Ozren Bogdanovic
@obog.bsky.social
Principal Investigator at https://www.cabd.es | Interested in developmental epigenomics | Coordinator of the DANIO-ReCODE MSCA DN | https://danio-recode.eu | @daniorecode.bsky.social | webpage: www.bogdanoviclab.org
Pinned
Ozren Bogdanovic
@obog.bsky.social
· Oct 14
A single-cell multiomics roadmap of zebrafish spermatogenesis reveals regulatory principles of male germline formation | Molecular Systems Biology
imageimageA multiomics study of zebrafish spermatogenesis integrating scRNA-seq, scATAC-seq, and base-resolution DNA methylomes defines the chromatin and transcriptional states of germ cells, revealing the regulatory dynamics of this continuous ...
www.embopress.org
Reposted by Ozren Bogdanovic
🐟Meet the DANIO-ReCODE team!🐟
This week: Martina Sevo and Prof Blaz Zupan from University of Ljubljana
Martina´s research focuses on conversational AI for exploring complex data in tissue regeneration research
📢Stay tuned! #DANIO #MSCA @obog.bsky.social @cabd-upo-csic.bsky.social
This week: Martina Sevo and Prof Blaz Zupan from University of Ljubljana
Martina´s research focuses on conversational AI for exploring complex data in tissue regeneration research
📢Stay tuned! #DANIO #MSCA @obog.bsky.social @cabd-upo-csic.bsky.social
November 24, 2025 at 12:49 PM
🐟Meet the DANIO-ReCODE team!🐟
This week: Martina Sevo and Prof Blaz Zupan from University of Ljubljana
Martina´s research focuses on conversational AI for exploring complex data in tissue regeneration research
📢Stay tuned! #DANIO #MSCA @obog.bsky.social @cabd-upo-csic.bsky.social
This week: Martina Sevo and Prof Blaz Zupan from University of Ljubljana
Martina´s research focuses on conversational AI for exploring complex data in tissue regeneration research
📢Stay tuned! #DANIO #MSCA @obog.bsky.social @cabd-upo-csic.bsky.social
Reposted by Ozren Bogdanovic
Photosynthetic sea slugs can decapitate themselves & regenerate whole body from the detached head (without the heart or guts), while the shed body do not regenerate. The process takes ~2-3 weeks. A new model for regeneration?
From: www.cell.com/current-biol...
From: www.cell.com/current-biol...
Extreme autotomy and whole-body regeneration in photosynthetic sea slugs
Autotomy, the voluntary shedding of a body part, is common among animals. Mitoh and
Yusa report an extreme case of autotomy with the shedding of the main body, including
the whole heart, and subsequen...
www.cell.com
November 22, 2025 at 4:00 PM
Photosynthetic sea slugs can decapitate themselves & regenerate whole body from the detached head (without the heart or guts), while the shed body do not regenerate. The process takes ~2-3 weeks. A new model for regeneration?
From: www.cell.com/current-biol...
From: www.cell.com/current-biol...
Reposted by Ozren Bogdanovic
Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9
Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes - Nature Genetics
Long-read sequencing in 18 unicellular eukaryotes reveals that 6mA is widespread across eukaryotes and is enriched at transcriptionally permissive regions, which are also marked by H3K4me3.
www.nature.com
November 18, 2025 at 12:00 PM
Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9
Reposted by Ozren Bogdanovic
piRNA-directed DNA methylation may not be a mammalian invention, but can already be found in the germline of axolotl salamanders
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
November 13, 2025 at 11:54 AM
piRNA-directed DNA methylation may not be a mammalian invention, but can already be found in the germline of axolotl salamanders
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
Reposted by Ozren Bogdanovic
🗨️ Just published in Nature Biotechnology: Our CellWhisperer AI enables chat-based analysis of single-cell sequencing data. You can talk to your cells & figure out the biology without writing any computer code. Paper here: www.nature.com/articles/s41.... Annotated walkthrough in a thread below (1/11)
November 11, 2025 at 12:52 PM
🗨️ Just published in Nature Biotechnology: Our CellWhisperer AI enables chat-based analysis of single-cell sequencing data. You can talk to your cells & figure out the biology without writing any computer code. Paper here: www.nature.com/articles/s41.... Annotated walkthrough in a thread below (1/11)
Reposted by Ozren Bogdanovic
🐟Meet the DANIO-ReCODE team!🐟
This week:Parth Bhatia and Prof @ferencmueller.bsky.social from @unibirmingham.bsky.social
Parth´s research focuses on the annotation,characterisation and dynamics of cis-regulatory elements (CREs) in telencephalon injury
📢Stay tuned! #DANIO #MSCA @obog.bsky.social
This week:Parth Bhatia and Prof @ferencmueller.bsky.social from @unibirmingham.bsky.social
Parth´s research focuses on the annotation,characterisation and dynamics of cis-regulatory elements (CREs) in telencephalon injury
📢Stay tuned! #DANIO #MSCA @obog.bsky.social
November 11, 2025 at 8:30 AM
🐟Meet the DANIO-ReCODE team!🐟
This week:Parth Bhatia and Prof @ferencmueller.bsky.social from @unibirmingham.bsky.social
Parth´s research focuses on the annotation,characterisation and dynamics of cis-regulatory elements (CREs) in telencephalon injury
📢Stay tuned! #DANIO #MSCA @obog.bsky.social
This week:Parth Bhatia and Prof @ferencmueller.bsky.social from @unibirmingham.bsky.social
Parth´s research focuses on the annotation,characterisation and dynamics of cis-regulatory elements (CREs) in telencephalon injury
📢Stay tuned! #DANIO #MSCA @obog.bsky.social
Reposted by Ozren Bogdanovic
Some hardcore mechanism, for the aficionados (from Peter Jones @vai.org and Ting-Hai Xu @slu-official.bsky.social labs) @natsmb.nature.com www.nature.com/articles/s41...
Mechanisms of DNMT3A–3L-mediated de novo DNA methylation on chromatin - Nature Structural & Molecular Biology
Yan et al. use cryo-EM to obtain structures that reveal how DNMT3A2 and DNMT3L cooperate to read histone signals and bind chromatin, illustrating a mechanism that controls DNA methylation and shapes e...
www.nature.com
November 4, 2025 at 2:55 PM
Some hardcore mechanism, for the aficionados (from Peter Jones @vai.org and Ting-Hai Xu @slu-official.bsky.social labs) @natsmb.nature.com www.nature.com/articles/s41...
Reposted by Ozren Bogdanovic
#CABDseminars
"Rewriting Cell Identity Through TET2 Chromatin Profiling and DNA Methylation Editing" by José Luis Sardina @jlsardinalab.bsky.social, @carrerasijc.bsky.social
🗓️ November 7th
⏰ 12 pm
📍sala Grado, edificio 25 (biblioteca UPO) ‼️
Hosted by @obog.bsky.social
"Rewriting Cell Identity Through TET2 Chromatin Profiling and DNA Methylation Editing" by José Luis Sardina @jlsardinalab.bsky.social, @carrerasijc.bsky.social
🗓️ November 7th
⏰ 12 pm
📍sala Grado, edificio 25 (biblioteca UPO) ‼️
Hosted by @obog.bsky.social
November 3, 2025 at 2:01 PM
#CABDseminars
"Rewriting Cell Identity Through TET2 Chromatin Profiling and DNA Methylation Editing" by José Luis Sardina @jlsardinalab.bsky.social, @carrerasijc.bsky.social
🗓️ November 7th
⏰ 12 pm
📍sala Grado, edificio 25 (biblioteca UPO) ‼️
Hosted by @obog.bsky.social
"Rewriting Cell Identity Through TET2 Chromatin Profiling and DNA Methylation Editing" by José Luis Sardina @jlsardinalab.bsky.social, @carrerasijc.bsky.social
🗓️ November 7th
⏰ 12 pm
📍sala Grado, edificio 25 (biblioteca UPO) ‼️
Hosted by @obog.bsky.social
Reposted by Ozren Bogdanovic
Part 6: For decades, the zebrafish has helped scientists unlock the mysteries of genetics, development, & disease. But the fish that power most discoveries have spent generations inside lab tanks. This video captures footage of zebrafish in their natural environment in Nepal.
youtu.be/cCZhZpPALqw
youtu.be/cCZhZpPALqw
Zebrafish in the wild
YouTube video by John Rawls
youtu.be
October 28, 2025 at 2:09 PM
Part 6: For decades, the zebrafish has helped scientists unlock the mysteries of genetics, development, & disease. But the fish that power most discoveries have spent generations inside lab tanks. This video captures footage of zebrafish in their natural environment in Nepal.
youtu.be/cCZhZpPALqw
youtu.be/cCZhZpPALqw
Reposted by Ozren Bogdanovic
Two back-to-back stories on mitosis led by my incredible postdoc @krunovuk.bsky.social at @institutrb.bsky.social, in which we challenge the gliding model of CENP-E-driven chromosome congression! Today in @natcomms.nature.com
doi.org/10.1038/s414...
doi.org/10.1038/s414...
doi.org/10.1038/s414...
doi.org/10.1038/s414...
October 21, 2025 at 11:14 AM
Two back-to-back stories on mitosis led by my incredible postdoc @krunovuk.bsky.social at @institutrb.bsky.social, in which we challenge the gliding model of CENP-E-driven chromosome congression! Today in @natcomms.nature.com
doi.org/10.1038/s414...
doi.org/10.1038/s414...
doi.org/10.1038/s414...
doi.org/10.1038/s414...
Reposted by Ozren Bogdanovic
💥 Another fruitful collaboration!
Along with @obog.bsky.social & Juan Tena’s teams we provide a multiomics study of zebrafish spermatogenesis
🐟#meiosis
👇
www.embopress.org/doi/full/10....
Along with @obog.bsky.social & Juan Tena’s teams we provide a multiomics study of zebrafish spermatogenesis
🐟#meiosis
👇
www.embopress.org/doi/full/10....
October 16, 2025 at 6:10 PM
💥 Another fruitful collaboration!
Along with @obog.bsky.social & Juan Tena’s teams we provide a multiomics study of zebrafish spermatogenesis
🐟#meiosis
👇
www.embopress.org/doi/full/10....
Along with @obog.bsky.social & Juan Tena’s teams we provide a multiomics study of zebrafish spermatogenesis
🐟#meiosis
👇
www.embopress.org/doi/full/10....
We’re looking for a Research Assistant / Lab Manager to join the 🧬 Developmental Epigenomics lab at the Andalusian Centre for Developmental Biology (CABD, Seville 🇪🇸)!
🐟 Work with zebrafish, CRISPR–Cas9, and genomics technologies
💫 3-year fully funded position
Details 👉 www.bogdanoviclab.org
🐟 Work with zebrafish, CRISPR–Cas9, and genomics technologies
💫 3-year fully funded position
Details 👉 www.bogdanoviclab.org
Bogdanovic Lab
www.bogdanoviclab.org
October 6, 2025 at 12:34 PM
We’re looking for a Research Assistant / Lab Manager to join the 🧬 Developmental Epigenomics lab at the Andalusian Centre for Developmental Biology (CABD, Seville 🇪🇸)!
🐟 Work with zebrafish, CRISPR–Cas9, and genomics technologies
💫 3-year fully funded position
Details 👉 www.bogdanoviclab.org
🐟 Work with zebrafish, CRISPR–Cas9, and genomics technologies
💫 3-year fully funded position
Details 👉 www.bogdanoviclab.org
Reposted by Ozren Bogdanovic
🐟Meet the DANIO-ReCODE team!🐟
This week: Dario González and Dr Csilla Várnai from @unibirmingham.bsky.social
Dario studies the annotation, characterisation, and conservation of 3D chromatin topology in telencephalon injury
📢Stay tuned!
#DANIO #MSCA @obog.bsky.social @cabd-upo-csic.bsky.social
This week: Dario González and Dr Csilla Várnai from @unibirmingham.bsky.social
Dario studies the annotation, characterisation, and conservation of 3D chromatin topology in telencephalon injury
📢Stay tuned!
#DANIO #MSCA @obog.bsky.social @cabd-upo-csic.bsky.social
October 6, 2025 at 8:55 AM
🐟Meet the DANIO-ReCODE team!🐟
This week: Dario González and Dr Csilla Várnai from @unibirmingham.bsky.social
Dario studies the annotation, characterisation, and conservation of 3D chromatin topology in telencephalon injury
📢Stay tuned!
#DANIO #MSCA @obog.bsky.social @cabd-upo-csic.bsky.social
This week: Dario González and Dr Csilla Várnai from @unibirmingham.bsky.social
Dario studies the annotation, characterisation, and conservation of 3D chromatin topology in telencephalon injury
📢Stay tuned!
#DANIO #MSCA @obog.bsky.social @cabd-upo-csic.bsky.social
Reposted by Ozren Bogdanovic
❓Can a father’s environmental exposures before conception influence their offspring?
We systematically tackled this - identifying effects of paternal age, environment and genetics on early embryos - as well as confounding influences
www.embopress.org/doi/full/10....
We systematically tackled this - identifying effects of paternal age, environment and genetics on early embryos - as well as confounding influences
www.embopress.org/doi/full/10....
Embryonic signatures of intergenerational epigenetic inheritance across paternal environments and genetic backgrounds | The EMBO Journal
imageimagePaternal environmental exposures have been linked with modulation of phenotype and
disease risk in offspring via largely unclear mechanisms. This study employs in vitro
fertilization and sin...
www.embopress.org
September 27, 2025 at 7:28 AM
❓Can a father’s environmental exposures before conception influence their offspring?
We systematically tackled this - identifying effects of paternal age, environment and genetics on early embryos - as well as confounding influences
www.embopress.org/doi/full/10....
We systematically tackled this - identifying effects of paternal age, environment and genetics on early embryos - as well as confounding influences
www.embopress.org/doi/full/10....
Reposted by Ozren Bogdanovic
Very excited to share an excellent review from @teresa-urli.bsky.social, published one week before her PhD defense! We did a deep dive into the fascinating biology of the variant Polycomb complex, PRC1.6 (1/5) journals.plos.org/plosgenetics...
Epigenetic relay: Polycomb-directed DNA methylation in mammalian development
In mammals, repression of germline-specific gene expression is essential for preserving somatic cell identity and preventing disease. Germline gene silencing is often dependent on the presence of prom...
journals.plos.org
September 15, 2025 at 7:04 PM
Very excited to share an excellent review from @teresa-urli.bsky.social, published one week before her PhD defense! We did a deep dive into the fascinating biology of the variant Polycomb complex, PRC1.6 (1/5) journals.plos.org/plosgenetics...
Reposted by Ozren Bogdanovic
Very happy to have contributed to this review on "non-CG" #methylation in animals now out in @natgenet.nature.com. Working again with @obog.bsky.social and Tirsa is always a pleasure. We think this not so well studied form of methylation should be more widely considered, please read: rdcu.be/eFAEk
Non-CG DNA methylation in animal genomes
Nature Genetics - This Review discusses noncanonical DNA methylation (mCH) in animal genomes and highlights the remaining need to clarify whether mCH represents a conserved regulatory layer or a...
rdcu.be
September 11, 2025 at 10:11 AM
Very happy to have contributed to this review on "non-CG" #methylation in animals now out in @natgenet.nature.com. Working again with @obog.bsky.social and Tirsa is always a pleasure. We think this not so well studied form of methylation should be more widely considered, please read: rdcu.be/eFAEk
Reposted by Ozren Bogdanovic
Reposted by Ozren Bogdanovic
Many people were essential, I can only tag a handful here! @caseywdunn.bsky.social @stevehaddock.bsky.social @colinjanthony.bsky.social @rebeccarhelm.bsky.social @catmunro.bsky.social @amandine-oceano.bsky.social @scientifikita.bsky.social @guillermodelia.bsky.social & Yale Peabody Museum
June 19, 2025 at 7:51 PM
Many people were essential, I can only tag a handful here! @caseywdunn.bsky.social @stevehaddock.bsky.social @colinjanthony.bsky.social @rebeccarhelm.bsky.social @catmunro.bsky.social @amandine-oceano.bsky.social @scientifikita.bsky.social @guillermodelia.bsky.social & Yale Peabody Museum
Reposted by Ozren Bogdanovic
Excited to share our study on sailing siphonophores, AKA bluebottles or man-o'-war! 🌊 we received hundreds of samples from scientists around the world, part of a huge effort to sequence genomes and test for multiple species 🧬 out today in @currentbiology.bsky.social doi.org/10.1016/j.cu... 🦑🧪📌
June 19, 2025 at 7:51 PM
Excited to share our study on sailing siphonophores, AKA bluebottles or man-o'-war! 🌊 we received hundreds of samples from scientists around the world, part of a huge effort to sequence genomes and test for multiple species 🧬 out today in @currentbiology.bsky.social doi.org/10.1016/j.cu... 🦑🧪📌
Reposted by Ozren Bogdanovic
🚨 Just out in Nature Communications:
Cholangiocytes contribute to hepatocyte regeneration after partial #liver #injury during growth in #zebrafish
We challenge old assumptions on liver regeneration!
🔗 nature.com/articles/s41...
🧵(1/8)
Cholangiocytes contribute to hepatocyte regeneration after partial #liver #injury during growth in #zebrafish
We challenge old assumptions on liver regeneration!
🔗 nature.com/articles/s41...
🧵(1/8)
Cholangiocytes contribute to hepatocyte regeneration after partial liver injury during growth spurt in zebrafish - Nature Communications
During partial liver injury in growing zebrafish, cholangiocytes regenerate hepatocytes through transdifferentiation, revealing a stage-specific regeneration mechanism regulated by mTORC1 signaling.
nature.com
June 6, 2025 at 11:39 AM
🚨 Just out in Nature Communications:
Cholangiocytes contribute to hepatocyte regeneration after partial #liver #injury during growth in #zebrafish
We challenge old assumptions on liver regeneration!
🔗 nature.com/articles/s41...
🧵(1/8)
Cholangiocytes contribute to hepatocyte regeneration after partial #liver #injury during growth in #zebrafish
We challenge old assumptions on liver regeneration!
🔗 nature.com/articles/s41...
🧵(1/8)
Reposted by Ozren Bogdanovic
EPIGENETIC HULK READY TO SMASH AGAIN! GET IN LOSERS!
June 13, 2025 at 4:30 AM
EPIGENETIC HULK READY TO SMASH AGAIN! GET IN LOSERS!
Reposted by Ozren Bogdanovic
Sequence-alignment is not the best way to detect conserved cis-regulatory elements?
Tobi Zehnder from Vingron-Lab developed #IPP a synteny based algorithm with @ferencmueller.bsky.social, @borislenhard.bsky.social& @da-bar.bsky.social
We used it to find conserved enhancers with diverged sequences
Tobi Zehnder from Vingron-Lab developed #IPP a synteny based algorithm with @ferencmueller.bsky.social, @borislenhard.bsky.social& @da-bar.bsky.social
We used it to find conserved enhancers with diverged sequences
May 27, 2025 at 12:19 PM
Sequence-alignment is not the best way to detect conserved cis-regulatory elements?
Tobi Zehnder from Vingron-Lab developed #IPP a synteny based algorithm with @ferencmueller.bsky.social, @borislenhard.bsky.social& @da-bar.bsky.social
We used it to find conserved enhancers with diverged sequences
Tobi Zehnder from Vingron-Lab developed #IPP a synteny based algorithm with @ferencmueller.bsky.social, @borislenhard.bsky.social& @da-bar.bsky.social
We used it to find conserved enhancers with diverged sequences
Reposted by Ozren Bogdanovic
I am super excited to announce the first (brief) pre-print purely from my group:
Start right to end right: authentic open reading frame selection matters
www.biorxiv.org/content/10.1...
This marks a return to NMD research for me. NMD detects early stop codons but we need to find the true stop!
Start right to end right: authentic open reading frame selection matters
www.biorxiv.org/content/10.1...
This marks a return to NMD research for me. NMD detects early stop codons but we need to find the true stop!
June 11, 2025 at 10:40 PM
I am super excited to announce the first (brief) pre-print purely from my group:
Start right to end right: authentic open reading frame selection matters
www.biorxiv.org/content/10.1...
This marks a return to NMD research for me. NMD detects early stop codons but we need to find the true stop!
Start right to end right: authentic open reading frame selection matters
www.biorxiv.org/content/10.1...
This marks a return to NMD research for me. NMD detects early stop codons but we need to find the true stop!
Reposted by Ozren Bogdanovic
So excited that our latest work is out! We have been working to understand how damaged tissue exits regeneration and returns to normal gene expression, and found a major role for the pioneer transcription factor Zelda in flies. Kudos to @anishbose.bsky.social @keatonschuster.bsky.social et al!
The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila
The pioneer factor Zelda activates a specific set of developmental and structural genes to end tissue regeneration.
www.science.org
June 14, 2025 at 12:47 AM
So excited that our latest work is out! We have been working to understand how damaged tissue exits regeneration and returns to normal gene expression, and found a major role for the pioneer transcription factor Zelda in flies. Kudos to @anishbose.bsky.social @keatonschuster.bsky.social et al!