Eric Lubeck

SCALLOPS improves processing of optical pooled screens by enabling efficient alignment and analysis of large-scale image data, demonstrating superior performance over existing methods.

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.

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.

This paper introduces a pooled CRISPR screening platform combined with self-supervised deep learning to infer gene function from morphological phenotypes without target-specific biomarkers.

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.

This study uses seqFISH to image nascent transcription active sites in single mouse embryonic stem cells, revealing dynamic spatial distribution and variability in transcription activity.