Ozren Bogdanović

The paper investigates the evolution of CTCF's role in chromatin organization across species, finding that vertebrate CTCF enables loop extrusion but requires additional factors for full genome architecture.

This study shows that paternal cardiac injury in vertebrates triggers inflammatory signals to the gonads, leading to intergenerational cardiac effects in offspring.

This study presents a multi-omic atlas of the siphonophore Physalia utriculus, revealing the regulatory mechanisms of colonial division of labour and the molecular basis of venom activity.

The paper introduces Cornetto, a method using targeted long-read sequencing to improve genome assembly quality and completeness, particularly for challenging regions and sample types.

This study presents a single-cell multiomics atlas of zebrafish spermatogenesis, identifying key transcriptional states, DNA methylation changes, and chromatin accessibility patterns involved in male germline formation.

The paper sequences 133 Physalia genomes and analyzes citizen-science images to reveal five distinct lineages and four species, with geographic population structure and long-distance dispersal.

This study investigates DNA methylation dynamics during lamprey embryogenesis, revealing extensive maternal-to-paternal epigenome remodeling and its link to programmed genome rearrangement.

The paper compares DNA methylation dynamics in medaka and zebrafish embryos, showing conserved remodelling patterns without global erasure, and identifies conserved non-canonical methylation reprogramming.

The paper presents a high-quality chromosome-level genome assembly, DNA methylome, and cranial morphology analysis of an Alpine dingo, supporting its status as an archetype for evolutionary studies.

The paper investigates 5hmC and TET enzyme function in non-vertebrate deuterostomes, showing conserved 5mC removal from regulatory regions across species.

The paper creates a central repository for zebrafish developmental genomics data, identifies new cis-regulatory elements, and compares regulatory elements between zebrafish and mouse.

The paper presents a desert dingo genome assembly and compares it to domestic dog genomes, identifying structural variants and physiological differences linked to ecological roles.

The paper analyzes gene network bifurcation during optic cup morphogenesis in zebrafish, identifying regulatory mechanisms and conserved TF recruitment sequences in RPE specification.

The paper presents two high-quality Basenji genome assemblies and compares structural variations across three dog breeds, highlighting the impact of reference genome choice on variant detection.

This study identifies mCH accumulation at CAC trinucleotides in zebrafish brain development and shows Dnmt3a's role in mCAC deposition, demonstrating evolutionary conservation of mCH dynamics.

The paper shows that during zygotic genome activation, embryos exhibit temporary splicing failures in DNA damage response genes, regulated by Snrpb and Snrpd2, which reduce DNA damage response.

The paper identifies pervasive non-CpG methylation at zebrafish mosaic satellite repeats, showing enrichment at TGCT positions in various tissues.

This paper uses a zebrafish model to study the in vivo effects of human A20 variants, showing that specific mutations impact A20 function and disease relevance.

Forcing DNA methylation onto thousands of human promoters with a zinc finger-DNMT3A fusion often fails to repress them, and the mark is quickly erased at H3K4me3-marked promoters.