Jose Alquicira Hernandez
@joseah.bsky.social
Postdoctoral fellow at Harvard Medical School and Brigham Women’s Hospital with Soumya Raychaudhuri.
Statistical genetics | Single cell genomics | Immunogenomics
Statistical genetics | Single cell genomics | Immunogenomics
Reposted by Jose Alquicira Hernandez
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...
Reposted by Jose Alquicira Hernandez
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 Jose Alquicira Hernandez
A population-scale atlas of blood and tissue in lupus nephritis https://www.biorxiv.org/content/10.1101/2025.08.11.669754v1
August 15, 2025 at 3:17 AM
A population-scale atlas of blood and tissue in lupus nephritis https://www.biorxiv.org/content/10.1101/2025.08.11.669754v1
Reposted by Jose Alquicira Hernandez
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 Jose Alquicira Hernandez
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 Jose Alquicira Hernandez
Excited about our new preprint: 1st successful genome-wide study of >61,000 panic attack and 29,000 panic disorder cases. www.medrxiv.org/content/10.1... We find 17 associations & evidence that peripheral neurons in eye, lungs and heart are involved in panic & other psychiatric disorders 1/n
June 17, 2025 at 10:50 AM
Excited about our new preprint: 1st successful genome-wide study of >61,000 panic attack and 29,000 panic disorder cases. www.medrxiv.org/content/10.1... We find 17 associations & evidence that peripheral neurons in eye, lungs and heart are involved in panic & other psychiatric disorders 1/n
Reposted by Jose Alquicira Hernandez
📣 Latest from the lab: Performance of deep-learning-based approaches to improve polygenic scores www.nature.com/articles/s41...
Its thought deep learning will substantially improve PGS but the reality is MANY have tried but no/little gain has been seen so far. Here we report our negative results.
Its thought deep learning will substantially improve PGS but the reality is MANY have tried but no/little gain has been seen so far. Here we report our negative results.
June 5, 2025 at 1:37 PM
📣 Latest from the lab: Performance of deep-learning-based approaches to improve polygenic scores www.nature.com/articles/s41...
Its thought deep learning will substantially improve PGS but the reality is MANY have tried but no/little gain has been seen so far. Here we report our negative results.
Its thought deep learning will substantially improve PGS but the reality is MANY have tried but no/little gain has been seen so far. Here we report our negative results.
Reposted by Jose Alquicira Hernandez
Do you have an interest in B cells and immune-mediated diseases? We generated a multiomics resource of human B cell activation and showed its utility for elucidating disease mechanisms. Check out our manuscript led by @vitoraguiar.bsky.social and Marcella Franco: www.medrxiv.org/content/10.1...
A multi-omics resource of B cell activation reveals genetic mechanisms for immune-mediated diseases
Most genetic variants that confer risk of complex immune-mediated diseases (IMD) affect gene regulation in specific cell types. Their target genes and focus cell types are often unknown, partially bec...
www.medrxiv.org
May 24, 2025 at 4:33 PM
Do you have an interest in B cells and immune-mediated diseases? We generated a multiomics resource of human B cell activation and showed its utility for elucidating disease mechanisms. Check out our manuscript led by @vitoraguiar.bsky.social and Marcella Franco: www.medrxiv.org/content/10.1...
Reposted by Jose Alquicira Hernandez
📢 new preprint alert: So so excited to share our analysis on the impact of common and rare variants on single-cell gene expression in blood, using WGS and scRNA-seq data from nearly 2,000 individuals and 5.4m cells as part of TenK10K phase 1 🧬 www.medrxiv.org/content/10.1...
🧵👇 (1/n)
🧵👇 (1/n)
March 24, 2025 at 7:47 AM
📢 new preprint alert: So so excited to share our analysis on the impact of common and rare variants on single-cell gene expression in blood, using WGS and scRNA-seq data from nearly 2,000 individuals and 5.4m cells as part of TenK10K phase 1 🧬 www.medrxiv.org/content/10.1...
🧵👇 (1/n)
🧵👇 (1/n)
Reposted by Jose Alquicira Hernandez
📣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 2:21 AM
📣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🧵
Reposted by Jose Alquicira Hernandez
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 Jose Alquicira Hernandez
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