TIVAN: tissue-specific cis-eQTL single nucleotide variant annotation and prediction. - Li Chen 029; Ye Wang 024; Bing Yao; Amit Mitra; Xu Wang 026; Xiao Qin 001 (Bioinform., 2019)

A novel deep learning method for predictive modeling of microbiome data. - Ye Wang 024; Tathagata Bhattacharya; Yuchao Jiang; Xiao Qin 001; Yue Wang; Yunlong Liu; Andrew J. Saykin; Li Chen 029 (Briefings Bioinform., 2021)

WEVar: a novel statistical learning framework for predicting noncoding regulatory variants. - Ye Wang 024; Yuchao Jiang; Bing Yao; Kun Huang; Yunlong Liu; Yue Wang; Xiao Qin 001; Andrew J. Saykin; Li Chen 029 (Briefings Bioinform., 2021)

Exploiting deep transfer learning for the prediction of functional non-coding variants using genomic sequence. - Li Chen 029; Ye Wang 024; Fengdi Zhao (Bioinform., 2022)

Performance modeling for I/O-intensive applications on virtual machines. - Tathagata Bhattacharya; Xiaopu Peng; Jianzhou Mao; Chaowei Zhang 001; Taha Takreeti; Ye Wang 024; Ting Cao; Xiao Qin 001 (Concurr. Comput. Pract. Exp., 2022)

A Transformer-based Generative Model for De Novo Molecular Design. - Wenlu Wang; Ye Wang 024; Honggang Zhao; Simone Sciabola (CoRR, 2022)

DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome. - Ye Wang 024; Li Chen 029 (Bioinform., 2022)

Large-scale Pretraining Improves Sample Efficiency of Active Learning based Molecule Virtual Screening. - Zhonglin Cao; Simone Sciabola; Ye Wang 024 (CoRR, 2023)

Prospective Validation of Machine Learning Algorithms for Absorption, Distribution, Metabolism, and Excretion Prediction: An Industrial Perspective. - Cheng Fang; Ye Wang 024; Richard Grater; Sudarshan Kapadnis; Cheryl Black; Patrick E. Trapa; Simone Sciabola (J. Chem. Inf. Model., 2023)

ROSHAMBO: Open-Source Molecular Alignment and 3D Similarity Scoring. - Rasha Atwi; Ye Wang 024; Simone Sciabola; Adam Antoszewski (J. Chem. Inf. Model., 2024)

ACEGEN: Reinforcement Learning of Generative Chemical Agents for Drug Discovery. - Albert Bou; Morgan Thomas; Sebastian Dittert; Carles Navarro; Maciej Majewski; Ye Wang 024; Shivam Patel; Gary Tresadern; Mazen Ahmad; Vincent Moens; Woody Sherman; Simone Sciabola; et al. (J. Chem. Inf. Model., 2024)

Large-Scale Pretraining Improves Sample Efficiency of Active Learning-Based Virtual Screening. - Zhonglin Cao; Simone Sciabola; Ye Wang 024 (J. Chem. Inf. Model., 2024)