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Items: 25

1.

High-throughput identification of human SNPs affecting regulatory element activity.

van Arensbergen J, Pagie L, FitzPatrick VD, de Haas M, Baltissen MP, Comoglio F, van der Weide RH, Teunissen H, Võsa U, Franke L, de Wit E, Vermeulen M, Bussemaker HJ, van Steensel B.

Nat Genet. 2019 Jul;51(7):1160-1169. doi: 10.1038/s41588-019-0455-2. Epub 2019 Jun 28.

2.

Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs.

Leemans C, van der Zwalm MCH, Brueckner L, Comoglio F, van Schaik T, Pagie L, van Arensbergen J, van Steensel B.

Cell. 2019 May 2;177(4):852-864.e14. doi: 10.1016/j.cell.2019.03.009. Epub 2019 Apr 11.

3.

The large fraction of heterochromatin in Drosophila neurons is bound by both B-type lamin and HP1a.

Pindyurin AV, Ilyin AA, Ivankin AV, Tselebrovsky MV, Nenasheva VV, Mikhaleva EA, Pagie L, van Steensel B, Shevelyov YY.

Epigenetics Chromatin. 2018 Nov 1;11(1):65. doi: 10.1186/s13072-018-0235-8.

4.

Massive reshaping of genome-nuclear lamina interactions during oncogene-induced senescence.

Lenain C, de Graaf CA, Pagie L, Visser NL, de Haas M, de Vries SS, Peric-Hupkes D, van Steensel B, Peeper DS.

Genome Res. 2017 Oct;27(10):1634-1644. doi: 10.1101/gr.225763.117. Epub 2017 Sep 15.

5.

Small chromosomal regions position themselves autonomously according to their chromatin class.

van de Werken HJG, Haan JC, Feodorova Y, Bijos D, Weuts A, Theunis K, Holwerda SJB, Meuleman W, Pagie L, Thanisch K, Kumar P, Leonhardt H, Marynen P, van Steensel B, Voet T, de Laat W, Solovei I, Joffe B.

Genome Res. 2017 Jun;27(6):922-933. doi: 10.1101/gr.213751.116. Epub 2017 Mar 24.

6.

Genome-wide mapping of autonomous promoter activity in human cells.

van Arensbergen J, FitzPatrick VD, de Haas M, Pagie L, Sluimer J, Bussemaker HJ, van Steensel B.

Nat Biotechnol. 2017 Feb;35(2):145-153. doi: 10.1038/nbt.3754. Epub 2016 Dec 26.

7.

High-throughput assessment of context-dependent effects of chromatin proteins.

Brueckner L, van Arensbergen J, Akhtar W, Pagie L, van Steensel B.

Epigenetics Chromatin. 2016 Oct 18;9:43. eCollection 2016.

8.

Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila.

Pindyurin AV, Pagie L, Kozhevnikova EN, van Arensbergen J, van Steensel B.

Nucleic Acids Res. 2016 Jul 8;44(12):5646-57. doi: 10.1093/nar/gkw176. Epub 2016 Mar 21.

9.

Genome-wide maps of nuclear lamina interactions in single human cells.

Kind J, Pagie L, de Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, de Graaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny LA, Jalink K, Dekker J, van Oudenaarden A, van Steensel B.

Cell. 2015 Sep 24;163(1):134-47. doi: 10.1016/j.cell.2015.08.040. Epub 2015 Sep 10.

10.

Corrigendum: using TRIP for genome-wide position effect analysis in cultured cells.

Akhtar W, Pindyurin AV, de Jong J, Pagie L, Ten Hoeve J, Berns A, Wessels LF, van Steensel B, van Lohuizen M.

Nat Protoc. 2015 Apr;10(4):643. doi: 10.1038/nprot0415-644c. Epub 2015 Mar 26. No abstract available.

PMID:
25811898
11.

Using TRIP for genome-wide position effect analysis in cultured cells.

Akhtar W, Pindyurin AV, de Jong J, Pagie L, Ten Hoeve J, Berns A, Wessels LF, van Steensel B, van Lohuizen M.

Nat Protoc. 2014;9(6):1255-81. doi: 10.1038/nprot.2014.072. Epub 2014 May 8. Erratum in: Nat Protoc. 2015 Apr;10(4):643.

PMID:
24810036
12.

Chromatin position effects assayed by thousands of reporters integrated in parallel.

Akhtar W, de Jong J, Pindyurin AV, Pagie L, Meuleman W, de Ridder J, Berns A, Wessels LF, van Lohuizen M, van Steensel B.

Cell. 2013 Aug 15;154(4):914-27. doi: 10.1016/j.cell.2013.07.018.

13.

Single-cell dynamics of genome-nuclear lamina interactions.

Kind J, Pagie L, Ortabozkoyun H, Boyle S, de Vries SS, Janssen H, Amendola M, Nolen LD, Bickmore WA, van Steensel B.

Cell. 2013 Mar 28;153(1):178-92. doi: 10.1016/j.cell.2013.02.028. Epub 2013 Mar 21.

14.

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence.

Meuleman W, Peric-Hupkes D, Kind J, Beaudry JB, Pagie L, Kellis M, Reinders M, Wessels L, van Steensel B.

Genome Res. 2013 Feb;23(2):270-80. doi: 10.1101/gr.141028.112. Epub 2012 Nov 2.

15.

Glucosylated hydroxymethyluracil, DNA base J, prevents transcriptional readthrough in Leishmania.

van Luenen HG, Farris C, Jan S, Genest PA, Tripathi P, Velds A, Kerkhoven RM, Nieuwland M, Haydock A, Ramasamy G, Vainio S, Heidebrecht T, Perrakis A, Pagie L, van Steensel B, Myler PJ, Borst P.

Cell. 2012 Aug 31;150(5):909-21. doi: 10.1016/j.cell.2012.07.030.

16.

Interactions among Polycomb domains are guided by chromosome architecture.

Tolhuis B, Blom M, Kerkhoven RM, Pagie L, Teunissen H, Nieuwland M, Simonis M, de Laat W, van Lohuizen M, van Steensel B.

PLoS Genet. 2011 Mar;7(3):e1001343. doi: 10.1371/journal.pgen.1001343. Epub 2011 Mar 24.

17.

The insulator protein SU(HW) fine-tunes nuclear lamina interactions of the Drosophila genome.

van Bemmel JG, Pagie L, Braunschweig U, Brugman W, Meuleman W, Kerkhoven RM, van Steensel B.

PLoS One. 2010 Nov 24;5(11):e15013. doi: 10.1371/journal.pone.0015013.

18.

Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation.

Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Gräf S, Flicek P, Kerkhoven RM, van Lohuizen M, Reinders M, Wessels L, van Steensel B.

Mol Cell. 2010 May 28;38(4):603-13. doi: 10.1016/j.molcel.2010.03.016.

19.

Histone H1 binding is inhibited by histone variant H3.3.

Braunschweig U, Hogan GJ, Pagie L, van Steensel B.

EMBO J. 2009 Dec 2;28(23):3635-45. doi: 10.1038/emboj.2009.301. Epub 2009 Oct 15.

20.

High-resolution mapping of heterochromatin redistribution in a Drosophila position-effect variegation model.

Vogel MJ, Pagie L, Talhout W, Nieuwland M, Kerkhoven RM, van Steensel B.

Epigenetics Chromatin. 2009 Jan 29;2(1):1. doi: 10.1186/1756-8935-2-1.

21.

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions.

Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de Laat W, van Steensel B.

Nature. 2008 Jun 12;453(7197):948-51. doi: 10.1038/nature06947. Epub 2008 May 7. Erratum in: Nature. 2013 Aug 8;500(7461):242.

PMID:
18463634
22.

Chemical warfare between microbes promotes biodiversity.

Czárán TL, Hoekstra RF, Pagie L.

Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):786-90. Epub 2002 Jan 15.

23.

Individual- and population-based diversity in restriction-modification systems.

Pagie L, Hogeweg P.

Bull Math Biol. 2000 Jul;62(4):759-74.

PMID:
10938631
24.

Colicin diversity: a result of eco-evolutionary dynamics.

Pagie L, Hogeweg P.

J Theor Biol. 1999 Jan 21;196(2):251-61.

PMID:
10049618
25.

Evolutionary consequences of coevolving targets

Pagie L, Hogeweg P.

Evol Comput. 1997 Winter;5(4):401-18.

PMID:
10021765

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