Brooks Benard

A single-cell framework identifies functionally and molecularly distinct multipotent progenitors in adult human hematopoiesis Ediriwickrema et al. conducted a systematic evaluation of human bone marrow cells and provide an updated model of adult hematopoiesis, which includes distinct, immunophenotypically defined, multipoten...

New #majetilab publication!

Asiri identifies 3 human MPP subsets from adult bone marrow and evaluates their engraftment + differentiation potential. Bonus: a single-cell multi-omics resource.

Check it out here ➡️ bit.ly/4mFSBEa

@stanforddeptmed.bsky.social @cp-cellreports.bsky.social

All clinical and expression data, along with cell type proportion associations with outcomes, are publicly available at precog.stanford.edu.

We integrated our existing pediatric data along with a newly curated ICI PRECOG resource into the PRECOG website, in addition to giving the site a UI overhaul.

Additionally, the recent advent of immune checkpoint inhibitor (ICI) therapies in cancer nominates novel biomarkers of clinical response, and prompted us to update PRECOG for the immunotherapy age.

Complimentary work from our group and others has provided similar expression-based biomarkers of outcomes in pediatric cancers (Pediatric PRECOG). However, this resource was never integrated into our online tool, limiting its accessibility and usefulness.

www.mdpi.com/2072-6694/13...

The prognostic landscape of genes and infiltrating immune cells across human cancers - Nature Medicine A searchable pan-cancer resource generated using data from nearly 18,000 human tumors reveals links between tumor infiltration by particular leukocyte subsets, tumor expression of particular gene sign...

PRECOG has been a valuable resource for highlighting clinically relevant biomarkers across adult cancers. Additionally, it was one of the first comprehensive reports on the prognostic importance of the immune system in cancer.

www.nature.com/articles/nm....

PRECOG update: An augmented resource of clinical outcome associations with gene expression for pediatric and immunotherapy cohorts Gene expression can be used to define prognostic and predictive biomarkers across cancers and treatment modalities. PRECOG (https://precog.stanford.edu) is a compendium of datasets with gene expressio...

Excited to share that, a decade after its initial release, PRECOG has an update!

www.biorxiv.org/content/10.1...

Looking forward to celebrating 80 years of federally funded science, technology and innovation @standupforscience.bsky.social SF, March 7, Civic Center, 1-3 pm 🧪 🧫 🧬

The immunometabolic topography of tuberculosis granulomas governs cellular organization and bacterial control Despite being heavily infiltrated by immune cells, tuberculosis (TB) granulomas often subvert the host response to Mycobacterium tuberculosis (Mtb) infection and support bacterial persistence. We prev...

Happy to share a preprint from the Angelo lab many years in the making. Read on for a saga of multiplexed imaging, immunometabolism, and TB granulomas with some fun side quests into the realms of geographical information sciences and transcriptomics… (1/20) doi.org/10.1101/2025...

AI provides a universal framework that leverages data and compute at scale to uncover higher-order patterns

Today, @arcinstitute.org in collaboration with Nvidia releases Evo 2—a fully open source biological foundation model trained on genomes spanning the entire tree of life.

Spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis - Nature Genetics Xenium spatial transcriptomic profiling of pulmonary fibrosis characterizes cell composition dynamics and histopathological features associated with the disease.

Excited to post my first #skySplain about our recent work published yesterday in Nature Genetics! www.nature.com/articles/s41.... One of the first authors of this study - Annika Vannan – actually wrote this breakdown, but she's not yet over here on bluesky and asked me to post!

Temporal and spatial composition of the tumor microenvironment predicts response to immune checkpoint inhibition Immune checkpoint inhibition (ICI) has fundamentally changed cancer treatment. However, only a minority of patients with metastatic triple negative breast cancer (TNBC) benefit from ICI, and the deter...

I’m super excited to share what I’ve been working on for the last (many) years: a spatial + genomic + transcriptomic characterization of how the breast cancer microenvironment evolves through immunotherapy! (1/x) 🧪🧬 🖥️ #AcademicSky #MLSky #ImmunoSky www.biorxiv.org/content/10.1...