Riddhiman Garge

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. 🧵 👇

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

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...

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.

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) ...

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/...

Thanks GSA for blogging about our work!

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

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...

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!

If you're interested in hearing more about this work, I will be speaking at the #2023MasterBrewers Meeting in October! Please come by!

Finally, I can't thank my mentors @edwardmarcotte.bsky.social and @maitreya.bsky.social enough for all their support and encouragement without which none of this would have been possible!

Always grateful to Chip, Dusan and Thorin @LiveOakBrewing (Twitter) for enthusiastically supporting us even through tough pandemic times and showing me that interesting scientific questions aren't restricted to the lab.

A huge thank you to my fellow authors, @reneegeck.bsky.social, Joe Armstrong, Barbara Dunn, Daniel Boutz, Anna Battenhouse, @MarioLeutert (Twitter),
@vyqtdang (Twitter), @pyjiang (Twitter), Dusan Kwiatkowski, Thorin Peiser, and Chip McElroy for their help and assistance!

We're really excited to share this resource with the community, and thanks to @MarioLeutert (Twitter), we have this website for exploring the data! brewing-yeast-proteomics.ccbb.utexas.edu

-We gain insights into adaptation by uncovering pathways/processes changing across serial repitching (a practice breweries use to harvest and reuse yeast from a prior fermentation batch). Finally, we have a global view of how proteins complexes are regulated across fermentation.

So what did we learn from making over 64,000 protein abundance measurements across 17 different timepoints? -We now have a global view of the temporal protein changes in yeast across brewing including when and which processes change most between timepoints.

Sample collection was particularly fun because it required sampling directly from fermentation tanks!

Our work directly profiles the actual brewing yeast populations from fermentation tanks to understand how yeast proteomes temporally (and globally) change over fermentation. We used proteomics to profile brewing yeast both across fermentation cycles and serial repitching.

The majority of previous fermentation yeast omics studies characterize the domestication history, genetic differences across strains, and understand how proteins and metabolites in beer influence flavor.

It was purely a labor-of-love driven by curiosity and conversations with biochemist and founder Chip McElroy from @LiveOakBrewing (Twitter) wanting to know what molecular changes yeast cells go through during fermentation and brewing.

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...