BionoiNet: ligand-binding site classification with off-the-shelf deep neural network. - Wentao Shi; Jeffrey Mitchell Lemoine; Abd-El-Monsif A. Shawky; Manali Singha; Limeng Pu; Shuangyan Yang; J. Ramanujam; Michal Brylinski (Bioinform., 2020)

GraphDTI: A robust deep learning predictor of drug-target interactions from multiple heterogeneous data. - Guannan Liu; Manali Singha; Limeng Pu; Prasanga Neupane; Joseph Feinstein; Hsiao-Chun Wu; J. Ramanujam; Michal Brylinski (J. Cheminformatics, 2021)

Fine-Tuning Optimization of Small Language Models: A Novel Graph-Theoretical Approach for Efficient Prompt Engineering. - Venkata Gadiraju; Hao-Yu Tsai; Hsiao-Chun Wu; Manali Singha; Scott Chih-Hao Huang; Guannan Liu; Shih Yu Chang; Yiyan Wu 001 (BMSB, 2024)