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Boyan Bonev

@boyanbonev.bsky.social
410 followers 198 following 25 posts

Group Leader at Helmholtz Center Munich * Brain Epigenomics

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Reposted by Boyan Bonev
Helmholtz Munich @helmholtzmunich.bsky.social · 20/05/2026
#M1 Launches First Funding Period & Advances Translation in Munich🚀 Seven projects receive €7.45 million through the M1 – Munich Medicine Alliance. #HelmholtzMunich is involved in four funded projects. 👉 t1p.de/disle @tum.de @lmu.de @boyanbonev.bsky.social @erturklab.bsky.social #MunichMedicine
M1 Launches First Funding Period & Advances Translation in Munich
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Enard/Hellmann Lab @enardhellmannwg.bsky.social · 25/11/2025
Out now: we’re happy to share our new preprint on CroCoNet (Cross-species Comparison of Networks), a framework for robust comparative network analyses. 👉 doi.org/10.1101/2025...
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Alex Pollen @brainevodevo.bsky.social · 07/11/2025
Our new manuscript, led by Emily Corrigan, examines inhibitory neuron diversity across approximately 160 million years of evolutionary divergence, as part of BRAIN Initiative Cell Atlas Network (BICAN) developing brain atlas package: www.nature.com/articles/s41...
nature.com
Conservation and alteration of mammalian striatal interneurons - Nature
An analysis of cell-type diversity in brain samples from a variety of mammalian species, both during development and in adult animals, reveals that the TAC3 initial class of striatal interneurons is c...
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Boyan Bonev @boyanbonev.bsky.social · 05/11/2025
🚀 𝗣𝗼𝘀𝘁𝗱𝗼𝗰 𝗢𝗽𝗲𝗻𝗶𝗻𝗴 We’re recruiting an ERC-funded Postdoctoral Researcher to explore how 3D gene regulatory networks evolved during human and primate brain development, using cutting-edge single-cell multiomics, organoid models, and CRISPR screens. 👉 Apply by Nov 30 | www.bonevlab.com/join
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The Hassan Brain Development Team @hassanbraindevlab.bsky.social · 28/10/2025
A wonderful collaboration with @alexbaffet.bsky.social @boyanbonev.bsky.social and @neurogenesis-i3s.bsky.social labs
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Hamperl Lab @hamperllab.bsky.social · 04/08/2025
Our latest research is online in the @biorxivpreprint.bsky.social! 🧬🎉 🔎 We have developed a novel, single-cell real-time approach to monitor R-loop generated TRCs, and we have shown R-loop-mediated, replisome-controlled transcription repression. www.biorxiv.org/cgi/content/...
biorxiv.org
Replisome progression regulates R-loop mediated transcriptional repression
Maintaining cellular proliferation necessitates the synchronized activity of diverse molecular machineries operating in parallel on the genome. Wide-spread transcription and R-loop formation can inter...
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ME Torres-Padilla @metorrespadilla.bsky.social · 15/07/2025
🎤 Apply to speak @our TALENT FORUM by July 31! Showcase YOUR research in Epigenetics & NucleicAcids @www.helmholtz-munich.de & connect with leading scientists 🧳Travel+accommodation covered if selected! 📝 Info+how to apply: lnkd.in/drkRvz7N #postdoc #career #groupleader #HelmholtzMunich #research
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Christian Mayer @chr-mayer.bsky.social · 08/07/2025
Now out in @natneuro.nature.com: Temporal control of progenitor competence shapes maturation in GABAergic neuron development in mice. Congrats to first authors @annrosebright.bsky.social, Yana Kotlyarenko, @flo-neuhaus.bsky.social, and thanks to all collaborators! www.nature.com/articles/s41... 1/n
nature.com
Temporal control of progenitor competence shapes maturation in GABAergic neuron development in mice - Nature Neuroscience
Unlike cortical progenitors, ventral telencephalic progenitors retain the ability to generate diverse neuron types during neurogenesis. Here, the authors show that ventral telencephalic progenitor mat...
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ME Torres-Padilla @metorrespadilla.bsky.social · 12/06/2025
Are you @ the late stages of your postdoc ? Want to pursue a PI career ? Then this 👇👇 is for you ! Apply for a spot @ our Talent Forum www.helmholtz-munich.de/en/stem-cell... Peer-networking / Career orientation and more !!! Please distribute :) 🙂
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Boyan Bonev @boyanbonev.bsky.social · 15/05/2025
Looking forward to it!
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Lars Velten @larsplus.bsky.social · 08/05/2025
Out in Cell @cp-cell.bsky.social: Design principles of cell-state-specific enhancers in hematopoiesis 🧬🩸 screen of fully synthetic enhancers in blood progenitors 🤖 AI that creates new cell state specific enhancers 🔍 negative synergies between TFs lead to specificity! www.cell.com/cell/fulltex... 🧵
cell.com
Design principles of cell-state-specific enhancers in hematopoiesis
Screen of minimalistic enhancers in blood progenitor cells demonstrates widespread dual activator-repressor function of transcription factors (TFs) and enables the model-guided design of cell-state-sp...
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Arnau Sebé-Pedrós @arnausebe.bsky.social · 07/05/2025
Check out our latest work on the evolution of animal genome regulation out today in @nature.com. Nicely summarized below by @ianakim.bsky.social. www.nature.com/articles/s41... This is a major output from our ERC-StG project Evocellmap @erc.europa.eu at @crg.eu
nature.com
Chromatin loops are an ancestral hallmark of the animal regulatory genome - Nature
The physical organization of the genome in non-bilaterian animals and their closest unicellular relatives is characterized; comparative analysis shows chromatin looping is a conserved feature of ...
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Epigenetics Podcast @epigeneticspod.bsky.social · 14/04/2025
In the most recent episode we talked with @boyanbonev.bsky.social from @bonevlab.bsky.social at @epihmgu.bsky.social about his work on neuroepigenetics, focusing on gene regulation, chromatin architecture, and primate epigenome evolution. #epigenetics Listen here: activemotif.com/podcasts-boy...
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Boyan Bonev @boyanbonev.bsky.social · 04/04/2025
This was a great collaboration between the @bonevlab.bsky.social and the lab of Amos Tanay, led by Yonatan and Florian with substantial contribution from @silviavangelisti.bsky.social, Faye and Aviezer. If you found this study of interest, please RT, comment and share! All feedback is welcome. 14/14
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Boyan Bonev @boyanbonev.bsky.social · 04/04/2025
Code and data to reproduce all figures, or browse and reanalyze, is available at github.com/tanaylab/mmcortex, either separately or in a standalone docker container. You can also explore the data interactively at apps.tanaylab.com/MCV/mmcortex/. 13/14
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Boyan Bonev @boyanbonev.bsky.social · 04/04/2025
Finally, we assayed the activity of thousands of CREs isolated from their genomic context across multiple timepoints in vivo using a cell-type-specific massively parallel reporter assay. We showed that cell type-specificity is encoded in the sequence, in agreement with our quantitative model. 12/14
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Boyan Bonev @boyanbonev.bsky.social · 04/04/2025
We also show explicitly that NSC methylation has a repressive effect on IPC accessibility, and that cooperativity between proximal CREs is correlated with accessibility both in terms of sequence content and total proximal activation. 11/14
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Boyan Bonev @boyanbonev.bsky.social · 04/04/2025
We developed a machine-learning model that integrates sequence (putative TF motifs, dinucleotide content) and epigenomic features (ATAC, methylation, proximal activity) to predict NSC<->IPC specificity of CREs, that yields R^2 = 0.62 on held-out data. 10/14
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Boyan Bonev @boyanbonev.bsky.social · 04/04/2025
Moreover, temporally activating CREs in NSCs get compacted significantly closer over time to astrocyte- or NSC-specific TSSs, an effect not observed with IPC TSSs. 9/14
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Boyan Bonev @boyanbonev.bsky.social · 04/04/2025
Our Hi-C analysis shows that while overall chromatin topology is conserved across time in NSCs, there are specific hotspots whose differential insulation across time is correlated with the presence or depletion of proximal CREs. 8/14
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Boyan Bonev @boyanbonev.bsky.social · 04/04/2025
Temporally activating CREs are significant: they are enriched with astrocyte-specific CREs, and astro CREs undergo extensive demethylation within NSCs across time, in contrast to other cell type-specific CREs. 7/14
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Boyan Bonev @boyanbonev.bsky.social · 04/04/2025
We found that ATAC-activating CREs are tightly concomitant with methylation decrease. But the opposite was not true! Deactivating CREs in NSCs stay unmethylated across our time series, and this is not due to absence of DNMTs. 6/14
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Boyan Bonev @boyanbonev.bsky.social · 04/04/2025
Furthermore, we were able to identify CREs with dynamic accessibility within cell types, across time. We focused on CREs that either activate/increase accessibility, or deactivate over time in NSCs. 5/14
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Boyan Bonev @boyanbonev.bsky.social · 04/04/2025
Our metacell model of ATAC states provides a high-resolution timeline of cis-regulatory element (CRE) accessibility in corticogenesis. We use it to show that CREs specific to corticofugal neurons are activated late in maturation, in stark contrast to callosal projection neuron-specific CREs. 4/14
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Boyan Bonev @boyanbonev.bsky.social · 04/04/2025
We show that astrocyte genes in NSCs are upregulated gradually over time, not suddenly, along with erosion of NSC proliferative capacity. This erosion is also correlated with lengthening of the cell cycle, suggesting that NSC fate bias is coupled to the cell cycle. 3/14
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Boyan Bonev @boyanbonev.bsky.social · 04/04/2025
We have generated one of the most comprehensive multiome datasets in the context of brain development, integrating time-series measurements of scRNA-seq, scATAC-seq, 5mC methylation and Hi-C of mouse somatosensory cortex across 6 developmental timepoints. 2/14
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Boyan Bonev @boyanbonev.bsky.social · 04/04/2025
Can a stem cell change its epigenome while proliferating? In collaboration with the lab of Amos Tanay, we demonstrate that yes, the epigenome of neural stem cells (NSCs) is continuously remodeled, across multiple layers, during mouse corticogenesis. 1/14 www.biorxiv.org/content/10.1...
biorxiv.org
Neural stem cell epigenomes and fate bias are temporally coordinated during corticogenesis
The cerebral cortex orchestrates complex cognitive functions, yet how its distinct temporal lineages are molecularly patterned during development remains unresolved. Here, we integrate single-cell tra...
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Ludovico Rizzuti @ludoritz.bsky.social · 03/04/2025
I'm happy to share our work on the neurodevelopmental impact of ADNP mutations in ASD and beyond. It has been an exciting ride to share with @alessandrovitriolo.bsky.social, Mariana, and the people of the Testa and Poot Labs. Full paper here: www.biorxiv.org/content/10.1... Thread below 🧵
biorxiv.org
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Kaessmann Lab @kaessmannlab.bsky.social · 16/03/2025
How does gene regulation shape brain evolution? Our new preprint dives into this question in the context of mammalian cerebellum development! rb.gy/dbcxjz Led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social
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mareikealbert.bsky.social @mareikealbert.bsky.social · 13/03/2025
💫 New preprint from the lab: Comparing great ape cerebral organoids, we found that human-specific morphoregulatory signatures in basal radial glia characterise neocortex evolution. Fantastic work from super-talented PhD student Theresa Schütze! www.biorxiv.org/content/10.1...
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Boyan Bonev @boyanbonev.bsky.social · 13/03/2025
This was a heroic effort by my very first PhD student - Silvia, with a significant contribution from other lab members and a great collaboration with the Enard lab @enardhellmannwg.bsky.social. Stay tuned for more exciting research from the @bonevlab.bsky.social very soon!
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Boyan Bonev @boyanbonev.bsky.social · 13/03/2025
Overall, we systematically link 3D epigenome evolution to gene expression changes in the context of primate brain development. This integrative approach significantly advances our understanding of how divergent regulatory networks and epigenome dynamics contribute to human brain evolution
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Boyan Bonev @boyanbonev.bsky.social · 13/03/2025
Species-specific genes were often associated with multiple differentially accessible regions, suggesting that synergistic enhancer activation is a key mechanism driving epigenome evolution. #EnhancerSynergy #GeneRegulation
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Boyan Bonev @boyanbonev.bsky.social · 13/03/2025
High-resolution Hi-C revealed unexpected global shifts in 3D genome architecture in the chimpanzee and gorilla NSC, while topologically associating domains remained remarkably conserved. #3DGenome #HiC
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Boyan Bonev @boyanbonev.bsky.social · 13/03/2025
Using ChromBPNet @anshulkundaje.bsky.social, we modeled the complex regulatory grammar at cis-regulatory elements — and found that epigenome evolution is influenced not only by sequence changes, but also by local genomic context, shaping species- and cell type-specific regulation.
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Boyan Bonev @boyanbonev.bsky.social · 13/03/2025
We also proposed the emergence of novel TF motifs and specific class of transposable elements - SVA, as one of the key drivers of species- and cell type-specific chromatin accessibility — linking DNA sequence to epigenome evolution.
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Boyan Bonev @boyanbonev.bsky.social · 13/03/2025
We identified novel human-biased genes and epigenetic signatures and further validated them using cortical organoids and MPRA data to generate a set of highly confident putative enhancers - paving the way for future functional studies of human brain development. #ComparativeGenomics
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Boyan Bonev @boyanbonev.bsky.social · 13/03/2025
We have generated one of the most comprehensive datasets of primate epigenome evolution to date — profiling and integrating genome-wide 3D genome organization, chromatin accessibility and gene expression in human, chimpanzee, gorilla and macaque IPSC and neural stem cells (NSC).
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Boyan Bonev @boyanbonev.bsky.social · 13/03/2025
🚨New preprint from @bonevlab.bsky.social 🚨: What are the key epigenetic mechanisms that drive species-specific gene regulation during primate neurogenesis - and how do they contribute to the evolution of the human neocortex? Here’s what we discovered 👇 www.biorxiv.org/content/10.1...
biorxiv.org
3D Epigenome Evolution Underlies Divergent Gene Regulatory Programs in Primate Neural Development
The expansion of the neocortex is a hallmark of human evolution and is closely linked to neural stem cell biology. Yet, the epigenetic mechanisms driving divergent gene regulation during primate neuro...
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