Ross SE, Bogdanovic O. Generation and Molecular Characterization of Transient tet1/2/3 Zebrafish Knockouts. Methods in Molecular Biology. 2021;2272:281-317. full text
Skvortsova K, Bogdanovic O. TAB-seq and ACE-seq Data Processing for Genome-Wide DNA hydroxymethylation Profiling. Methods in Molecular Biology. 2021;2272:163-178. book chapter
Ogawa M, Geng FS, Humphreys DT, Kristianto E, Sheng DZ, Hui SP, Zhang Y, Sugimoto K, Nakayama M, Zheng D, Hesselson D, Hodson MP, Bogdanovic O, Kikuchi K. Krüppel-like factor 1 is a core cardiomyogenic trigger in zebrafish. Science. 2021 Apr 9;372(6538):201-205. journal
Ross SE, Hesselson D, Bogdanovic O. Developmental Accumulation of Gene Body and Transposon Non-CpG Methylation in the Zebrafish Brain. Frontiers in Cell and Developmental Biology. 2021 Mar 4;9:643603. full text
de Mendoza A, Poppe D, Buckberry S, Pflueger J, Albertin CB, Daish T, Bertrand S, de la Calle-Mustienes E, Gómez-Skarmeta JL, Nery JR, Ecker JR, Baer B, Ragsdale CW, Grützner F, Escriva H, Venkatesh B, Bogdanovic O, Lister R. The emergence of the brain non-CpG methylation system in vertebrates. Nature Ecology and Evolution. 2021 Mar;5(3):369-378. journal
Ross SE, Angeloni A, Geng FS, de Mendoza A, Bogdanovic O^. Developmental remodelling of non-CG methylation at satellite DNA repeats. Nucleic Acids Research. doi: 10.1093/nar/gkaa1135. full text
de Mendoza A^, Lister R, Bogdanovic O^. Evolution of DNA Methylome Diversity in Eukaryotes. Journal of Molecular Biology. 2019 Nov 11:S0022-2836(19)30659-X. journal
Skvortsova K, Tarbashevich K, Stehling M, Lister R, Irimia M, Raz E, Bogdanovic O^. Retention of paternal DNA methylome in the developing zebrafish germline. Nature Communications. 2019 Jul 11;10(1):3054. doi: 10.1038/s41467-019-10895-6. full text
Marlétaz F*, Firbas PN*, Maeso I*, Tena JJ*, Bogdanovic O*, Perry M*, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, Jimenez-Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech-Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Gutiérrez È, Cañestro C, Castro F, D’Aniello S, Ferrier DEK, Huang S, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu A, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fernàndez J, Lister R, Lenhard B, Holland PWH, Escriva H, Gómez-Skarmeta JL, Irimia M. Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature. 2018 Nov 21. doi: 10.1038/s41586-018-0734-6. full text
Skvortsova K, Iovino N^, Bogdanovic O^. Functions and mechanisms of epigenetic inheritance in animals. Nature Reviews Molecular Cell Biology. 2018 Dec;19(12):774-790 journal
Zenk F, Loeser E, Schiavo R, Kilpert F, Bogdanovic O, Iovino N. Germ line–inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition. Science. 2017 Jul 14;357(6347):212-216 journal
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^, 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
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
Bogdanovic 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
Bogdanovic 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
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