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ORCIDLei Xie 0006
Person information
- affiliation: City University of New York, Department of Computer Science, Hunter College, NY, USA
- affiliation (former): University of California, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, La Jolla, CA, USA
Other persons with the same name
- Lei Xie — disambiguation page
- Lei Xie 0001
![[0000-0001-8234-0823]](https://dblp.org/img/orcid-mark.12x12.png "0000-0001-8234-0823")
— Northwestern Polytechnical University, School of Computer Science, Xi'an, China (and 4 more) - Lei Xie 0002 — Xi'an Jiaotong University, China
- Lei Xie 0003 — Zhejiang University, College of Information Science and Electronic Engineering, Hangzhou, China
- Lei Xie 0004 — Nanjing University, State Key Laboratory for Novel Software Technology, China
- Lei Xie 0005 — Delft University of Technology, Laboratory of Computer Engineering, The Netherlands
- Lei Xie 0007 — Zhejiang University, State Key Laboratory of Industrial Control Technology, Hangzhou, China (and 2 more)
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2020 – today
- 2023
[j42]Tian Cai, Li Xie, Shuo Zhang, Muge Chen, Di He, Amitesh Badkul, Yang Liu, Hari Krishna Namballa, Michael Dorogan, Wayne W. Harding, Cameron Mura, Philip E. Bourne, Lei Xie:
End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins. PLoS Comput. Biol. 19(1) (2023)- [j41]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) - [c11]Jyoti Yadav, Aparna S. Varde, Lei Xie:
Comprehensive cough data analysis on CODA TB. IEEE Big Data 2023: 6311-6313 - [i9]Shuo Zhang, Yang Liu, Li Xie, Lei Xie:
Learning Universal and Robust 3D Molecular Representations with Graph Convolutional Networks. CoRR abs/2307.12491 (2023) - [i8]Shuo Zhang, Yang Liu, Lei Xie:
A Universal Framework for Accurate and Efficient Geometric Deep Learning of Molecular Systems. CoRR abs/2311.11228 (2023) - 2022
- [j40]Yang Liu, Hansaim Lim, Lei Xie:
Exploration of chemical space with partial labeled noisy student self-training and self-supervised graph embedding. BMC Bioinform. 23-S(3): 158 (2022) - [j39]Qiao Liu, Bohyun Lee, Lei Xie:
Small molecule modulation of microbiota: a systems pharmacology perspective. BMC Bioinform. 23-S(3): 403 (2022) - [j38]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): 223-224 (2022) - [j37]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): 879-892 (2022) - [j36]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): 100441 (2022) - [j35]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) - [c10]Kenna Reagan, Aparna S. Varde, Lei Xie:
Evolving Perceptions of Mental Health on Social Media and their Medical Impacts. IEEE Big Data 2022: 5328-5337 - [c9]Thai-Hoang Pham, Lei Xie, Ping Zhang:
FAME: Fragment-based Conditional Molecular Generation for Phenotypic Drug Discovery. SDM 2022: 720-728 - [i7]Shuo Zhang, Yang Liu, Lei Xie:
Efficient and Accurate Physics-aware Multiplex Graph Neural Networks for 3D Small Molecules and Macromolecule Complexes. CoRR abs/2206.02789 (2022) - [i6]Shuo Zhang, Yang Liu, Lei Xie:
Physics-aware Graph Neural Network for Accurate RNA 3D Structure Prediction. CoRR abs/2210.16392 (2022) - 2021
- [j34]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): 204-210 (2021) - [j33]Yang Liu, You Wu, Xiaoke Shen, Lei Xie:
COVID-19 Multi-Targeted Drug Repurposing Using Few-Shot Learning. Frontiers Bioinform. 1 (2021) - [j32]Tian Cai, Hansaim Lim, Kyra Alyssa Abbu, Yue Qiu, Ruth Nussinov, Lei Xie:
MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization. J. Chem. Inf. Model. 61(4): 1570-1582 (2021) - [j31]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): 247-257 (2021) - [j30]Qiao Liu, Lei Xie:
TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations. PLoS Comput. Biol. 17(2) (2021) - [j29]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): 126-137 (2021) - [i5]Di He, Lei Xie:
CODE-AE: A Coherent De-confounding Autoencoder for Predicting Patient-Specific Drug Response From Cell Line Transcriptomics. CoRR abs/2102.00538 (2021) - [i4]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 abs/2111.14283 (2021) - 2020
- [j28]Yue Qiu, Tianhuan Lu, Hansaim Lim, Lei Xie:
A Bayesian approach to accurate and robust signature detection on LINCS L1000 data. Bioinform. 36(9): 2787-2795 (2020) - [c8]Shuo Zhang, Lei Xie:
Improving Attention Mechanism in Graph Neural Networks via Cardinality Preservation. IJCAI 2020: 1395-1402 - [i3]Di He, Lei Xie:
A Cross-Level Information Transmission Network for Predicting Phenotype from New Genotype: Application to Cancer Precision Medicine. CoRR abs/2010.04824 (2020) - [i2]Shuo Zhang, Yang Liu, Lei Xie:
Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures. CoRR abs/2011.07457 (2020)
2010 – 2019
- 2019
- [j27]Mohamed Ayed, Hansaim Lim, Lei Xie:
Biological representation of chemicals using latent target interaction profile. BMC Bioinform. 20-S(24): 674 (2019) - [j26]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): 453-462 (2019) - [j25]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) - [j24]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) - [i1]Shuo Zhang, Lei Xie:
Improving Attention Mechanism in Graph Neural Networks via Cardinality Preservation. CoRR abs/1907.02204 (2019) - 2018
- [j23]Xiaoming Liu, Lei Xie, Zhijin Wu, Kai Wang, Zhongming Zhao, Jianhua Ruan, Degui Zhi:
The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications. BMC Bioinform. 19-S(17): 492:1-492:3 (2018) - [j22]Annie Wang, Hansaim Lim, Shu-Yuan Cheng, Lei Xie:
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. 15(6): 1960-1967 (2018) - [c7]Hansaim Lim, Lei Xie:
Target Gene Prediction of Transcription Factor Using a New Neighborhood-regularized Tri-factorization One-class Collaborative Filtering Algorithm. BCB 2018: 1-10 - 2017
- [j21]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): 3080-3087 (2017) - [j20]Chen Chen, Hanghang Tong, Lei Xie, Lei Ying, Qing He:
Cross-Dependency Inference in Multi-Layered Networks: A Collaborative Filtering Perspective. ACM Trans. Knowl. Discov. Data 11(4): 42:1-42:26 (2017) - [c6]Zhaoheng Ni, Ahmet Cem Yuksel, Xiuyan Ni, Michael I. Mandel, Lei Xie:
Confused or not Confused?: Disentangling Brain Activity from EEG Data Using Bidirectional LSTM Recurrent Neural Networks. BCB 2017: 241-246 - [c5]Qiao Liu, Chen Chen, Annie Gao, Hanghang Tong, Lei Xie:
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. BIBM 2017: 2177-2182 - 2016
- [j19]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: 90 (2016) - [j18]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) - [c4]Chen Chen, Hanghang Tong, Lei Xie, Lei Ying, Qing He:
FASCINATE: Fast Cross-Layer Dependency Inference on Multi-layered Networks. KDD 2016: 765-774 - 2015
- [j17]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): 2106-2114 (2015) - [c3]Yuechang Liu, Hanghang Tong, Lei Xie, Yong Tang:
Supervised Link Prediction Using Random Walks. SMP 2015: 107-118 - 2014
- [j16]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) - [c2]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: 136-147 - 2013
- [j15]Roger L. Chang, Lei Xie, Philip E. Bourne, Bernhard O. Palsson:
Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst. Biol. 7: 102 (2013) - 2012
- [c1]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: 32-39 - 2011
- [j14]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): 408-419 (2011) - [j13]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): 1195-1197 (2011) - [j12]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) - 2010
- [j11]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): 441-444 (2010) - [j10]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) - [j9]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) - [j8]Sarah L. Kinnings, Li Xie, Kingston H. Fung, Richard M. Jackson, Lei Xie, Philip E. Bourne:
The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications. PLoS Comput. Biol. 6(11) (2010)
2000 – 2009
- 2009
- [j7]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) - [j6]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) - [j5]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) - 2007
- [j4]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) - [j3]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) - 2006
- [j2]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): 302-305 (2006) - 2005
- [j1]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)
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