Lei Xie
Orcid: 0000-0001-9051-2111Affiliations:
- City University of New York, Department of Computer Science, Hunter College, NY, USA
- University of California, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, La Jolla, CA, USA (former)
According to our database1,
Lei Xie
authored at least 61 papers
between 2005 and 2023.
Collaborative distances:
Collaborative distances:
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Bibliography
2023
End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins.
PLoS Comput. Biol., January, 2023
Elucidation of genome-wide understudied proteins targeted by PROTAC-induced degradation using interpretable machine learning.
PLoS Comput. Biol., 2023
A Universal Framework for Accurate and Efficient Geometric Deep Learning of Molecular Systems.
CoRR, 2023
Learning Universal and Robust 3D Molecular Representations with Graph Convolutional Networks.
CoRR, 2023
Proceedings of the IEEE International Conference on Big Data, 2023
2022
A context-aware deconfounding autoencoder for robust prediction of personalized clinical drug response from cell-line compound screening.
Nat. Mac. Intell., October, 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.
PLoS Comput. Biol., 2022
Chemical-induced gene expression ranking and its application to pancreatic cancer drug repurposing.
Patterns, 2022
Correction to "Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants".
J. Chem. Inf. Model., 2022
CoRR, 2022
Efficient and Accurate Physics-aware Multiplex Graph Neural Networks for 3D Small Molecules and Macromolecule Complexes.
CoRR, 2022
BMC Bioinform., 2022
Exploration of chemical space with partial labeled noisy student self-training and self-supervised graph embedding.
BMC Bioinform., 2022
Proceedings of the 2022 SIAM International Conference on Data Mining, 2022
Proceedings of the IEEE International Conference on Big Data, 2022
2021
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., 2021
TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations.
PLoS Comput. Biol., 2021
A deep learning framework for high-throughput mechanism-driven phenotype compound screening and its application to COVID-19 drug repurposing.
Nat. Mach. Intell., 2021
MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization.
J. Chem. Inf. Model., 2021
Frontiers Bioinform., 2021
Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology.
CoRR, 2021
CODE-AE: A Coherent De-confounding Autoencoder for Predicting Patient-Specific Drug Response From Cell Line Transcriptomics.
CoRR, 2021
A cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype.
Bioinform., 2021
2020
Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures.
CoRR, 2020
A Cross-Level Information Transmission Network for Predicting Phenotype from New Genotype: Application to Cancer Precision Medicine.
CoRR, 2020
Bioinform., 2020
Proceedings of the Twenty-Ninth International Joint Conference on Artificial Intelligence, 2020
2019
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., 2019
Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology.
PLoS Comput. Biol., 2019
Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants.
J. Chem. Inf. Model., 2019
BMC Bioinform., 2019
2018
ANTENNA, a Multi-Rank, Multi-Layered Recommender System for Inferring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide as a Targeted Anti-Cancer Therapy.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018
The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications.
BMC Bioinform., 2018
Target Gene Prediction of Transcription Factor Using a New Neighborhood-regularized Tri-factorization One-class Collaborative Filtering Algorithm.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018
2017
Cross-Dependency Inference in Multi-Layered Networks: A Collaborative Filtering Perspective.
ACM Trans. Knowl. Discov. Data, 2017
JDINAC: joint density-based non-parametric differential interaction network analysis and classification using high-dimensional sparse omics data.
Bioinform., 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.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017
Confused or not Confused?: Disentangling Brain Activity from EEG Data Using Bidirectional LSTM Recurrent Neural Networks.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017
2016
Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing.
PLoS Comput. Biol., 2016
Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology.
BMC Bioinform., 2016
Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2016
2015
A new method to improve network topological similarity search: applied to fold recognition.
Bioinform., 2015
Proceedings of the Social Media Processing - 4th National Conference, 2015
2014
Towards Structural Systems Pharmacology to Study Complex Diseases and Personalized Medicine.
PLoS Comput. Biol., 2014
Anti-Infectious Drug Repurposing Using an Integrated Chemical Genomics and Structural Systems Biology Approach.
Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014
2013
BMC Syst. Biol., 2013
2012
An integrated workflow for proteome-wide off-target identification and polypharmacology drug design.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012
2011
Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir.
PLoS Comput. Biol., 2011
Correction to "A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing".
J. Chem. Inf. Model., 2011
A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing.
J. Chem. Inf. Model., 2011
2010
The <i>Mycobacterium tuberculosis</i> Drugome and Its Polypharmacological Implications.
PLoS Comput. Biol., 2010
A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology.
PLoS Comput. Biol., 2010
Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model.
PLoS Comput. Biol., 2010
SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison.
Nucleic Acids Res., 2010
2009
Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors.
PLoS Comput. Biol., 2009
Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis.
PLoS Comput. Biol., 2009
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., 2009
2007
In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators.
PLoS Comput. Biol., 2007
A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites.
BMC Bioinform., 2007
2006
2005
Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models.
PLoS Comput. Biol., 2005