The paper uses spatial transcriptomics to analyze molecular differences in mood disorders and biological sex in the human prefrontal cortex, identifying sex- and disorder-specific gene expression patterns.

bioRxiv · Oct 24, 2026 · PreprintNeuroscience

BatchSVG: identifying batch-biased genes in the application of spatially variable gene detection

Kinnary Shah, Christine Hou, Jacqueline R. Thompson, Stephanie C. Hicks

BatchSVG identifies batch-biased genes in spatially variable gene detection to improve downstream analyses by removing technical artifacts.

Bioinformatics · Jul 1, 2026Peer-reviewedGenomics

SpatialArtifacts: a computational framework for tissue artifact detection in spatial transcriptomics data

Jiali Harriet He, Jacqueline R. Thompson, Michael S. Totty, Stephanie C. Hicks

SpatialArtifacts identifies and classifies tissue artifacts in spatial transcriptomics data using MAD-based outlier detection and mathematical morphology operations.

bioRxiv · May 18, 2026 · PreprintBioinformatics

An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus

Jacqueline R. Thompson, Erik D. Nelson, Madhavi Tippani, Anthony D. Ramnauth, Heena R. Divecha, Ryan A. Miller, Nicholas J. Eagles, Elizabeth A. Pattie, Sang‐Ho Kwon, Svitlana V. Bach, Uma M. Kaipa, Jianing Yao, Christine Hou, Joel E. Kleinman, Leonardo Collado‐Torres, , Stephanie C. Hicks

The paper integrates single-nucleus and spatial transcriptomics data to map the molecular landscape of the human hippocampus, identifying cell types and spatial domains.

Nature Neuroscience · Jul 30, 2025Peer-reviewedNeuroscience

Spatiotemporal analysis of gene expression in the human dentate gyrus reveals age-associated changes in cellular maturation and neuroinflammation

Anthony D. Ramnauth, Madhavi Tippani, Heena R. Divecha, Alexis R. Papariello, Ryan A. Miller, Erik D. Nelson, Jacqueline R. Thompson, Elizabeth A. Pattie, Joel E. Kleinman, Kristen R. Maynard, Leonardo Collado‐Torres, Thomas M. Hyde, Keri Martinowich, Stephanie C. Hicks, Stephanie C. Page

This study analyzes age-related changes in gene expression in the human dentate gyrus, identifying shifts in neurogenesis, maturation, and neuroinflammation across the lifespan.

Cell Reports · Feb 1, 2025Peer-reviewedNeuroscience

Spatiotemporal Mapping and Molecular Basis of Whole-brain Circuit Maturation

Jian Xue, Andrew T. Brawner, Jacqueline R. Thompson, Tushar Devanand Yelhekar, Kyra T. Newmaster, Qiang Qiu, Yonatan A. Cooper, C. Ron Yu, Yasir H. Ahmed-Braima, Yongsoo Kim, Yingxi Lin

This study creates DevATLAS to map spatiotemporal circuit maturation in postnatal mouse brains and identifies molecular mechanisms and impairments in neurodevelopmental disorders.

bioRxiv · Jan 3, 2024 · PreprintNeuroscience

Vertex-wise characterization of Non-Human Primate cortical development with prenatal insights.

Julian S.B. Ramirez, Robert J. M. Hermosillo, Elina Thomas, Jennifer Y. Zhu, Darrick Sturgeon, Emma Schifsky, Anthony Galassi, Jacqueline R. Thompson, Jennifer L. Bagley, Michael Peter Milham, Óscar Miranda-Domínguez, Samantha Papadakis, Muhammed Bah, A. J. Mitchell, Ting Xu, , Damien A. Fair

This study characterizes cortical thickness development in Japanese macaques using latent growth models and identifies how maternal diet and inflammation influence regional cortical maturation patterns.

bioRxiv · Sep 23, 2021 · PreprintNeuroscience