Shannon Coy

The paper investigates somatic copy number variants (CNVs) in human neurons across development, finding that perinatal elimination of neurons with aberrant genomes reduces CNV prevalence and targets dosage-sensitive genes.

The paper introduces v-CyCIF, a method for 3D spatial profiling of human FFPE tissue, enabling detailed analysis of tumor, stroma, and immune structures.

This study uses 3D reconstruction and optimal transport modeling to analyze TLS development in TB-infected lungs, revealing distinct maturation trajectories and spatial dynamics.

This paper introduces a human-in-the-loop framework using AI foundation models and sparse autoencoders to interpret H&E histology images and integrate them with molecular spatial profiling.

This study identifies epigenetic dysregulation of metabolic programs in liposarcoma, linking IGF1 loss and PPARG2 deficiency to dedifferentiation and proposing IGF1R-targeted therapy.

The paper introduces statistical tools to analyze immune cluster patterns in prostate cancer and finds high-grade tumors show more immune infiltration and active immune features.

This paper introduces a method that combines autoencoders with segmentation to improve single-cell analysis of multiplexed tissue images by capturing morphology and reducing signal spillover.

This study uses spatial profiling to show immune suppression and microenvironment changes in fallopian tube precursors of high-grade serous ovarian cancer.

The paper identifies a subset of mismatch repair proficient colorectal cancers with high immune infiltration that may benefit from immune checkpoint inhibitors, using spatial profiling and genomics.

The paper shows nuclear rupture is common in cancer, especially glioblastoma, and links it to lamin proteins and immune signaling.

This study quantifies cell proliferation in tumors using multiplexed imaging and identifies spatial and temporal patterns of cell cycle regulation.