Soumya Raychaudhuri সৌম্য রায়চৌধুরী
@soumya-boston.bsky.social
Mapping response eQTLs in data sets using single-cell statistical models! Congrats to Cristian Valencia and team!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
www.nature.com
October 27, 2025 at 12:39 AM
Mapping response eQTLs in data sets using single-cell statistical models! Congrats to Cristian Valencia and team!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
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
September 28, 2025 at 8:50 PM
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...
danafarber.jimmyfund.org/site/TR?px=2...
Reposted by Soumya Raychaudhuri সৌম্য রায়চৌধুরী
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
August 29, 2025 at 6:15 PM
Excited to share our preprint studying the genetics of T cell receptors! bit.ly/tcrdiversity with @soumya-boston.bsky.social @broadinstitute.org 🧵
Reposted by Soumya Raychaudhuri সৌম্য রায়চৌধুরী
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
September 3, 2025 at 4:46 PM
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...
Our exciting new manuscript disentangling the human TCR locus!
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
September 2, 2025 at 7:40 PM
Our exciting new manuscript disentangling the human TCR locus!
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
August 18, 2025 at 7:56 PM
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...
Reposted by Soumya Raychaudhuri সৌম্য রায়চৌধুরী
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
August 7, 2025 at 5:03 PM
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
Reposted by Soumya Raychaudhuri সৌম্য রায়চৌধুরী
Nature research paper: Precisely defining disease variant effects in CRISPR-edited single cells
go.nature.com/44M3ygX
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
July 29, 2025 at 6:38 PM
Nature research paper: Precisely defining disease variant effects in CRISPR-edited single cells
go.nature.com/44M3ygX
go.nature.com/44M3ygX
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...
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
July 23, 2025 at 11:34 PM
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...
www.nature.com/articles/s41...
Reposted by Soumya Raychaudhuri সৌম্য রায়চৌধুরী
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...
July 16, 2025 at 7:50 PM
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...
Reposted by Soumya Raychaudhuri সৌম্য রায়চৌধুরী
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!
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...
July 17, 2025 at 5:09 PM
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!
Excited to be at the #HCA2025GM meeting!
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
June 9, 2025 at 1:12 AM
Excited to be at the #HCA2025GM meeting!
Check out @saorisakaue.bsky.social ‘s study today demonstrating the differences in early RNA and late RNA eQTLs!
📣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🧵
@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🧵
February 27, 2025 at 2:55 AM
Check out @saorisakaue.bsky.social ‘s study today demonstrating the differences in early RNA and late RNA eQTLs!
Reposted by Soumya Raychaudhuri সৌম্য রায়চৌধুরী
#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
February 16, 2025 at 9:50 PM
#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.
Check out our latest from @yakirreshef.bsky.social!
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
February 12, 2025 at 4:28 AM
Check out our latest from @yakirreshef.bsky.social!
Reposted by Soumya Raychaudhuri সৌম্য রায়চৌধুরী
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
February 12, 2025 at 4:21 AM
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