Zhi Huang

Brain Proteomic Analysis Implicates Actin Filament Processes and Injury Response in Resilience to Alzheimer’s Disease [paper]
Zhi Huang, Gennifer E. Merrihew, Eric B. Larson, Jea Park, Deanna Plubell, Edward J. Fox, Kathleen S. Montine, C Dirk Keene, James Zou, Michael J. MacCoss, Thomas J. Montine
Nature Communications, 14 (1), 2747 (2023).

This work was selected as one of the only 9 projects in Stanford Catalyst 2023 cohort.
A human–AI collaboration framework enhances digital pathology [research website]
Zhi Huang, Eric Yang, Jeanne Shen, Dita Gratzinger, Frederick Eyerer, Brooke Liang, Jeffrey Nirschl, David Bingham, Alex M. Dussaq, Christian Kunder, Rebecca Rojansky, Aubre Gilbert, Alexandra L. Chang-Graham, Brooke Howitt, Ying Liu, Emily E. Ryan, Troy B. Tenney, Xiaoming Zhang, Ann Folkins, Edward J. Fox, Kathleen S. Montine, Thomas J. Montine, James Zou
In revision at Nature Biomedical Engineering (2023).
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Artificial Intelligence Reveals Features Associated with Breast Cancer Neoadjuvant Chemotherapy Responses from Multi-stain Histopathologic Images [paper] [news]
Zhi Huang, Wei Shao, Zhi Han, Ahmad Mahmoud Alkashash, Carlo De la Sancha, Anil V. Parwani, Hiroaki Nitta, Yanjun Hou, Tongxin Wang, Paul Salama, Maher Rizkalla, Jie Zhang, Kun Huang, and Zaibo Li
NPJ Precision Oncology, 7, no. 14 (2023)

TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining [paper] [github] [software]
Zhi Huang, Zhi Han, Tongxin Wang, Wei Shao, Shunian Xiang, Paul Salama, Maher Rizkalla, Kun Huang, and Jie Zhang
Genomics, Proteomics and Bioinformatics, 19, no. 6, (2021).

SALMON: Survival Analysis Learning with Multi-Omics Neural Networks on Breast Cancer [paper] [github]
Zhi Huang, Xiaohui Zhan, Shunian Xiang, Travis Johnson, Bryan Helm, Christina Yu, Jie Zhang, Paul Salama, Maher Rizkalla, Zhi Han, and Kun Huang
Frontiers in genetics 10 (2019): 166.

Deep Learning-based Cancer Survival Prognosis from RNA-seq Data: Approaches and Evaluations [paper]
Zhi Huang, Travis S. Johnson, Zhi Han, Bryan Helm, Sha Cao, Chi Zhang, Paul Salama, Maher Rizkalla, Christina Y. Yu, Jun Cheng, Shunian Xiang, Xiaohui Zhan, Jie Zhang, and Kun Huang
BMC medical genomics 13, no. 5 (2020): 1-12.

Systematic Pan-cancer Analysis of Mutation-Treatment Interactions using Large Real-world Clinicogenomics Data [paper] [precision-cancer]
Ruishan Liu, Shemra Rizzo, Sarah Waliany, Marius Rene Garmhausen, Navdeep Pal, Zhi Huang, Nayan Chaudhary, Lisa Wang, Chris Harbron, Joel Neal, Ryan Copping, and James Zou
Nature Medicine volume 28 (2022): 1656-1661.