Publications

SELECTED PUBLICATIONS

Ford E, Grimmer MR, Stolzenburg S, Bogdanovic O, de Mendoza A, Farnham PJ, Blancafort P, Lister R. Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation. bioRxiv doi: https://doi.org/10.1101/17050.  full text

Zenk F, Loeser E, Schiavo R, Kilpert F, Bogdanović O, Iovino N. Germ line–inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition. Science2017 Jul 14;357(6347): 212-216 journal

Bogdanović O^, Lister R^. DNA methylation and the preservation of cell identity. Curr Opin Genet Dev. doi: 10.1016/j.gde.2017.06.007 journal

Elurbe DM, Paranjpe SS, Georgiou G, van Kruijsbergen I, Bogdanovic O, Gibeaux R, Heald R, Lister R, Huynen MA, van Heeringen SJ, Veenstra GJ. Regulatory remodeling in the allo-tetraploid frog Xenopus laevis. bioRxiv. doi: https://doi.org/10.1101/120212 full text

Bogdanović O^. Tet proteins: master regulators of vertebrate body plan formation? Epigenomics. 2017 Feb;9(2):93-96 full text

Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C, Kitzman J, Nakayama T, Izutsu Y, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJ, Fujiyama A, Harland RM, Taira M, Rokhsar DS. Genome evolution in the allotetraploid frog Xenopus laevis. Nature. 2016 Oct 19;538(7625):336-343 full text  DNA  cover art

Bogdanovic O, van Heeringen SJ. ChIP-seq Data Processing for PcG Proteins and Associated Histone Modifications. Methods Mol Biol. 2016;1480:37-53 journal

Bogdanović O^, Smits AH, de la Calle Mustienes E, Tena JJ, Ford E, Williams R, Senanayake U, Schultz MD, Hontelez S, van Kruijsbergen I, Rayon T, Gnerlich F, Carell T, Veenstra GJ, Manzanares M, Sauka-Spengler T, Ecker JR, Vermeulen M^, Gómez-Skarmeta JL^, Lister R^ (2016) Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nature Genetics. Apr;48(4):417-26  journal  DNA  protein

de la Calle Mustienes E, Gómez-Skarmeta JL, Bogdanović O^ (2015) Genome-wide epigenetic cross-talk between DNA methylation and H3K27me3 in zebrafish embryos. Genomics Data. Jul 22;6:7-9 full text  DNA

Hontelez S, van Kruijsbergen I, Georgiou G, van Heeringen SJ, Bogdanovic O, Lister R, Veenstra GJ (2015) Embryonic transcription is controlled by maternally defined chromatin state. Nature Communications. Dec 18;6:10148 full text  DNA

Bogdanović O, Lister R (2015) Of Mice and Man: Differential DNMT Dependence in Mammalian ESCs. Cell Stem Cell. May 7;16(5):459-60 full text

Bogdanović O*, Fernández-Miñán A*, Tena JJ*, de la Calle-Mustienes E, Gómez-Skarmeta JL (2013) The developmental epigenomics toolbox: ChIP-seq and MethylCap-seq profiling of early zebrafish embryos. Methods. Aug 15;62(3):207-15 journal  DNA

Bogdanović O*, Delfino-Machín M*, Nicolás-Pérez M, Gavilán MP, Gago-Rodrigues I, Fernández-Miñán A, Lillo C, Ríos RM, Wittbrodt J, Martínez-Morales JR (2012) Numb/Numbl-Opo antagonism controls retinal epithelium morphogenesis by regulating integrin endocytosis. Developmental Cell. Oct 16;23(4):782-95 full text  cover art

Bogdanović O (2012) DNA methylation and methyl-CpG binding proteins during early development. ISBN: 978-94-6182-087-7 full text

Bogdanovic O, Fernandez-Miñán A, Tena JJ, de la Calle-Mustienes E, Hidalgo C, van Kruysbergen I, van Heeringen SJ, Veenstra GJ, Gómez-Skarmeta JL (2012) Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. Genome Research Oct;22(10):2043-53 full text  DNA

Bogdanović O, van Heeringen SJ, Veenstra GJ (2012) The epigenome in early vertebrate development. Genesis. Mar;50(3):192-206 full text

Bogdanovic O, Long SW, van Heeringen SJ, Brinkman AB, Gómez-Skarmeta JL, Stunnenberg HG, Jones PL, Veenstra GJ (2011) Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis. Genome Research Aug;21(8):1313-27 full text  DNA

Bogdanović O, Veenstra GJ (2009) DNA methylation and methyl-CpG binding proteins: developmental requirements and function. Chromosoma. Oct;118(5):549-65 full text

Complete list of publications can be accessed here

^ corresponding author

* equal contribution