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...

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)

Early immune cell development precedes gastrulation in annual killifish

During embryogenesis, cell types arise in a predictable order because developmental regulators act sequentially. But how evolutionary changes in morphogenesis reshape the signaling environments that a...

doi.org

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...

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.

nature.com

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?...

Brain Health accelerator: a new way to study brain disease to find new treatments for it

YouTube video by allen institute

youtu.be

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.

allen institute@alleninstitute.org · 2mo ago

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?...

“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...

Summary of Key Changes in OMB’s Proposed Federal Financial Assistance Rule

Russell Vought is going destroy American Science

elizabethginexi.substack.com

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...

www.nature.com/articles/s41...

Widespread DNA off-targeting confounds RNA chromatin occupancy studies - Nature Biotechnology

Many long noncoding RNA–DNA binding peaks detected using common assays arise from technical artifacts.

nature.com

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.

medRxivpreprint@medrxivpreprint.bsky.social · 3mo ago

Multi-ancestral GWAS with the VA Million Veteran Program enables functional interpretation of rheumatoid arthritis alleles https://www.medrxiv.org/content/10.64898/2026.04.22.26351423v1

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

Pool-packaged AAV libraries exhibit extensive length-dependent and homology-dependent chimerism - Nature Biotechnology

Pooled production of recombinant AAV vectors leads to frequent genetic recombination.

go.nature.com

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...

The proteomic landscape and temporal dynamics of human and mouse gastruloid development - Nature Cell Biology

Garge et al. use experimentally matched mass spectrometry and RNA-sequencing to quantify proteins, phosphosites and transcripts across four key stages of human and mouse gastruloid development.

nature.com

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...

The proteomic landscape and temporal dynamics of human and mouse gastruloid development - Nature Cell Biology

Garge et al. use experimentally matched mass spectrometry and RNA-sequencing to quantify proteins, phosphosites and transcripts across four key stages of human and mouse gastruloid development.

nature.com

@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

Early Career Faculty Program | Freeman Hrabowski Scholars | HHMI

The Freeman Hrabowski Scholars Program offers comprehensive support to outstanding early career faculty committed to scientific excellence in their own research, and to fostering labs that expand the ...

bit.ly

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. 🦎

Nature Methods@natmethods.nature.com · 4mo ago

CREsted: an efficient and user-friendly toolbox for analysis, modeling and design of cell-type-specific enhancers. www.nature.com/articles/s41...

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...

Nitrogen, Ammonia, and the Strait of Hormuz

science.org