Jose Alquicira Hernandez

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.

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...

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...

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 https://www.biorxiv.org/content/10.1101/2025.08.11.669754v1

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...

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...

talk poster

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...

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

📣 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.

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...

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...

📢 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)

📣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🧵

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

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...

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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