By Associate Professor Ozren Bogdanovic

Book Chapters

Bogdanovic O; Vermeulen M, 2021, 'Erratum: Correction to: TET Proteins and DNA Demethylation (Methods in molecular biology (Clifton, N.J.) (2021) 2272 (29-44))', in , pp. C1, http://dx.doi.org/10.1007/978-1-0716-1294-1_18

Ross SE; Bogdanovic O, 2021, 'Generation and Molecular Characterization of Transient TET1/2/3 Zebrafish Knockouts', in TET Proteins and DNA Demethylation: Methods and Protocols, pp. 281 - 317, http://dx.doi.org/10.1007/978-1-0716-1294-1_17

Skvortsova K; Bogdanovic O, 2021, 'TAB-seq and ACE-seq Data Processing for Genome-Wide DNA hydroxymethylation Profiling', in TET Proteins and DNA Demethylation: Methods and Protocols, pp. 163 - 178, http://dx.doi.org/10.1007/978-1-0716-1294-1_9

Journal articles

Angeloni A; Fissette S; Kaya D; Hammond JM; Gamaarachchi H; Deveson IW; Klose RJ; Li W; Zhang X; Bogdanovic O, 2024, 'Extensive DNA methylome rearrangement during early lamprey embryogenesis', Nature Communications, 15, http://dx.doi.org/10.1038/s41467-024-46085-2

Filipe EC; Velayuthar S; Philp A; Nobis M; Latham SL; Parker AL; Murphy KJ; Wyllie K; Major GS; Contreras O; Mok ETY; Enriquez RF; McGowan S; Feher K; Quek LE; Hancock SE; Yam M; Tran E; Setargew YFI; Skhinas JN; Chitty JL; Phimmachanh M; Han JZR; Cadell AL; Papanicolaou M; Mahmodi H; Kiedik B; Junankar S; Ross SE; Lam N; Coulson R; Yang J; Zaratzian A; Da Silva AM; Tayao M; Chin IL; Cazet A; Kansara M; Segara D; Parker A; Hoy AJ; Harvey RP; Bogdanovic O; Timpson P; Croucher DR; Lim E; Swarbrick A; Holst J; Turner N; Choi YS; Kabakova IV; Philp A; Cox TR, 2024, 'Tumor Biomechanics Alters Metastatic Dissemination of Triple Negative Breast Cancer via Rewiring Fatty Acid Metabolism', Advanced Science, 11, http://dx.doi.org/10.1002/advs.202307963

Ross SE; Vázquez-Marín J; Gert KRB; González-Rajal Á; Dinger ME; Pauli A; Martínez-Morales JR; Bogdanovic O, 2023, 'Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species', Nucleic Acids Research, 51, pp. 9658 - 9671, http://dx.doi.org/10.1093/nar/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, 2023, 'The little skate genome and the evolutionary emergence of wing-like fins', Nature, 616, pp. 495 - 503, http://dx.doi.org/10.1038/s41586-023-05868-1

Hastings JF; Latham SL; Kamili A; Wheatley MS; Han JZR; Wong-Erasmus M; Phimmachanh M; Nobis M; Pantarelli C; Cadell AL; O’Donnell YEI; Leong KH; Lynn S; Geng FS; Cui L; Yan S; Achinger-Kawecka J; Stirzaker C; Norris MD; Haber M; Trahair TN; Speleman F; De Preter K; Cowley MJ; Bogdanovic O; Timpson P; Cox TR; Kolch W; Fletcher JI; Fey D; Croucher DR, 2023, 'Memory of stochastic single-cell apoptotic signaling promotes chemoresistance in neuroblastoma', Science Advances, 9, http://dx.doi.org/10.1126/sciadv.abp8314

Ballard JOW; 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', GigaScience, 12, http://dx.doi.org/10.1093/gigascience/giad018

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, 2022, 'Active DNA demethylation of developmental cis-regulatory regions predates vertebrate origins', Science Advances, 8, http://dx.doi.org/10.1126/sciadv.abn2258

de Mendoza A; Nguyen TV; Ford E; Poppe D; Buckberry S; Pflueger J; Grimmer MR; Stolzenburg S; Bogdanovic O; Oshlack A; Farnham PJ; Blancafort P; Lister R, 2022, 'Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability', Genome Biology, 23, http://dx.doi.org/10.1186/s13059-022-02728-5

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, 2022, 'Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements', Nature Genetics, 54, pp. 1037 - 1050, http://dx.doi.org/10.1038/s41588-022-01089-w

Wyatt CDR; Pernaute B; Gohr A; Miret-Cuesta M; Goyeneche L; Rovira Q; Salzer MC; Boke E; Bogdanovic O; Bonnal S; Irimia M, 2022, 'A developmentally programmed splicing failure contributes to DNA damage response attenuation during mammalian zygotic genome activation', Science Advances, 8, http://dx.doi.org/10.1126/sciadv.abn4935

Field MA; Yadav S; Dudchenko O; Esvaran M; Rosen BD; Skvortsova K; Edwards RJ; Keilwagen J; Cochran BJ; Manandhar B; Bustamante S; Rasmussen JA; Melvin RG; Chernoff B; Omer A; Colaric Z; Chan EKF; Minoche AE; Smith TPL; Gilbert MTP; Bogdanovic O; Zammit RA; Thomas T; Aiden EL; Ballard JWO, 2022, 'The Australian dingo is an early offshoot of modern breed dogs', Science Advances, 8, http://dx.doi.org/10.1126/sciadv.abm5944

Angeloni A; Ferguson J; Bogdanovic O, 2022, 'Nanopore Sequencing and Data Analysis for Base-Resolution Genome-Wide 5-Methylcytosine Profiling', , 2458, pp. 75 - 94, http://dx.doi.org/10.1007/978-1-0716-2140-0_5

Buono L; Corbacho J; Naranjo S; Almuedo-Castillo M; Moreno-Marmol T; de la Cerda B; Sanbria-Reinoso E; Polvillo R; Díaz-Corrales FJ; Bogdanovic O; Bovolenta P; Martínez-Morales JR, 2021, 'Analysis of gene network bifurcation during optic cup morphogenesis in zebrafish', Nature Communications, 12, http://dx.doi.org/10.1038/s41467-021-24169-7

Buono L; Corbacho J; Naranjo S; Almuedo-Castillo M; Moreno-Marmol T; de la Cerda B; Sanabria-Reinoso E; Polvillo R; Díaz-Corrales FJ; Bogdanovic O; Bovolenta P; Martínez-Morales JR, 2021, 'Author Correction: Analysis of gene network bifurcation during optic cup morphogenesis in zebrafish (Nature Communications, (2021), 12, 1, (3866), 10.1038/s41467-021-24169-7)', Nature Communications, 12, http://dx.doi.org/10.1038/s41467-021-24834-x

Edwards RJ; Field MA; Ferguson JM; Dudchenko O; Keilwagen J; Rosen BD; Johnson GS; Rice ES; Hillier LD; Hammond JM; Towarnicki SG; Omer A; Khan R; Skvortsova K; Bogdanovic O; Zammit RA; Aiden EL; Warren WC; Ballard JWO, 2021, 'Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome', BMC Genomics, 22, http://dx.doi.org/10.1186/s12864-021-07493-6

Angeloni A; Bogdanovic O, 2021, 'Sequence determinants, function, and evolution of CpG islands', Biochemical Society Transactions, 49, pp. 1109 - 1119, http://dx.doi.org/10.1042/BST20200695

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, 2021, 'Krüppel-like factor 1 is a core cardiomyogenic trigger in zebrafish', Science, 372, http://dx.doi.org/10.1126/science.abe2762

Ross SE; Hesselson D; Bogdanovic O, 2021, 'Developmental Accumulation of Gene Body and Transposon Non-CpG Methylation in the Zebrafish Brain', Frontiers in Cell and Developmental Biology, 9, http://dx.doi.org/10.3389/fcell.2021.643603

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, 2021, 'The emergence of the brain non-CpG methylation system in vertebrates', Nature Ecology and Evolution, 5, pp. 369 - 378, http://dx.doi.org/10.1038/s41559-020-01371-2

Ross SE; Angeloni A; Geng FS; de Mendoza A; Bogdanovic O, 2020, 'Developmental remodelling of non-CG methylation at satellite DNA repeats', Nucleic Acids Research, 48, pp. 12675 - 12688, http://dx.doi.org/10.1093/nar/gkaa1135

Geng F-S; de la Calle-Mustienes E; Gómez-Skarmeta JL; Lister R; Bogdanovic O, 2020, 'Depletion of Foxk transcription factors causes genome-wide transcriptional misregulation and developmental arrest in zebrafish embryos.', MicroPubl Biol, 2020, http://dx.doi.org/10.17912/micropub.biology.000341

Cultrone D; Zammit NW; Self E; Postert B; Han JZR; Bailey J; Warren J; Croucher DR; Kikuchi K; Bogdanovic O; Chtanova T; Hesselson D; Grey ST, 2020, 'A zebrafish functional genomics model to investigate the role of human A20 variants in vivo', Scientific Reports, 10, http://dx.doi.org/10.1038/s41598-020-75917-6

Bogdanovic O; Irimia M, 2020, 'José Luis Gómez-Skarmeta (1966-2020)', Nature genetics, 52, pp. 1267 - 1268, http://dx.doi.org/10.1038/s41588-020-00743-5

Edwards RJ; Field M; Ferguson J; Dudchenko O; Keilwagen J; Rosen B; Johnston G; Rice E; Hillier L; Hammond J; Towarnicki S; Omer A; Skvortsova K; Bogdanovic O; Zammit R; Aiden E; Warren W; Ballard B, 2020, 'Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome', bioRxiv, pp. 2020.11.11.379073, http://dx.doi.org/10.1101/2020.11.11.379073

Field MA; Rosen BD; Dudchenko O; Chan EKF; Minoche AE; Edwards RJ; Barton K; Lyons RJ; Tuipulotu DE; Hayes VM; Omer AD; Colaric Z; Keilwagen J; Skvortsova K; Bogdanovic O; Smith MA; Aiden EL; Smith TPL; Zammit RA; Ballard JWO, 2020, 'Canfam-GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C', GigaScience, 9, http://dx.doi.org/10.1093/gigascience/giaa027

de Mendoza A; Lister R; Bogdanovic O, 2020, 'Evolution of DNA Methylome Diversity in Eukaryotes', Journal of Molecular Biology, 432, pp. 1687 - 1705, http://dx.doi.org/10.1016/j.jmb.2019.11.003

Wyatt C; Pernaute B; Gohr A; Miret-Cuesta M; Goyeneche L; Rovira Q; Bogdanovic O; Bonnal S; Irimia M, 2020, 'A developmentally programmed splicing failure attenuates the DNA damage response during mammalian zygotic genome activation', , http://dx.doi.org/10.1101/2020.11.25.397794

Cultrone D; Zammit N; Self E; Postert B; Han JZR; Bailey J; Warren J; Croucher D; Kikuchi K; Bogdanovic O; Chtanova T; Hesselson D; Grey S, 2020, 'A zebrafish functional genomics model to investigate the role of human A20 variantsin vivo', , http://dx.doi.org/10.1101/2020.02.23.961763

Buono L; Naranjo S; Moreno-Marmol T; de la Cerda B; Polvillo R; Díaz-Corrales F-J; Bogdanovic O; Bovolenta P; Martínez-Morales J-R, 2020, 'Analysis of gene network bifurcation during optic cup morphogenesis in zebrafish', , http://dx.doi.org/10.1101/2020.05.28.121038

Ross S; Ross S; Hesselson D; Bogdanovic O, 2020, 'Developmental accumulation of gene body and transposon non-CpG methylation in the zebrafish brain', , http://dx.doi.org/10.1101/2020.12.17.423365

Ross S; Angeloni A; de Mendoza A; Bogdanovic O, 2020, 'Pervasive non-CpG methylation at zebrafish mosaic satellite repeats', , http://dx.doi.org/10.1101/2020.05.13.093203

Skvortsova K; Tarbashevich K; Stehling M; Lister R; Irimia M; Raz E; Bogdanovic O, 2019, 'Retention of paternal DNA methylome in the developing zebrafish germline', Nature Communications, 10, http://dx.doi.org/10.1038/s41467-019-10895-6

de Mendoza A; Hatleberg WL; Pang K; Leininger S; Bogdanovic O; Pflueger J; Buckberry S; Technau U; Hejnol A; Adamska M; Degnan BM; Degnan SM; Lister R, 2019, 'Convergent evolution of a vertebrate-like methylome in a marine sponge', Nature Ecology and Evolution, 3, pp. 1464 - 1473, http://dx.doi.org/10.1038/s41559-019-0983-2

Angeloni A; Bogdanovic O, 2019, 'Enhancer DNA methylation: implications for gene regulation.', Essays Biochem, 63, pp. 707 - 715, http://dx.doi.org/10.1042/EBC20190030

Skvortsova K; Masle-Farquhar E; Luu PL; Song JZ; Qu W; Zotenko E; Gould CM; Du Q; Peters TJ; Colino-Sanguino Y; Pidsley R; Nair SS; Khoury A; Smith GC; Miosge LA; Reed JH; Kench JG; Rubin MA; Horvath L; Bogdanovic O; Lim SM; Polo JM; Goodnow CC; Stirzaker C; Clark SJ, 2019, 'DNA Hypermethylation Encroachment at CpG Island Borders in Cancer Is Predisposed by H3K4 Monomethylation Patterns', Cancer Cell, 35, pp. 297 - 314.e8, http://dx.doi.org/10.1016/j.ccell.2019.01.004

Ross SE; Bogdanovic O, 2019, 'TET enzymes, DNA demethylation and pluripotency', Biochemical Society Transactions, 47, pp. 875 - 885, http://dx.doi.org/10.1042/BST20180606

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, 2018, 'Amphioxus functional genomics and the origins of vertebrate gene regulation', Nature, 564, pp. 64 - 70, http://dx.doi.org/10.1038/s41586-018-0734-6

Skvortsova K; Iovino N; Bogdanović O, 2018, 'Functions and mechanisms of epigenetic inheritance in animals', Nature Reviews Molecular Cell Biology, 19, pp. 774 - 790, http://dx.doi.org/10.1038/s41580-018-0074-2

Elurbe DM; Paranjpe SS; Georgiou G; van Kruijsbergen I; Bogdanovic O; Gibeaux R; Heald R; Lister R; Huynen MA; van Heeringen SJ; Veenstra GJC, 2017, 'Regulatory remodeling in the allo-tetraploid frog Xenopus laevis', Genome biology, 18, pp. 198, http://dx.doi.org/10.1186/s13059-017-1335-7

Bogdanović O; Lister R, 2017, 'DNA methylation and the preservation of cell identity', Current Opinion in Genetics and Development, 46, pp. 9 - 14, http://dx.doi.org/10.1016/j.gde.2017.06.007

Zenk F; Loeser E; Schiavo R; Kilpert F; Bogdanovic O; Iovino N, 2017, 'Germ line–inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition', Science, 357, pp. 212 - 216, http://dx.doi.org/10.1126/science.aam5339

Westhorpe F; Tiengwe C; Hunsberger H; Jain G; Wells M; Yu M; Bogdanovic O; Absalon S; Sen P; Madrigal P; Natarajan K, 2017, 'Postdocs, What Would You Tell Your Younger Self?', CELL, 168, pp. 745 - 748, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000396284800002&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Bogdanović O, 2017, 'Tet proteins: Master regulators of vertebrate body plan formation?', Epigenomics, 9, pp. 93 - 96, http://dx.doi.org/10.2217/epi-2016-0164

Crisp PA; Ganguly DR; Smith AB; Murray KD; Estavillo GM; Searle I; Ford E; Bogdanović O; Lister R; Borevitz JO; Eichten SR; Pogson BJ, 2017, 'Rapid recovery gene downregulation during excess-light stress and recovery in arabidopsis', Plant Cell, 29, pp. 1836 - 1863, http://dx.doi.org/10.1105/tpc.16.00828

Ford E; Grimmer M; Stolzenburg S; Bogdanovic O; Mendoza AD; Farnham P; Blancafort P; Lister R, 2017, 'Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation', , http://dx.doi.org/10.1101/170506

Elurbe D; Paranjpe S; Georgiou G; van Kruijsbergen I; Bogdanovic O; Gibeaux R; Heald R; Lister R; Huynen M; van Heeringen S; Veenstra GJ, 2017, 'Regulatory remodeling in the allo-tetraploid frog Xenopus laevis', , http://dx.doi.org/10.1101/120212

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 GJC; Fujiyama A; Harland RM; Taira M; Rokhsar DS, 2016, 'Genome evolution in the allotetraploid frog Xenopus laevis', Nature, 538, pp. 336 - 343, http://dx.doi.org/10.1038/nature19840

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