. 2012 Apr 11;485(7398):381-5. doi: 10.1038/nature11049.

2.

Evidence for transcript networks composed of chimeric RNAs in human cells.

Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, Lin C, Bell I, Dumais E, Drenkow J, Tress ML, Gelpí JL, Orozco M, Valencia A, van Berkum NL, Lajoie BR, Vidal M, Stamatoyannopoulos J, Batut P, Dobin A, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis SE, Guigó R, Gingeras TR.

PLoS One. 2012;7(1):e28213. doi: 10.1371/journal.pone.0028213. Epub 2012 Jan 4.

3.

Mediator and cohesin connect gene expression and chromatin architecture.

Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, Ebmeier CC, Goossens J, Rahl PB, Levine SS, Taatjes DJ, Dekker J, Young RA.

Nature. 2010 Sep 23;467(7314):430-5. doi: 10.1038/nature09380. Epub 2010 Aug 18. Erratum in: Nature. 2011 Apr 14;472(7342):247.

4.

A consensus of core protein complex compositions for Saccharomyces cerevisiae.

Benschop JJ, Brabers N, van Leenen D, Bakker LV, van Deutekom HW, van Berkum NL, Apweiler E, Lijnzaad P, Holstege FC, Kemmeren P.

Mol Cell. 2010 Jun 25;38(6):916-28. doi: 10.1016/j.molcel.2010.06.002.

5.

Hi-C: a method to study the three-dimensional architecture of genomes.

van Berkum NL, Lieberman-Aiden E, Williams L, Imakaev M, Gnirke A, Mirny LA, Dekker J, Lander ES.

J Vis Exp. 2010 May 6;(39). pii: 1869. doi: 10.3791/1869.

6.

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J.

Science. 2009 Oct 9;326(5950):289-93. doi: 10.1126/science.1181369.

7.

My5C: web tools for chromosome conformation capture studies.

Lajoie BR, van Berkum NL, Sanyal A, Dekker J.

Nat Methods. 2009 Oct;6(10):690-1. doi: 10.1038/nmeth1009-690. No abstract available.

8.

Determining spatial chromatin organization of large genomic regions using 5C technology.

van Berkum NL, Dekker J.

Methods Mol Biol. 2009;567:189-213. doi: 10.1007/978-1-60327-414-2_13. Review.

9.

Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit.

Radonjic M, Andrau JC, Lijnzaad P, Kemmeren P, Kockelkorn TT, van Leenen D, van Berkum NL, Holstege FC.

Mol Cell. 2005 Apr 15;18(2):171-83.

10.

A high resolution protein interaction map of the yeast Mediator complex.

Guglielmi B, van Berkum NL, Klapholz B, Bijma T, Boube M, Boschiero C, Bourbon HM, Holstege FC, Werner M.

Nucleic Acids Res. 2004 Oct 11;32(18):5379-91. Print 2004.

11.

Protein interaction verification and functional annotation by integrated analysis of genome-scale data.

Kemmeren P, van Berkum NL, Vilo J, Bijma T, Donders R, Brazma A, Holstege FC.

Mol Cell. 2002 May;9(5):1133-43.

12.

DNA microarrays: raising the profile.

van Berkum NL, Holstege FC.

Curr Opin Biotechnol. 2001 Feb;12(1):48-52. Review.

PMID:
11167072
13.

Isolation and characterization of human orthologs of yeast CCR4-NOT complex subunits.

Albert TK, Lemaire M, van Berkum NL, Gentz R, Collart MA, Timmers HT.

Nucleic Acids Res. 2000 Feb 1;28(3):809-17.

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