Estimation of ADME Properties with Substructure Pattern Recognition. - Jie Shen 006; Feixiong Cheng; You Xu; Weihua Li 005; Yun Tang 001 (J. Chem. Inf. Model., 2010)

Classification of Cytochrome P450 Inhibitors and Noninhibitors Using Combined Classifiers. - Feixiong Cheng; Yue Yu; Jie Shen 006; Lei Yang; Weihua Li 005; Guixia Liu; Philip W. Lee; Yun Tang 001 (J. Chem. Inf. Model., 2011)

Insights into Molecular Basis of Cytochrome P450 Inhibitory Promiscuity of Compounds. - Feixiong Cheng; Yue Yu; Yadi Zhou; Zhonghua Shen; Wen Xiao; Guixia Liu; Weihua Li 005; Philip W. Lee; Yun Tang 001 (J. Chem. Inf. Model., 2011)

In Silico Assessment of Chemical Biodegradability. - Feixiong Cheng; Yutaka Ikenaga; Yadi Zhou; Yue Yu; Weihua Li 005; Jie Shen 006; Zheng Du; Lei Chen 019; Congying Xu; Guixia Liu; Philip W. Lee; Yun Tang 001 (J. Chem. Inf. Model., 2012)

admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties. - Feixiong Cheng; Weihua Li 005; Yadi Zhou; Jie Shen 006; Zengrui Wu; Guixia Liu; Philip W. Lee; Yun Tang 001 (J. Chem. Inf. Model., 2012)

Unbinding Pathways of GW4064 from Human Farnesoid X Receptor As Revealed by Molecular Dynamics Simulations. - Weihua Li 005; Jing Fu; Feixiong Cheng; Mingyue Zheng; Jian Zhang 037; Guixia Liu; Yun Tang 001 (J. Chem. Inf. Model., 2012)

In silico Prediction of Chemical Ames Mutagenicity. - Congying Xu; Feixiong Cheng; Lei Chen 019; Zheng Du; Weihua Li 005; Guixia Liu; Philip W. Lee; Yun Tang 001 (J. Chem. Inf. Model., 2012)

Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference. - Feixiong Cheng; Chuang Liu; Jing Jiang; Weiqiang Lu; Weihua Li 005; Guixia Liu; Wei-Xing Zhou; Jin Huang; Yun Tang 001 (PLoS Comput. Biol., 2012)

Prediction of Polypharmacological Profiles of Drugs by the Integration of Chemical, Side Effect, and Therapeutic Space. - Feixiong Cheng; Weihua Li 005; Zengrui Wu; Xichuan Wang; Chen Zhang; Jie Li; Guixia Liu; Yun Tang 001 (J. Chem. Inf. Model., 2013)

Adverse Drug Events: Database Construction and in Silico Prediction. - Feixiong Cheng; Weihua Li 005; Xichuan Wang; Yadi Zhou; Zengrui Wu; Jie Shen 006; Yun Tang 001 (J. Chem. Inf. Model., 2013)

In Silico Prediction of Chemical Acute Oral Toxicity Using Multi-Classification Methods. - Xiao Li 010; Lei Chen 019; Feixiong Cheng; Zengrui Wu; Hanping Bian; Congying Xu; Weihua Li 005; Guixia Liu; Xu Shen; Yun Tang 001 (J. Chem. Inf. Model., 2014)

A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3, 000 Cancer Genomes across 9 Cancer Types. - Feixiong Cheng; Chuang Liu; Chen-Ching Lin; Junfei Zhao; Peilin Jia; Wen-Hsiung Li; Zhongming Zhao (PLoS Comput. Biol., 2015)

SGDriver: a novel structural genomics-based approach to prioritize cancer related and potentially druggable somatic mutations. - Junfei Zhao; Feixiong Cheng; Zhongming Zhao (BMC Bioinform., 2015)

Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. - Feixiong Cheng; Junfei Zhao; Zhongming Zhao (Briefings Bioinform., 2016)

Systematic dissection of dysregulated transcription factor-miRNA feed-forward loops across tumor types. - Wei Jiang 023; Ramkrishna Mitra; Chen-Ching Lin; Quan Wang 004; Feixiong Cheng; Zhongming Zhao (Briefings Bioinform., 2016)

Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach. - Feixiong Cheng; Chuang Liu; Bairong Shen; Zhongming Zhao (BMC Syst. Biol., 2016)

A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes. - Feixiong Cheng; Junfei Zhao; Michaela Fooksa; Zhongming Zhao (J. Am. Medical Informatics Assoc., 2016)

ccmGDB: a database for cancer cell metabolism genes. - Pora Kim; Feixiong Cheng; Junfei Zhao; Zhongming Zhao (Nucleic Acids Res., 2016)

Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis. - Feixiong Cheng; James L. Murray; Junfei Zhao; Jinsong Sheng; Zhongming Zhao; Donald H. Rubin (PLoS Comput. Biol., 2016)

Individualized network-based drug repositioning infrastructure for precision oncology in the panomics era. - Feixiong Cheng; Huixiao Hong; Sheng-Yong Yang; Yuquan Wei (Briefings Bioinform., 2017)

SDTNBI: an integrated network and chemoinformatics tool for systematic prediction of drug-target interactions and drug repositioning. - Zengrui Wu; Feixiong Cheng; Jie Li; Weihua Li 005; Guixia Liu; Yun Tang 001 (Briefings Bioinform., 2017)

Entropy-based consensus clustering for patient stratification. - Hongfu Liu 001; Rui Zhao; Hongsheng Fang; Feixiong Cheng; Yun Fu 001; Yang-Yu Liu (Bioinform., 2017)

Quantitative and Systems Pharmacology. 1. In Silico Prediction of Drug-Target Interactions of Natural Products Enables New Targeted Cancer Therapy. - Jiansong Fang; Zengrui Wu; Chuipu Cai; Qi Wang; Yun Tang 001; Feixiong Cheng (J. Chem. Inf. Model., 2017)

In silico polypharmacology of natural products. - Jiansong Fang; Chuang Liu; Qi Wang; Ping Lin; Feixiong Cheng (Briefings Bioinform., 2018)

In Silico Pharmacoepidemiologic Evaluation of Drug-Induced Cardiovascular Complications Using Combined Classifiers. - Chuipu Cai; Jiansong Fang; Pengfei Guo; Qi Wang; Huixiao Hong; Javid Moslehi; Feixiong Cheng (J. Chem. Inf. Model., 2018)

deepDR: a network-based deep learning approach to in silico drug repositioning. - Xiangxiang Zeng; Siyi Zhu; Xiangrong Liu; Yadi Zhou; Ruth Nussinov; Feixiong Cheng (Bioinform., 2019)

Deep Learning-Based Prediction of Drug-Induced Cardiotoxicity. - Chuipu Cai; Pengfei Guo; Yadi Zhou; Jingwei Zhou; Qi Wang; Fengxue Zhang; Jiansong Fang; Feixiong Cheng (J. Chem. Inf. Model., 2019)

Correction to "admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties". - Feixiong Cheng; Weihua Li 005; Yadi Zhou; Jie Shen 006; Zengrui Wu; Guixia Liu; Philip W. Lee; Yun Tang 001 (J. Chem. Inf. Model., 2019)

Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers. - Ruth Nussinov; Hyunbum Jang; Chung-Jung Tsai; Feixiong Cheng (PLoS Comput. Biol., 2019)

Correction: Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers. - Ruth Nussinov; Hyunbum Jang; Chung-Jung Tsai; Feixiong Cheng (PLoS Comput. Biol., 2019)

A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications. - He Peng; Xiangxiang Zeng; Yadi Zhou; Defu Zhang; Ruth Nussinov; Feixiong Cheng (PLoS Comput. Biol., 2019)

Network-based prediction of drug-target interactions using an arbitrary-order proximity embedded deep forest. - Xiangxiang Zeng; Siyi Zhu; Yuan Hou; Pengyue Zhang; Lang Li 001; Jing Li; L. Frank Huang; Stephen J. Lewis; Ruth Nussinov; Feixiong Cheng (Bioinform., 2020)

Repurpose Open Data to Discover Therapeutics for COVID-19 using Deep Learning. - Xiangxiang Zeng; Xiang Song 003; Tengfei Ma 002; Xiaoqin Pan; Yadi Zhou; Yuan Hou; Zheng Zhang 001; George Karypis; Feixiong Cheng (CoRR, 2020)

iDrug: Integration of drug repositioning and drug-target prediction via cross-network embedding. - Huiyuan Chen; Feixiong Cheng; Jing Li 002 (PLoS Comput. Biol., 2020)

Individualized genetic network analysis reveals new therapeutic vulnerabilities in 6, 700 cancer genomes. - Chuang Liu 001; Junfei Zhao; Weiqiang Lu; Yao Dai; Jennifer Hockings; Yadi Zhou; Ruth Nussinov; Charis Eng; Feixiong Cheng (PLoS Comput. Biol., 2020)

Artificial Intelligence for Drug Discovery. - Jian Tang 005; Fei Wang 001; Feixiong Cheng (KDD, 2021)

A network-based deep learning methodology for stratification of tumor mutations. - Chuang Liu 001; Zhen Han; Zi-Ke Zhang; Ruth Nussinov; Feixiong Cheng (Bioinform., 2021)

Comprehensively modeling heterogeneous symptom progression for Parkinson's disease subtyping. - Chang Su 002; Yu Hou; Jielin Xu; Matthew Brendel; Jacqueline R. M. A. Maasch; Zilong Bai; Yingying Zhu 003; Claire Henchcliffe; Feixiong Cheng; Fei Wang 001 (AMIA, 2022)

Deep learning for drug repurposing: methods, databases, and applications. - Xiaoqin Pan; Xuan Lin; Dongsheng Cao 001; Xiangxiang Zeng; Philip S. Yu; Lifang He 001; Ruth Nussinov; Feixiong Cheng (CoRR, 2022)

Multimodal Machine Learning in Precision Health. - Adrienne S. Kline; Hanyin Wang; Yikuan Li; Saya R. Dennis; Meghan Hutch; Zhenxing Xu; Fei Wang 001; Feixiong Cheng; Yuan Luo 001 (CoRR, 2022)

Multimodal machine learning in precision health: A scoping review. - Adrienne S. Kline; Hanyin Wang; Yikuan Li; Saya R. Dennis; Meghan Hutch; Zhenxing Xu; Fei Wang 001; Feixiong Cheng; Yuan Luo 001 (npj Digit. Medicine, 2022)

Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease. - Chirag Gupta; Jielin Xu; Ting Jin; Saniya Khullar; Xiaoyu Liu; Sayali Alatkar; Feixiong Cheng; Daifeng Wang (PLoS Comput. Biol., 2022)

Accurate prediction of molecular properties and drug targets using a self-supervised image representation learning framework. - Xiangxiang Zeng; Hongxin Xiang; Linhui Yu; Jianmin Wang 016; Kenli Li 001; Ruth Nussinov; Feixiong Cheng (Nat. Mac. Intell., 2022)

A Deep Multimodal Representation Learning Framework for Accurate Molecular Properties Prediction. - Yuxin Yang 001; Zixu Wang; Pegah Ahadian; Abby Jerger; Jeremy Zucker; Song Feng; Feixiong Cheng; Qiang Guan (ACM Great Lakes Symposium on VLSI, 2024)

Multi-view biomedical foundation models for molecule-target and property prediction. - Parthasarathy Suryanarayanan; Yunguang Qiu; Shreyans Sethi; Diwakar Mahajan; Hongyang Li; Yuxin Yang; Elif K. Eyigöz; Aldo Guzmán-Sáenz; Daniel E. Platt; Timothy H. Rumbell; Kenney Ng; Sanjoy Dey; et al. (CoRR, 2024)

Identification of Parkinson's disease PACE subtypes and repurposing treatments through integrative analyses of multimodal data. - Chang Su 002; Yu Hou; Jielin Xu; Zhenxing Xu; Manqi Zhou; Alison Ke; Haoyang Li 001; Jie Xu 012; Matthew Brendel; Jacqueline R. M. A. Maasch; Zilong Bai; Haotan Zhang; et al. (npj Digit. Medicine, 2024)

A Deep Subgrouping Framework for Precision Drug Repurposing via Emulating Clinical Trials on Real-world Patient Data. - Seungyeon Lee 002; Ruoqi Liu; Feixiong Cheng; Ping Zhang 016 (KDD (1), 2025)

Prediction of Protein Three-dimensional Structures via a Hardware-Executable Quantum Computing Framework. - Yuqi Zhang; Yuxin Yang; William Martin 011; Kingsten Lin; Zixu Wang; Cheng-Chang Lu; Weiwen Jiang; Ruth Nussinov; Joseph Loscalzo; Qiang Guan; Feixiong Cheng (CoRR, 2025)

QDockBank: A Dataset for Ligand Docking on Protein Fragments Predicted on Utility-Level Quantum Computers. - Yuqi Zhang; Yuxin Yang; Cheng-Chang Lu; Weiwen Jiang; Feixiong Cheng; Bo Fang 002; Qiang Guan (CoRR, 2025)