This was so fun to be a part of! Just an amazing feat of collaboration with a bunch of brilliant scientists. ♥️ 🧬

Jay Shendure@jshendure.bsky.social · 5d ago

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

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

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...

1/n What fraction of the human genome is essential for cells? Excited to share our preprint that explores this question by combining an unusual CRISPR system, phage promoters, and thousands of deletion launchpads. @sudpinglay.bsky.social @jshendure.bsky.social www.biorxiv.org/content/10.6...

A decade on from the launch of an ambitious project, it’s time to revisit the reasons for constructing a human genome from scratch, says synthetic biologist Sudarshan Pinglay. go.nature.com/4uRxXVQ

Why a synthetic human genome is still worth building

A decade on from the launch of an ambitious project, it’s time to revisit the reasons for constructing a human genome from scratch.

go.nature.com

Latest from Shendure & Qiu labs (@cxqiu.bsky.social) )! We combined a new 4M cell mouse whole embryo scATAC-seq atlas (E10-P0), millions of 'evolutionarily coherent' orthologs from 241 mammalian genomes (Zoonomia), and the CREsted CNN framework (@steinaerts.bsky.social).

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!

So honored to have received this award! Thank you to the Experiement Foundation and @navigation.org

Bloom lab@jbloomlab.bsky.social · 6mo ago

I’d also like to note that @ckikawa.bsky.social was recently given a Beyond the Journal Award for the way she has been sharing these and similar data on GitHub in real-time as they are generated: www.experiment.foundation/beyond

Check out our new protocol paper on molecular recording of transcriptional events in genomic DNA! Super fun pulling this together with @jennynathans.bsky.social @chenomics.bsky.social and @jshendure.bsky.social

Nature Protocols@natprot.nature.com · 6mo ago

New Article! Multichannel genomic recording of biological information with ENGRAM

We have significantly improved the protocol for recording CRE activities and orders with ENGRAM. We also designed new plasmids for easier cloning. Great work with @jennynathans.bsky.social, @troymcdiarmid.bsky.social and @jshendure.bsky.social . Happy recording!!

Jenny Nathans@jennynathans.bsky.social · 6mo ago

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.

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.

Nature Protocols@natprot.nature.com · 6mo ago

New Article! Multichannel genomic recording of biological information with ENGRAM

The amazing @shawnfayer.bsky.social has developed a saturation genome editing method in iPSCs enabling MAVEs in differentiated cell types and diploid contexts. Please check it out! And, for some lucky department, Shawn is on the faculty job market!

Shawn Fayer@shawnfayer.bsky.social · 9mo ago

The effects of genetic variants primarily occur in differentiated cells meaning we need to access these cell types to measure variant effects for most disease genes. We developed saturation genome editing in stem cells (iPSC-SGE) to enable phenotyping in diverse genetic and cell contexts at scale!

A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording - @jshendure.bsky.social @troymcdiarmid.bsky.social @uwgenome.bsky.social go.nature.com/49eTPCu

A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording - Nature Biotechnology

Prime editing in mammalian cells benefits from a comprehensive list of genetic parts.

go.nature.com

Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies” shorturl.at/H3Qww This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon. Bluetorial below.

Thrilled to share I’ve started my lab at Dartmouth’s Geisel School of Medicine! We focus on mapping cellular trajectories & TF networks in development and Mendelian disorders, exploring new therapies. Join us—postdocs, grads, and scientists welcome! sites.dartmouth.edu/qiulab/

Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here: www.biorxiv.org/content/10.1...

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...

Check out our new paper by postdoc Debasish Paul, out now in @Nature.com. Cells need a boost of energy to jumpstart the cell cycle, but how can this happen while the APC/C is inhibiting glycolysis? We found cells solve this paradox through a highly dynamic mechanism. www.nature.com/articles/s41...

Transient APC/C inactivation by mTOR boosts glycolysis during cell cycle entry - Nature

APC/C activity is transiently inhibited to generate a pulse of glycolysis that is required for mammalian cell cycle entry.

nature.com