DiffCircaPipeline: a framework for multifaceted characterization of differential rhythmicity. - Xiangning Xue; Wei Zong; Zhiguang Huo; Kyle D. Ketchesin; Madeline R. Scott; Kaitlyn A Petersen; Ryan W. Logan; Marianne L. Seney; Colleen A. Mcclung; George C. Tseng (Bioinform., 2023)

Comprehensive evaluation and practical guideline of gating methods for high-dimensional cytometry data: manual gating, unsupervised clustering, and auto-gating. - Peng Liu; Yuchen Pan; Hung-Ching Chang; Wenjia Wang; Yusi Fang; Xiangning Xue; Jian Zou; Jessica M. Toothaker; Oluwabunmi Olaloye; Eduardo Gonzalez Santiago; Black McCourt; Vanessa Mitsialis; et al. (Briefings Bioinform., 2024)

Beyond Retrieval: Ensembling Cross-Encoders and GPT Rerankers with LLMs for Biomedical QA. - Shashank Verma; Fengyi Jiang; Xiangning Xue (CoRR, 2025)