iiinova — where your digital self keeps evolving

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Jay Shendure @jshendure.bsky.social · 30/07/2026

New preprint from Shendure Lab on Locus-Scale aka Long-@$$ MPRAs led by the amazing Abby McGee & @carinabiar.bsky.social Most MPRAs test ~300 bp fragments next to a promoter. But real enhancers are bigger, act combinatorially and from a distance. 1/n www.biorxiv.org/content/10.6...

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Jay Shendure @jshendure.bsky.social · 31/07/2026

Thrilled to post thread re: new single-cell lineage of mouse embryo reconstructed w/ DNA Typewriter. One animal, zygote to late organogenesis (E13.5). Tree has 1,340,794 transcriptionally profiled, annotated tips (cells), 1,142,588 dated internal nodes, rooted at zygote 1/n

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Jenny Nathans @jennynathans.bsky.social · 13/02/2026

Super happy to share our protocol for ENGRAM is out in Nature Protocols! This was fun to write with @chenomics.bsky.social @troymcdiarmid.bsky.social @jshendure.bsky.social. In it we describe how to record CRE identity, activity, and order in mammalian cells.

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Troy McDiarmid @troymcdiarmid.bsky.social · 02/04/2026

Stoked to announce that I’m starting a lab as an Assistant Professor in the School of Biomedical Engineering and Centre for Brain Health at UBC! mcdiarmid-lab.sbme.ubc.ca Recruiting at all levels - please share the word! Cheers and happy long weekend all!

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cxqiu.bsky.social @cxqiu.bsky.social · 09/04/2026

New preprint @cxqiu.bsky.social @jshendure.bsky.social ! Can we learn regulatory grammars of human cell types — by training on mouse development and transferring across 241 mammalian genomes? Introducing STEAM & a whole-organism scATAC-seq atlas from E10 to birth. www.biorxiv.org/content/10.6...

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Nobu Hamazaki @nobuhamazaki.bsky.social · 26/09/2025

New paper from my lab and @jshendure.bsky.social lab! Led by the brilliant @zukailiu.bsky.social and @cxqiu.bsky.social. We tackled how anterior and posterior progenitor cells cooperate to self-organize into an embryonic structure (termed AP-gastruloid). (1/n) www.biorxiv.org/content/10.1...

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Agnel Sfeir @agnelsfeir.bsky.social · 10/03/2025

Combining bacterial end joining with programmable nucleases, we induced mtDNA deletions in human cells at varying heteroplasmy and examined their metabolic and cellular effects. Simple tool to apply across any cell type and engineer pathogenic mtDNA deletions. www.sciencedirect.com/science/arti...

sciencedirect.com

Engineering mtDNA deletions by reconstituting end joining in human mitochondria

Recent breakthroughs in the genetic manipulation of mitochondrial DNA (mtDNA) have enabled precise base substitutions and the efficient elimination of…

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Yi Fu @yi-fu.bsky.social · 12/03/2025

Another part of my PhD work in @agnelsfeir.bsky.social lab is finally out! Combining DNA breaks and end joining, we engineered mtDNA deletions in human cells and explored their impact on cellular metabolism and transcription. 📄: authors.elsevier.com/c/1kkg7L7PXu... 🧵: x.com/Yi__Fu/statu...

authors.elsevier.com

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Pedro Rocha @pedroprocha.bsky.social · 26/02/2025

Here is the peer-reviewed version of our study showing how some TAD borders are essential for gene regulation and development. Loss of a single CTCF motif is sufficient to cause embryonic lethality. www.sciencedirect.com/science/arti...

sciencedirect.com

Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development

Chromatin domains delimited by CTCF can restrict the range of enhancer action. However, disruption of some domain boundaries results in mild gene dysr…

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