Lei Xie

Publication Activity (10 Years)

Years Active: 2005-2024
Publications (10 Years): 25

Top Topics

Gene Prediction

Top Venues

PLoS Comput. Biol.

Publications

You Wu, Lei Xie
AI-driven multi-omics integration for multi-scale predictive modeling of causal genotype-environment-phenotype relationships. CoRR (2024)
Shuo Zhang, Yang Liu, Lei Xie
A Universal Framework for Accurate and Efficient Geometric Deep Learning of Molecular Systems. CoRR (2023)
Li Xie, Lei Xie
Elucidation of genome-wide understudied proteins targeted by PROTAC-induced degradation using interpretable machine learning. PLoS Comput. Biol. 19 (8) (2023)
Shuo Zhang, Yang Liu, Li Xie, Lei Xie
Learning Universal and Robust 3D Molecular Representations with Graph Convolutional Networks. CoRR (2023)
Jyoti Yadav, Aparna S. Varde, Lei Xie
Comprehensive cough data analysis on CODA TB. BigData (2023)
Di He, Qiao Liu, You Wu, Lei Xie
A context-aware deconfounding autoencoder for robust prediction of personalized clinical drug response from cell-line compound screening. Nat. Mac. Intell. 4 (10) (2022)
Qiao Liu, Bohyun Lee, Lei Xie
Small molecule modulation of microbiota: a systems pharmacology perspective. BMC Bioinform. (3) (2022)
Yang Liu, Hansaim Lim, Lei Xie
Exploration of chemical space with partial labeled noisy student self-training and self-supervised graph embedding. BMC Bioinform. (3) (2022)
Thai-Hoang Pham, Yue Qiu, Jiahui Liu, Steven Zimmer, Eric E. O'Neill, Lei Xie, Ping Zhang
Chemical-induced gene expression ranking and its application to pancreatic cancer drug repurposing. Patterns 3 (4) (2022)
Zheng Zhao, Lei Xie, Philip E. Bourne
Correction to "Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants". J. Chem. Inf. Model. 62 (1) (2022)
You Wu, Qiao Liu, Yue Qiu, Lei Xie
Deep learning prediction of chemical-induced dose-dependent and context-specific multiplex phenotype responses and its application to personalized alzheimer's disease drug repurposing. PLoS Comput. Biol. 18 (8) (2022)
Thai-Hoang Pham, Lei Xie, Ping Zhang
FAME: Fragment-based Conditional Molecular Generation for Phenotypic Drug Discovery. SDM (2022)
Thai-Hoang Pham, Yue Qiu, Jucheng Zeng, Lei Xie, Ping Zhang
A deep learning framework for high-throughput mechanism-driven phenotype compound screening and its application to COVID-19 drug repurposing. Nat. Mach. Intell. 3 (3) (2021)
Hansaim Lim, Lei Xie
A New Weighted Imputed Neighborhood-Regularized Tri-Factorization One-Class Collaborative Filtering Algorithm: Application to Target Gene Prediction of Transcription Factors. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (1) (2021)
Tian Cai, Li Xie, Muge Chen, Yang Liu, Di He, Shuo Zhang, Cameron Mura, Philip E. Bourne, Lei Xie
Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology. CoRR (2021)
Di He, Lei Xie
CODE-AE: A Coherent De-confounding Autoencoder for Predicting Patient-Specific Drug Response From Cell Line Transcriptomics. CoRR (2021)
Di He, Lei Xie
A cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype. Bioinform. 38 (1) (2021)
Di He, Lei Xie
A Cross-Level Information Transmission Network for Predicting Phenotype from New Genotype: Application to Cancer Precision Medicine. CoRR (2020)
Zheng Zhao, Lei Xie, Philip E. Bourne
Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants. J. Chem. Inf. Model. 59 (1) (2019)
Hansaim Lim, Di He, Yue Qiu, Patrycja Krawczuk, Xiaoru Sun, Lei Xie
Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology. PLoS Comput. Biol. 15 (6) (2019)
Qiao Liu, Di He, Lei Xie
Prediction of off-target specificity and cell-specific fitness of CRISPR-Cas System using attention boosted deep learning and network-based gene feature. PLoS Comput. Biol. 15 (10) (2019)
Jiadong Ji, Di He, Yang Feng, Yong He, Fuzhong Xue, Lei Xie
JDINAC: joint density-based non-parametric differential interaction network analysis and classification using high-dimensional sparse omics data. Bioinform. 33 (19) (2017)
Zheng Zhao, Che L. Martin, Raymond Fan, Philip E. Bourne, Lei Xie
Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology. BMC Bioinform. 17 (2016)
Hansaim Lim, Aleksandar Poleksic, Yuan Yao, Hanghang Tong, Di He, Luke Zhuang, Patrick Meng, Lei Xie
Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing. PLoS Comput. Biol. 12 (10) (2016)
John Lhota, Ruth Hauptman, Thomas Hart, Clara Ng, Lei Xie
A new method to improve network topological similarity search: applied to fold recognition. Bioinform. 31 (13) (2015)
Clara Ng, Ruth Hauptman, Yinliang Zhang, Philip E. Bourne, Lei Xie
Anti-Infectious Drug Repurposing Using an Integrated Chemical Genomics and Structural Systems Biology Approach. Pacific Symposium on Biocomputing (2014)
Lei Xie, Xiaoxia Ge, Hepan Tan, Li Xie, Yinliang Zhang, Thomas Hart, Xiaowei Yang, Philip E. Bourne
Towards Structural Systems Pharmacology to Study Complex Diseases and Personalized Medicine. PLoS Comput. Biol. 10 (5) (2014)
Roger L. Chang, Lei Xie, Philip E. Bourne, Bernhard O. Palsson
Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst. Biol. 7 (2013)
Thomas Evangelidis, Philip E. Bourne, Li Xie, Lei Xie
An integrated workflow for proteome-wide off-target identification and polypharmacology drug design. BIBM Workshops (2012)
Sarah L. Kinnings, Nina Liu, Peter J. Tonge, Richard M. Jackson, Lei Xie, Philip E. Bourne
Correction to "A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing". J. Chem. Inf. Model. 51 (5) (2011)
Li Xie, Thomas Evangelidis, Lei Xie, Philip E. Bourne
Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir. PLoS Comput. Biol. 7 (4) (2011)
Sarah L. Kinnings, Nina Liu, Peter J. Tonge, Richard M. Jackson, Lei Xie, Philip E. Bourne
A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing. J. Chem. Inf. Model. 51 (2) (2011)
Jacob D. Durrant, Rommie E. Amaro, Lei Xie, Michael D. Urbaniak, Michael A. J. Ferguson, Antti Haapalainen, Zhijun Chen, Anne Marie Di Guilmi, Frank Wunder, Philip E. Bourne, James Andrew McCammon
A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. PLoS Comput. Biol. 6 (1) (2010)
Jingyuan Ren, Lei Xie, Wilfred W. Li, Philip E. Bourne
SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Sarah L. Kinnings, Li Xie, Kingston H. Fung, Richard M. Jackson, Lei Xie, Philip E. Bourne
Drugome and Its Polypharmacological Implications. PLoS Comput. Biol. 6 (11) (2010)
Roger L. Chang, Li Xie, Lei Xie, Philip E. Bourne, Bernhard Ø. Palsson
Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model. PLoS Comput. Biol. 6 (9) (2010)
Li Xie, Jerry Li, Lei Xie, Philip E. Bourne
Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors. PLoS Comput. Biol. 5 (5) (2009)
Sarah L. Kinnings, Nina Liu, Nancy Buchmeier, Peter J. Tonge, Lei Xie, Philip E. Bourne
Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis. PLoS Comput. Biol. 5 (7) (2009)
Lei Xie, Li Xie, Philip E. Bourne
A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery. Bioinform. 25 (12) (2009)
Lei Xie, Philip E. Bourne
A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. BMC Bioinform. 8 (S-4) (2007)
Lei Xie, Jian Wang, Philip E. Bourne
In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators. PLoS Comput. Biol. 3 (11) (2007)
Andrei Kouranov, Lei Xie, Joanna de la Cruz, Li Chen, John D. Westbrook, Philip E. Bourne, Helen M. Berman
The RCSB PDB information portal for structural genomics. Nucleic Acids Res. 34 (Database-Issue) (2006)
Lei Xie, Philip E. Bourne
Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models. PLoS Comput. Biol. 1 (3) (2005)