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...

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

☕ @riddhiman.bsky.social et al. use experimentally matched mass-spec and RNA-seq to quantify proteins, phosphosites & transcripts across 4 stages of human & mouse gastruloid development. @jshendure.bsky.social @leastarita.bsky.social @nobuhamazaki.bsky.social @dschweppe.bsky.social bit.ly/4dAYyA1

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.

bit.ly

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

Previously a #preprint, now a peer reviewed @dschweppe.bsky.social work a fine, insightful, useful reference for the growing #gastruloid community . Proteomics, protein-RNA discordances, mouse-human comparison www.nature.com/articles/s41... Insights into human embryos for a growing #SCBEM community

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

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

We are deeply saddened to share the news of the passing of David Botstein, a towering figure in modern #genetics and a foundational force behind SGD. www.yeastgenome.org/blog/in-memo... #yeast #modelOrganism

I was sad to learn that my postdoctoral mentor, David Botstein, died yesterday. I started with David as a postdoc in 1998, and he had a profound effect on both my life and scientific career. He was a giant in the field of genetics, making seminal contributions in both yeast and human genetics. 1/

Scientists have seen Asgard archaea crawling for the first time. When it comes to the origin of eukaryotes, this is like seeing a feathered dinosaur in the wild. (Video courtesy of Philipp Ralder)

Very happy to share our latest led by the relentless @shawnfayer.bsky.social! We developed multiplexed assays to measure variant effects across diverse genetic and cell contexts in stem cell and differentiated cells. 🧵 👇

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!

Congratulations to Karel Svoboda and @jshendure.bsky.social on their election to the National Academy of Medicine (@nam.edu)! Election to the Academy is one of the highest honors in health and medicine. #NAMmtg More on their journeys to this achievement: alleninstitute.org/news/karel-s...

Karel Svoboda and Jay Shendure elected to National Academy of Medicine

The honor recognizes leaders who have demonstrated outstanding achievement and made lasting contributions to the advancement of the medical sciences, health care, and public health

alleninstitute.org

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...

It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.

Now out in @science.org w/ @jshendure.bsky.social we present 'Genome-shuffle-seq': a method to shuffle mammalian genomes and characterize the impact of structural variants (SVs) with single-cell resolution in one experiment. www.science.org/doi/10.1126/...

Multiplex generation and single-cell analysis of structural variants in mammalian genomes

Studying the functional consequences of structural variants (SVs) in mammalian genomes is challenging because (i) SVs arise much less commonly than single-nucleotide variants or small indels and (ii) ...

science.org

Thanks GSA for blogging about our work!

Maitreya Dunham@maitreya.bsky.social · 2y ago

Nice article about our brewing yeast proteomics paper with @riddhiman.bsky.social and @edwardmarcotte.bsky.social! Beer brewers and geneticists collaborate on study of yeast changes during commercial fermentation genestogenomes.org/beer-brewers...

How appropriate that our G3 paper with @riddhiman.bsky.social and @edwardmarcotte.bsky.social et al came out in final form while I'm at #TAGC24! Systematic profiling of ale yeast protein dynamics across fermentation and repitching academic.oup.com/g3journal/ar...

Systematic profiling of ale yeast protein dynamics across fermentation and repitching

Abstract. Studying the genetic and molecular characteristics of brewing yeast strains is crucial for understanding their domestication history and adaptations a

academic.oup.com

Very grateful to be amongst this amazing cohort of scientists! Many thanks to @wrfseattle for the opportunity to learn and grow in this diverse program. Finally, I can't thank my mentors @jshendure.bsky.social and @lea_starita at UW Genome Sciences enough for their support!

Finally on BlueSky! Thrilled to share our work profiling Ale yeast protein dynamics across fermentation and serial repitching! biorxiv.org/content/10.1... @maitreya.bsky.social @edwardmarcotte.bsky.social @LiveOakBrewing #BeerYeast #SystemsBiology #Proteomics Sneek Peak🧵 below-

Super fun project with @riddhimankg (twitter), @edwardmarcotte.bsky.social, @LiveOakBrewing (twitter), and friends! Systematic Profiling of Ale Yeast Protein Dynamics across Fermentation and Repitching www.biorxiv.org/content/10.1...