Xie, Lei

Publications

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selected publications

Agomelatine drives sex-specific neuroprotection and reduced pathology in rat and human Alzheimer's models. 2026 GET IT
BT-11 targets the LANCL2 pathway to attenuate cognitive deficits and hippocampal pathology in Alzheimer's transgenic rats. Scientific reports. 2025 Academic Article GET IT
Multimodal out-of-distribution individual uncertainty quantification enhances binding affinity prediction for polypharmacology. Nature machine intelligence. 2025 Academic Article GET IT
Integrating explainable artificial intelligence with multiomics systems biology and electronic health record data mining for personalized drug repurposing in Alzheimer's disease. Briefings in bioinformatics. 2025 Academic Article GET IT
AI-powered programmable virtual humans toward human physiologically-based drug discovery. Drug discovery today. 2025 Review GET IT
Discovery of a selective α2C-AR scaffold from a molecular hybridization approach. Bioorganic & medicinal chemistry. 2025 Academic Article GET IT
Cross-level Cross-Scale Inference and Imputation of Single-cell Spatial Proteomics. 2025 GET IT
ContraDTI: Improved drug-target interaction prediction via multi-view contrastive learning. Artificial intelligence in medicine. 2025 Academic Article GET IT
NNKcat: deep neural network to predict catalytic constants (Kcat) by integrating protein sequence and substrate structure with enhanced data imbalance handling. Briefings in bioinformatics. 2025 Academic Article GET IT
AI-Driven Applications in Clinical Pharmacology and Translational Science: Insights From the ASCPT 2024 AI Preconference. Clinical and translational science. 2025 Review GET IT
Times cited: 10
Integrating Interpretable Machine Learning and Multi-omics Systems Biology for Personalized Biomarker Discovery and Drug Repurposing in Alzheimer's Disease. 2025 GET IT
Corrigendum to "AI-driven multi-omics integration for multi-scale predictive modeling of genotype-environment-phenotype relationships" [Comput Struct Biotechnol J 27 (2025) 265-277]. 2025 GET IT
Times cited: 1
MolGene-E: Inverse Molecular Design to Modulate Single Cell Transcriptomics. 2025 GET IT
Brain-penetrant histone deacetylase inhibitor RG2833 improves spatial memory in females of an Alzheimer's disease rat model. Journal of Alzheimer's disease : JAD. 2025 Academic Article GET IT
Times cited: 4
AI-driven multi-omics integration for multi-scale predictive modeling of genotype-environment-phenotype relationships. Computational and structural biotechnology journal. 2025 Review GET IT
Times cited: 64
BT-11 repurposing potential for Alzheimer's disease and insights into its mode of actions. 2024 GET IT
Semi-supervised meta-learning elucidates understudied molecular interactions. Communications biology. 2024 Academic Article GET IT
Times cited: 7
Model Agnostic Semi-Supervised Meta-Learning Elucidates Understudied Out-of-distribution Molecular Interactions. 2024 GET IT
Potential Alzheimer's early biomarkers in a transgenic rat model and benefits of diazoxide/dibenzoylmethane co-treatment on spatial memory and AD-pathology. Scientific reports. 2024 Academic Article GET IT
Times cited: 7
Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants. GigaScience. 2024 Academic Article GET IT
Times cited: 12
Histone deacetylase inhibitor RG2833 has therapeutic potential for Alzheimer's disease in females. 2023 GET IT
A universal framework for accurate and efficient geometric deep learning of molecular systems. Scientific reports. 2023 Academic Article GET IT
Times cited: 16
Elucidation of genome-wide understudied proteins targeted by PROTAC-induced degradation using interpretable machine learning. PLoS computational biology. 2023 Academic Article GET IT
Times cited: 16
Deciphering Phage-Host Specificity Based on the Association of Phage Depolymerases and Bacterial Surface Glycan with Deep Learning. 2023 GET IT
Hierarchical multi-omics data integration and modeling predict cell-specific chemical proteomics and drug responses. Cell reports methods. 2023 Academic Article GET IT
Times cited: 12
Repurposing ibudilast to mitigate Alzheimer's disease by targeting inflammation. Brain : a journal of neurology. 2023 Academic Article GET IT
Times cited: 49
Elucidation of Genome-wide Understudied Proteins targeted by PROTAC-induced degradation using Interpretable Machine Learning. 2023 GET IT
Times cited: 122
End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins. PLoS computational biology. 2023 Academic Article GET IT
Times cited: 18
A Tribute to Phil Bourne-Scientist and Human. Biomolecules. 2023 Editorial Article GET IT
Sc2Mol: a scaffold-based two-step molecule generator with variational autoencoder and transformer. Bioinformatics (Oxford, England). 2023 Academic Article GET IT
Times cited: 22
Females exhibit higher GluA2 levels and outperform males in active place avoidance despite increased amyloid plaques in TgF344-Alzheimer's rats. Scientific reports. 2022 Academic Article GET IT
Times cited: 20
A context-aware deconfounding autoencoder for robust prediction of personalized clinical drug response from cell-line compound screening. Nature machine intelligence. 2022 Academic Article GET IT
Times cited: 64
Small molecule modulation of microbiota: a systems pharmacology perspective. BMC bioinformatics. 2022 Academic Article GET IT
Times cited: 3
Timapiprant, a prostaglandin D2 receptor antagonist, ameliorates pathology in a rat Alzheimer's model. Life science alliance. 2022 Academic Article GET IT
Times cited: 15
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 computational biology. 2022 Academic Article GET IT
Times cited: 23
Reinforcement learning for systems pharmacology-oriented and personalized drug design. Expert opinion on drug discovery. 2022 Review GET IT
Times cited: 39
Exploration of chemical space with partial labeled noisy student self-training and self-supervised graph embedding. BMC bioinformatics. 2022 Academic Article GET IT
Times cited: 10
DeepREAL: a deep learning powered multi-scale modeling framework for predicting out-of-distribution ligand-induced GPCR activity. Bioinformatics (Oxford, England). 2022 Academic Article GET IT
Times cited: 18
Chemical-induced gene expression ranking and its application to pancreatic cancer drug repurposing. Patterns (New York, N.Y.). 2022 Academic Article GET IT
Times cited: 21
FAME: Fragment-based Conditional Molecular Generation for Phenotypic Drug Discovery. Proceedings of the ... SIAM International Conference on Data Mining. SIAM International Conference on Data Mining. 2022 Academic Article GET IT
A cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype. Bioinformatics (Oxford, England). 2021 Academic Article GET IT
Times cited: 13
Correction to "Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants". 2021 GET IT
Times cited: 3
Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology. 2021 GET IT
COVID-19 Multi-Targeted Drug Repurposing Using Few-Shot Learning. Frontiers in bioinformatics. 2021 Academic Article GET IT
Times cited: 19
MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization. Journal of chemical information and modeling. 2021 Academic Article GET IT
Times cited: 19
TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations. PLoS computational biology. 2021 Academic Article GET IT
Times cited: 149
A New Weighted Imputed Neighborhood-Regularized Tri-Factorization One-Class Collaborative Filtering Algorithm: Application to Target Gene Prediction of Transcription Factors. IEEE/ACM transactions on computational biology and bioinformatics. 2021 Academic Article GET IT
Times cited: 8
A deep learning framework for high-throughput mechanism-driven phenotype compound screening and its application to COVID-19 drug repurposing. Nature machine intelligence. 2021 Academic Article GET IT
Times cited: 163
A deep learning framework for high-throughput mechanism-driven phenotype compound screening. 2020 GET IT
Improving Attention Mechanism in Graph Neural Networks via Cardinality Preservation. IJCAI : proceedings of the conference. 2020 Academic Article GET IT
A Bayesian approach to accurate and robust signature detection on LINCS L1000 data. Bioinformatics (Oxford, England). 2020 Academic Article GET IT
Times cited: 18
The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View. Trends in cancer. 2020 Review GET IT
Times cited: 198
Heterogeneous Multi-Layered Network Model for Omics Data Integration and Analysis. Frontiers in genetics. 2020 Review GET IT
Times cited: 86
Database of adverse events associated with drugs and drug combinations. Scientific reports. 2019 Academic Article GET IT
Times cited: 24
Biological representation of chemicals using latent target interaction profile. BMC bioinformatics. 2019 Academic Article GET IT
Times cited: 11
Prediction of off-target specificity and cell-specific fitness of CRISPR-Cas System using attention boosted deep learning and network-based gene feature. PLoS computational biology. 2019 Academic Article GET IT
Times cited: 65
Pathway-Centric Structure-Based Multi-Target Compound Screening for Anti-Virulence Drug Repurposing. International journal of molecular sciences. 2019 Academic Article GET IT
Times cited: 10
Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology. PLoS computational biology. 2019 Academic Article GET IT
Times cited: 40
Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants. Journal of chemical information and modeling. 2019 Academic Article GET IT
Times cited: 51
Omics Data Integration and Analysis for Systems Pharmacology. Methods in molecular biology (Clifton, N.J.). 2019 Academic Article GET IT
Times cited: 10
A new insight into underlying disease mechanism through semi-parametric latent differential network model. BMC bioinformatics. 2018 Academic Article GET IT
Times cited: 7
The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications. BMC bioinformatics. 2018 Editorial Article GET IT
Predicting serious rare adverse reactions of novel chemicals. Bioinformatics (Oxford, England). 2018 Academic Article GET IT
Times cited: 18
Exploring Landscape of Drug-Target-Pathway-Side Effect Associations. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2018 Academic Article GET IT
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 transactions on computational biology and bioinformatics. 2018 Academic Article GET IT
Times cited: 29
Target Gene Prediction of Transcription Factor Using a New Neighborhood-regularized Tri-factorization One-class Collaborative Filtering Algorithm. ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine. 2018 Academic Article GET IT
Times cited: 3
JDINAC: joint density-based non-parametric differential interaction network analysis and classification using high-dimensional sparse omics data. Bioinformatics (Oxford, England). 2017 Academic Article GET IT
Times cited: 22
Confused or not Confused?: Disentangling Brain Activity from EEG Data Using Bidirectional LSTM Recurrent Neural Networks. ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine. 2017 Academic Article GET IT
Times cited: 63
Cross-Dependency Inference in Multi-Layered Networks: A Collaborative Filtering Perspective. ACM transactions on knowledge discovery from data. 2017 Academic Article GET IT
Times cited: 7
Insights into the binding mode of MEK type-III inhibitors. A step towards discovering and designing allosteric kinase inhibitors across the human kinome. PloS one. 2017 Academic Article GET IT
Times cited: 42
Determining Cysteines Available for Covalent Inhibition Across the Human Kinome. Journal of medicinal chemistry. 2017 Academic Article GET IT
Times cited: 109
Improved genome-scale multi-target virtual screening via a novel collaborative filtering approach to cold-start problem. Scientific reports. 2016 Academic Article GET IT
Times cited: 41
Molecular mechanisms involved in the side effects of fatty acid amide hydrolase inhibitors: a structural phenomics approach to proteome-wide cellular off-target deconvolution and disease association. NPJ systems biology and applications. 2016 Academic Article GET IT
Times cited: 14
Harnessing Big Data for Systems Pharmacology. Annual review of pharmacology and toxicology. 2016 Review GET IT
Times cited: 53
Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing. PLoS computational biology. 2016 Academic Article GET IT
Times cited: 70
Toward High-Throughput Predictive Modeling of Protein Binding/Unbinding Kinetics. Journal of chemical information and modeling. 2016 Academic Article GET IT
Times cited: 28
Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach. Journal of medicinal chemistry. 2016 Academic Article GET IT
Times cited: 40
Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology. BMC bioinformatics. 2016 Academic Article GET IT
Times cited: 44
Protein-fold recognition using an improved single-source K diverse shortest paths algorithm. Proteins. 2016 Academic Article GET IT
Times cited: 5
Toward Repurposing Metformin as a Precision Anti-Cancer Therapy Using Structural Systems Pharmacology. Scientific reports. 2016 Academic Article GET IT
Times cited: 43
Providing data science support for systems pharmacology and its implications to drug discovery. Expert opinion on drug discovery. 2016 Review GET IT
Times cited: 32
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. Bioinformatics (Oxford, England). 2015 Academic Article GET IT
Times cited: 45
Developing multi-target therapeutics to fine-tune the evolutionary dynamics of the cancer ecosystem. Frontiers in pharmacology. 2015 Academic Article GET IT
Times cited: 45
A new method to improve network topological similarity search: applied to fold recognition. Bioinformatics (Oxford, England). 2015 Academic Article GET IT
Times cited: 13
Towards structural systems pharmacology to study complex diseases and personalized medicine. PLoS computational biology. 2014 Review GET IT
Times cited: 64
Anti-infectious drug repurposing using an integrated chemical genomics and structural systems biology approach. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2014 Academic Article GET IT
Times cited: 22
Antibacterial mechanisms identified through structural systems pharmacology. BMC systems biology. 2013 Academic Article GET IT
Times cited: 22
Novel computational approaches to polypharmacology as a means to define responses to individual drugs. Annual review of pharmacology and toxicology. 2011 Review GET IT
Times cited: 188

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Background

education and training

M.S., Rutgers-The State University of New Jersey 2000
Ph.D., Rutgers-The State University of New Jersey 2000
B.S., University of Science and Technology of China (China) 1990

Contact

full name

Lei Xie

primary email

lex4001@med.cornell.edu

VIVO Weill Cornell Medical College

Lei Xie Adjunct Professor of Neuroscience

Publications

selected publications

Background

education and training

Contact

full name

primary email