Dr Manvendra Singh

Defending US democracy: the role of scientists
@science.org
www.science.org/doi/10.1126/...

GitHub - lh3/longdust: Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome - lh3/longdust

lh3/longdust: Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome github.com/lh3/longdust 🧬🖥️🧪

A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function - Nature Biotechnology RNA-binding motifs in eukaryotic proteins are presented in a comprehensive resource.

New in @natbiotech.nature.com: a team led by scientists at MSK and ‪University of Toronto have developed a new platform to facilitate the study of RNA-biding proteins (RBPs) across hundreds of species of plants, insects, and animals.

A single-cell transposable element atlas of human cell identity Reyes-Gopar et al. introduce Stellarscope, a computational approach for quantifying locus-specific transposable element expression in single-cell RNA sequencing data. The authors profile human PBMCs a...

🧵1/ Introducing Stellarscope: an EM-based tool for quantifying locus-specific transposable element expression in single cells.

A single-cell transposable element atlas of human cell identity: Cell Reports Methods www.cell.com/cell-reports...

@hamarillo.bsky.social #TEHub #singlecell #genomics

Exactly two weeks left to submit your abstract to the EMBO Mobile Genome Workshop.
☝️this year we will select from abstracts 2 “long” talks to highlight last minute breakthrough from early career scientists. Apply! July 29th

Think of HERVH as an ancient “virus scrap” in our DNA—not GMO. In early embryos, it wakes up at pluripotency, not to make viruses but to turn on antiviral “guards” (like APOBEC enzymes). So it’s less “virus attack” and more “viral parts repurposed to help protect our embryos. Cool repurposing!

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

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

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

Phenomenal work! Congrats, Juliane and all authors 🎉

Identification of proliferating neural progenitors in the adult human hippocampus Continuous adult hippocampal neurogenesis is involved in memory formation and mood regulation but is challenging to study in humans. Difficulties finding proliferating progenitor cells called into que...

Woohoo! From superstars ionut and Marta in the Frisén lab! www.science.org/doi/10.1126/... can’t wait to see what the anti-neurogenesis folks say about it 😃

Cell type and cell signalling innovations underlying mammalian pregnancy - Nature Ecology & Evolution Single-cell transcriptomes from the fetal–maternal interface of six species of mammals reveal a conserved gene expression signature of invasive trophoblast, stepwise evolution of decidual stromal cell...

😲

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Complete genome sequences for 6 apes species

Complete ape genomes! 🦍🦧 Our closest relatives get the deluxe sequencing treatment, resolving the most complex & often most interesting parts of the genome.
Happy to make a tiny contribution alongside @panpan100.bsky.social to awesome teamwork & fantastic resource.
www.nature.com/articles/s41...

😬 oops, sorry. I am probably not the only who made that mistake. I’ll correct it. Thanks for letting us know

Gag proteins encoded by endogenous retroviruses are required for zebrafish development | PNAS Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound of TE-derived sequences repurposed for organismal function. ...

💥🥳 At long last, our latest paper is out!

Gag proteins of endogenous retroviruses are required for zebrafish development

www.pnas.org/doi/10.1073/...

Led heroically by Sylvia Chang & @jonowells.bsky.social

A study which has changed the way I think of #transposons! No less! 🧵 1/n

Lovely! The addiction model 😍
So glad to see it out.
Big Congrats to Sylvia and @jonowells.bsky.social

Two rejuvenating days of exciting science, fun times, and beautiful sights in Tuebingen 🇩🇪
THANKS to Vikas Bansal & Daniel Sauter @unituebingen.bsky.social
and Susana Coelho @maxplanckcampus.bsky.social for hosting & @manusingh.bsky.social for joining 🙏😊

Sonoepigenetics: Spatiotemporal Calcium Dynamics and cAMP Signaling Driven by High Frequency Nanomechanostimulation Regulates Transient Epigenetic Modifications and Early Osteogenic Commitment in Mese... Cells effectively balance and integrate numerous pathways to adapt to external signals in an attempt to regain homeostasis, although the complex nuclear mechanotransduction mechanism through which thi...

I am Absolutely delighted to share the preprint of our last collaborative efforts where we investigated the impact of sonostimulation of Mesenchymal Stem Cells. Thread -1-

www.biorxiv.org/content/10.1...

🤯 cryo-ET of copia viral-like particles lurking at the nuclear pore of intact Drosophila eggs!
Amazing work by @svenklumpe.bsky.social & more cool findings in this collaborative paper illuminating the replication cycle of an iconic retrotransposon!
www.cell.com/cell/fulltex...

The below average intelligence - trump confidently blabbed in public about fundings to research on transgender mice when they are just transgenic mice .
I weep for future

I turned off the news and put a serial killer documentary for relaxing

Today is a devastating reminder that infectious diseases don’t care what your ‘beliefs’ are. Everyone is likely to be affected directly or indirectly. Serious challenges require serious people at the helm. Protect your loved ones. Educate. Advocate. The cost of not doing so will be too much to bear.

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

Its all about HERVH 😍

Welcome to the BlueSky. Btw, after German election results, I am changing my slide colors to big red 😀

Great thread of our most recent paper about how Transposons may make some people HIV-resistant, none other than by our @cedricfeschotte.bsky.social

Plenty of good reads here ⬇️

Transposable elements may enhance antiviral resistance in HIV-1 elite controllers - Genome Biology Background Less than 0.5% of people living with HIV-1 are elite controllers (ECs)—individuals who maintain undetectable plasma viremia without antiretroviral therapy, despite having replication-compet...

Feels awkward but necessary to celebrate scientific progress in this imperiled time for US biomedical research.

Proud of our latest paper out today exploring the role of transposable elements in antiviral resistance to HIV 🦠

genomebiology.biomedcentral.com/articles/10....
🧵1/n

Awesome teamwork co-led brilliantly by @manusingh.bsky.social & Sabrina Leddy; in collaboration with Doug Nixon’s lab - and of course funded by NIH. Thank you all! 🙏🙏🙏

Paper out !!🥳big thanks to all authors @marliesoomen.bsky.social @diego-rt.bsky.social @kaessmannlab.bsky.social @jonathangoeke.bsky.social @lorenzamottes.bsky.social & 'bluesky-less'

Lots of interesting new TE (& genes) biology

Data fully browsable💻 👉 embryo.helmholtz-munich.de/shiny_embryo/