The paper uses spatial multi-omics and single-cell transcriptomics to identify senescence-associated programs in colon adenoma to cancer progression, finding GDF15 mediates senescence-stemness coupling and immune exclusion.

bioRxiv · Sep 4, 2026 · PreprintCancer Biology

Prototype-based AI triage for 3D pathology

Renao Yan, Gan Gao, Andrew H. Song, Huai-Ching Hsieh, Yujie Zhao, Cristina Almagro-Pérez, David Brenes, Sarah S. L. Chow, Jeanne Shen, Deepti Reddi, Lawrence D. True, Priti Lal, Anant Madabhushi, Faisal Mahmood, Jonathan T.C. Liu

SCOPE improves AI triage in 3D pathology by using morphology-aware prototypes to identify high-risk 2D slices for pathologist review.

bioRxiv · Jul 15, 2026 · PreprintPathology

3D pathology-guided microdissection

Huai-Ching Hsieh, Gan Gao, Qinghua Han, David Brenes, Elena Baraznenok, Renao Yan, Robert Serafin, Kevin W. Bishop, Rui Wang, Eric Quentin Konnick, Colin C. Pritchard, Sandy Figiel, Freddie Charles Hamdy, Ian Geoffrey Mills, Nicholas P. Reder, , Jonathan T.C. Liu

This paper introduces a 3D microdissection method combining CNC milling and light-sheet microscopy to study tumor evolution in complex 3D structures.

Nature Methods · Jun 22, 2026Peer-reviewedBioengineering

Deep-learning triage of 3D pathology datasets for comprehensive and efficient pathologist assessments

Gan Gao, Renao Yan, Andrew H. Song, Huai-Ching Hsieh, Lindsey A. Erion Barner, Fiona Wang, David Brenes, Sarah S. L. Chow, Rui Wang, Kevin W. Bishop, Yongjun Liu, Xavier Farré, Mukul K. Divatia, Michelle R. Downes, Funda Vakar‐Lopez, , Jonathan T.C. Liu

CARP3D uses deep learning to prioritize high-risk 2D sections in 3D pathology data, improving disease detection while reducing pathologist workload.

bioRxiv · Jul 20, 2025 · PreprintPathology