By Associate Professor Ozren Bogdanovic

Journal articles

Hontelez S; van Kruijsbergen I; Georgiou G; van Heeringen SJ; Bogdanovic O; Lister R; Veenstra GJC, 2016, 'Embryonic transcription is controlled by maternally defined chromatin state (vol 6, 10148, 2015)', NATURE COMMUNICATIONS, 7, http://dx.doi.org/10.1038/ncomms12208

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 GJC; 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, 48, pp. 417 - 426, http://dx.doi.org/10.1038/ng.3522

Bogdanović O; Van Heeringen SJ, 2016, 'ChiP-seq data processing for PcG proteins and associated Histone modifications', Methods in Molecular Biology, 1480, pp. 37 - 53, http://dx.doi.org/10.1007/978-1-4939-6380-5_4

Hontelez S; Van Kruijsbergen I; Georgiou G; Van Heeringen SJ; Bogdanovic O; Lister R; Veenstra GJC, 2015, 'Embryonic transcription is controlled by maternally defined chromatin state', Nature Communications, 6, http://dx.doi.org/10.1038/ncomms10148

Marcos S; González-Lázaro M; Beccari L; Carramolino L; Martin-Bermejo MJ; Amarie O; Martı́n DMS; Torroja C; Bogdanović O; Doohan R; Puk O; de Angelis MH; Graw J; Gomez-Skarmeta JL; Casares F; Torres M; Bovolenta P, 2015, 'Meis1 coordinates a network of genes implicated in eye development and microphthalmia', Development (Cambridge), 142, pp. 3009 - 3020, http://dx.doi.org/10.1242/dev.122176

Bogdanović O; Lister R, 2015, 'Of mice and man: Differential DNMT dependence in mammalian ESCs', Cell Stem Cell, 16, pp. 459 - 460, http://dx.doi.org/10.1016/j.stem.2015.04.009

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, 6, pp. 7 - 9, http://dx.doi.org/10.1016/j.gdata.2015.07.020

Bogdanović O, 2014, 'Invertebrate epigenomics: The brave new world of the spineless', Briefings in Functional Genomics, 13, pp. 189 - 190, http://dx.doi.org/10.1093/bfgp/elu008

Bogdanović O; Gómez-Skarmeta JL, 2014, 'Embryonic DNA methylation: Insights from the genomics era', Briefings in Functional Genomics, 13, pp. 121 - 130, http://dx.doi.org/10.1093/bfgp/elt039

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, 62, pp. 207 - 215, http://dx.doi.org/10.1016/j.ymeth.2013.04.011

Irimia M; Tena JJ; Alexis MS; Fernandez-Miñan A; Maeso I; Bogdanović O; De La Calle-Mustienes E; Roy SW; Gómez-Skarmeta JL; Fraser HB, 2012, 'Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints', Genome Research, 22, pp. 2356 - 2367, http://dx.doi.org/10.1101/gr.139725.112

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, 23, pp. 782 - 795, http://dx.doi.org/10.1016/j.devcel.2012.09.004

Bogdanović O; Veenstra GJC, 2011, 'Affinity-based enrichment strategies to assay methyl-CpG binding activity and DNA methylation in early Xenopus embryos.', BMC Res Notes, 4, pp. 300, http://dx.doi.org/10.1186/1756-0500-4-300

Working Papers

Edwards R; Field M; Ferguson J; Dudchenko O; Keilwagen J; Rosen B; Johnson G; Rice E; Hillier L; Hammond J; Towarnicki S; Omer A; Khan R; Skvortsova K; Bogdanovic O; Zammit R; Aiden EL; Warren W; Ballard W, 2021, Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome, BioMed Central, http://dx.doi.org10.1186/s12864-021-07493-6

Yadav S; Dudchenko O; Esvaran M; Rosen B; Field M; Skvortsova K; Gopalakrishnan S; Keilwagen J; Cochran B; Manandhar B; Bucknall M; Bustamante S; Rasmussen J; Melvin R; Omer A; Colaric Z; Chan E; Minoche A; Smith T; Gilbert T; Bogdanovic O; Zammit R; Thomas T; Aiden E; Ballard B; Edwards R, 2020, Desert Dingo (Canis lupus dingo) genome provides insights into their role in the Australian ecosystem, Cold Spring Harbor, http://dx.doi.org10.1101/2020.11.15.384057, https://www.biorxiv.org/content/10.1101/2020.11.15.384057v1

Preprints

Church SH; Abedon RB; Ahuja N; Anthony CJ; Ramirez DA; Rojas LM; Albinsson ME; Álvarez Trasobares I; Bergemann RE; Bogdanovic O; Burdick DR; Cunha TJ; Damian-Serrano A; D’Elía G; Dion KB; Doyle TK; Gonçalves JM; Gonzalez Rajal A; Haddock SHD; Helm RR; Gouvello DL; Lewis ZR; Magalhães BIMM; Mańko MK; de Mendoza A; Moura CJ; Nel R; Perelman JN; Prieto L; Munro C; Oguchi K; Pitt KA; Schaeffer A; Schmidt AL; Sellanes J; Wilson NG; Yamamoto G; Lazo-Wasem EA; Simon C; Decker MB; Coughlan JM; Dunn CW, 2024, Global genomics of the man-o’-war (Physalia) reveals biodiversity at the ocean surface, , http://dx.doi.org/10.1101/2024.07.10.602499

Cahn J; Lloyd JPB; Karemaker ID; Jansen PWTC; Pflueger J; Duncan O; Petereit J; Bogdanovic O; Millar AH; Vermeulen M; Lister R, 2023, Characterization of DNA methylation reader proteins ofArabidopsis thaliana, , http://dx.doi.org/10.1101/2023.12.05.570080

Ballard JWO; Field MA; Edwards RJ; Wilson LAB; Koungoulos LG; Rosen BD; Chernoff B; Dudchenko O; Omer A; Keilwagen J; Skvortsova K; Bogdanovic O; Chan E; Zammit R; Hayes V; Aiden EL, 2023, The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology., , http://dx.doi.org/10.1101/2023.01.26.525801

Ross S; Vázquez-Marín J; Gert KRB; González-Rajal Á; Dinger M; Pauli A; Martínez-Morales JR; Bogdanovic O, 2023, Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species, , http://dx.doi.org/10.1101/2023.05.24.542066

Angeloni A; Fissette S; Kaya D; Hammond J; Gamaarachchi H; Deveson I; Klose R; Li W; Zhang X; Bogdanovic O, 2023, Extensive DNA methylome rearrangement during early lamprey embryogenesis, , http://dx.doi.org/10.1101/2023.05.25.542242

Marletaz F; de la Calle-Mustienes E; Acemel R; Nakamura T; Paliou C; Naranjo S; Martinez-Garcia P; Cases I; Sleight V; Hirschberger C; Marcet-Houben M; Navon D; Andrescavage A; Skvortsova K; Duckett P; Gonzalez-Rajal A; Bogdanovic O; Gibcus J; Yang L; Gallardo-Fuentes L; Sospedra I; Lopez-Rios J; Darbellay F; Visel A; Dekker J; Shubin N; Gabaldon T; Tena J; Lupianez D; Rokhsar D; Gomez-Skarmeta J, 2022, The little skate genome and the evolutionary emergence of wing-like fin appendages, , http://dx.doi.org/10.1101/2022.03.21.485123

Skvortsova K; Bertrand S; Voronov D; Duckett PE; Ross SE; Magri MS; Maeso I; Weatheritt RJ; Gomez-Skarmeta JL; Arnone MI; Escriva H; Bogdanovic O, 2021, Active DNA demethylation of developmental cis-regulatory regions predates vertebrate origins, , http://dx.doi.org/10.1101/2021.11.07.467601

Baranasic D; Hörtenhuber M; Balwierz P; Zehnder T; Mukarram AK; Nepal C; Varnai C; Hadzhiev Y; Jimenez-Gonzalez A; Li N; Wragg J; D’Orazio F; Díaz N; Hernández-Rodríguez B; Chen Z; Stoiber M; Dong M; Stevens I; Ross SE; Eagle A; Martin R; Obasaju P; Rastegar S; McGarvey AC; Kopp W; Chambers E; Wang D; Kim HR; Acemel RD; Naranjo S; Lapinski M; Chong V; Mathavan S; Peers B; Sauka-Spengler T; Vingron M; Carninci P; Ohler U; Lacadie SA; Burgess S; Winata C; van Eeden F; Vaquerizas JM; Gómez-Skarmeta JL; Onichtchouk D; Brown BJ; Bogdanovic O; Westerfield M; Wardle FC; Daub CO; Lenhard B; Müller F, 2021, Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish, , http://dx.doi.org/10.1101/2021.08.09.454869

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