Selected Publications

Modeling patient tissues at molecular resolution with Eva

Yufan Liu, Rishabh Sharma, Matthew Bieniosek, Amy Kang, Eric Wu, Peter Chou, Irene Li, Maha Rahim, Erica Bauer, Ran Ji, Wei Duan, Li Qian, Ruibang Luo, Padmanee Sharma, Renu Dhanasekaran, Christian M. Schürch, Gregory Charville, Aaron T. Mayer, James Zou, Alexandro E. Trevino*, Zhenqin Wu*

preprint: 10.64898/2025.12.10.693553, code available at: https://github.com/YAndrewL/Eva

HOPE: Interpretable Histology Analysis with Spatial Omics-Derived Signatures for Precision Oncology

Tianyi Wang, Matthew Bieniosek, Tamara J. Krpicak, Mingyuan Luan, Benjamin Ruf, Christian M. Schürch, Aaron T. Mayer, Ruibang Luo, Alexandro E. Trevino, Zhenqin Wu

preprint in preparation, code available at: https://github.com/wangtyi/HOPE

Best student paper (extended abstract) at CVAMD@ICCV2025

OmicsNavigator: an auditable scientific partner for scalable hypothesis validation in spatial omics

Li Yiyao, Nirvi Vakharia, Weixin Liang, Aaron T. Mayer, Ruibang Luo, Alexandro E. Trevino, Zhenqin Wu.

preprint (v1): 10.1101/2025.07.21.665821, code and data available at: https://github.com/yyli-leo/OmicsAnnotator

Spatial multi-omics and deep learning reveal fingerprints of immunotherapy response and resistance in hepatocellular carcinoma

Zhenqin Wu, Joseph Boen, Sonali Jindal, Sreyashi Basu, Matthew Bieniosek, Siyu He, Michael LaPelusa, Aaron T Mayer, Ahmed O Kaseb, James Zou, Padmanee Sharma, Alexandro E Trevino

preprint: 10.1101/2025.06.11.656869, data available at: https://zenodo.org/records/15392699

ROSIE: AI generation of multiplex immunofluorescence staining from histopathology images

Eric Wu, Matthew Bieniosek, Zhenqin Wu, Nitya Thakkar, Gregory W. Charville, Ahmad Makky, Christian M. Schürch, Jeroen R. Huyghe, Ulrike Peters, Christopher I. Li, Li Li, Hannah Giba, Vivek Behera, Arjun Raman, Alexandro E. Trevino, Aaron T. Mayer and James Zou.

Nature Communications, 2025.

DOI: 10.1038/s41467-025-62346-0, preprint: 10.1101/2024.11.10.622859

Code available at: https://gitlab.com/enable-medicine-public/rosie

Characterizing tissue structures from spatial omics with spatial cellular graph partition

Zhenqin Wu, Ayano Kondo, Monee McGrady, Ethan A. G. Baker, Benjamin Chidester, Eric Wu, Maha K. Rahim, Nathan A. Bracey, Vivek Charu, Raymond J. Cho, Jeffrey B. Cheng, Maryam Afkarian, James Zou, Aaron T. Mayer, and Alexandro E. Trevino.

Cell Reports Methods, 2024.

DOI: 10.1016/j.crmeth.2024.100838, preprint:10.1101/2023.09.05.556133

Code available at: https://gitlab.com/enable-medicine-public/scgp, datasets available at: https://doi.org/10.5281/zenodo.12682727

Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens

Zhenqin Wu*, Alexandro E Trevino*, Eric Wu, Kyle Swanson, Honesty J Kim, H Blaize D’Angio, Ryan Preska, Gregory W Charville, Piero D Dalerba, Ann Marie Egloff, Ravindra Uppaluri, Umamaheswar Duvvuri, Aaron T Mayer, and James Zou.

Nature Biomedical Engineering, 2022

DOI: 10.1038/s41551-022-00951-w, preprint: 10.1101/2022.05.12.491707

Code available at: https://gitlab.com/enable-medicine-public/space-gm, datasets available at: https://doi.org/10.5281/zenodo.13179600