publications

2026

1. Agents’ Last Exam

   Yiyou Sun, Xinyang Han, Weichen Zhang, and 8 more authors

   arXiv preprint arXiv:2606.05405, 2026
2. Under Review

   SCOPE: Localizing fate-decision states and their regulatory drivers in single-cell differentiation

   Yimin Zhao, Connor Finkbeiner, Manu Setty, and 1 more author

   2026

   Under review at Nature Communications

   Abs Bib Code

   Computational method to localize branch point in cell development based on conformal inference, semi-supervised learning and density clustering.

   @article{zhao2026scope,
     title = {SCOPE: Localizing fate-decision states and their regulatory drivers in single-cell differentiation},
     author = {Zhao, Yimin and Finkbeiner, Connor and Setty, Manu and Lin, Kevin Z.},
     year = {2026},
     note = {Under review at Nature Communications},
   }

3. Under Review

   PanCanBench: A Comprehensive Benchmark for Evaluating Large Language Models in Pancreatic Oncology

   Yimin Zhao, Sheela R Damle, Simone E Dekker, and 13 more authors

   2026

   Under review at NEJM AI

   Abs arXiv Bib Website

   End-to-end pipeline to collect, standardize, and polish expert-rubric annotations for evaluating LLM responses to patient-focused pancreatic cancer questions.

   @article{zhao2026pancan,
     title = {PanCanBench: A Comprehensive Benchmark for Evaluating Large Language Models in Pancreatic Oncology},
     author = {Zhao, Yimin and Damle, Sheela R and Dekker, Simone E and Geng, Scott and Silva, Karly Williams and Hubbard, Jesse J and Fernandez, Manuel F and Zelada-Arenas, Fatima and Alvarez, Alejandra and Flores, Brianne and Rodriguez, Alexis and Salerno, Stephen and Wright, Carrie and Wang, Zihao and Koh, Pang Wei and Leek, Jeffrey T},
     year = {2026},
     note = {Under review at NEJM AI},
   }

2025

1. Nat Commun

   A minimal gene set characterizes multiple classes of tumor-specific TIL among different cancer types

   Zhen Zeng, Tianbei Zhang, Jiajia Zhang, and 16 more authors

   Nature Communications, 2025

   DOI Bib HTML

   @article{zeng2025minimal,
     title = {A minimal gene set characterizes multiple classes of tumor-specific TIL among different cancer types},
     author = {Zeng, Zhen and Zhang, Tianbei and Zhang, Jiajia and Li, Shuai and Connor, Sydney and Zhang, Boyang and Zhao, Yimin and Wilson, Jordan and Singh, Dipika and Kulikauskas, Rima and Church, Candice D. and Pulliam, Thomas H. and Jani, Saumya and Nghiem, Paul and Topalian, Suzanne L. and Forde, Patrick M. and Pardoll, Drew M. and Ji, Hongkai and Smith, Kellie N.},
     journal = {Nature Communications},
     volume = {16},
     number = {1},
     pages = {1070},
     year = {2025},
     publisher = {Nature Publishing Group UK London},
     doi = {10.1038/s41467-025-55956-3},
   }

2020

1. Bioinformatics

   scTIM: seeking cell-type-indicative marker from single cell RNA-seq data by consensus optimization

   Zhanying Feng, Xianwen Ren, Yuan Fang, and 4 more authors

   Bioinformatics, 2020

   DOI Bib HTML

   @article{feng2020sctim,
     title = {scTIM: seeking cell-type-indicative marker from single cell RNA-seq data by consensus optimization},
     author = {Feng, Zhanying and Ren, Xianwen and Fang, Yuan and Yin, Yining and Huang, Chutian and Zhao, Yimin and Wang, Yong},
     journal = {Bioinformatics},
     volume = {36},
     number = {8},
     pages = {2474--2485},
     year = {2020},
     publisher = {Oxford University Press},
     doi = {10.1093/bioinformatics/btz896},
   }