Andréanne Gagné

Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis

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

Compositional and interpretable representation of histology using AI foundation models and sparse autoencoders

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.

Spatial statistics for identifying and scoring immune clusters in high-plex profiles of primary prostate cancer

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.

Multiomic analysis identifies suppressive myeloid cell populations in human TB granulomas.

This study identifies suppressive myeloid cell populations in human TB granulomas using spatial transcriptomics and single-cell immunophenotyping, revealing IDO1+ dendritic cells as key regulators of immune suppression.

Integrating spatial profiles and cancer genomics to identify immune-infiltrated mismatch repair proficient colorectal cancers

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.