Tools for comparative protein structure modeling and analysis. - Narayanan Eswar; Bino John; Nebojsa Mirkovic; András Fiser; Valentin A. Ilyin; Ursula Pieper 001; Ashley C. Stuart; Marc A. Martí-Renom; Mallur S. Madhusudhan; Bozidar Yerkovich; Andrej Sali (Nucleic Acids Res., 2003)

Regulatory Circuit of Human MicroRNA Biogenesis. - Ji Lee; Zhihua Li; Rachel A. Brower-Sinning; Bino John (PLoS Comput. Biol., 2007)

Automated family-based naming of small RNAs for next generation sequencing data using a modified MD5-digest algorithm - Guodong Liu; Zhihua Li; Yuefeng Lin; Bino John (CoRR, 2012)

Hierarchical Clustering Split for Low-Bias Evaluation of Drug-Target Interaction Prediction. - Peizhen Bai; Filip Miljkovic; Yan Ge; Nigel Greene; Bino John; Haiping Lu (BIBM, 2021)

PHEE: A Dataset for Pharmacovigilance Event Extraction from Text. - Zhaoyue Sun; Jiazheng Li 002; Gabriele Pergola; Byron C. Wallace; Bino John; Nigel Greene; Joseph Kim; Yulan He 001 (EMNLP, 2022)

Interpretable bilinear attention network with domain adaptation improves drug-target prediction. - Peizhen Bai; Filip Miljkovic; Bino John; Haiping Lu (Nat. Mac. Intell., 2023)

Multimodal AI predicts clinical outcomes of drug combinations from preclinical data. - Yepeng Huang; Xiao-Rui Su 001; Varun Ullanat; Ivy Liang; Lindsay Clegg; Damilola Olabode; Nicholas Ho; Bino John; Megan Gibbs; Marinka Zitnik (CoRR, 2025)