Soumya Raychaudhuri সৌম্য রায়চৌধুরী
@soumya-boston.bsky.social
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Mapping response eQTLs in data sets using single-cell statistical models! Congrats to Cristian Valencia and team!
www.nature.com/articles/s41...
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Modeling heterogeneity in single-cell perturbation states enhances detection of response eQTLs - Nature Genetics
Modeling of per-cell perturbation states in single-cell RNA sequencing datasets enhances detection of response expression quantitative trait loci and helps prioritize genetic regulatory effects in dis...
https://www.nature.com/articles/s41588-025-02344-6
3 months ago
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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...
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I am walking for Dana-Farber patients
Together against cancer at the Jimmy Fund Walk
https://danafarber.jimmyfund.org/site/TR?px=2821198&pg=personal&fr_id=2380&s_hasSecureSession=true
4 months ago
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reposted by
Soumya Raychaudhuri সৌম্য রায়চৌধুরী
5 months ago
Excited to share our preprint studying the genetics of T cell receptors!
bit.ly/tcrdiversity
with
@soumya-boston.bsky.social
@broadinstitute.org
🧵
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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...
https://doi.org/10.1101/2025.08.20.671277
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reposted by
Soumya Raychaudhuri সৌম্য রায়চৌধুরী
5 months ago
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...
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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.
https://nature.com/articles/s41592-025-02793-1
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Our exciting new manuscript disentangling the human TCR locus!
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5 months ago
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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...
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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...
https://www.biorxiv.org/content/10.1101/2025.08.11.669754v1
5 months ago
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reposted by
Soumya Raychaudhuri সৌম্য রায়চৌধুরী
Broad Institute
6 months ago
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
6 months ago
Nature research paper: Precisely defining disease variant effects in CRISPR-edited single cells
go.nature.com/44M3ygX
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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.
https://go.nature.com/44M3ygX
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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...
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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...
https://www.nature.com/articles/s41586-025-09313-3
6 months ago
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reposted by
Soumya Raychaudhuri সৌম্য রায়চৌধুরী
Broad Institute
6 months ago
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...
0
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reposted by
Soumya Raychaudhuri সৌম্য রায়চৌধুরী
Tom Ulrich (he/him)
6 months ago
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!
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Excited to be at the
#HCA2025GM
meeting!
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8 months ago
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Check out
@saorisakaue.bsky.social
‘s study today demonstrating the differences in early RNA and late RNA eQTLs!
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11 months ago
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reposted by
Soumya Raychaudhuri সৌম্য রায়চৌধুরী
ProPublica
11 months ago
#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.
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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…
https://propub.li/4k4hlVY
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Check out our latest from
@yakirreshef.bsky.social
!
add a skeleton here at some point
11 months ago
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reposted by
Soumya Raychaudhuri সৌম্য রায়চৌধুরী
Yakir Reshef
11 months ago
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
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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...
https://www.biorxiv.org/content/10.1101/2025.02.07.637149v1
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