Spectacular preprint led by @sydsat.bsky.social in @ohnolog.bsky.social lab, @uwgenome.bsky.social. Neutrophils precede gastrulation in killifish and rapidly patrol the yolk. (1/2)

22/n On a personal note, I’ll soon start an independent research group in the Genome Biology Unit at EMBL Heidelberg. If you enjoy this type of work and want to engineer genomes at the largest scale, please reach out! jonas-koeppel.github.io/koeppellab/ www.embl.org/groups/koepp...

How much of the human genome is essential? Two pieces out today from our lab: 1) a method to map essential genomic intervals at gigabase scale, and 2) an argument that it's time to consider synthesizing a minimal human genome. biorxiv.org/content/10.6... nature.com/articles/d41...

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...

Brain disease is tragic, but it doesn’t have to be. It’s time for a new approach to #brainhealth research. That’s why we and our partners are launching the Brain Health accelerator. 🎥 youtu.be/wnTG5Sg8AKY?...

This week’s launch of the #BrainHealth accelerator marks an important step forward for neuroscience. I’m excited to see this ambitious effort rally teams around a shared goal: building a deeper understanding of brain disease and accelerating progress toward better therapies.

“AlphaFold 3's representational coherence is deeply tied to evolutionary scaffolding, suggesting it functions similarly to an advanced fold-recognition system and highlighting that protein structure prediction from sequence alone is not yet fully solved.”

And, here, in much more detail. This is an absolutely critical read for all federally funded scientists and institutions. Now is not the time to sit in the corner, hoping you won't be noticed - now is the time for action. elizabethginexi.substack.com/p/summary-of...

NIH funded peeps: This is insane and coming for us.

Game over, phylogeneticists! New DNA foundation model "Carbon" reconstructs the tree of life. 🙃 huggingface.co/spaces/Huggi...

Last year two preprints from @jshendure.bsky.social and @arjunraj.bsky.social www.biorxiv.org/content/10.1... and www.biorxiv.org/content/10.1... perhaps began to shed light on this question. One of them has been updated. Their findings are important.

Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.

An important piece from my neighbor, colleague and friend Will DeWitt et al. @wsdewitt.github.io www.biorxiv.org/content/10.6...

New preprint! 📣We performed the largest multi-ancestry GWAS of rheumatoid arthritis (RA), the most common autoimmune disease, by analyzing the VA Million Veteran Program (MVP) with international RA cohorts.

Pool-packaged AAV libraries exhibit extensive length-dependent and homology-dependent chimerism - @jshendure.bsky.social @uwgenome.bsky.social go.nature.com/4cMTnLP

1/ Thrilled to share our latest: an exciting collaboration across the @jshendure.bsky.social, @leastarita.bsky.social, @nobuhamazaki.bsky.social and @dschweppe.bsky.social labs! 🧵 below- #SystemsBiology #SCBEM #MultiOmics #Gastruloids www.nature.com/articles/s41...

Excited to see @riddhiman.bsky.social's gastruloid multiomics paper out now at Nature Cell Bio! Riddhiman used proteomics, phosphoproteomics, and RNAseq to profile stem-cell-derived embryo models to identify protein, complex, and signaling regulators of development. www.nature.com/articles/s41...

@hhmi-science.bsky.social's #FreemanHrabowski Scholars Program offers early career faculty up to $10M over 10 yrs, plus salary & benefits Stable, sustained support can transform your career: Senior Postdoc? This year's competition has a program for you too. Applications open 11/3! bit.ly/4vhC0LA

HHMI CEO: "diamond funding should be deployed to sustain repositories [i.e. preprint servers] and connective infrastructure that focus on researcher-shared outputs" zenodo.org/records/1960...

Excited to share our new paper @nature.com! We developed PerturbFate, a scalable single-cell platform to discover how diverse genetic perturbations converge on a shared drug-resistant cell state, and key programs driving it, led by our incredible Zihan Xu from @rockefeller.edu rdcu.be/fdC14

CREsted is finally out! You can find the article, together with a summarizing Research Briefing, in thread. 🦎

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).

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...

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!

1/ 🚀 Excited to release: napari-mcp - agentic control of napari from any MCP-capable AI assistant! Use it for interactive image processing, analysis, and visualisation! Really cool project from @ilan-theodoro.bsky.social from my team! #napari #bioimageanalysis #MCP @biohub

AP-1 mediates cellular adaptation and memory formation @natcomms.nature.com @pennmedicine.bsky.social @arjunraj.bsky.social @penngenetics.bsky.social www.nature.com/articles/s41...

I mean, these are always good. But this is So Good. Nitrogen, Ammonia, and the Strait of Hormuz | Science | AAAS www.science.org/content/blog...

Very happy to see this out. 👏 @yinanwan.bsky.social Bogdan Bintu and team. Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis | free link Science www.science.org/eprint/5MHTM...

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!!

Happy to share that our review on mammalian genome writing with Jack Atwater, Ran Brosh, Jef Boeke, @jshendure.bsky.social and Matt Maurano is now out in @cellpress.bsky.social! www.sciencedirect.com/science/arti...

Calling all rising juniors & seniors: Interested in biological or biomedical research? Applications for our ’26 Summer Undergraduate Research Experience Program are now open! Nine weeks, hands-on research, & mentorship from some of the nation’s top scientists — learn more: bit.ly/CechFellows

Happy Birthday to the Seattle Hub for Synthetic Biology! 🎂🎉 OTD with @chanzuckerberg.bsky.social and @uwmedicine.bsky.social, we launched #SeaSynBio with the goal to build tech that allows cells to record their own histories. 🔗 https://alleninstitute.org/division/seattle-hub-for-synthetic-biology

We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below: (TLDR; low-affinity motifs matter as pioneers!)

Our work developing a parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording is now out @natbiotech.nature.com

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

🚀 Very excited to share the first major work from my PhD!! We combined MPRA and CRISPRa in excitatory neurons to test and validate cis-regulation therapies for hundreds of haploinsufficient neurodevelopmental disorder genes. 🧬🔬 www.biorxiv.org/content/10.1...

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/

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...

This is one of the coolest figures I've seen in a while

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...

Developmental Biology and Disability. “Developmental biology is fundamentally beautiful. We are no less beautiful for our variation. Instead, perhaps we are more so. Perhaps we are remarkable. Perhaps we are full of wonder.” Insightful post by Bethan ⬇️👀 thenode.biologists.com/developmenta...

awesome new work by my @gladstoneinst.bsky.social and @ucsanfrancisco.bsky.social colleagues incl @vram142.bsky.social on how chromatin remodelers affect mesoscale chromatin organization www.science.org/doi/10.1126/...

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...

Hugely thankful for this 🙏. We will do our best to make the most of it. @erc.europa.eu!

Our latest research is out today on ‪@medrxivpreprint.bsky.social: www.medrxiv.org/content/10.1... Saturation genome editing of BRCA1 across cell types accurately resolves cancer risk. Led by the amazing Phoebe Dace. This one’s packed full of data, so check out the paper. Quick highlights… 🧵 1/n

Thrilled at the news of @10xgenomics.bsky.social ' acquisition of Scale Bio which I co-founded with Frank Steemers (ex-Illumina), @coletrapnell.bsky.social and Garry Nolan . Further thrilled to joining 10X Genomics as an scientific advisor and for the synergies that lie ahead!

Two new preprints from the @arjunraj.bsky.social‬ on #gastruloids. Both excellent. Exploring the relationship between macroscopic reproducibility v microscopic heterogeneity. Stunning experiments and much to think about biorxiv.org/content/earl... biorxiv.org/content/earl...

🚨 Most variant screens measure growth or abundance. What do they miss? That variants impact a spectrum of protein and cellular phenotypes. Variant in situ sequencing (VIS-seq) finds what’s missing: image cells 🔬 first, decode later, revealing multi-scale phenotypes for thousands of variants.👇 1/9