Donuts, scratches and blanks: robust model-based segmentation of microarray images. - Qunhua Li; Chris Fraley; Roger Eugene Bumgarner; Ka Yee Yeung; Adrian E. Raftery (Bioinform., 2005)

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. - Timothy Bailey; Pawel Krajewski; Istvan Ladunga; Céline Lefebvre; Qunhua Li; Tao Liu 022; Pedro Madrigal; Cenny Taslim; Jie Zhang (PLoS Comput. Biol., 2013)

A semi-parametric statistical model for integrating gene expression profiles across different platforms. - Yafei Lyu; Qunhua Li (BMC Bioinform., 2016)

A continuous threshold expectile model. - Feipeng Zhang; Qunhua Li (Comput. Stat. Data Anal., 2017)

powerTCR: A model-based approach to comparative analysis of the clone size distribution of the T cell receptor repertoire. - Hillary Koch; Dmytro Starenki; Sara J. Cooper; Richard M. Myers; Qunhua Li (PLoS Comput. Biol., 2018)

Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network. - Yafei Lyu; Lingzhou Xue; Feipeng Zhang; Hillary Koch; Laura M. Saba; Katerina J. Kechris; Qunhua Li (PLoS Comput. Biol., 2018)

Individualized Modeling to Distinguish Between High and Low Arousal States Using Physiological Data. - Ame Osotsi; Zita Oravecz; Qunhua Li; Joshua M. Smyth; Timothy R. Brick (J. Heal. Informatics Res., 2020)

RCFGL: Rapid Condition adaptive Fused Graphical Lasso and application to modeling brain region co-expression networks. - Souvik Seal; Qunhua Li; Elle Butler Basner; Laura M. Saba; Katerina J. Kechris (PLoS Comput. Biol., 2023)

An Analyst-Inspector Framework for Evaluating Reproducibility of LLMs in Data Science. - Qiuhai Zeng; Claire Jin; Xinyue Wang; Yuhan Zheng; Qunhua Li (CoRR, 2025)