Feixiong Cheng

50 papers A* 1A 1Misc 1Journal 45Unranked 2

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	A Deep Subgrouping Framework for Precision Drug Repurposing via Emulating Clinical Trials on Real-world Patient Data. KDD (1) Seungyeon Lee, Ruoqi Liu, Feixiong Cheng, Ping Zhang
2025	J	`jnl`	Prediction of Protein Three-dimensional Structures via a Hardware-Executable Quantum Computing Framework. CoRR Yuqi Zhang, Yuxin Yang, William Martin, Kingsten Lin, Zixu Wang, Cheng-Chang Lu, Weiwen Jiang, Ruth Nussinov, Joseph Loscalzo, Qiang Guan, Feixiong Cheng
2025	J	`jnl`	QDockBank: A Dataset for Ligand Docking on Protein Fragments Predicted on Utility-Level Quantum Computers. CoRR Yuqi Zhang, Yuxin Yang, Cheng-Chang Lu, Weiwen Jiang, Feixiong Cheng, Bo Fang, Qiang Guan
2025	A	`conf`	QDockBank: A dataset for Ligand Docking on Protein Fragments Predicted on Utility-Level Quantum Computers. SC Yuqi Zhang, Yuxin Yang, Cheng-Chang Lu, Weiwen Jiang, Feixiong Cheng, Bo Fang, Qiang Guan
2024	—	`conf`	A Deep Multimodal Representation Learning Framework for Accurate Molecular Properties Prediction. ACM Great Lakes Symposium on VLSI Yuxin Yang, Zixu Wang, Pegah Ahadian, Abby Jerger, Jeremy Zucker, Song Feng, Feixiong Cheng, Qiang Guan
2024	J	`jnl`	A Deep Subgrouping Framework for Precision Drug Repurposing via Emulating Clinical Trials on Real-world Patient Data. CoRR Seungyeon Lee, Ruoqi Liu, Feixiong Cheng, Ping Zhang
2024	J	`jnl`	Identification of Parkinson's disease PACE subtypes and repurposing treatments through integrative analyses of multimodal data. npj Digit. Medicine Chang Su, Yu Hou, Jielin Xu, Zhenxing Xu, Manqi Zhou, Alison Ke, Haoyang Li, Jie Xu, Matthew Brendel, Jacqueline R. M. A. Maasch, Zilong Bai, Haotan Zhang, Yingying Zhu, Molly C. Cincotta, Xinghua Shi, Claire Henchcliffe, James B. Leverenz, Jeffrey Cummings, Michael S. Okun, Jiang Bian, Feixiong Cheng, Fei Wang
2024	J	`jnl`	Multi-view biomedical foundation models for molecule-target and property prediction. CoRR 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, Myson Burch, Bum Chul Kwon, Pablo Meyer, Feixiong Cheng, Jianying Hu, Joseph A. Morrone
2022	J	`jnl`	Accurate prediction of molecular properties and drug targets using a self-supervised image representation learning framework. Nat. Mac. Intell. Xiangxiang Zeng, Hongxin Xiang, Linhui Yu, Jianmin Wang, Kenli Li, Ruth Nussinov, Feixiong Cheng
2022	Misc	`conf`	Comprehensively modeling heterogeneous symptom progression for Parkinson's disease subtyping. AMIA Chang Su, Yu Hou, Jielin Xu, Matthew Brendel, Jacqueline R. M. A. Maasch, Zilong Bai, Yingying Zhu, Claire Henchcliffe, Feixiong Cheng, Fei Wang
2022	J	`jnl`	Deep learning for drug repurposing: methods, databases, and applications. CoRR Xiaoqin Pan, Xuan Lin, Dongsheng Cao, Xiangxiang Zeng, Philip S. Yu, Lifang He, Ruth Nussinov, Feixiong Cheng
2022	J	`jnl`	Multimodal Machine Learning in Precision Health. CoRR Adrienne S. Kline, Hanyin Wang, Yikuan Li, Saya R. Dennis, Meghan Hutch, Zhenxing Xu, Fei Wang, Feixiong Cheng, Yuan Luo
2022	J	`jnl`	Multimodal machine learning in precision health: A scoping review. npj Digit. Medicine Adrienne S. Kline, Hanyin Wang, Yikuan Li, Saya R. Dennis, Meghan Hutch, Zhenxing Xu, Fei Wang, Feixiong Cheng, Yuan Luo
2022	J	`jnl`	Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease. PLoS Comput. Biol. Chirag Gupta, Jielin Xu, Ting Jin, Saniya Khullar, Xiaoyu Liu, Sayali Alatkar, Feixiong Cheng, Daifeng Wang
2021	J	`jnl`	A network-based deep learning methodology for stratification of tumor mutations. Bioinform. Chuang Liu, Zhen Han, Zi-Ke Zhang, Ruth Nussinov, Feixiong Cheng
2021	A*	`conf`	Artificial Intelligence for Drug Discovery. KDD Jian Tang, Fei Wang, Feixiong Cheng
2020	J	`jnl`	Individualized genetic network analysis reveals new therapeutic vulnerabilities in 6, 700 cancer genomes. PLoS Comput. Biol. Chuang Liu, Junfei Zhao, Weiqiang Lu, Yao Dai, Jennifer Hockings, Yadi Zhou, Ruth Nussinov, Charis Eng, Feixiong Cheng
2020	J	`jnl`	Network-based prediction of drug-target interactions using an arbitrary-order proximity embedded deep forest. Bioinform. Xiangxiang Zeng, Siyi Zhu, Yuan Hou, Pengyue Zhang, Lang Li, Jing Li, L. Frank Huang, Stephen J. Lewis, Ruth Nussinov, Feixiong Cheng
2020	J	`jnl`	Repurpose Open Data to Discover Therapeutics for COVID-19 using Deep Learning. CoRR Xiangxiang Zeng, Xiang Song, Tengfei Ma, Xiaoqin Pan, Yadi Zhou, Yuan Hou, Zheng Zhang, George Karypis, Feixiong Cheng
2020	J	`jnl`	iDrug: Integration of drug repositioning and drug-target prediction via cross-network embedding. PLoS Comput. Biol. Huiyuan Chen, Feixiong Cheng, Jing Li
2019	J	`jnl`	A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications. PLoS Comput. Biol. He Peng, Xiangxiang Zeng, Yadi Zhou, Defu Zhang, Ruth Nussinov, Feixiong Cheng
2019	J	`jnl`	Correction to "admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties". J. Chem. Inf. Model. Feixiong Cheng, Weihua Li, Yadi Zhou, Jie Shen, Zengrui Wu, Guixia Liu, Philip W. Lee, Yun Tang
2019	J	`jnl`	Correction: Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers. PLoS Comput. Biol. Ruth Nussinov, Hyunbum Jang, Chung-Jung Tsai, Feixiong Cheng
2019	J	`jnl`	Deep Learning-Based Prediction of Drug-Induced Cardiotoxicity. J. Chem. Inf. Model. Chuipu Cai, Pengfei Guo, Yadi Zhou, Jingwei Zhou, Qi Wang, Fengxue Zhang, Jiansong Fang, Feixiong Cheng
2019	J	`jnl`	Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers. PLoS Comput. Biol. Ruth Nussinov, Hyunbum Jang, Chung-Jung Tsai, Feixiong Cheng
2019	J	`jnl`	deepDR: a network-based deep learning approach to in silico drug repositioning. Bioinform. Xiangxiang Zeng, Siyi Zhu, Xiangrong Liu, Yadi Zhou, Ruth Nussinov, Feixiong Cheng
2018	J	`jnl`	In Silico Pharmacoepidemiologic Evaluation of Drug-Induced Cardiovascular Complications Using Combined Classifiers. J. Chem. Inf. Model. Chuipu Cai, Jiansong Fang, Pengfei Guo, Qi Wang, Huixiao Hong, Javid Moslehi, Feixiong Cheng
2018	J	`jnl`	In silico polypharmacology of natural products. Briefings Bioinform. Jiansong Fang, Chuang Liu, Qi Wang, Ping Lin, Feixiong Cheng
2017	J	`jnl`	Entropy-based consensus clustering for patient stratification. Bioinform. Hongfu Liu, Rui Zhao, Hongsheng Fang, Feixiong Cheng, Yun Fu, Yang-Yu Liu
2017	J	`jnl`	Individualized network-based drug repositioning infrastructure for precision oncology in the panomics era. Briefings Bioinform. Feixiong Cheng, Huixiao Hong, Sheng-Yong Yang, Yuquan Wei
2017	J	`jnl`	Quantitative and Systems Pharmacology. 1. J. Chem. Inf. Model. Jiansong Fang, Zengrui Wu, Chuipu Cai, Qi Wang, Yun Tang, Feixiong Cheng
2017	J	`jnl`	SDTNBI: an integrated network and chemoinformatics tool for systematic prediction of drug-target interactions and drug repositioning. Briefings Bioinform. Zengrui Wu, Feixiong Cheng, Jie Li, Weihua Li, Guixia Liu, Yun Tang
2016	J	`jnl`	A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes. J. Am. Medical Informatics Assoc. Feixiong Cheng, Junfei Zhao, Michaela Fooksa, Zhongming Zhao
2016	J	`jnl`	Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. Briefings Bioinform. Feixiong Cheng, Junfei Zhao, Zhongming Zhao
2016	J	`jnl`	Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach. BMC Syst. Biol. Feixiong Cheng, Chuang Liu, Bairong Shen, Zhongming Zhao
2016	J	`jnl`	Systematic dissection of dysregulated transcription factor-miRNA feed-forward loops across tumor types. Briefings Bioinform. Wei Jiang, Ramkrishna Mitra, Chen-Ching Lin, Quan Wang, Feixiong Cheng, Zhongming Zhao
2016	J	`jnl`	Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis. PLoS Comput. Biol. Feixiong Cheng, James L. Murray, Junfei Zhao, Jinsong Sheng, Zhongming Zhao, Donald H. Rubin
2016	J	`jnl`	ccmGDB: a database for cancer cell metabolism genes. Nucleic Acids Res. Pora Kim, Feixiong Cheng, Junfei Zhao, Zhongming Zhao
2015	J	`jnl`	A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3, 000 Cancer Genomes across 9 Cancer Types. PLoS Comput. Biol. Feixiong Cheng, Chuang Liu, Chen-Ching Lin, Junfei Zhao, Peilin Jia, Wen-Hsiung Li, Zhongming Zhao
2015	J	`jnl`	SGDriver: a novel structural genomics-based approach to prioritize cancer related and potentially druggable somatic mutations. BMC Bioinform. Junfei Zhao, Feixiong Cheng, Zhongming Zhao
2013	J	`jnl`	Adverse Drug Events: Database Construction and in Silico Prediction. J. Chem. Inf. Model. Feixiong Cheng, Weihua Li, Xichuan Wang, Yadi Zhou, Zengrui Wu, Jie Shen, Yun Tang
2013	J	`jnl`	Prediction of Polypharmacological Profiles of Drugs by the Integration of Chemical, Side Effect, and Therapeutic Space. J. Chem. Inf. Model. Feixiong Cheng, Weihua Li, Zengrui Wu, Xichuan Wang, Chen Zhang, Jie Li, Guixia Liu, Yun Tang
2012	J	`jnl`	In Silico Assessment of Chemical Biodegradability. J. Chem. Inf. Model. Feixiong Cheng, Yutaka Ikenaga, Yadi Zhou, Yue Yu, Weihua Li, Jie Shen, Zheng Du, Lei Chen, Congying Xu, Guixia Liu, Philip W. Lee, Yun Tang
2012	J	`jnl`	In silico Prediction of Chemical Ames Mutagenicity. J. Chem. Inf. Model. Congying Xu, Feixiong Cheng, Lei Chen, Zheng Du, Weihua Li, Guixia Liu, Philip W. Lee, Yun Tang
2012	J	`jnl`	Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference. PLoS Comput. Biol. Feixiong Cheng, Chuang Liu, Jing Jiang, Weiqiang Lu, Weihua Li, Guixia Liu, Wei-Xing Zhou, Jin Huang, Yun Tang
2012	J	`jnl`	Unbinding Pathways of GW4064 from Human Farnesoid X Receptor As Revealed by Molecular Dynamics Simulations. J. Chem. Inf. Model. Weihua Li, Jing Fu, Feixiong Cheng, Mingyue Zheng, Jian Zhang, Guixia Liu, Yun Tang
2012	J	`jnl`	admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties. J. Chem. Inf. Model. Feixiong Cheng, Weihua Li, Yadi Zhou, Jie Shen, Zengrui Wu, Guixia Liu, Philip W. Lee, Yun Tang
2011	J	`jnl`	Classification of Cytochrome P450 Inhibitors and Noninhibitors Using Combined Classifiers. J. Chem. Inf. Model. Feixiong Cheng, Yue Yu, Jie Shen, Lei Yang, Weihua Li, Guixia Liu, Philip W. Lee, Yun Tang
2011	J	`jnl`	Insights into Molecular Basis of Cytochrome P450 Inhibitory Promiscuity of Compounds. J. Chem. Inf. Model. Feixiong Cheng, Yue Yu, Yadi Zhou, Zhonghua Shen, Wen Xiao, Guixia Liu, Weihua Li, Philip W. Lee, Yun Tang
2010	J	`jnl`	Estimation of ADME Properties with Substructure Pattern Recognition. J. Chem. Inf. Model. Jie Shen, Feixiong Cheng, You Xu, Weihua Li, Yun Tang