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Riddhiman Garge

@riddhiman.bsky.social
271 followers 539 following 30 posts

K99/R00 Fellow w/ @jshendure.bsky.social, @leastarita.bsky.social & @dschweppe.bsky.social | @uwgenome.bsky.social, @cegs-cmap.bsky.social & @brotmanbaty.bsky.social |PhD w/ @edwardmarcotte.bsky.social |Musician, vinyl collector, RCB & Utd outside the lab.

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Reposted by Riddhiman Garge
Jay Shendure @jshendure.bsky.social · 31/07/2026
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
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Jay Shendure @jshendure.bsky.social · 30/07/2026
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...
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Sudarshan Pinglay @sudpinglay.bsky.social · 04/06/2026
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...
nature.com
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.
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Nature Cell Biology @natcellbio.nature.com · 11/05/2026
☕ @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
bit.ly
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.
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Devin Schweppe @dschweppe.bsky.social · 24/04/2026
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...
nature.com
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.
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Reposted by Riddhiman Garge
Alfonso Martinez Arias @amartinezarias.bsky.social · 25/04/2026
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
nature.com
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.
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Riddhiman Garge @riddhiman.bsky.social · 25/04/2026
15/ Last but no means least, thanks to @uwgenome.bsky.social @cegs-cmap.bsky.social @brotmanbaty.bsky.social for amazing colleagues and resources!
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Riddhiman Garge @riddhiman.bsky.social · 25/04/2026
14/ Grateful for the insightful and exciting conversations w/ @nobuhamazaki.bsky.social and @dschweppe.bsky.social and the unconditional support from their amazing labs. As always, huge thanks to my mentors @jshendure.bsky.social and @leastarita.bsky.social for their constant mentorship and advice!
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Riddhiman Garge @riddhiman.bsky.social · 25/04/2026
13/ More broadly, our work adds to a growing body of work phenotyping proteome dynamics in stem cell derived embryo models. #SCBEM
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Riddhiman Garge @riddhiman.bsky.social · 25/04/2026
12/ Our co-regulation network placed 8 Commander subunits alongside 23 cooperative proteins, including DPYSL4 & PRKACB. Knocking out Commander subunits or cooperative partners produced gastruloids with similar morphological defects including reduced size, shortened axes.
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Riddhiman Garge @riddhiman.bsky.social · 25/04/2026
11/ Intersecting our data with developmental disease databases, we find disease genes tend to be co-regulated. We zoomed in on the Commander complex, linked to congenital defects including intellectual disability and Ritscher-Schinzel syndrome.
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Riddhiman Garge @riddhiman.bsky.social · 25/04/2026
10/ For example, our data suggested that MAPKAPK2’s activity increased during gastruloid development. On inhibiting MAPKAPK2, we observed that gastruloids failed to elongate, formed with multi-axes, & had high SOX2 suggesting that it regulates symmetry breaking & pluripotency exit in gastruloids.
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Riddhiman Garge @riddhiman.bsky.social · 25/04/2026
9/ With phosphoproteomics, we profiled how phosphorylation states change over gastruloid development. Excitingly, using these datasets we predicted kinase activity (including those poorly characterized in developmental contexts) across gastruloid development.
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Riddhiman Garge @riddhiman.bsky.social · 25/04/2026
8/ With experimentally matched RNA-seq, we find transcript & protein abundance are only modestly correlated. Discordance peaks at peri-gastrulation & is especially strong for metabolic and mitochondrial genes, pointing to active post-transcriptional remodeling during fate transitions.
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Riddhiman Garge @riddhiman.bsky.social · 25/04/2026
7/ By computing co-regulation across all protein pairs, we map which sets of proteins move together during gastruloid development. The network recovers known complexes (26S proteasome, TCA cycle, ribosome) & nominates "cooperative" proteins linked to each.
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Riddhiman Garge @riddhiman.bsky.social · 25/04/2026
6/ Quantifying ~7.3K human & ~8.7K mouse proteins, we see thousands of differentially expressed proteins across stages, often in coordinated temporal shifts. e.g., the systematic downregulation of mitochondrial OxPhos proteins over gastruloid development.
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Riddhiman Garge @riddhiman.bsky.social · 25/04/2026
5/ To fill this gap, we used multi-omics to profile proteins, phosphosites, & RNA (in a experimentally matched fashion) across 4 stages in mouse & human gastruloids.
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Riddhiman Garge @riddhiman.bsky.social · 25/04/2026
4/ We & others have profiled gastruloids extensively with scRNA-seq & imaging. But proteins, (the workhorses of the cell) have been largely uncharted. RNA only modestly predicts protein levels, & misses PTMs entirely.
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Riddhiman Garge @riddhiman.bsky.social · 25/04/2026
3/ @nobuhamazaki.bsky.social and Wei Yang showed that a discontinuous pulse of retinoic acid induces human gastruloids with embryo-like features including neural tube & segmented somites. www.nature.com/articles/s41...
nature.com
Retinoic acid induces human gastruloids with posterior embryo-like structures - Nature Cell Biology
Hamazaki, Yang et al. report that an early pulse of retinoic acid robustly induces human gastruloids with a neural tube, segmented somites and more advanced cell types than conventional gastruloids.
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Riddhiman Garge @riddhiman.bsky.social · 25/04/2026
2/ Gastrulation is when the embryo breaks symmetry, forms the 3 germ layers, & lays down the body plan. Ethical & technical challenges make it hard to study gastrulations. Gastruloids are stem-cell-based embryo models #SCBEM that have emerged as powerful models to gain insights into gastrulation.
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Riddhiman Garge @riddhiman.bsky.social · 25/04/2026
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...
nature.com
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.
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Saccharomyces Genome Database @yeastgenome.bsky.social · 02/03/2026
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
a headshot of David Botstein
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Gavin Sherlock @gsherloc.bsky.social · 28/02/2026
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/
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Carl Zimmer @carlzimmer.com · 18/02/2026
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)
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Riddhiman Garge @riddhiman.bsky.social · 22/11/2025
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. 🧵 👇
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Reposted by Riddhiman Garge
allen institute @alleninstitute.org · 20/10/2025
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...
alleninstitute.org
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
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Jay Shendure @jshendure.bsky.social · 14/10/2025
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...
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Nobu Hamazaki @nobuhamazaki.bsky.social · 26/09/2025
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...
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Sri Kosuri @srikosuri.bsky.social · 08/02/2025
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.
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Sudarshan Pinglay @sudpinglay.bsky.social · 31/01/2025
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/...
science.org
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) ...
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Riddhiman Garge @riddhiman.bsky.social · 10/05/2024
Thanks GSA for blogging about our work!
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Reposted by Riddhiman Garge
Maitreya Dunham @maitreya.bsky.social · 07/03/2024
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...
academic.oup.com
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
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Riddhiman Garge @riddhiman.bsky.social · 14/12/2023
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!
wrfseattle.org
Washington Research Foundation announces its largest ever cohort of WRF Postdoctoral Fellows for 202...
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Riddhiman Garge @riddhiman.bsky.social · 23/09/2023
If you're interested in hearing more about this work, I will be speaking at the #2023MasterBrewers Meeting in October! Please come by!
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Riddhiman Garge @riddhiman.bsky.social · 23/09/2023
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!
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Riddhiman Garge @riddhiman.bsky.social · 23/09/2023
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.
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Riddhiman Garge @riddhiman.bsky.social · 23/09/2023
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!
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Riddhiman Garge @riddhiman.bsky.social · 23/09/2023
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
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Riddhiman Garge @riddhiman.bsky.social · 23/09/2023
-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.
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Riddhiman Garge @riddhiman.bsky.social · 23/09/2023
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.
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Riddhiman Garge @riddhiman.bsky.social · 23/09/2023
Sample collection was particularly fun because it required sampling directly from fermentation tanks!
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Riddhiman Garge @riddhiman.bsky.social · 23/09/2023
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.
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Riddhiman Garge @riddhiman.bsky.social · 23/09/2023
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.
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Riddhiman Garge @riddhiman.bsky.social · 23/09/2023
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.
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Riddhiman Garge @riddhiman.bsky.social · 23/09/2023
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-
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Maitreya Dunham @maitreya.bsky.social · 22/09/2023
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...
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