The paper uses cryo-electron tomography to directly visualize paracellular claudin-15 pores in tight junctions, confirming their structure and spacing.

Biophysical Journal · Jun 24, 2026Peer-reviewedPhysiology

Histopathologic Evaluation and Single-Cell Spatial Transcriptomics of the Colon Reveal Cellular and Molecular Abnormalities Linked to J-Pouch Failure in Patients with Inflammatory Bowel Disease.

Andrea D. Olivas, Patricia Ngai, Emily Schahrer, Junjie Xing, Mobarakeh Ghadiri, Kinga S. Olortegui, John Cursio, Shintaro Akiyama, Eugene B. Chang, Le Shen, Konstantin Umanskiy, David T. Rubin, David Zemmour, Christopher R. Weber

This study identifies histopathological and molecular features linked to J-pouch failure in IBD patients using single-cell spatial transcriptomics.

Cellular and Molecular Gastroenterology and Hepatology · Jan 1, 2025Peer-reviewedPathology

ATAT: Automated Tissue Alignment and Traversal in Spatial Transcriptomics with Self-Supervised Learning

Steven Song, Emaan Mohsin, Renyu Zhang, Andrey Kuznetsov, Le Shen, Robert L. Grossman, Christopher R. Weber, Aly Azeem Khan

ATAT automates spatial transcriptomics analysis by aligning and traversing tissue samples using self-supervised learning, improving gene expression modeling without manual annotation.

bioRxiv · Dec 8, 2023 · PreprintBioinformatics

Novel hemorrhage models of cerebral cavernous malformations

Matthew R. Detter, Robert Shenkar, Christian R. Benavides, Catherine A. Neilson, Thomas Moore, Rhonda Lightle, Nicholas Hobson, Le Shen, Ying Jun Cao, Romuald Girard, Dongdong Zhang, Erin Griffin, Carol J. Gallione, Issam A. Awad, Douglas A. Marchuk

This paper develops new mouse models of cerebral cavernous malformations (CCMs) to better study drug therapies for CCM formation and hemorrhage.

bioRxiv · Feb 12, 2020 · PreprintGenetics