SELECTED PUBLICATIONS
Dirk Schübeler

Arnold P, Schöler A, Pachkov M, Balwierz PJ, Jorgensen H, Stadler MB, van Nimwegen E*, Schübeler D* (2013) Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting.
Genome Res 23:60-73
(*=corresponding authors)

Schübeler D (2012) Epigenetic islands in a genetic ocean.
Science, 338, 756-757

Krebs A, Schübeler D (2012) Tracking the evolution of cancer methylomes.
Nat Genet. 44:1173-4

Tippmann SC, Ivanek R, Gaidatzis D, Schöler A, Hoerner L, van Nimwegen E, Stadler PF, Stadler MB, Schübeler D (2012) Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA level.
Mol Syst Biol. 17;8:593

Tiwari VK, Burger L, Nikoletopoulou V, Deogracias R, Thakurela S, Wirbelauer C, Kaut J, Terranova R, Hoerner L, Mielke C, Boege F, Murr R, Peters AH, Yves-Alain Barde, Schübeler D (2012) Genomic targets of Topoisomerase IIbeta regulate neuronal differentiation and survival and are defined by their chromatin state.
PNAS, 109:E934-43

Tiwari VK, Stadler MB*, Wirbelauer C, Paro R, Schübeler D*, Beisel C (2012) A chromatin-modifying function for JNK at NF-Y bound Promoters during Stem Cell Differentiation.
Nature Genetics, 44, 94-100
(*corr. authors)

Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, van Nimwegen E, Wirbelauer C, Oakeley EJ, Gaidatzis D, Tiwari VK, Schübeler D (2011) DNA binding factors shape the mouse methylome at distal regulatory regions.
Nature, 480, 490-495

Lienert F, Wirbelauer C, Som I, Dean A, Mohn F, Schübeler D. (2011) Identification of genetic elements that autonomously determine DNA methylation states.
Nat Genet. 43(11):1091-7

Bell O, Tiwari VK, Thomä NH, Schübeler D (2011) Determinants and dynamics of genome accessibility.
Nat Rev Genet. 2011 Jul 12. doi: 10.1038/nrg3017. [Epub ahead of print]

Lienert F., Mohn F., Tiwari, V., Baubec, T., Roloff, T., Gaidatzis, D., Stadler, M. and Schübeler, D (2011) Genomic prevalence of heterochromatic H3K9me2 and transcription do not discriminate pluripotent from terminally differentiated cells.
PLoS Genetics 7(6): e1002090.

Dirk Schübeler (2010) Chromatin in Multicolor.
Cell 143: 183-4

Bell O, Schwaiger M, Oakeley EJ, Lienert F, Beisel C, Stadler MB, Schübeler D (2010) DNA accessibility discriminates sites of PcG repression, H4K16 acetylation and replication initiation throughout the genome.
Nat Struct Mol Biol 17: 894-900

Schübeler D (2009) Epigenomics: Methylation matters.
Nature 462:296-297

Schwaiger M, Stadler M, Bell O, Kohler H, Oakeley E, Schübeler D (2009) Chromatin state marks cell-type and gender specific replication of the Drosophila genome.
Genes Dev 23:589-601

Mohn F, Weber M, Rebhan M, Roloff TC, Richter J, Stadler MB, Bibel M, Schübeler D (2008) Polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors.
Molecular Cell 30: 755-766

Bell O, Wirbelauer C, Hild M, Scharf AN, Schwaiger M, Macalpine DM, Zilbermann F, van Leeuwen F, Bell SP, Imhof A, Garza D Peters AH, Schübeler D (2007) Localized H3K36 methylation states define histone H4K16 acetylation during transcriptional elongation in Drosophila.
EMBO J 26:4974-4984

Weber M, Hellmann I, Stadler MB, Ramos L, Pääbo S, Rebhan M, Schübeler D (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome.
Nature Genet (39, 457 - 466)

Weber M, Davies J, Wittig D, Oakeley E, Haase M, Lam WL, Schübeler D (2005) Chromosome-wide and promoter-specific analyses reveal sites of differential DNA methylation in normal and transformed human cells.
Nature Genet (37:853-862)

Wirbelauer C, Bell O, Schübeler D (2005) Variant histone H3.3 is deposited at sites of nucleosomal displacement throughout transcribed genes while active histone modifications show a promoter-proximal bias.
Genes Dev (19:1761-1766)

Schübeler D, MacAlpine D, Scalzo D, Wirbelauer C, Kooperberg C, van Leeuwen F, Gottschling D, O'Neill L, Turner B, Delrow J, Bell SP, Groudine M (2004) The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote.
Genes Dev 18:1263-1271

Schübeler D, Scalzo D, Kooperberg C, van Steensel B, Delrow J, Groudine M (2002) Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing.
Nature Genet 32:438-442

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