The paper generates a molecular neuroanatomical map of the human prefrontal cortex using spatial transcriptomics and single nucleus RNA-sequencing, revealing novel spatial domains and cell-cell interactions linked to psychiatric disorders.

Science · May 23, 2024Peer-reviewedNeuroscience

The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics

Lukas M. Weber, Heena R. Divecha, Matthew Nguyen Tran, Sang‐Ho Kwon, Abby Spangler, Kelsey D. Montgomery, Madhavi Tippani, Rahul A. Bharadwaj, Joel E. Kleinman, Stephanie C. Page, Thomas M. Hyde, Leonardo Collado‐Torres, Kristen R. Maynard, Keri Martinowich, Stephanie C. Hicks

The paper characterizes the molecular landscape of the human locus coeruleus using spatially-resolved transcriptomics and single-nucleus RNA-sequencing, providing a publicly accessible resource.

eLife · Feb 3, 2023Peer-reviewedNeuroscience

VistoSeg: processing utilities for high-resolution Visium/Visium-IF images for spatial transcriptomics data

Madhavi Tippani, Heena R. Divecha, Joseph L Catallini II, Sang H. Kwon, Lukas M. Weber, Abby Spangler, Andrew E. Jaffe, Thomas M. Hyde, Joel E. Kleinman, Stephanie C. Hicks, Keri Martinowich, Leonardo Collado‐Torres, Stephanie C. Page, Kristen R. Maynard

VistoSeg processes high-resolution Visium/Visium-IF images to integrate image-derived metrics with spatial gene expression data for spatial transcriptomics analysis.

Biological Imaging · Jan 1, 2023Peer-reviewedBioinformatics

spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

Brenda Pardo, Abby Spangler, Lukas M. Weber, Stephanie C. Page, Stephanie C. Hicks, Andrew E. Jaffe, Keri Martinowich, Kristen R. Maynard, Leonardo Collado‐Torres

spatialLIBD provides an R/Bioconductor package for interactive visualization of spatially-resolved transcriptomics data from the 10x Genomics Visium platform.

BMC Genomics · Jun 10, 2022Peer-reviewedBioinformatics

Reconstruction of dynamic regulatory networks reveals signaling-induced topology changes associated with germ layer specification

Emily Y. Su, Abby Spangler, Qin Bian, Jessica Y. Kasamoto, Patrick Cahan

The paper introduces Epoch, a tool for dynamic GRN reconstruction, and shows it identifies topology changes in mouse ESC differentiation networks driven by signaling pathways.

Stem Cell Reports · Jan 27, 2022Peer-reviewedSystems Biology

Single-nucleus transcriptome analysis reveals cell type-specific molecular signatures across reward circuitry in the human brain

Matthew Nguyen Tran, Kristen R. Maynard, Abby Spangler, Louise A. Huuki-Myers, Kelsey D. Montgomery, Vijay Sadashivaiah, Madhavi Tippani, Brianna K. Barry, Dana B. Hancock, Stephanie C. Hicks, Joel E. Kleinman, Thomas M. Hyde, Leonardo Collado‐Torres, Andrew E. Jaffe, Keri Martinowich

The paper uses snRNA-seq to analyze five human brain regions, identifies novel neuronal subpopulations, and links them to psychiatric and substance use risks.

Neuron · Sep 27, 2021Peer-reviewedNeuroscience

Quantitative comparison of in vitro and in vivo embryogenesis at a single cell resolution

Yuqi Tan, Abby Spangler, Michael Farid, Da Peng, Patrick Cahan

The paper compares in vitro and in vivo embryogenesis using scRNA-seq data and computational tools to evaluate stem cell differentiation protocols.

bioRxiv · May 7, 2021 · PreprintDevelopmental Biology