iiinova — where your digital self keeps evolving

Manvendra Singh @manusingh.bsky.social · 28/09/2026

8/8 Huge credit to first author @cakirumut.bsky.social for driving this work, and to @mfederica.bsky.social and @souad-youjilabadi.bsky.social from #RETROGEN Lab @inem-necker.bsky.social @institutimagine.bsky.social @cnrs.fr & our collaborators at UCLA and MPI. Preprint: doi.org/10.64898/202...

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Manvendra Singh @manusingh.bsky.social · 28/09/2026

7/8 Together, the atlas maps where a pro-neurogenic signal reshapes chromatin and points to TE-derived sequences as possible parts of the regulatory network. We hope this cell-type-resolved resource helps others explore the adult hippocampus.

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Manvendra Singh @manusingh.bsky.social · 28/09/2026

6/8 Several TE families were bound by neurogenic transcription factors. Their nearby genes are linked to neuronal differentiation and synapse formation. We propose these TE-derived sequences as candidate regulatory elements—not yet proven causal switches.

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Manvendra Singh @manusingh.bsky.social · 28/09/2026

5/8 Here’s the striking TE result: transposable elements overlapped ~20% of candidate regulatory regions at baseline, but ~50% of regions that gained accessibility after rhEPO. Ancient mobile DNA was strongly enriched in the response.

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Manvendra Singh @manusingh.bsky.social · 28/09/2026

4/8 The response was highly uneven: more than half of 39,404 regions with altered accessibility were in pyramidal neurons. Within that lineage, chromatin remodelling was strongest in newly formed neurons, rather than mature ones.

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Manvendra Singh @manusingh.bsky.social · 28/09/2026

3/8 We profiled ~35,000 hippocampal nuclei with snATAC-seq and integrated the data with ~120,000 matched snRNA-seq nuclei. This gave us a cell-type-resolved view of chromatin accessibility across 11 major hippocampal lineages.

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Manvendra Singh @manusingh.bsky.social · 28/09/2026

2/8 Adult hippocampal neurogenesis can respond to external signals. We used recombinant human erythropoietin (rhEPO) as a defined pro-neurogenic stimulus and asked: which cells change their chromatin, and could transposable elements be part of that response?

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Manvendra Singh @manusingh.bsky.social · 28/09/2026

1/8 Proud and super thrilled to share our preprint, “A single-nucleus regulatory atlas links transposons to adult hippocampal neurogenesis.”, led by Umut, Fede, and Souad, the FIRST from our #RETROGEN lab @inem-necker.bsky.social . www.biorxiv.org/content/10.6... shrt thread on what we found 🧵

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Manvendra Singh @manusingh.bsky.social · 26/08/2026

A Planet of Viruses. 🦠🌍 Scary but had a lot of fun talking about viruses today. They are everywhere, they have been with us forever, and they have even become part of our own genome. I have a feeling we’ll be talking a lot more about them in the years ahead. 😄 #Virology #HERVs #Genomics #Scienc

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Manvendra Singh @manusingh.bsky.social · 25/07/2026

What happened in India today teaches us a valuable lesson - To learn something new, one has to break their arrogance and pride, and Genz taught this #CJP

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Manvendra Singh @manusingh.bsky.social · 10/07/2026

Proud moment for the RetroGen Lab! 🎉 Congratulations to Federica Mantovani on her selection for an oral presentation at the CNET meeting in Montpellier—a well-deserved recognition of her hard work and a fantastic opportunity to represent our lab. Bravo! 👏 #ProudPI

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Manvendra Singh @manusingh.bsky.social · 15/06/2026

Three Species in One House is Endless Entertainment One delegate refuses to acknowledge the other. The other delegate is desperately trying to make friends. And I’m the confused moderator wondering why nobody is speaking the same language.

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Manvendra Singh @manusingh.bsky.social · 05/06/2026

📍5 minutes before journal club. Today’s paper was… let’s say, not exactly light one of our PhD students sat down at the piano and played to calm everyone’s neurons before we wrestled with the paper. 🎹📖 Lucky to work with them. #AcademicLife #PhDLife #JournalClub #Science #ResearchLife #LabLife

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Manvendra Singh @manusingh.bsky.social · 08/03/2026

Happy Women’s Day 🎊🎊😊to all of us and especially three outstanding women leading science at the highest level around our Necker Campus. Fabiola, Bana, and Yasmine, the directors of Necker, IMAGINE and Pasteur Institutes, respectively. Proud to be part of this cluster.

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Manvendra Singh @manusingh.bsky.social · 05/03/2026

Happy Holi everyone 🌈 A festival where poetry meets science as every color carries meaning, every wavelength shapes how we see the world. Train your eyes with colors and your heart with kindness. May peace, harmony, and love spread across every spectrum of humanity.

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Manvendra Singh @manusingh.bsky.social · 03/03/2026

In a mouse model of Primrose syndrome, rhEPO reverses. This is preclinical & could be the first tangible therapeutic path. Huge thanks to Justus, @cakirumut.bsky.social , Klaus and Hannelore and to an amazing team. DOI: 10.1172/jci.insight.200021 #RareDisease #Neurobiology #TranslationalResearch

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Manvendra Singh @manusingh.bsky.social · 27/01/2026

Gave a talk at @institutcurie.bsky.social on Friday and honestly… it felt unreal. Speaking in the same place where Marie Curie carried out her radiation experiments reminds how long science lasts beyond us. Thnks Elena Zueva, @mburbage.bsky.social , Sebastian Amigorena, Josh Waterfall and Lorena 🙏🏽

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Manvendra Singh @manusingh.bsky.social · 05/01/2026

Finally, to cross-validate - Independent TF ChIP-seq shows neurogenic TFs (FOXG1, NEUROD1/2, NEUROG2, ASCL1) selectively bind TE-derived sequences, thus supporting a model where EPO engages a transposon-based regulatory reservoir to drive adult neurogenesis.🧵8/8

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Manvendra Singh @manusingh.bsky.social · 05/01/2026

Here’s the twist we’re most excited about: A sizeable fraction of EPO-responsive regulatory elements overlaps ancient transposable elements (LINEs/SINEs). These aren’t “genomic fossils” but they behave like reusable regulatory modules the brain can recruit during plasticity. 🧵7/8

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Manvendra Singh @manusingh.bsky.social · 05/01/2026

The most striking effect sits in newly formed / immature pyramidal neurons. EPO preferentially boosts accessibility and gene programs that look like a neurogenic push plus synaptic integration 🧵6/8

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Manvendra Singh @manusingh.bsky.social · 05/01/2026

The strongest remodeling concentrates in excitatory neuronal lineages in dentate gyrus, with distinct responses across glia and neuroimmune compartments. This is why bulk approaches miss the story 🧵5/8

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Manvendra Singh @manusingh.bsky.social · 05/01/2026

We see broad, lineage-resolved chromatin opening (differential accessibility) that aligns with transcriptional activation of programs linked to neuronal differentiation, synaptogenesis, and plasticity. And a major portion of accessibility changes occurred around Transposons near these genes. 🧵4/8

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Manvendra Singh @manusingh.bsky.social · 05/01/2026

Our atlas resolves diverse lineages and their cell-type-specific regulatory “grammar” (motifs/TF programs) through specific regulatory codes. 🧵3/8

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Manvendra Singh @manusingh.bsky.social · 05/01/2026

We built a matched snRNA-seq + snATAC-seq atlas after rhEPO vs placebo to see which regulatory switches flip. 🧠✨ 🧵2/8

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Manvendra Singh @manusingh.bsky.social · 05/01/2026

🔥🎉 🧠 SuperThrilled to share our paper (preprint) - Human erythropoietin (rhEPO) reshapes the adult hippocampal chromatin landscape, around transposons to promote neurogenesis. 🧵1/8 Massive kudos to #UmutCakir who drove multi-omics through dark roads of the genome. www.biorxiv.org/content/10.1...

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Manvendra Singh @manusingh.bsky.social · 02/01/2026

Happy new year and 3 more days to apply for Computational biology post doc position in my lab #Paris #transpoosns @inem-necker.bsky.social @institutimagine.bsky.social

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Manvendra Singh @manusingh.bsky.social · 20/12/2025

This is the view where we shall have our regular lab meetings. Maybe this persuades you to join our team. #hiring #postdoc #computationalBiology #multiomics #deeplearning

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Manvendra Singh @manusingh.bsky.social · 10/12/2025

#hiring #postdoc #bioinformatics We’re opening a Computational/Bioinformatics postdoc position in my new lab at INEM in Paris, connected with Imagine and Institut Pasteur. The big theme: 👉 How do endogenous retroviruses and other mobile DNA rewire human immune regulation and genome control? 👇⬇️🧵

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Manvendra Singh @manusingh.bsky.social · 04/12/2025

#NewPI #Neuroscience #Immunology #Transposons #SciComm #HERVs Stay tuned, a few postdoctoral, both molecular and computational biology positions are gonna be advertised soon.

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Manvendra Singh @manusingh.bsky.social · 23/09/2025

I'd be leaving soon for the new challenges Before I go, here are a few brain’s stories on the table: 1 out in Nat Comm, 1 in press at Mol Psy, and 🤞 for the third. Preprints here: www.biorxiv.org/content/10.1...; www.biorxiv.org/content/10.1...; www.biorxiv.org/content/10.1...; Onwards. 🖤

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Manvendra Singh @manusingh.bsky.social · 15/07/2025

The backbone and most attractive part of HERVs existence in genomes can be explained by the addiction hypothesis proposed by Cedric, so we do acknowledge it 🧵3/3

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Manvendra Singh @manusingh.bsky.social · 15/07/2025

In morula, KRAB-ZNF/TRIM28 could be locking HERVH down; in the inner cell mass, pluripotency factors free it. Freed HERVH lncRNA then helps drive APOBEC3 enzymes that cripple retroelements, a tidy self-reinforcing antiviral loop. 🧵2/3

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Manvendra Singh @manusingh.bsky.social · 15/07/2025

Just dropped our Mobile DNA review on HERVH, an ancient retrovirus now repurposed to build and defend the early human embryo. Call it genomic up-cycling! I felt HERVH went unnoticed this year, so we published this as a refresher; two fresh data papers - coming soon. 🔗 doi.org/10.1186/s131... 🧵1/3

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Manvendra Singh @manusingh.bsky.social · 25/02/2025

This humour is way too dark for me. I am even scared to put any caption on it!

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Manvendra Singh @manusingh.bsky.social · 13/02/2025

It was amazing to have interacted with Jeff Boeke, from NYU and also witnessed his phenomenal talk at @mdc-bimsb.bsky.social He has now put all human chromosomes in yeast, One by one. Also, they made parrots have conversation in five languages English, French, German, Swedish and Spanish 😂

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Manvendra Singh @manusingh.bsky.social · 09/01/2025

Help desk when you missed your flight

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Manvendra Singh @manusingh.bsky.social · 26/12/2024

My Xmas gift 💝 I like it coz I like watching GOT with some Single Malt

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Manvendra Singh @manusingh.bsky.social · 20/12/2024

I was on Vacation in India but then had privilege interacting with new students from 4 institutes located in SE, SW, North and Central India. Not just a great hospitality but the curiosity and knowledge students have these days, my mind is flabbergasted. happy for the next generation of scientists

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Manvendra Singh @manusingh.bsky.social · 21/11/2024

Plotting becomes tidy in R , good read for trainees. www.biorxiv.org/content/10.1...

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Manvendra Singh @manusingh.bsky.social · 21/11/2024

I believe that Fathers have realized it ☺️ jamanetwork.com/journals/jam....

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Manvendra Singh @manusingh.bsky.social · 17/11/2024

Almost a full moon today! Stars are less visible, that’s pollution. A metaphor of how things are at X

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Manvendra Singh @manusingh.bsky.social · 16/11/2024

Hey bsky family, Happy weekends! here is the view from our #MPINAT campus in Gottingen

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Manvendra Singh @manusingh.bsky.social · 14/11/2024

A good review should always teach you something new, even if you have been in the field for a long time rdcu.be/d0aKY

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