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Soumya Raychaudhuri সৌম্য রায়চৌধুরী @soumya-boston.bsky.social · 10d

Dear friends, I will be participating in the Jimmy Fund walk to support @DanaFarber. Please use the link below to donate anything you are comfortable with to this worthy cause, and please share. Thanks so much in advance for your support!

danafarber.jimmyfund.org/site/TR?px=2...

I am walking for Dana-Farber patients

Together against cancer at the Jimmy Fund Walk

danafarber.jimmyfund.org

Reposted by Soumya Raychaudhuri সৌম্য রায়চৌধুরী

sreekarmantena.bsky.social @sreekarmantena.bsky.social · Aug 29

Excited to share our preprint studying the genetics of T cell receptors! bit.ly/tcrdiversity with @soumya-boston.bsky.social @broadinstitute.org 🧵

TCR germline diversity reveals evidence of natural selection on variable and joining alpha chain genes

T cell receptors (TCRs) orchestrate adaptive immunity, yet the complex, repetitive architecture of the TCR loci has impeded systematic characterization of human genetic variation in the genes encoding...

doi.org

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Reposted by Soumya Raychaudhuri সৌম্য রায়চৌধুরী

dkotliar.bsky.social @dkotliar.bsky.social · Sep 3

Paper from me, Michelle Curtis, @soumya-boston.bsky.social and co out now in @natmethods.nature.com! We now call it starCAT instead of *CAT but the strategy is the same: Build a catalog of ~50 interpretable T cell gene expression programs + use them to interpret new data nature.com/articles/s41...

Reproducible single-cell annotation of programs underlying T cell subsets, activation states and functions - Nature Methods

TCAT is a pipeline that can simultaneously capture gene expression programs related to T cell subsets and activation states for accurate T cell characterization.

nature.com

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Soumya Raychaudhuri সৌম্য রায়চৌধুরী @soumya-boston.bsky.social · Sep 2

Our exciting new manuscript disentangling the human TCR locus!

sreekarmantena.bsky.social @sreekarmantena.bsky.social · Aug 29

Excited to share our preprint studying the genetics of T cell receptors! bit.ly/tcrdiversity with @soumya-boston.bsky.social @broadinstitute.org 🧵

TCR germline diversity reveals evidence of natural selection on variable and joining alpha chain genes

T cell receptors (TCRs) orchestrate adaptive immunity, yet the complex, repetitive architecture of the TCR loci has impeded systematic characterization of human genetic variation in the genes encoding...

doi.org

1

Soumya Raychaudhuri সৌম্য রায়চৌধুরী @soumya-boston.bsky.social · Aug 18

So excited to share our latest with Betty Diamond and many colleagues from the AMP RA/SLE consortium, NIAMS, and @niaidnews.bsky.social! A large-scale blood and tissue atlas of Lupus Nephritis! www.biorxiv.org/content/10.1...

A population-scale atlas of blood and tissue in lupus nephritis

Lupus nephritis (LN), a severe manifestation of Systemic lupus erythematosus (SLE), is a heterogeneous disease driven by diverse immune and tissue cell types. Current treatments of LN are non-specific...

www.biorxiv.org

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Reposted by Soumya Raychaudhuri সৌম্য রায়চৌধুরী

Broad Institute @broadinstitute.org · Aug 7

Next week! Join us on Thursday, August 14 at 6PM ET in Cambridge, MA (or online) for a Broad Discovery Series talk with @soumya-boston.bsky.social, “Arthritis, autoimmunity, and how the genome works.” Register: broadinstitute.swoogo.com/DiscoverySeries25

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Reposted by Soumya Raychaudhuri সৌম্য রায়চৌধুরী

Nature @nature.com · Jul 29

Nature research paper: Precisely defining disease variant effects in CRISPR-edited single cells

go.nature.com/44M3ygX

Precisely defining disease variant effects in CRISPR-edited single cells - Nature

A plate-based assay called CRAFTseq has been developed that uses ‘multi-omic’ single-cell RNA sequencing and direct genotyping of CRISPR edits to test the functional effects of genetic variants on cell state and function.

go.nature.com

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Soumya Raychaudhuri সৌম্য রায়চৌধুরী @soumya-boston.bsky.social · Jul 23

So excited to share our latest study on defining the function of disease variants by editing single cells, and assuming them with CRAFT-seq! Special thanks to @zpmu.bsky.social and @baglaenkolab.bsky.social! @broadinstitute.org

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

Precisely defining disease variant effects in CRISPR-edited single cells - Nature

A plate-based assay called CRAFTseq has been developed that uses ‘multi-omic’ single-cell RNA sequencing and direct genotyping of CRISPR edits to test the functional effects of genetic variants o...

www.nature.com

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Reposted by Soumya Raychaudhuri সৌম্য রায়চৌধুরী

Broad Institute @broadinstitute.org · Jul 16

Join us on Thursday, August 14 at 6 PM ET in Cambridge, MA – or online – for a Broad Discovery Series talk with @soumya-boston.bsky.social : “Arthritis, autoimmunity, and how the genome works.” Register: broadinstitute.swoogo.com/DiscoverySer...

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Reposted by Soumya Raychaudhuri সৌম্য রায়চৌধুরী

Tom Ulrich (he/him) @scribblertom.com · Jul 17

I've always found @soumya-boston.bsky.social's research to be absolutely fascinating, and I'm excited to bring him on-stage for the next talk in the @broadinstitute.org's Broad Discovery Series. Join us in-person or online on 8/14!

Broad Institute @broadinstitute.org · Jul 16

Join us on Thursday, August 14 at 6 PM ET in Cambridge, MA – or online – for a Broad Discovery Series talk with @soumya-boston.bsky.social : “Arthritis, autoimmunity, and how the genome works.” Register: broadinstitute.swoogo.com/DiscoverySer...

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Soumya Raychaudhuri সৌম্য রায়চৌধুরী @soumya-boston.bsky.social · Jun 9

Excited to be at the #HCA2025GM meeting!

Human Cell Atlas @humancellatlas.org · Jun 9

We’re excited to start the 2025 HCA General Meeting today. Looking forward to many insightful discussions and collaborations. You can still register to attend virtually at buff.ly/eZiIwaB #HCA2025GM

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Soumya Raychaudhuri সৌম্য রায়চৌধুরী @soumya-boston.bsky.social · Feb 27

Check out @saorisakaue.bsky.social ‘s study today demonstrating the differences in early RNA and late RNA eQTLs!

Saori Sakaue @saorisakaue.bsky.social · Feb 27

📣Excited to share my last postdoc paper with
@soumya-boston.bsky.social on eQTL mechanisms depending on where the RNA is in the cell! @broadinstitute.org @harvardmed.bsky.social
TL;DR:Early RNA eQTL variants in the nucleus and late RNA eQTL variants in the cytosol have distinct molecular mechanism🧵

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Reposted by Soumya Raychaudhuri সৌম্য রায়চৌধুরী

ProPublica @propublica.org · Feb 16

#ICYMI: ProPublica has confirmed the names and roles of more than 30 Musk-affiliated staffers who are helping the world’s richest man dismantle or downsize federal agencies one by one.

The Staffers Helping Elon Musk Dismantle and Downsize the U.S. Government, One Agency at a Time

Musk and his lieutenants are reshaping the government and its mission with the blessing of President Trump. ProPublica has confirmed the names and roles of more than 30 staffers affiliated with the…

propub.li

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Soumya Raychaudhuri সৌম্য রায়চৌধুরী @soumya-boston.bsky.social · Feb 12

Check out our latest from @yakirreshef.bsky.social!

Yakir Reshef @yakirreshef.bsky.social · Feb 12

Excited to tell you about VIMA (Variational Inference-based Microniche Analysis), our deep learning + stats hybrid for case-control analysis of multi-sample spatial molecular datasets. 🧵👇 www.biorxiv.org/content/10.1... @soumya-boston.bsky.social @broadinstitute.org

Powerful and accurate case-control analysis of spatial molecular data with deep learning-defined tissue microniches

As spatial molecular data grow in scope and resolution, there is a pressing need to identify key spatial structures associated with disease. Current approaches often rely on hand-crafted features such...

www.biorxiv.org

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Reposted by Soumya Raychaudhuri সৌম্য রায়চৌধুরী

Yakir Reshef @yakirreshef.bsky.social · Feb 12

Excited to tell you about VIMA (Variational Inference-based Microniche Analysis), our deep learning + stats hybrid for case-control analysis of multi-sample spatial molecular datasets. 🧵👇 www.biorxiv.org/content/10.1... @soumya-boston.bsky.social @broadinstitute.org

Powerful and accurate case-control analysis of spatial molecular data with deep learning-defined tissue microniches

As spatial molecular data grow in scope and resolution, there is a pressing need to identify key spatial structures associated with disease. Current approaches often rely on hand-crafted features such...

www.biorxiv.org

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