Lisa M. McGinnis

A Spatial Proteomic Atlas of Tertiary Lymphoid Structures in Non-Small Cell Lung Cancer Identifies a Novel Predictive Class of Lymphoid Aggregates

The paper identifies a novel class of mature lymphoid aggregates in NSCLC using spatial proteomics and develops a classifier to improve CPI biomarker eligibility.

Spatiotemporal profiling reveals the role of inflammatory niche in driving prostate cancer

This study uses single-cell and spatial profiling to show that inflammatory signals from macrophages and fibroblasts drive CD8 T cell exhaustion and resistance to immune checkpoint blockade in prostate cancer.

Spatial Decoding of Tertiary Lymphoid Structure Maturation in Non-Small Cell Lung Cancer Using Deep Neural Networks

The paper develops a framework to decode TLS maturation in NSCLC using spatial omics data and deep learning, identifying two distinct spatial ecosystems linked to patient outcomes.

Dictionary of human intestinal organoid responses to secreted niche factors at single cell resolution

The paper builds a dictionary of human intestinal organoid responses to 81 secreted niche factors using scRNA-seq, mapping perturbations and identifying cell type-specific pathways in an IBD context.

Fibroblastic FLT3L supports lymph node dendritic cells in the interfollicular niche

The paper identifies Grem1-expressing fibroblastic reticular cells as a source of FLT3L that supports dendritic cell homeostasis and function in lymph nodes.

SpatialAgent: An Autonomous AI Agent for Spatial Biology

SpatialAgent integrates large language models with dynamic tool retrieval, multimodal interpretation, and claim verification to automate end-to-end spatial biology workflows from gene-panel design to tissue annotation and hypothesis generation.

SPEX: A modular end-to-end platform for high-plex tissue spatial omics analysis

SPEX provides a web-based platform for spatial omics analysis, enabling modular and user-friendly processing of spatial transcriptomics and proteomics data.

Highly multiplexed, image-based pooled screens in primary cells and tissues with PerturbView

PerturbView enables highly multiplexed optical pooled screens in primary cells and tissues by improving barcode amplification, revealing regulators of NFκB signaling and enabling spatial transcriptomics integration.

A single cell framework for multi-omic analysis of disease identifies malignant regulatory signatures in mixed phenotype acute leukemia

This paper develops a single-cell multi-omic framework to identify malignant regulatory signatures in mixed phenotype acute leukemia by analyzing transcriptomic and epigenetic data.