Lei Xie - RankMe

68 papers A* 2A 1B 2Misc 1Journal 56Unranked 6

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Adaptive Individual Uncertainty under Out-Of-Distribution Shift with Expert-Routed Conformal Prediction. CoRR Amitesh Badkul, Lei Xie
2025	J	`jnl`	Programmable Virtual Humans Toward Human Physiologically-Based Drug Discovery. CoRR You Wu, Philip E. Bourne, Lei Xie
2024	J	`jnl`	AI-driven multi-omics integration for multi-scale predictive modeling of causal genotype-environment-phenotype relationships. CoRR You Wu, Lei Xie
2024	—	`conf`	Audiovisual Multimodal Cough Data Analysis for Tuberculosis Detection. IISA Jyoti Yadav, Aparna S. Varde, Hao Liu, George Antoniou, Lei Xie
2023	J	`jnl`	A Universal Framework for Accurate and Efficient Geometric Deep Learning of Molecular Systems. CoRR Shuo Zhang, Yang Liu, Lei Xie
2023	B	`conf`	Comprehensive cough data analysis on CODA TB. IEEE Big Data Jyoti Yadav, Aparna S. Varde, Lei Xie
2023	J	`jnl`	Elucidation of genome-wide understudied proteins targeted by PROTAC-induced degradation using interpretable machine learning. PLoS Comput. Biol. Li Xie, Lei Xie
2023	J	`jnl`	End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins. PLoS Comput. Biol. 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
2023	J	`jnl`	Learning Universal and Robust 3D Molecular Representations with Graph Convolutional Networks. CoRR Shuo Zhang, Yang Liu, Li Xie, Lei Xie
2023	J	`jnl`	Protein Language Model-Powered 3D Ligand Binding Site Prediction from Protein Sequence. CoRR Shuo Zhang, Lei Xie
2022	J	`jnl`	A context-aware deconfounding autoencoder for robust prediction of personalized clinical drug response from cell-line compound screening. Nat. Mac. Intell. Di He, Qiao Liu, You Wu, Lei Xie
2022	J	`jnl`	Chemical-induced gene expression ranking and its application to pancreatic cancer drug repurposing. Patterns Thai-Hoang Pham, Yue Qiu, Jiahui Liu, Steven Zimmer, Eric E. O'Neill, Lei Xie, Ping Zhang
2022	J	`jnl`	Correction to "Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants". J. Chem. Inf. Model. Zheng Zhao, Lei Xie, Philip E. Bourne
2022	J	`jnl`	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. You Wu, Qiao Liu, Yue Qiu, Lei Xie
2022	J	`jnl`	DeepREAL: a deep learning powered multi-scale modeling framework for predicting out-of-distribution ligand-induced GPCR activity. Bioinform. Tian Cai, Kyra Alyssa Abbu, Yang Liu, Lei Xie
2022	J	`jnl`	Efficient and Accurate Physics-aware Multiplex Graph Neural Networks for 3D Small Molecules and Macromolecule Complexes. CoRR Shuo Zhang, Yang Liu, Lei Xie
2022	B	`conf`	Evolving Perceptions of Mental Health on Social Media and their Medical Impacts. IEEE Big Data Kenna Reagan, Aparna S. Varde, Lei Xie
2022	J	`jnl`	Exploration of chemical space with partial labeled noisy student self-training and self-supervised graph embedding. BMC Bioinform. Yang Liu, Hansaim Lim, Lei Xie
2022	A	`conf`	FAME: Fragment-based Conditional Molecular Generation for Phenotypic Drug Discovery. SDM Thai-Hoang Pham, Lei Xie, Ping Zhang
2022	J	`jnl`	Physics-aware Graph Neural Network for Accurate RNA 3D Structure Prediction. CoRR Shuo Zhang, Yang Liu, Lei Xie
2022	J	`jnl`	Small molecule modulation of microbiota: a systems pharmacology perspective. BMC Bioinform. Qiao Liu, Bohyun Lee, Lei Xie
2021	J	`jnl`	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. Hansaim Lim, Lei Xie
2021	J	`jnl`	A cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype. Bioinform. Di He, Lei Xie
2021	J	`jnl`	A deep learning framework for high-throughput mechanism-driven phenotype compound screening and its application to COVID-19 drug repurposing. Nat. Mach. Intell. Thai-Hoang Pham, Yue Qiu, Jucheng Zeng, Lei Xie, Ping Zhang
2021	J	`jnl`	CODE-AE: A Coherent De-confounding Autoencoder for Predicting Patient-Specific Drug Response From Cell Line Transcriptomics. CoRR Di He, Lei Xie
2021	J	`jnl`	COVID-19 Multi-Targeted Drug Repurposing Using Few-Shot Learning. Frontiers Bioinform. Yang Liu, You Wu, Xiaoke Shen, Lei Xie
2021	J	`jnl`	Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology. CoRR Tian Cai, Li Xie, Muge Chen, Yang Liu, Di He, Shuo Zhang, Cameron Mura, Philip E. Bourne, Lei Xie
2021	J	`jnl`	MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization. J. Chem. Inf. Model. Tian Cai, Hansaim Lim, Kyra Alyssa Abbu, Yue Qiu, Ruth Nussinov, Lei Xie
2021	J	`jnl`	TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations. PLoS Comput. Biol. Qiao Liu, Lei Xie
2020	J	`jnl`	A Bayesian approach to accurate and robust signature detection on LINCS L1000 data. Bioinform. Yue Qiu, Tianhuan Lu, Hansaim Lim, Lei Xie
2020	J	`jnl`	A Cross-Level Information Transmission Network for Predicting Phenotype from New Genotype: Application to Cancer Precision Medicine. CoRR Di He, Lei Xie
2020	A*	`conf`	Improving Attention Mechanism in Graph Neural Networks via Cardinality Preservation. IJCAI Shuo Zhang, Lei Xie
2020	J	`jnl`	Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures. CoRR Shuo Zhang, Yang Liu, Lei Xie
2019	J	`jnl`	Biological representation of chemicals using latent target interaction profile. BMC Bioinform. Mohamed Ayed, Hansaim Lim, Lei Xie
2019	J	`jnl`	Improving Attention Mechanism in Graph Neural Networks via Cardinality Preservation. CoRR Shuo Zhang, Lei Xie
2019	J	`jnl`	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. Qiao Liu, Di He, Lei Xie
2019	J	`jnl`	Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology. PLoS Comput. Biol. Hansaim Lim, Di He, Yue Qiu, Patrycja Krawczuk, Xiaoru Sun, Lei Xie
2019	J	`jnl`	Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants. J. Chem. Inf. Model. Zheng Zhao, Lei Xie, Philip E. Bourne
2018	J	`jnl`	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. Annie Wang, Hansaim Lim, Shu-Yuan Cheng, Lei Xie
2018	—	`conf`	Target Gene Prediction of Transcription Factor Using a New Neighborhood-regularized Tri-factorization One-class Collaborative Filtering Algorithm. BCB Hansaim Lim, Lei Xie
2018	J	`jnl`	The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications. BMC Bioinform. Xiaoming Liu, Lei Xie, Zhijin Wu, Kai Wang, Zhongming Zhao, Jianhua Ruan, Degui Zhi
2017	—	`conf`	Confused or not Confused?: Disentangling Brain Activity from EEG Data Using Bidirectional LSTM Recurrent Neural Networks. BCB Zhaoheng Ni, Ahmet Cem Yuksel, Xiuyan Ni, Michael I. Mandel, Lei Xie
2017	J	`jnl`	Cross-Dependency Inference in Multi-Layered Networks: A Collaborative Filtering Perspective. ACM Trans. Knowl. Discov. Data Chen Chen, Hanghang Tong, Lei Xie, Lei Ying, Qing He
2017	J	`jnl`	JDINAC: joint density-based non-parametric differential interaction network analysis and classification using high-dimensional sparse omics data. Bioinform. Jiadong Ji, Di He, Yang Feng, Yong He, Fuzhong Xue, Lei Xie
2017	—	`conf`	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 Qiao Liu, Chen Chen, Annie Gao, Hanghang Tong, Lei Xie
2016	J	`jnl`	Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology. BMC Bioinform. Zheng Zhao, Che L. Martin, Raymond Fan, Philip E. Bourne, Lei Xie
2016	A*	`conf`	FASCINATE: Fast Cross-Layer Dependency Inference on Multi-layered Networks. KDD Chen Chen, Hanghang Tong, Lei Xie, Lei Ying, Qing He
2016	J	`jnl`	Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing. PLoS Comput. Biol. Hansaim Lim, Aleksandar Poleksic, Yuan Yao, Hanghang Tong, Di He, Luke Zhuang, Patrick Meng, Lei Xie
2015	J	`jnl`	A new method to improve network topological similarity search: applied to fold recognition. Bioinform. John Lhota, Ruth Hauptman, Thomas Hart, Clara Ng, Lei Xie
2015	—	`conf`	Supervised Link Prediction Using Random Walks. SMP Yuechang Liu, Hanghang Tong, Lei Xie, Yong Tang
2014	Misc	`conf`	Anti-Infectious Drug Repurposing Using an Integrated Chemical Genomics and Structural Systems Biology Approach. Pacific Symposium on Biocomputing Clara Ng, Ruth Hauptman, Yinliang Zhang, Philip E. Bourne, Lei Xie
2014	J	`jnl`	Towards Structural Systems Pharmacology to Study Complex Diseases and Personalized Medicine. PLoS Comput. Biol. Lei Xie, Xiaoxia Ge, Hepan Tan, Li Xie, Yinliang Zhang, Thomas Hart, Xiaowei Yang, Philip E. Bourne
2013	J	`jnl`	Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst. Biol. Roger L. Chang, Lei Xie, Philip E. Bourne, Bernhard O. Palsson
2012	—	`conf`	An integrated workflow for proteome-wide off-target identification and polypharmacology drug design. BIBM Workshops Thomas Evangelidis, Philip E. Bourne, Li Xie, Lei Xie
2011	J	`jnl`	A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing. J. Chem. Inf. Model. Sarah L. Kinnings, Nina Liu, Peter J. Tonge, Richard M. Jackson, Lei Xie, Philip E. Bourne
2011	J	`jnl`	Correction to "A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing". J. Chem. Inf. Model. Sarah L. Kinnings, Nina Liu, Peter J. Tonge, Richard M. Jackson, Lei Xie, Philip E. Bourne
2011	J	`jnl`	Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir. PLoS Comput. Biol. Li Xie, Thomas Evangelidis, Lei Xie, Philip E. Bourne
2010	J	`jnl`	A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. PLoS Comput. Biol. 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
2010	J	`jnl`	Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model. PLoS Comput. Biol. Roger L. Chang, Li Xie, Lei Xie, Philip E. Bourne, Bernhard Ø. Palsson
2010	J	`jnl`	SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison. Nucleic Acids Res. Jingyuan Ren, Lei Xie, Wilfred W. Li, Philip E. Bourne
2010	J	`jnl`	The PLoS Comput. Biol. Sarah L. Kinnings, Li Xie, Kingston H. Fung, Richard M. Jackson, Lei Xie, Philip E. Bourne
2009	J	`jnl`	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. Lei Xie, Li Xie, Philip E. Bourne
2009	J	`jnl`	Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors. PLoS Comput. Biol. Li Xie, Jerry Li, Lei Xie, Philip E. Bourne
2009	J	`jnl`	Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis. PLoS Comput. Biol. Sarah L. Kinnings, Nina Liu, Nancy Buchmeier, Peter J. Tonge, Lei Xie, Philip E. Bourne
2007	J	`jnl`	A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. BMC Bioinform. Lei Xie, Philip E. Bourne
2007	J	`jnl`	In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators. PLoS Comput. Biol. Lei Xie, Jian Wang, Philip E. Bourne
2006	J	`jnl`	The RCSB PDB information portal for structural genomics. Nucleic Acids Res. Andrei Kouranov, Lei Xie, Joanna de la Cruz, Li Chen, John D. Westbrook, Philip E. Bourne, Helen M. Berman
2005	J	`jnl`	Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models. PLoS Comput. Biol. Lei Xie, Philip E. Bourne