2025

Brethouwer T, de Mendoza A, Bogdanovic O. Non-CG DNA methylation in animal genomes. Nat Genet. 2025 Sep 11. doi: 10.1038/s41588-025-02303-1.

2024

Angeloni A, Fissette S, Kaya D, Hammond JM, Gamaarachchi H, Deveson IW, Klose RJ, Li W, Zhang X, Bogdanovic O. Extensive DNA methylome rearrangement during early lamprey embryogenesis. Nat Commun. 2024 Mar 4;15(1):1977.

2023

Ross SE, Vázquez-Marín J, Gert KRB, González-Rajal A, Dinger ME, Pauli A, Martínez-Morales JR, Bogdanovic O^. Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species. Nucleic Acids Research. 2023 Aug 24:gkad695.

Marlétaz F, de la Calle-Mustienes E, Acemel RD, Paliou C, Naranjo S, Martínez-García PM, Cases I, Sleight VA, Hirschberger C, Marcet-Houben M, Navon D, Andrescavage A, Skvortsova K, Duckett PE, González-Rajal Á, Bogdanovic O, Gibcus JH, Yang L, Gallardo-Fuentes L, Sospedra I, Lopez-Rios J, Darbellay F, Visel A, Dekker J, Shubin N, Gabaldón T, Nakamura T, Tena JJ, Lupiáñez DG, Rokhsar DS, Gómez-Skarmeta JL. The little skate genome and the evolutionary emergence of wing-like fins. Nature. 2023 Apr;616(7957):495-503.

2022

Skvortsova K, Bertrand S, Voronov D, Duckett PE, Ross SE, Magri MS, Maeso I, Weatheritt RJ, Gómez Skarmeta JL, Arnone MI, Escriva H, Bogdanovic O. Active DNA demethylation of developmental cis-regulatory regions predates vertebrate origins. Science Advances. 2022 Dec 2;8(48):eabn2258.

Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N, Wragg J, D’Orazio FM, Relic D, Pachkov M, Díaz N, Hernández-Rodríguez B, Chen Z, Stoiber M, Dong M, Stevens I, Ross SE, Eagle A, Martin R, Obasaju O, Rastegar S, McGarvey AC, Kopp W, Chambers E, Wang D, Kim HR, Acemel RD, Naranjo S, Łapiński M, Chong V, Mathavan S, Peers B, Sauka-Spengler T, Vingron M, Carninci P, Ohler U, Lacadie SA, Burgess SM, Winata C, van Eeden F, Vaquerizas JM, Gómez-Skarmeta JL, Onichtchouk D, Brown BJ, Bogdanovic O, van Nimwegen E, Westerfield M, Wardle FC, Daub CO, Lenhard B, Müller F. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nature Genetics . 2022 Jul;54(7):1037-1050.

2021

Ross SE, Bogdanovic O. Generation and Molecular Characterization of Transient tet1/2/3 Zebrafish Knockouts. Methods in Molecular Biology. 2021;2272:281-317.

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.

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.

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.

2020

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.

2019

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.

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.

2018

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.

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.

2017

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.

2016

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.

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.

2015

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.

Complete list of publications can be accessed here