CERENKOV: Computational Elucidation of the Regulatory Noncoding Variome. - Yao Yao 007; Zheng Liu; Satpreet Singh; Qi Wei 006; Stephen A. Ramsey (BCB, 2017)

Res2s2aM: Deep residual network-based model for identifying functional noncoding SNPs in trait-associated regions. - Zheng Liu; Yao Yao 007; Qi Wei 006; Benjamin Weeder; Stephen A. Ramsey (PSB, 2019)

CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features. - Yao Yao 007; Zheng Liu; Qi Wei 006; Stephen A. Ramsey (BMC Bioinform., 2019)

CERENKOV3: Clustering and Molecular Network-Derived Features Improve Computational Predictionof Functional Noncoding SNPs. - Yao Yao 007; Stephen A. Ramsey (PSB, 2020)

BioThings SDK: a toolkit for building high-performance data APIs in biomedical research. - Sebastien Lelong; Xinghua Zhou; Cyrus Afrasiabi; Zhongchao Qian; Marco Alvarado Cano; Ginger Tsueng; Jiwen Xin; Julia Mullen; Yao Yao 007; Ricardo Avila; Greg Taylor; Andrew I. Su; et al. (Bioinform., 2022)

BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs. - Jackson Callaghan; Colleen H. Xu; Jiwen Xin; Marco Alvarado Cano; Anders Riutta; Eric Zhou; Rohan Juneja; Yao Yao 007; Madhumita Narayan; Kristina Hanspers; Ayushi Agrawal; Alexander R. Pico; et al. (Bioinform., 2023)