Elena Dvoretskova
@elena-dvoretskova.bsky.social
postdoctoral researcher at the MPI for biological intelligence I development & evolution of the brain I interactions of transcription factors
Pinned
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...
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www.nature.com/articles/s41...
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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...
www.nature.com
How is the progression of maturation regulated in forebrain inhibitory neurons? Excited to share our new study from the Mayer lab — stable differentiation, dynamic maturation, and stage-specific chromatin changes in GABAergic neurons.
#GABA #Neuroscience #scATACseq #scRNAseq
#GABA #Neuroscience #scATACseq #scRNAseq
Reposted by Elena Dvoretskova
📣 I hereby make my Bluesky debut to announce that our work linking DNA binding affinities and kinetics 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 and 𝘪𝘯 𝘷𝘪𝘷𝘰 for the human transcription factor KLF1 just got published in Cell! @cp-cell.bsky.social
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
November 27, 2025 at 1:17 PM
📣 I hereby make my Bluesky debut to announce that our work linking DNA binding affinities and kinetics 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 and 𝘪𝘯 𝘷𝘪𝘷𝘰 for the human transcription factor KLF1 just got published in Cell! @cp-cell.bsky.social
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
Reposted by Elena Dvoretskova
Do you have an exciting new chromatin/transcription story that you'd like to share with the #FN community?
Fill out this form to be considered for a talk in our Jan-June 2026 schedule! forms.gle/TBi38UgYxPAB...
Please repost and share!
Fill out this form to be considered for a talk in our Jan-June 2026 schedule! forms.gle/TBi38UgYxPAB...
Please repost and share!
Application to speak in the Fragile Nucleosome series
Thank you for your interest in our seminar series!
We use a variety of different session formats but, in general, trainees can plan for a ~15 min talk + 5min Q/A and PIs can plan for a ~25min talk +...
forms.gle
November 24, 2025 at 1:50 PM
Do you have an exciting new chromatin/transcription story that you'd like to share with the #FN community?
Fill out this form to be considered for a talk in our Jan-June 2026 schedule! forms.gle/TBi38UgYxPAB...
Please repost and share!
Fill out this form to be considered for a talk in our Jan-June 2026 schedule! forms.gle/TBi38UgYxPAB...
Please repost and share!
Reposted by Elena Dvoretskova
Reposted by Elena Dvoretskova
New paper “Proteome-wide model for human disease genetics” is now live at Nature Genetics: rdcu.be/eRu7K
popEVE (pop.evemodel.org) finds the needles in the haystacks of human genetic variation:
popEVE (pop.evemodel.org) finds the needles in the haystacks of human genetic variation:
November 24, 2025 at 2:53 PM
New paper “Proteome-wide model for human disease genetics” is now live at Nature Genetics: rdcu.be/eRu7K
popEVE (pop.evemodel.org) finds the needles in the haystacks of human genetic variation:
popEVE (pop.evemodel.org) finds the needles in the haystacks of human genetic variation:
Reposted by Elena Dvoretskova
Fun week for DNA methylation research! Here is a thread of three cool papers that came out, all with an evolution angle. And a bonus 4th that examines DNAme/PcG interplay (certainly an interest for our lab!) #Epigenetics
November 19, 2025 at 9:48 AM
Fun week for DNA methylation research! Here is a thread of three cool papers that came out, all with an evolution angle. And a bonus 4th that examines DNAme/PcG interplay (certainly an interest for our lab!) #Epigenetics
Reposted by Elena Dvoretskova
Good to see the peer reviewed version of this in print
The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube
A global temporal chromatin program operates across the vertebrate nervous system to control neural cell diversity
www.cell.com/developmenta...
The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube
A global temporal chromatin program operates across the vertebrate nervous system to control neural cell diversity
www.cell.com/developmenta...
The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube
Zhang et al. identify a global temporal chromatin program that operates across the
developing vertebrate nervous system to control neural cell diversity. This mechanism,
which involves Nr6a1 and NFIA/...
www.cell.com
November 18, 2025 at 8:59 AM
Good to see the peer reviewed version of this in print
The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube
A global temporal chromatin program operates across the vertebrate nervous system to control neural cell diversity
www.cell.com/developmenta...
The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube
A global temporal chromatin program operates across the vertebrate nervous system to control neural cell diversity
www.cell.com/developmenta...
Reposted by Elena Dvoretskova
Our latest paper has just been published in Cell!
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
November 5, 2025 at 5:20 PM
Our latest paper has just been published in Cell!
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
Reposted by Elena Dvoretskova
🚀 Our new Science paper is out (w/ B DeMeo, D Burkhardt, A Shalek, M Cortes): www.science.org/doi/10.1126/...
We show that active learning + transcriptomic perturbations can guide which exps to run next, boosting phenotypic hit rates >13x. AI not just predicting bio, but designing it. 🔁
We show that active learning + transcriptomic perturbations can guide which exps to run next, boosting phenotypic hit rates >13x. AI not just predicting bio, but designing it. 🔁
October 25, 2025 at 1:24 PM
🚀 Our new Science paper is out (w/ B DeMeo, D Burkhardt, A Shalek, M Cortes): www.science.org/doi/10.1126/...
We show that active learning + transcriptomic perturbations can guide which exps to run next, boosting phenotypic hit rates >13x. AI not just predicting bio, but designing it. 🔁
We show that active learning + transcriptomic perturbations can guide which exps to run next, boosting phenotypic hit rates >13x. AI not just predicting bio, but designing it. 🔁
Reposted by Elena Dvoretskova
Thrilled to share my main postdoc work with @jamesbriscoe.bsky.social
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
Hierarchical lineage architecture of human and avian spinal cord revealed by single-cell genomic barcoding
The formation of neural circuits depends on the precise spatial and temporal organisation of neuronal populations during development. In the vertebrate spinal cord, progenitors are patterned into mole...
www.biorxiv.org
October 26, 2025 at 5:15 PM
Thrilled to share my main postdoc work with @jamesbriscoe.bsky.social
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
Reposted by Elena Dvoretskova
🧵1/ Excited to share our new paper introducing a new #singlecell assay: scTF-seq, a high-throughput single-cell approach to explore how transcription factor (TF) dose shapes cell identity and reprogramming outcomes. 🔗 www.nature.com/articles/s41... Big congrats to the entire team @EPFL & @SIAT_China
Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq - Nature Genetics
This study introduces single-cell transcription factor (TF) sequencing, a single-cell barcoded and doxycycline-inducible TF overexpression approach that reveals dose-sensitive functional classes of TFs and cellular heterogeneity by mapping TF dose-dependent transcriptomic changes during the reprogramming of mouse embryonic multipotent stromal cells.
www.nature.com
October 6, 2025 at 6:57 AM
🧵1/ Excited to share our new paper introducing a new #singlecell assay: scTF-seq, a high-throughput single-cell approach to explore how transcription factor (TF) dose shapes cell identity and reprogramming outcomes. 🔗 www.nature.com/articles/s41... Big congrats to the entire team @EPFL & @SIAT_China
Reposted by Elena Dvoretskova
Today in @nature.com, we present our work leveraging functional genomics and human blastoids to uncover a human-specific mechanism in preimplantation development driven by the endogenous retrovirus HERVK.
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD
A human-specific regulatory mechanism revealed in a pre-implantation model
Nature - Genetic manipulation of blastoids reveals the role of recently emerged transposable elements and genes in human development.
rdcu.be
October 1, 2025 at 6:08 PM
Today in @nature.com, we present our work leveraging functional genomics and human blastoids to uncover a human-specific mechanism in preimplantation development driven by the endogenous retrovirus HERVK.
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD
Reposted by Elena Dvoretskova
Genes are not On/Off switches. In a new preprint we show that HDAC3 is key to establish correct transcriptional dose in development. Gr8 work from N. Stamidis @ucph.bsky.social and collab. @jamiehackett.bsky.social @gregersenlab.bsky.social . Huge thx to all authors! www.biorxiv.org/content/10.1...
HDAC3 prevents enhancer hyperactivation to enable developmental transitions
Dynamic gene regulation requires precise cooperation between transcription factors and chromatin modifiers at regulatory elements to achieve not only activation or repression, but also appropriate tra...
www.biorxiv.org
September 18, 2025 at 9:55 AM
Genes are not On/Off switches. In a new preprint we show that HDAC3 is key to establish correct transcriptional dose in development. Gr8 work from N. Stamidis @ucph.bsky.social and collab. @jamiehackett.bsky.social @gregersenlab.bsky.social . Huge thx to all authors! www.biorxiv.org/content/10.1...
Reposted by Elena Dvoretskova
Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
September 18, 2025 at 4:14 PM
Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
Reposted by Elena Dvoretskova
Out today. 🙏 again to everyone for this wonderful piece of work, in particular to Aurelie @aurhin.bsky.social Chase @chasebolt.bsky.social and Brent @homeobox.bsky.social. 🙏 also to the Harris lab @fish4walking.bsky.social and @neilshubin.bsky.social @biology-unige.bsky.social @college-de-france.fr
September 17, 2025 at 5:30 PM
Out today. 🙏 again to everyone for this wonderful piece of work, in particular to Aurelie @aurhin.bsky.social Chase @chasebolt.bsky.social and Brent @homeobox.bsky.social. 🙏 also to the Harris lab @fish4walking.bsky.social and @neilshubin.bsky.social @biology-unige.bsky.social @college-de-france.fr
Reposted by Elena Dvoretskova
Thrilled to share that our work is now published in Science! ✨
We found a preference for visual objects in the mouse spatial navigation system where they dynamically refine head-direction coding. In short, objects boost our inner compass! 🧭
www.science.org/doi/10.1126/...
🧵1/
We found a preference for visual objects in the mouse spatial navigation system where they dynamically refine head-direction coding. In short, objects boost our inner compass! 🧭
www.science.org/doi/10.1126/...
🧵1/
September 11, 2025 at 8:14 PM
Thrilled to share that our work is now published in Science! ✨
We found a preference for visual objects in the mouse spatial navigation system where they dynamically refine head-direction coding. In short, objects boost our inner compass! 🧭
www.science.org/doi/10.1126/...
🧵1/
We found a preference for visual objects in the mouse spatial navigation system where they dynamically refine head-direction coding. In short, objects boost our inner compass! 🧭
www.science.org/doi/10.1126/...
🧵1/
Reposted by Elena Dvoretskova
We're super excited to announce the entire lineup for the Fall season of Fragile Nucleosome Seminars, starting on Sept 10th at 1200 EDT / 1600 UTC with @gracebower.bsky.social and @creminslab.bsky.social!
register here for the entire series: us06web.zoom.us/webinar/regi...
register here for the entire series: us06web.zoom.us/webinar/regi...
September 1, 2025 at 2:59 PM
We're super excited to announce the entire lineup for the Fall season of Fragile Nucleosome Seminars, starting on Sept 10th at 1200 EDT / 1600 UTC with @gracebower.bsky.social and @creminslab.bsky.social!
register here for the entire series: us06web.zoom.us/webinar/regi...
register here for the entire series: us06web.zoom.us/webinar/regi...
Reposted by Elena Dvoretskova
I'm really happy to announce that my two main postdoctoral works have been published in the same issue of Developmental Cell! First, the final form of the mouse cortical organoid protocol (tinyurl.com/bddfmx8n), which I recently presented at Development presents (tinyurl.com/36udcpme) and…
tinyurl.com
August 27, 2025 at 4:25 PM
I'm really happy to announce that my two main postdoctoral works have been published in the same issue of Developmental Cell! First, the final form of the mouse cortical organoid protocol (tinyurl.com/bddfmx8n), which I recently presented at Development presents (tinyurl.com/36udcpme) and…
Reposted by Elena Dvoretskova
Excited to share our latest work on brain evolution, where we dive into the evolution of Cajal-Retzius cells! If you are interested in cell type evolution and cerebral cortex evo-devo, please read on… www.biorxiv.org/content/10.1... 🧵 1/7
Evolution of Cajal-Retzius Cells in Vertebrates from an Ancient Class of Tp73+ Neurons
In the developing cerebral cortex, Cajal Retzius (CR) cells are early-born neurons that orchestrate the development of mammalian-specific cortical features. However, this cell type has not been conclu...
www.biorxiv.org
August 25, 2025 at 7:43 PM
Excited to share our latest work on brain evolution, where we dive into the evolution of Cajal-Retzius cells! If you are interested in cell type evolution and cerebral cortex evo-devo, please read on… www.biorxiv.org/content/10.1... 🧵 1/7
Reposted by Elena Dvoretskova
Hiding in plain sight - how close are we to mapping ALL 🧬enhancers🧬 in the genome?
Our new paper by Mannion et al. takes a systematic look at "hidden enhancers" and why they remain so hard to find. With @mosterwalder.bsky.social, @jlopezrios.bsky.social & many more
www.nature.com/articles/s41...
Our new paper by Mannion et al. takes a systematic look at "hidden enhancers" and why they remain so hard to find. With @mosterwalder.bsky.social, @jlopezrios.bsky.social & many more
www.nature.com/articles/s41...
August 8, 2025 at 6:10 PM
Hiding in plain sight - how close are we to mapping ALL 🧬enhancers🧬 in the genome?
Our new paper by Mannion et al. takes a systematic look at "hidden enhancers" and why they remain so hard to find. With @mosterwalder.bsky.social, @jlopezrios.bsky.social & many more
www.nature.com/articles/s41...
Our new paper by Mannion et al. takes a systematic look at "hidden enhancers" and why they remain so hard to find. With @mosterwalder.bsky.social, @jlopezrios.bsky.social & many more
www.nature.com/articles/s41...
Reposted by Elena Dvoretskova
August 7, 2025 at 4:00 PM
Reposted by Elena Dvoretskova
🚨 First paper from the Bocchi lab out now in @natcomms.nature.com!
We show that astrocytes in the cortex arise from not one, but two distinct progenitor lineages, each giving rise to specialized subtypes with distinct roles.
Here the story📖 doi.org/10.1038/s414...
We show that astrocytes in the cortex arise from not one, but two distinct progenitor lineages, each giving rise to specialized subtypes with distinct roles.
Here the story📖 doi.org/10.1038/s414...
Dual lineage origins contribute to neocortical astrocyte diversity - Nature Communications
Astrocytes display diverse molecular and functional features in the brain, but the developmental origins of this heterogeneity are not well understood. Here, the authors show that two separate progeni...
doi.org
July 31, 2025 at 7:17 AM
🚨 First paper from the Bocchi lab out now in @natcomms.nature.com!
We show that astrocytes in the cortex arise from not one, but two distinct progenitor lineages, each giving rise to specialized subtypes with distinct roles.
Here the story📖 doi.org/10.1038/s414...
We show that astrocytes in the cortex arise from not one, but two distinct progenitor lineages, each giving rise to specialized subtypes with distinct roles.
Here the story📖 doi.org/10.1038/s414...
Reposted by Elena Dvoretskova
How do enhancer-gene contacts relate to transcription activation? In mouse embryonic stem cells, a combo of STED, oligoFISH & RNA FISH shows that 3% of Dppa3 alleles transcribe. For these, enhancers and promoters come closer (panel E). Stumberger ... Leonhardt & Harz www.biorxiv.org/content/10.1...
July 26, 2025 at 9:36 PM
How do enhancer-gene contacts relate to transcription activation? In mouse embryonic stem cells, a combo of STED, oligoFISH & RNA FISH shows that 3% of Dppa3 alleles transcribe. For these, enhancers and promoters come closer (panel E). Stumberger ... Leonhardt & Harz www.biorxiv.org/content/10.1...
Reposted by Elena Dvoretskova
Excited to share our latest work with @jamesbriscoe.bsky.social .
A global #cis-regulatory temporal program guides how spatial cues are interpreted in neural progenitors. We show how #space and #time can be integrated to generate cell type diversity in the #spinalcord.
Congrats to all authors.
A global #cis-regulatory temporal program guides how spatial cues are interpreted in neural progenitors. We show how #space and #time can be integrated to generate cell type diversity in the #spinalcord.
Congrats to all authors.
A study from @crick.ac.uk and @ucllifesciences.bsky.social reveals how timing mechanisms, not just spatial cues, shape cell identity during spinal cord development. The findings open up new avenues for both basic developmental biology and clinical applications.
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube
The vertebrate neural tube generates a large diversity of molecularly and functionally distinct neurons and glia from a small progenitor pool. While t…
www.sciencedirect.com
July 21, 2025 at 10:18 AM
Excited to share our latest work with @jamesbriscoe.bsky.social .
A global #cis-regulatory temporal program guides how spatial cues are interpreted in neural progenitors. We show how #space and #time can be integrated to generate cell type diversity in the #spinalcord.
Congrats to all authors.
A global #cis-regulatory temporal program guides how spatial cues are interpreted in neural progenitors. We show how #space and #time can be integrated to generate cell type diversity in the #spinalcord.
Congrats to all authors.
Reposted by Elena Dvoretskova
Our study on a male-essential microRNA and the evolution of other dosage compensation mechanisms in birds is now out in Nature! www.nature.com/articles/s41...
A male-essential miRNA is key for avian sex chromosome dosage compensation - Nature
Birds have evolved a unique sex chromosome dosage compensation mechanism involving the male-biased microRNA (miR-2954), which is essential for male survival by regulating the expression of dosage-sens...
www.nature.com
July 16, 2025 at 3:23 PM
Our study on a male-essential microRNA and the evolution of other dosage compensation mechanisms in birds is now out in Nature! www.nature.com/articles/s41...
Reposted by Elena Dvoretskova
Just published: The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube
A global temporal chromatin program, operating across the CNS, directs binding of specific spatial TFs & hence when/where neurons & glia are born
authors.elsevier.com/sd/article/S...
A global temporal chromatin program, operating across the CNS, directs binding of specific spatial TFs & hence when/where neurons & glia are born
authors.elsevier.com/sd/article/S...
ScienceDirect.com | Science, health and medical journals, full text articles and books.
authors.elsevier.com
July 17, 2025 at 10:07 AM
Just published: The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube
A global temporal chromatin program, operating across the CNS, directs binding of specific spatial TFs & hence when/where neurons & glia are born
authors.elsevier.com/sd/article/S...
A global temporal chromatin program, operating across the CNS, directs binding of specific spatial TFs & hence when/where neurons & glia are born
authors.elsevier.com/sd/article/S...