GESLM algorithm for detecting causal SNPs in GWAS with multiple phenotypes. - Ruiqi Lyu; Jianle Sun; Dong Xu; Qianxue Jiang; Chaochun Wei; Yue Zhang (Briefings Bioinform., 2021)

SMetABF: A rapid algorithm for Bayesian GWAS meta-analysis with a large number of studies included. - Jianle Sun; Ruiqi Lyu; Luojia Deng; Qianwen Li; Yang Zhao; Yue Zhang (PLoS Comput. Biol., 2022)

Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data. - Hunyong Cho; Yixiang Qu; Chuwen Liu; Boyang Tang; Ruiqi Lyu; Bridget M. Lin; Jeffrey Roach; M. Andrea Azcarate-Peril; Apoena Aguiar Ribeiro; Michael I. Love; Kimon Divaris; Di Wu 073 (Briefings Bioinform., 2023)

Federated epidemic surveillance. - Ruiqi Lyu; Roni Rosenfeld; Bryan Wilder (PLoS Comput. Biol., 2025)

Explaining Concept Shift with Interpretable Feature Attribution. - Ruiqi Lyu; Alistair Turcan; Bryan Wilder (CoRR, 2025)