Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models. - Lei Xie 006; Philip E. Bourne (PLoS Comput. Biol., 2005)

The RCSB PDB information portal for structural genomics. - Andrei Kouranov; Lei Xie 006; Joanna de la Cruz; Li Chen 022; John D. Westbrook; Philip E. Bourne; Helen M. Berman (Nucleic Acids Res., 2006)

A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. - Lei Xie 006; Philip E. Bourne (BMC Bioinform., 2007)

In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators. - Lei Xie 006; Jian Wang; Philip E. Bourne (PLoS Comput. Biol., 2007)

A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery. - Lei Xie 006; Li Xie 002; Philip E. Bourne (Bioinform., 2009)

Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis. - Sarah L. Kinnings; Nina Liu; Nancy Buchmeier; Peter J. Tonge; Lei Xie 006; Philip E. Bourne (PLoS Comput. Biol., 2009)

Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors. - Li Xie 002; Jerry Li 004; Lei Xie 006; Philip E. Bourne (PLoS Comput. Biol., 2009)

SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison. - Jingyuan Ren; Lei Xie 006; Wilfred W. Li; Philip E. Bourne (Nucleic Acids Res., 2010)

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model. - Roger L. Chang; Li Xie 002; Lei Xie 006; Philip E. Bourne; Bernhard Ø. Palsson (PLoS Comput. Biol., 2010)

A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. - Jacob D. Durrant; Rommie E. Amaro; Lei Xie 006; Michael D. Urbaniak; Michael A. J. Ferguson; Antti Haapalainen; Zhijun Chen; Anne Marie Di Guilmi; Frank Wunder; Philip E. Bourne; James Andrew McCammon (PLoS Comput. Biol., 2010)

The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications. - Sarah L. Kinnings; Li Xie 002; Kingston H. Fung; Richard M. Jackson; Lei Xie 006; Philip E. Bourne (PLoS Comput. Biol., 2010)

A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing. - Sarah L. Kinnings; Nina Liu; Peter J. Tonge; Richard M. Jackson; Lei Xie 006; Philip E. Bourne (J. Chem. Inf. Model., 2011)

Correction to "A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing". - Sarah L. Kinnings; Nina Liu; Peter J. Tonge; Richard M. Jackson; Lei Xie 006; Philip E. Bourne (J. Chem. Inf. Model., 2011)

Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir. - Li Xie 002; Thomas Evangelidis; Lei Xie 006; Philip E. Bourne (PLoS Comput. Biol., 2011)

An integrated workflow for proteome-wide off-target identification and polypharmacology drug design. - Thomas Evangelidis; Philip E. Bourne; Li Xie 002; Lei Xie 006 (BIBM Workshops, 2012)

Antibacterial mechanisms identified through structural systems pharmacology. - Roger L. Chang; Lei Xie 006; Philip E. Bourne; Bernhard O. Palsson (BMC Syst. Biol., 2013)

Anti-Infectious Drug Repurposing Using an Integrated Chemical Genomics and Structural Systems Biology Approach. - Clara Ng; Ruth Hauptman; Yinliang Zhang; Philip E. Bourne; Lei Xie 006 (Pacific Symposium on Biocomputing, 2014)

Towards Structural Systems Pharmacology to Study Complex Diseases and Personalized Medicine. - Lei Xie 006; Xiaoxia Ge; Hepan Tan; Li Xie 002; Yinliang Zhang; Thomas Hart; Xiaowei Yang; Philip E. Bourne (PLoS Comput. Biol., 2014)

Supervised Link Prediction Using Random Walks. - Yuechang Liu; Hanghang Tong; Lei Xie 006; Yong Tang 001 (SMP, 2015)

A new method to improve network topological similarity search: applied to fold recognition. - John Lhota; Ruth Hauptman; Thomas Hart; Clara Ng; Lei Xie 006 (Bioinform., 2015)

FASCINATE: Fast Cross-Layer Dependency Inference on Multi-layered Networks. - Chen Chen 022; Hanghang Tong; Lei Xie 006; Lei Ying 001; Qing He 011 (KDD, 2016)

Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology. - Zheng Zhao; Che L. Martin; Raymond Fan; Philip E. Bourne; Lei Xie 006 (BMC Bioinform., 2016)

Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing. - Hansaim Lim; Aleksandar Poleksic; Yuan Yao 001; Hanghang Tong; Di He 003; Luke Zhuang; Patrick Meng; Lei Xie 006 (PLoS Comput. Biol., 2016)

Confused or not Confused?: Disentangling Brain Activity from EEG Data Using Bidirectional LSTM Recurrent Neural Networks. - Zhaoheng Ni; Ahmet Cem Yuksel; Xiuyan Ni; Michael I. Mandel; Lei Xie 006 (BCB, 2017)

VariFunNet, an integrated multiscale modeling framework to study the effects of rare non-coding variants in genome-wide association studies: Applied to Alzheimer's disease. - Qiao Liu; Chen Chen 022; Annie Gao; Hanghang Tong; Lei Xie 006 (BIBM, 2017)

JDINAC: joint density-based non-parametric differential interaction network analysis and classification using high-dimensional sparse omics data. - Jiadong Ji; Di He 003; Yang Feng 002; Yong He; Fuzhong Xue; Lei Xie 006 (Bioinform., 2017)

Cross-Dependency Inference in Multi-Layered Networks: A Collaborative Filtering Perspective. - Chen Chen 022; Hanghang Tong; Lei Xie 006; Lei Ying 001; Qing He 011 (ACM Trans. Knowl. Discov. Data, 2017)

Target Gene Prediction of Transcription Factor Using a New Neighborhood-regularized Tri-factorization One-class Collaborative Filtering Algorithm. - Hansaim Lim; Lei Xie 006 (BCB, 2018)

The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications. - Xiaoming Liu; Lei Xie 006; Zhijin Wu; Kai Wang 063; Zhongming Zhao; Jianhua Ruan; Degui Zhi (BMC Bioinform., 2018)

ANTENNA, a Multi-Rank, Multi-Layered Recommender System for Inferring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide as a Targeted Anti-Cancer Therapy. - Annie Wang; Hansaim Lim; Shu-Yuan Cheng; Lei Xie 006 (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Biological representation of chemicals using latent target interaction profile. - Mohamed Ayed; Hansaim Lim; Lei Xie 006 (BMC Bioinform., 2019)

Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants. - Zheng Zhao; Lei Xie 006; Philip E. Bourne (J. Chem. Inf. Model., 2019)

Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology. - Hansaim Lim; Di He 003; Yue Qiu 002; Patrycja Krawczuk; Xiaoru Sun; Lei Xie 006 (PLoS Comput. Biol., 2019)

Prediction of off-target specificity and cell-specific fitness of CRISPR-Cas System using attention boosted deep learning and network-based gene feature. - Qiao Liu; Di He 003; Lei Xie 006 (PLoS Comput. Biol., 2019)

Improving Attention Mechanism in Graph Neural Networks via Cardinality Preservation. - Shuo Zhang 010; Lei Xie 006 (IJCAI, 2020)

A Bayesian approach to accurate and robust signature detection on LINCS L1000 data. - Yue Qiu 002; Tianhuan Lu; Hansaim Lim; Lei Xie 006 (Bioinform., 2020)

A Cross-Level Information Transmission Network for Predicting Phenotype from New Genotype: Application to Cancer Precision Medicine. - Di He 003; Lei Xie 006 (CoRR, 2020)

Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures. - Shuo Zhang 010; Yang Liu; Lei Xie 006 (CoRR, 2020)

A cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype. - Di He 003; Lei Xie 006 (Bioinform., 2021)

CODE-AE: A Coherent De-confounding Autoencoder for Predicting Patient-Specific Drug Response From Cell Line Transcriptomics. - Di He 003; Lei Xie 006 (CoRR, 2021)

Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology. - Tian Cai; Li Xie 002; Muge Chen; Yang Liu; Di He 003; Shuo Zhang 010; Cameron Mura; Philip E. Bourne; Lei Xie 006 (CoRR, 2021)

COVID-19 Multi-Targeted Drug Repurposing Using Few-Shot Learning. - Yang Liu; You Wu; Xiaoke Shen; Lei Xie 006 (Frontiers Bioinform., 2021)

MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization. - Tian Cai; Hansaim Lim; Kyra Alyssa Abbu; Yue Qiu 002; Ruth Nussinov; Lei Xie 006 (J. Chem. Inf. Model., 2021)

A deep learning framework for high-throughput mechanism-driven phenotype compound screening and its application to COVID-19 drug repurposing. - Thai-Hoang Pham; Yue Qiu 002; Jucheng Zeng; Lei Xie 006; Ping Zhang 016 (Nat. Mach. Intell., 2021)

TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations. - Qiao Liu; Lei Xie 006 (PLoS Comput. Biol., 2021)

A New Weighted Imputed Neighborhood-Regularized Tri-Factorization One-Class Collaborative Filtering Algorithm: Application to Target Gene Prediction of Transcription Factors. - Hansaim Lim; Lei Xie 006 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Evolving Perceptions of Mental Health on Social Media and their Medical Impacts. - Kenna Reagan; Aparna S. Varde; Lei Xie 006 (IEEE Big Data, 2022)

FAME: Fragment-based Conditional Molecular Generation for Phenotypic Drug Discovery. - Thai-Hoang Pham; Lei Xie 006; Ping Zhang 016 (SDM, 2022)

DeepREAL: a deep learning powered multi-scale modeling framework for predicting out-of-distribution ligand-induced GPCR activity. - Tian Cai; Kyra Alyssa Abbu; Yang Liu; Lei Xie 006 (Bioinform., 2022)

Exploration of chemical space with partial labeled noisy student self-training and self-supervised graph embedding. - Yang Liu; Hansaim Lim; Lei Xie 006 (BMC Bioinform., 2022)

Small molecule modulation of microbiota: a systems pharmacology perspective. - Qiao Liu; Bohyun Lee; Lei Xie 006 (BMC Bioinform., 2022)

Efficient and Accurate Physics-aware Multiplex Graph Neural Networks for 3D Small Molecules and Macromolecule Complexes. - Shuo Zhang 010; Yang Liu; Lei Xie 006 (CoRR, 2022)

Physics-aware Graph Neural Network for Accurate RNA 3D Structure Prediction. - Shuo Zhang 010; Yang Liu; Lei Xie 006 (CoRR, 2022)

Correction to "Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants". - Zheng Zhao; Lei Xie 006; Philip E. Bourne (J. Chem. Inf. Model., 2022)

Chemical-induced gene expression ranking and its application to pancreatic cancer drug repurposing. - Thai-Hoang Pham; Yue Qiu 002; Jiahui Liu; Steven Zimmer; Eric E. O'Neill; Lei Xie 006; Ping Zhang 016 (Patterns, 2022)

Deep learning prediction of chemical-induced dose-dependent and context-specific multiplex phenotype responses and its application to personalized alzheimer's disease drug repurposing. - You Wu; Qiao Liu; Yue Qiu 002; Lei Xie 006 (PLoS Comput. Biol., 2022)

A context-aware deconfounding autoencoder for robust prediction of personalized clinical drug response from cell-line compound screening. - Di He 003; Qiao Liu; You Wu; Lei Xie 006 (Nat. Mac. Intell., 2022)

Comprehensive cough data analysis on CODA TB. - Jyoti Yadav; Aparna S. Varde; Lei Xie 006 (IEEE Big Data, 2023)

Learning Universal and Robust 3D Molecular Representations with Graph Convolutional Networks. - Shuo Zhang 010; Yang Liu; Li Xie 002; Lei Xie 006 (CoRR, 2023)

A Universal Framework for Accurate and Efficient Geometric Deep Learning of Molecular Systems. - Shuo Zhang 010; Yang Liu; Lei Xie 006 (CoRR, 2023)

Protein Language Model-Powered 3D Ligand Binding Site Prediction from Protein Sequence. - Shuo Zhang 010; Lei Xie 006 (CoRR, 2023)

Elucidation of genome-wide understudied proteins targeted by PROTAC-induced degradation using interpretable machine learning. - Li Xie 002; Lei Xie 006 (PLoS Comput. Biol., 2023)

End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins. - Tian Cai; Li Xie 002; Shuo Zhang 010; Muge Chen; Di He 003; Amitesh Badkul; Yang Liu; Hari Krishna Namballa; Michael Dorogan; Wayne W. Harding; Cameron Mura; Philip E. Bourne; et al. (PLoS Comput. Biol., 2023)

Audiovisual Multimodal Cough Data Analysis for Tuberculosis Detection. - Jyoti Yadav; Aparna S. Varde; Hao Liu 054; George Antoniou; Lei Xie 006 (IISA, 2024)

AI-driven multi-omics integration for multi-scale predictive modeling of causal genotype-environment-phenotype relationships. - You Wu; Lei Xie 006 (CoRR, 2024)

Programmable Virtual Humans Toward Human Physiologically-Based Drug Discovery. - You Wu; Philip E. Bourne; Lei Xie 006 (CoRR, 2025)