A Fast Agglomerate Algorithm for Mining Functional Modules in Protein Interaction Networks. - Min Li 007; Jianxin Wang 001; Jianer Chen (BMEI (1), 2008)

An Improved Method Based on Maximal Clique for Predicting Interactions in Protein Interaction Networks. - Jianxin Wang 001; Zhao Cai; Min Li 007 (BMEI (1), 2008)

Greedily Mining l-dense Subgraphs in Protein Interaction Networks. - Min Li 007; Jianxin Wang 001; Jianer Chen; Bin Hu 001 (ICYCS, 2008)

A Graph-Theoretic Method for Mining Overlapping Functional Modules in Protein Interaction Networks. - Min Li 007; Jianxin Wang 001; Jianer Chen (ISBRA, 2008)

Modifying the DPClus algorithm for identifying protein complexes based on new topological structures. - Min Li 007; Jianer Chen; Jianxin Wang 001; Bin Hu 001; Gang Chen 010 (BMC Bioinform., 2008)

GO Semantic Similarity Based Analysis for Huaman Protein Interactions. - Gang Chen 010; Jianxin Wang 001; Min Li 007 (IJCBS, 2009)

GO Semantic Similarity-Based False Positive Reduction of Protein-Protein Interactions. - Jianxin Wang 001; Lijian Dai; Min Li 007 (IJCBS, 2009)

Hierarchical Organization of Functional Modules in Weighted Protein Interaction Networks Using Clustering Coefficient. - Min Li 007; Jianxin Wang 001; Jianer Chen; Yi Pan 001 (ISBRA, 2009)

Essential Proteins Discovery from Weighted Protein Interaction Networks. - Min Li 007; Jianxin Wang 001; Huan Wang; Yi Pan 001 (ISBRA, 2010)

An Agglomerate Algorithm for Mining Overlapping and Hierarchical Functional Modules in Protein Interaction Networks. - Jun Ren; Jianxin Wang 001; Jianer Chen; Min Li 007; Gang Chen 010 (ISBRA, 2010)

Identifying the overlapping complexes in protein interaction networks. - Min Li 007; Jianxin Wang 001; Jianer Chen; Zhao Cai; Gang Chen 010 (Int. J. Data Min. Bioinform., 2010)

Essential Protein Discovery Based on Network Motif and Gene Ontology. - Wooyoung Kim; Min Li 007; Jianxin Wang 001; Yi Pan 001 (BIBM, 2011)

A New Measurement for Evaluating Clusters in Protein Interaction Networks. - Min Li 007; Xuehong Wu; Jianxin Wang 001; Yi Pan 001 (BIBM, 2011)

Active Protein Interaction Network and Its Application on Protein Complex Detection. - Jianxin Wang 001; Xiaoqing Peng; Min Li 007; Yong Luo; Yi Pan 001 (BIBM, 2011)

Prediction of Essential Proteins by Integration of PPI Network Topology and Protein Complexes Information. - Jun Ren; Jianxin Wang 001; Min Li 007; Huan Wang; Binbin Liu (ISBRA, 2011)

A New Method for Identifying Essential Proteins Based on Edge Clustering Coefficient. - Huan Wang; Min Li 007; Jianxin Wang 001; Yi Pan 001 (ISBRA, 2011)

A comparison of the functional modules identified from time course and static PPI network data. - Xiwei Tang; Jianxin Wang 001; Binbin Liu; Min Li 007; Gang Chen 010; Yi Pan 001 (BMC Bioinform., 2011)

Biological network motif detection and evaluation. - Wooyoung Kim; Min Li 007; Jianxin Wang 001; Yi Pan 001 (BMC Syst. Biol., 2011)

Integration of breast cancer gene signatures based on graph centrality. - Jianxin Wang 001; Gang Chen 010; Min Li 007; Yi Pan 001 (BMC Syst. Biol., 2011)

A local average connectivity-based method for identifying essential proteins from the network level. - Min Li 007; Jianxin Wang 001; Xiang Chen; Huan Wang; Yi Pan 001 (Comput. Biol. Chem., 2011)

A Fast Hierarchical Clustering Algorithm for Functional Modules Discovery in Protein Interaction Networks. - Jianxin Wang 001; Min Li 007; Jianer Chen; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Identifying protein complexes based on local fitness method. - Jun Ren; Jianxin Wang 001; Min Li 007 (BIBM, 2012)

Sparse kernel logistic regression for β-turns prediction. - Murtada Khalafallah Elbashir; Jianxin Wang 001; Fang-Xiang Wu; Min Li 007 (ISB, 2012)

Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data. - Min Li 007; Xuehong Wu; Jianxin Wang 001; Yi Pan 001 (BMC Bioinform., 2012)

A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data. - Min Li 007; Hanhui Zhang; Jianxin Wang 001; Yi Pan 001 (BMC Syst. Biol., 2012)

Identification of Essential Proteins Based on Edge Clustering Coefficient. - Jianxin Wang 001; Min Li 007; Huan Wang; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Prioritization of candidate genes based on disease similarity and protein's proximity in PPI networks. - Gamage Upeksha Ganegoda; Jianxin Wang 001; Fang-Xiang Wu; Min Li 007 (BIBM, 2013)

Identifying dynamic protein complexes based on gene expression profiles and PPI networks. - Min Li 007; Weijie Chen; Jianxin Wang 001; Fang-Xiang Wu; Yi Pan 001 (BIBM, 2013)

A new method for predicting essential proteins based on topology potential. - Yu Lu; Min Li 007; Qi Li; Yi Pan 001; Jianxin Wang 001 (BIBM, 2013)

A clustering algorithm for identifying hierarchical and overlapping protein complexes in large PPI networks. - Jun Ren; Jianxin Wang 001; Min Li 007 (BIBM, 2013)

A novel algorithm for mining protein complex from the weighted network. - Xiwei Tang; Jianxin Wang 001; Min Li 007; Yiming He; Yi Pan 001 (BIBM, 2013)

Identifying protein complexes based on density and modularity in protein-protein interaction network. - Jun Ren; Jianxin Wang 001; Min Li 007; Lusheng Wang 001 (BMC Syst. Biol., 2013)

An effective method for refining predicted protein complexes based on protein activity and the mechanism of protein complex formation. - Jianxin Wang 001; Xiaoqing Peng; Qianghua Xiao; Min Li 007; Yi Pan 001 (BMC Syst. Biol., 2013)

Identification of Essential proteins from Weighted protein-protein Interaction Networks. - Min Li 007; Jianxin Wang 001; Huan Wang; Yi Pan 001 (J. Bioinform. Comput. Biol., 2013)

A logistic regression based algorithm for identifying human disease genes. - Bolin Chen; Min Li 007; Jianxin Wang 001; Fang-Xiang Wu (BIBM, 2014)

Searching SNP Combinations Related to Evolutionary Information of Human Populations on HapMap Data. - Xiaojun Ding; Haihua Gu; Zhen Zhang 024; Min Li 007; Fang-Xiang Wu (ISBRA, 2014)

Identification of Essential Proteins by Using Complexes and Interaction Network. - Min Li 007; Yu Lu; Zhibei Niu; Fang-Xiang Wu; Yi Pan 001 (ISBRA, 2014)

Drug Target Identification Based on Structural Output Controllability of Complex Networks. - Lin Wu; Yichao Shen; Min Li 007; Fang-Xiang Wu (ISBRA, 2014)

Prediction of disease genes using tissue-specified gene-gene network. - Gamage Upeksha Ganegoda; Jianxin Wang 001; Fang-Xiang Wu; Min Li 007 (BMC Syst. Biol., 2014)

Improving protein function prediction using domain and protein complexes in PPI networks. - Wei Peng 004; Jianxin Wang 001; Juan Cai; Lu Chen; Min Li 007; Fang-Xiang Wu (BMC Syst. Biol., 2014)

Detecting Protein Complexes Basedon Uncertain Graph Model. - Bihai Zhao; Jianxin Wang 001; Min Li 007; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

A two-step logistic regression algorithm for identifying individual-cancer-related genes. - Bolin Chen; Xuequn Shang 001; Min Li 007; Jianxin Wang 001; Fang-Xiang Wu (BIBM, 2015)

Predicting microRNA-disease associations by integrating multiple biological information. - Wei Lan; Jianxin Wang 001; Min Li 007; Jin Liu 012; Yi Pan 001 (BIBM, 2015)

EPGA2: memory-efficient de novo assembler. - Junwei Luo; Jianxin Wang 001; Weilong Li; Zhen Zhang 024; Fang-Xiang Wu; Min Li 007; Yi Pan 001 (Bioinform., 2015)

EPGA: de novo assembly using the distributions of reads and insert size. - Junwei Luo; Jianxin Wang 001; Zhen Zhang 024; Fang-Xiang Wu; Min Li 007; Yi Pan 001 (Bioinform., 2015)

CytoNCA: A cytoscape plugin for centrality analysis and evaluation of protein interaction networks. - Yu Tang; Min Li 007; Jianxin Wang 001; Yi Pan 001; Fang-Xiang Wu (Biosyst., 2015)

Re-alignment of the unmapped reads with base quality score. - Xiaoqing Peng; Jianxin Wang 001; Zhen Zhang 024; Qianghua Xiao; Min Li 007; Yi Pan 001 (BMC Bioinform., 2015)

Proteins involved in more domain types tend to be more essential. - Lu Chen; Yingjiao Cheng; Min Li 007; Jianxin Wang 001 (Int. J. Bioinform. Res. Appl., 2015)

Identifying protein complexes based on the integration of PPI network and gene expression data. - Weijie Chen; Min Li 007; Xuehong Wu; Jianxin Wang 001 (Int. J. Bioinform. Res. Appl., 2015)

Discovering essential proteins based on PPI network and protein complex. - Jun Ren; Jianxin Wang 001; Min Li 007; Fang-Xiang Wu (Int. J. Data Min. Bioinform., 2015)

A Topology Potential-Based Method for Identifying Essential Proteins from PPI Networks. - Min Li 007; Yu Lu; Jianxin Wang 001; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

ClusterViz: A Cytoscape APP for Cluster Analysis of Biological Network. - Jianxin Wang 001; Jiancheng Zhong; Gang Chen 010; Min Li 007; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

An Apache Spark Implementation of Block Power Method for Computing Dominant Eigenvalues and Eigenvectors of Large-Scale Matrices. - Hao Ji; Seth H. Weinberg; Min Li 007; Jianxin Wang 001; Yaohang Li (BDCloud-SocialCom-SustainCom, 2016)

Predicting microRNA-environmental factor interactions based on bi-random walk and multi-label learning. - Wei Lan; Jianxin Wang 001; Min Li 007; Chengqian Lu; Fang-Xiang Wu; Yi Pan 001 (BIBM, 2016)

Construction of the spatial and temporal active protein interaction network for identifying protein complexes. - Xiangmao Meng; Min Li 007; Jianxin Wang 001; Fang-Xiang Wu; Yi Pan 001 (BIBM, 2016)

The MSS of complex networks with centrality based preference and its application to biomolecular networks. - Lin Wu; Lingkai Tang; Min Li 007; Jianxin Wang 001; Fang-Xiang Wu (BIBM, 2016)

Identifying Essential Proteins by Purifying Protein Interaction Networks. - Min Li 007; Xiaopei Chen; Peng Ni; Jianxin Wang 001; Yi Pan 001 (ISBRA, 2016)

Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm. - Huimin Luo; Jianxin Wang 001; Min Li 007; Junwei Luo; Xiaoqing Peng; Fang-Xiang Wu; Yi Pan 001 (Bioinform., 2016)

C-DEVA: Detection, evaluation, visualization and annotation of clusters from biological networks. - Min Li 007; Yu Tang; Xuehong Wu; Jianxin Wang 001; Fang-Xiang Wu; Yi Pan 001 (Biosyst., 2016)

Predicting essential proteins based on subcellular localization, orthology and PPI networks. - Gaoshi Li; Min Li 007; Jianxin Wang 001; Jingli Wu; Fang-Xiang Wu; Yi Pan 001 (BMC Bioinform., 2016)

FLEXc: protein flexibility prediction using context-based statistics, predicted structural features, and sequence information. - Ashraf Yaseen; Mais Nijim; Brandon Williams; Lei Qian; Min Li 007; Jianxin Wang 001; Yaohang Li (BMC Bioinform., 2016)

Predicting drug-target interaction using positive-unlabeled learning. - Wei Lan; Jianxin Wang 001; Min Li 007; Jin Liu 012; Yaohang Li; Fang-Xiang Wu; Yi Pan 001 (Neurocomputing, 2016)

HybridDock: A Hybrid Protein-Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches. - Sheng-You Huang; Min Li 007; Jianxin Wang 001; Yi Pan 001 (J. Chem. Inf. Model., 2016)

An interpretable model for predicting side effects of analgesics for osteoarthritis. - Liangliang Liu 001; Jianxin Wang 001; Min Li 007; Fang-Xiang Wu; Hong-Dong Li; Ying Yu; Zhihui Fei (BIBM, 2017)

MEC: Misassembly error correction in contigs using a combination of paired-end reads and GC-contents. - Binbin Wu; Jianxin Wang 001; Junwei Luo; Min Li 007; Fang-Xiang Wu; Yi Pan 001 (BIBM, 2017)

LSLS: A Novel Scaffolding Method Based on Path Extension. - Min Li 007; Li Tang; Zhongxiang Liao; Junwei Luo; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (ICIC (2), 2017)

Construction of Protein Backbone Fragments Libraries on Large Protein Sets Using a Randomized Spectral Clustering Algorithm. - Wessam Elhefnawy; Min Li 007; Jianxin Wang 001; Yaohang Li (ISBRA, 2017)

Relating Diseases Based on Disease Module Theory. - Peng Ni; Min Li 007; Ping Zhong 002; Guihua Duan; Jianxin Wang 001; Yaohang Li; Fang-Xiang Wu (ISBRA, 2017)

LDAP: a web server for lncRNA-disease association prediction. - Wei Lan; Min Li 007; Kaijie Zhao; Jin Liu 012; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (Bioinform., 2017)

BOSS: a novel scaffolding algorithm based on an optimized scaffold graph. - Junwei Luo; Jianxin Wang 001; Zhen Zhang 024; Min Li 007; Fang-Xiang Wu (Bioinform., 2017)

VAliBS: a visual aligner for bisulfite sequences. - Min Li 007; Ping Huang; Xiaodong Yan; Jianxin Wang 001; Yi Pan 001; Fang-Xiang Wu (BMC Bioinform., 2017)

PECC: Correcting contigs based on paired-end read distribution. - Min Li 007; Binbin Wu; Xiaodong Yan; Junwei Luo; Yi Pan 001; Fang-Xiang Wu; Jianxin Wang 001 (Comput. Biol. Chem., 2017)

Complex Brain Network Analysis and Its Applications to Brain Disorders: A Survey. - Jin Liu 012; Min Li 007; Yi Pan 001; Wei Lan; Ruiqing Zheng; Fang-Xiang Wu; Jianxin Wang 001 (Complex., 2017)

ISEA: Iterative Seed-Extension Algorithm for De Novo Assembly Using Paired-End Information and Insert Size Distribution. - Min Li 007; Zhongxiang Liao; Yiming He; Jianxin Wang 001; Junwei Luo; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

United Complex Centrality for Identification of Essential Proteins from PPI Networks. - Min Li 007; Yu Lu; Zhibei Niu; Fang-Xiang Wu (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Predicting Protein Functions by Using Unbalanced Random Walk Algorithm on Three Biological Networks. - Wei Peng 004; Min Li 007; Lu Chen; Lusheng Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Protein Inference from the Integration of Tandem MS Data and Interactome Networks. - Jiancheng Zhong; Jianxin Wang 001; Xiaojun Ding; Zhen Zhang 024; Min Li 007; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Disease Inference with Symptom Extraction and Bidirectional Recurrent Neural Network. - Donglin Guo; Min Li 007; Ying Yu; Yaohang Li; Guihua Duan; Fang-Xiang Wu; Jianxin Wang 001 (BIBM, 2018)

A Deep Learning Framework for Identifying Essential Proteins Based on Protein-Protein Interaction Network and Gene Expression Data. - Min Zeng; Min Li 007; Zhihui Fei; Fang-Xiang Wu; Yaohang Li; Yi Pan 001 (BIBM, 2018)

Using Deep Neural Network to Predict Drug Sensitivity of Cancer Cell Lines. - Yake Wang; Min Li 007; Ruiqing Zheng; Xinghua Shi; Yaohang Li; Fang-Xiang Wu; Jianxin Wang 001 (ICIC (2), 2018)

Sprites2: Detection of Deletions Based on an Accurate Alignment Strategy. - Zhen Zhang 024; Jianxin Wang 001; Junwei Luo; Juan Shang; Min Li 007; Fang-Xiang Wu; Yi Pan 001 (ISBRA, 2018)

PBMarsNet: A Multivariate Adaptive Regression Splines Based Method to Reconstruct Gene Regulatory Networks. - Siyu Zhao; Ruiqing Zheng; Xiang Chen; Yaohang Li; Fang-Xiang Wu; Min Li 007 (ISBRA, 2018)

Multi-scale Deep Convolutional Neural Network for Stroke Lesions Segmentation on CT Images. - Liangliang Liu 001; Shuai Yang; Li Meng; Min Li 007; Jianxin Wang 001 (BrainLes@MICCAI (1), 2018)

Applications of deep learning to MRI images: A survey. - Jin Liu 012; Yi Pan 001; Min Li 007; Ziyue Chen; Lu Tang; Chengqian Lu; Jianxin Wang 001 (Big Data Min. Anal., 2018)

A survey of matrix completion methods for recommendation systems. - Andy Ramlatchan; Mengyun Yang; Quan Liu; Min Li 007; Jianxin Wang 001; Yaohang Li (Big Data Min. Anal., 2018)

DyNetViewer: a Cytoscape app for dynamic network construction, analysis and visualization. - Min Li 007; Jie Yang 057; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (Bioinform., 2018)

Prediction of lncRNA-disease associations based on inductive matrix completion. - Chengqian Lu; Mengyun Yang; Feng Luo 001; Fang-Xiang Wu; Min Li 007; Yi Pan 001; Yaohang Li; Jianxin Wang 001 (Bioinform., 2018)

Computational drug repositioning using low-rank matrix approximation and randomized algorithms. - Huimin Luo; Min Li 007; Shaokai Wang; Quan Liu; Yaohang Li; Jianxin Wang 001 (Bioinform., 2018)

CytoCtrlAnalyser: a Cytoscape app for biomolecular network controllability analysis. - Lin Wu; Min Li 007; Jianxin Wang 001; Fang-Xiang Wu (Bioinform., 2018)

Biomolecular Networks for Complex Diseases. - Fang-Xiang Wu; Jianxin Wang 001; Min Li 007; Haiying Wang 001 (Complex., 2018)

Predicting MicroRNA-Disease Associations Based on Improved MicroRNA and Disease Similarities. - Wei Lan; Jianxin Wang 001; Min Li 007; Jin Liu 012; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Classification of Alzheimer's Disease Using Whole Brain Hierarchical Network. - Jin Liu 012; Min Li 007; Wei Lan; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

DoRC: Discovery of rare cells from ultra-large scRNA-seq data. - Xiang Chen; Fang-Xiang Wu; Jin Chen 004; Min Li 007 (BIBM, 2019)

Classification of Schizophrenia by Iterative Random Forest Feature Selection Based on DNA Methylation Array Data. - Xinyu Hu; Min Li 007; Linconghua Wang; Xingyi Li; Fang-Xiang Wu; Jianxin Wang 001 (BIBM, 2019)

DualRank: multiplex network-based dual ranking for heterogeneous complex disease analysis. - Xingyi Li; Ju Xiang; Xinyu Hu; Fang-Xiang Wu; Min Li 007 (BIBM, 2019)

HNEDTI: Prediction of drug-target interaction based on heterogeneous network embedding. - Zhangli Lu; Yake Wang; Min Zeng; Min Li 007 (BIBM, 2019)

Detecting protein complex based on hierarchical compressing network embedding. - Xiangmao Meng; Xiaoqing Peng; Fang-Xiang Wu; Min Li 007 (BIBM, 2019)

Tentative diagnosis prediction via deep understanding of patient narratives. - Ying Yu; Min Li 007; Liangliang Liu 001; Fang-Xiang Wu; Jianxin Wang 001 (BIBM, 2019)

LncRNA-disease association prediction through combining linear and non-linear features with matrix factorization and deep learning techniques. - Min Zeng; Chengqian Lu; Fuhao Zhang; Zhangli Lu; Fang-Xiang Wu; Yaohang Li; Min Li 007 (BIBM, 2019)

Identification of Prognostic and Heterogeneous Breast Cancer Biomarkers Based on Fusion Network and Multiple Scoring Strategies. - Xingyi Li; Ju Xiang; Jianxin Wang 001; Fang-Xiang Wu; Min Li 007 (ICIC (2), 2019)

Control principles for complex biological networks. - Min Li 007; Hao Gao; Jianxin Wang 001; Fang-Xiang Wu (Briefings Bioinform., 2019)

Clinical big data and deep learning: Applications, challenges, and future outlooks. - Ying Yu; Min Li 007; Liangliang Liu 001; Yaohang Li; Jianxin Wang 001 (Big Data Min. Anal., 2019)

SCOP: a novel scaffolding algorithm based on contig classification and optimization. - Min Li 007; Li Tang; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (Bioinform., 2019)

BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks. - Ruiqing Zheng; Min Li 007; Xiang Chen; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (Bioinform., 2019)

SinNLRR: a robust subspace clustering method for cell type detection by non-negative and low-rank representation. - Ruiqing Zheng; Min Li 007; Zhenlan Liang; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (Bioinform., 2019)

DeepEP: a deep learning framework for identifying essential proteins. - Min Zeng; Min Li 007; Fang-Xiang Wu; Yaohang Li; Yi Pan 001 (BMC Bioinform., 2019)

Deep learning for biological/clinical data. - Fang-Xiang Wu; Min Li 007 (Neurocomputing, 2019)

Automatic ICD-9 coding via deep transfer learning. - Min Zeng; Min Li 007; Zhihui Fei; Ying Yu; Yi Pan 001; Jianxin Wang 001 (Neurocomputing, 2019)

Automatic ICD code assignment of Chinese clinical notes based on multilayer attention BiRNN. - Ying Yu; Min Li 007; Liangliang Liu 001; Zhihui Fei; Fang-Xiang Wu; Jianxin Wang 001 (J. Biomed. Informatics, 2019)

Decoding the Structural Keywords in Protein Structure Universe. - Wessam Elhefnawy; Min Li 007; Jianxin Wang 001; Yaohang Li (J. Comput. Sci. Technol., 2019)

Controllability and Its Applications to Biological Networks. - Lin Wu; Min Li 007; Jianxin Wang 001; Fang-Xiang Wu (J. Comput. Sci. Technol., 2019)

Correlation Analysis of Mental Health Status and Sleep Quality in Helicobacter pylori Positive Patients. - Min Li 007; Cai-Feng Luo (J. Medical Imaging Health Informatics, 2019)

Current challenges and solutions of de novo assembly. - Xingyu Liao; Min Li 007; You Zou; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (Quant. Biol., 2019)

Automated ICD-9 Coding via A Deep Learning Approach. - Min Li 007; Zhihui Fei; Min Zeng; Fang-Xiang Wu; Yaohang Li; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Construction of Refined Protein Interaction Network for Predicting Essential Proteins. - Min Li 007; Peng Ni; Xiaopei Chen; Jianxin Wang 001; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

A Novel Scaffolding Algorithm Based on Contig Error Correction and Path Extension. - Min Li 007; Li Tang; Zhongxiang Liao; Junwei Luo; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

MGT-SM: A Method for Constructing Cellular Signal Transduction Networks. - Min Li 007; Ruiqing Zheng; Yaohang Li; Fang-Xiang Wu; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Computational Drug Repositioning with Random Walk on a Heterogeneous Network. - Huimin Luo; Jianxin Wang 001; Min Li 007; Junwei Luo; Peng Ni; Kaijie Zhao; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

CSA: a web service for the complete process of ChIP-Seq analysis. - Min Li 007; Li Tang; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (BMC Bioinform., 2019)

A topological AUC-based biomarker ensemble method for the complex disease analysis. - Xingyi Li; Ju Xiang; Fang-Xiang Wu; Min Li 007 (BIBM, 2020)

A robust single cell clustering method based on subspace learning and partial imputation. - Ruiqing Zheng; Zhenlan Liang; Xiangmao Meng; Yu Tian; Min Li 007 (BIBM, 2020)

SPOC: Identification of Drug Targets in Biological Networks via Set Preference Output Control. - Hao Gao; Min Li 007; Fang-Xiang Wu (ISBRA, 2020)

Ess-NEXG: Predict Essential Proteins by Constructing a Weighted Protein Interaction Network Based on Node Embedding and XGBoost. - Nian Wang; Min Zeng; Jiashuai Zhang; Yiming Li; Min Li 007 (ISBRA, 2020)

Network-based methods for predicting essential genes or proteins: a survey. - Xingyi Li; Wenkai Li; Min Zeng; Ruiqing Zheng; Min Li 007 (Briefings Bioinform., 2020)

CircR2Cancer: a manually curated database of associations between circRNAs and cancers. - Wei Lan; Mingrui Zhu; Qingfeng Chen; Baoshan Chen; Jin Liu 012; Min Li 007; Yi-Ping Phoebe Chen (Database J. Biol. Databases Curation, 2020)

Protein-protein interaction site prediction through combining local and global features with deep neural networks. - Min Zeng; Fuhao Zhang; Fang-Xiang Wu; Yaohang Li; Jianxin Wang 001; Min Li 007 (Bioinform., 2020)

PROBselect: accurate prediction of protein-binding residues from proteins sequences via dynamic predictor selection. - Fuhao Zhang; Wenbo Shi; Jian Zhang 020; Min Zeng; Min Li 007; Lukasz A. Kurgan (Bioinform., 2020)

DeepFrag-k: a fragment-based deep learning approach for protein fold recognition. - Wessam Elhefnawy; Min Li 007; Jianxin Wang 001; Yaohang Li (BMC Bioinform., 2020)

MADA: a web service for analysing DNA methylation array data. - Xinyu Hu; Li Tang; Linconghua Wang; Fang-Xiang Wu; Min Li 007 (BMC Bioinform., 2020)

NEDD: a network embedding based method for predicting drug-disease associations. - Renyi Zhou; Zhangli Lu; Huimin Luo; Ju Xiang; Min Zeng; Min Li 007 (BMC Bioinform., 2020)

miRTRS: A Recommendation Algorithm for Predicting miRNA Targets. - Hui Jiang 008; Jianxin Wang 001; Min Li 007; Wei Lan; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

United Neighborhood Closeness Centrality and Orthology for Predicting Essential Proteins. - Gaoshi Li; Min Li 007; Jianxin Wang 001; Yaohang Li; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Identification of Protein Complexes by Using a Spatial and Temporal Active Protein Interaction Network. - Min Li 007; Xiangmao Meng; Ruiqing Zheng; Fang-Xiang Wu; Yaohang Li; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Improving de novo Assembly Based on Read Classification. - Xingyu Liao; Min Li 007; Junwei Luo; You Zou; Fang-Xiang Wu; Yi Pan 001; Feng Luo 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

An Efficient Trimming Algorithm based on Multi-Feature Fusion Scoring Model for NGS Data. - Xingyu Liao; Min Li 007; You Zou; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

GapReduce: A Gap Filling Algorithm Based on Partitioned Read Sets. - Junwei Luo; Jianxin Wang 001; Juan Shang; Huimin Luo; Min Li 007; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

MEC: Misassembly Error Correction in Contigs based on Distribution of Paired-End Reads and Statistics of GC-contents. - Binbin Wu; Min Li 007; Xingyu Liao; Junwei Luo; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

miRTMC: A miRNA Target Prediction Method Based on Matrix Completion Algorithm. - Hui Jiang 008; Mengyun Yang; Xiang Chen; Min Li 007; Yaohang Li; Jianxin Wang 001 (IEEE J. Biomed. Health Informatics, 2020)

Predicting Human lncRNA-Disease Associations Based on Geometric Matrix Completion. - Chengqian Lu; Mengyun Yang; Min Li 007; Yaohang Li; Fang-Xiang Wu; Jianxin Wang 001 (IEEE J. Biomed. Health Informatics, 2020)

A Hybrid Pooling Based Deep Learning Framework For Automated ICD Coding. - Sajida Raz Bhutto; Yifan Wu 008; Ying Yu; Akhtar Hussain Jalbani; Min Li 007 (BIBM, 2021)

DeepCI: a deep learning based clustering method for single cell RNA-seq data. - Zhenlan Liang; Ruiqing Zheng; Siqi Chen; Xuhua Yan; Min Li 007 (BIBM, 2021)

nPTAS: A Novel Platform for Text Annotation and Service. - Xuehong Wu; Junwen Duan; Jianhua Li; Min Li 007 (BIBM, 2021)

Improving human essential protein prediction using only protein sequences via ensemble learning. - Min Zeng; Nian Wang; Yifan Wu 008; Yiming Li; Fang-Xiang Wu; Min Li 007 (BIBM, 2021)

MKG: a mutual information based method to infer single cell gene regulatory network. - Yanping Zeng; Xuhua Yan; Zhenlan Liang; Ruiqing Zheng; Min Li 007 (BIBM, 2021)

Overlapping Protein Complexes Detection Based on Multi-level Topological Similarities. - Wenkang Wang; Xiangmao Meng; Ju Xiang; Min Li 007 (ISBRA, 2021)

Key residues influencing binding affinities of 2019-nCoV with ACE2 in different species. - Senbiao Fang; Ruoqian Zheng; Chuqi Lei; Jianxin Wang 001; Ruiqing Zheng; Min Li 007 (Briefings Bioinform., 2021)

Biomedical data and computational models for drug repositioning: a comprehensive review. - Huimin Luo; Min Li 007; Mengyun Yang; Fang-Xiang Wu; Yaohang Li; Jianxin Wang 001 (Briefings Bioinform., 2021)

DeepDTAF: a deep learning method to predict protein-ligand binding affinity. - Kaili Wang; Renyi Zhou; Yaohang Li; Min Li 007 (Briefings Bioinform., 2021)

NIDM: network impulsive dynamics on multiplex biological network for disease-gene prediction. - Ju Xiang; Jiashuai Zhang; Ruiqing Zheng; Xingyi Li; Min Li 007 (Briefings Bioinform., 2021)

Improving circRNA-disease association prediction by sequence and ontology representations with convolutional and recurrent neural networks. - Chengqian Lu; Min Zeng; Fang-Xiang Wu; Min Li 007; Jianxin Wang 001 (Bioinform., 2021)

BridgeDPI: A Novel Graph Neural Network for Predicting Drug-Protein Interactions. - Yifan Wu 008; Min Gao; Min Zeng; Feiyang Chen; Min Li 007; Jie Zhang 122 (CoRR, 2021)

A Pseudo Label-wise Attention Network for Automatic ICD Coding. - Yifan Wu 008; Min Zeng; Ying Yu; Min Li 007 (CoRR, 2021)

SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement. - Zhenlan Liang; Min Li 007; Ruiqing Zheng; Yu Tian; Xuhua Yan; Jin Chen 004; Fang-Xiang Wu; Jianxin Wang 001 (Genom. Proteom. Bioinform., 2021)

DeepPPF: A deep learning framework for predicting protein family. - Shehu Mohammed Yusuf; Fuhao Zhang; Min Zeng; Min Li 007 (Neurocomputing, 2021)

Essential Protein Prediction Based on node2vec and XGBoost. - Nian Wang; Min Zeng; Yiming Li; Fang-Xiang Wu; Min Li 007 (J. Comput. Biol., 2021)

DeepDSC: A Deep Learning Method to Predict Drug Sensitivity of Cancer Cell Lines. - Min Li 007; Yake Wang; Ruiqing Zheng; Xinghua Shi; Yaohang Li; Fang-Xiang Wu; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

FUNMarker: Fusion Network-Based Method to Identify Prognostic and Heterogeneous Breast Cancer Biomarkers. - Xingyi Li; Ju Xiang; Jianxin Wang 001; Jinyan Li 001; Fang-Xiang Wu; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

EPGA-SC : A Framework for de novo Assembly of Single-Cell Sequencing Reads. - Xingyu Liao; Min Li 007; Junwei Luo; You Zou; Fang-Xiang Wu; Yi Pan 001; Feng Luo 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

A Novel Drug Repositioning Approach Based on Collaborative Metric Learning. - Huimin Luo; Jianxin Wang 001; Cheng Yan; Min Li 007; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

A Deep Learning Framework for Identifying Essential Proteins by Integrating Multiple Types of Biological Information. - Min Zeng; Min Li 007; Zhihui Fei; Fang-Xiang Wu; Yaohang Li; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

DMFLDA: A Deep Learning Framework for Predicting lncRNA-Disease Associations. - Min Zeng; Chengqian Lu; Zhihui Fei; Fang-Xiang Wu; Yaohang Li; Jianxin Wang 001; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Deletion Detection Method Using the Distribution of Insert Size and a Precise Alignment Strategy. - Zhen Zhang 024; Junwei Luo; Juan Shang; Min Li 007; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

A Deep Learning Framework for Gene Ontology Annotations With Sequence- and Network-Based Information. - Fuhao Zhang; Hong Song; Min Zeng; Fang-Xiang Wu; Yaohang Li; Yi Pan 001; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

An Ensemble Method to Reconstruct Gene Regulatory Networks Based on Multivariate Adaptive Regression Splines. - Ruiqing Zheng; Min Li 007; Xiang Chen; Siyu Zhao; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Deep Matrix Factorization Improves Prediction of Human CircRNA-Disease Associations. - Chengqian Lu; Min Zeng; Fuhao Zhang; Fang-Xiang Wu; Min Li 007; Jianxin Wang 001 (IEEE J. Biomed. Health Informatics, 2021)

Protein interaction networks: centrality, modularity, dynamics, and applications. - Xiangmao Meng; Wenkai Li; Xiaoqing Peng; Yaohang Li; Min Li 007 (Frontiers Comput. Sci., 2021)

LDAGSO: Predicting 1ncRNA-Disease Associations from Graph Sequences and Disease Ontology via Deep Learning techniques. - Norah Saeed Awn; Yiming Li; Baoying Zhao; Min Zeng; Min Li 007 (BIBM, 2022)

BayesImpute: a Bayesian imputation method for single-cell RNA-seq data. - Siqi Chen; Ruiqing Zheng; Luyi Tian; Fang-Xiang Wu; Min Li 007 (BIBM, 2022)

MERAS: A method for entity recognition, alignment, and structuration from Chinese Electronic Medical Records. - Xuehong Wu; Yifan Wu 008; Min Li 007 (BIBM, 2022)

A single cell potency inference method based on the local cell-specific network entropy. - Ziwei Xu; Ruiqing Zheng; Yuxuan Chen; Edwin Wang; Min Li 007 (BIBM, 2022)

Coded Residual Transform for Generalizable Deep Metric Learning. - Shichao Kan; Yixiong Liang; Min Li 007; Yigang Cen; Jianxin Wang 001; Zhihai He (NeurIPS, 2022)

HyMM: hybrid method for disease-gene prediction by integrating multiscale module structure. - Ju Xiang; Xiangmao Meng; Yichao Zhao; Fang-Xiang Wu; Min Li 007 (Briefings Bioinform., 2022)

Biomedical data, computational methods and tools for evaluating disease-disease associations. - Ju Xiang; Jiashuai Zhang; Yichao Zhao; Fang-Xiang Wu; Min Li 007 (Briefings Bioinform., 2022)

GLOBE: a contrastive learning-based framework for integrating single-cell transcriptome datasets. - Xuhua Yan; Ruiqing Zheng; Min Li 007 (Briefings Bioinform., 2022)

A framework for predicting variable-length epitopes of human-adapted viruses using machine learning methods. - Rui Yin 002; Xianghe Zhu; Min Zeng; Pengfei Wu; Min Li 007; Chee Keong Kwoh 001 (Briefings Bioinform., 2022)

DeepLncLoc: a deep learning framework for long non-coding RNA subcellular localization prediction based on subsequence embedding. - Min Zeng; Yifan Wu 008; Chengqian Lu; Fuhao Zhang; Fang-Xiang Wu; Min Li 007 (Briefings Bioinform., 2022)

DeepDISOBind: accurate prediction of RNA-, DNA- and protein-binding intrinsically disordered residues with deep multi-task learning. - Fuhao Zhang; Bi Zhao; Wenbo Shi; Min Li 007; Lukasz A. Kurgan (Briefings Bioinform., 2022)

SEPA: signaling entropy-based algorithm to evaluate personalized pathway activation for survival analysis on pan-cancer data. - Xingyi Li; Min Li 007; Ju Xiang; Zhelin Zhao; Xuequn Shang 001 (Bioinform., 2022)

BACPI: a bi-directional attention neural network for compound-protein interaction and binding affinity prediction. - Min Li 007; Zhangli Lu; Yifan Wu 008; Yaohang Li (Bioinform., 2022)

BridgeDPI: a novel Graph Neural Network for predicting drug-protein interactions. - Yifan Wu 008; Min Gao; Min Zeng; Jie Zhang 122; Min Li 007 (Bioinform., 2022)

PGMG: A Pharmacophore-Guided Deep Learning Approach for Bioactive Molecular Generation. - Huimin Zhu; Renyi Zhou; Jing Tang 002; Min Li 007 (CoRR, 2022)

Guest editorial: Deep neural networks for precision medicine. - Fang-Xiang Wu; Min Li 007; Lukasz A. Kurgan; Luis Rueda 001 (Neurocomputing, 2022)

KAICD: A knowledge attention-based deep learning framework for automatic ICD coding. - Yifan Wu 008; Min Zeng; Zhihui Fei; Ying Yu; Fang-Xiang Wu; Min Li 007 (Neurocomputing, 2022)

EPIXplorer: A web server for prediction, analysis and visualization of enhancer-promoter interactions. - Li Tang; Zhizhou Zhong; Yisheng Lin; Yifei Yang; Jun Wang; James F. Martin; Min Li 007 (Nucleic Acids Res., 2022)

Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. - Zhipeng Cai 001; Min Li 007; Pavel Skums (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

In Silico Prediction of New Mutations That Can Improve the Binding Abilities Between 2019-nCoV Coronavirus and Human ACE2. - Senbiao Fang; Ruoqian Zheng; Chuqi Lei; Jianxin Wang 001; Renyi Zhou; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

NIMCE: A Gene Regulatory Network Inference Approach Based on Multi Time Delays Causal Entropy. - Haonan Feng; Ruiqing Zheng; Jianxin Wang 001; Fang-Xiang Wu; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

A Dual Ranking Algorithm Based on the Multiplex Network for Heterogeneous Complex Disease Analysis. - Xingyi Li; Ju Xiang; Fang-Xiang Wu; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Accurate Prediction of Human Essential Proteins Using Ensemble Deep Learning. - Yiming Li; Min Zeng; Yifan Wu 008; Yaohang Li; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

DPCMNE: Detecting Protein Complexes From Protein-Protein Interaction Networks Via Multi-Level Network Embedding. - Xiangmao Meng; Ju Xiang; Ruiqing Zheng; Fang-Xiang Wu; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Partner-Specific Drug Repositioning Approach Based on Graph Convolutional Network. - Xinliang Sun; Bei Wang 004; Jie Zhang 122; Min Li 007 (IEEE J. Biomed. Health Informatics, 2022)

A Pseudo Label-Wise Attention Network for Automatic ICD Coding. - Yifan Wu 008; Min Zeng; Ying Yu; Yaohang Li; Min Li 007 (IEEE J. Biomed. Health Informatics, 2022)

Temporal-Spatial Analysis of the Essentiality of Hub Proteins in Protein-Protein Interaction Networks. - Xiangmao Meng; Wenkai Li; Ju Xiang; Hayat Dino Bedru; Wenkang Wang; Fang-Xiang Wu; Min Li 007 (IEEE Trans. Netw. Sci. Eng., 2022)

DyNRW: Time-Series Dynamical Networks for Identifying HCC-Related Genes. - Jin A; Ju Xiang; Min Li 007 (BIBM, 2023)

Protein function prediction using graph neural network with multi-type biological knowledge. - Yuyan Shuai; Wenkang Wang; Yiming Li; Min Zeng; Min Li 007 (BIBM, 2023)

A flexible gene regulatory network reconstruction method based on autoencoder and graph attention network. - Ruiqing Zheng; Yanping Zeng; Weixing Zeng; Min Li 007 (BIBM, 2023)

End-to-end Task-oriented Dialogue: A Survey of Tasks, Methods, and Future Directions. - Libo Qin 001; Wenbo Pan; Qiguang Chen; Lizi Liao; Zhou Yu; Yue Zhang 004; Wanxiang Che; Min Li 007 (EMNLP, 2023)

Singularformer: Learning to Decompose Self-Attention to Linearize the Complexity of Transformer. - Yifan Wu 008; Shichao Kan; Min Zeng; Min Li 007 (IJCAI, 2023)

DTIAM: A unified framework for predicting drug-target interactions, binding affinities and activation/inhibition mechanisms. - Zhangli Lu; Chuqi Lei; Kaili Wang; Libo Qin 001; Jing Tang 002; Min Li 007 (CoRR, 2023)

Retrieve and rerank for automated ICD coding via Contrastive Learning. - Kunying Niu; Yifan Wu 008; Yaohang Li; Min Li 007 (J. Biomed. Informatics, 2023)

Structural Analysis and Prediction of Hematotoxicity Using Deep Learning Approaches. - Teng-Zhi Long; Shao-Hua Shi; Shao Liu; Ai-Ping Lu; Zhao-Qian Liu; Min Li 007; Tingjun Hou; Dong-Sheng Cao 001 (J. Chem. Inf. Model., 2023)

Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. - Zhipeng Cai 001; Min Li 007; Pavel Skums; Yanjie Wei (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

A Deep Learning Framework for Predicting Protein Functions With Co-Occurrence of GO Terms. - Min Li 007; Wenbo Shi; Fuhao Zhang; Min Zeng; Yaohang Li (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Bubble: a fast single-cell RNA-seq imputation using an autoencoder constrained by bulk RNA-seq data. - Siqi Chen; Xuhua Yan; Ruiqing Zheng; Min Li 007 (Briefings Bioinform., 2023)

GraphLncLoc: long non-coding RNA subcellular localization prediction using graph convolutional networks based on sequence to graph transformation. - Min Li 007; Baoying Zhao; Rui Yin 002; Chengqian Lu; Fei Guo 001; Min Zeng (Briefings Bioinform., 2023)

RLBind: a deep learning method to predict RNA-ligand binding sites. - Kaili Wang; Renyi Zhou; Yifan Wu 008; Min Li 007 (Briefings Bioinform., 2023)

DeepCellEss: cell line-specific essential protein prediction with attention-based interpretable deep learning. - Yiming Li; Min Zeng; Fuhao Zhang; Fang-Xiang Wu; Min Li 007 (Bioinform., 2023)

CLAIRE: contrastive learning-based batch correction framework for better balance between batch mixing and preservation of cellular heterogeneity. - Xuhua Yan; Ruiqing Zheng; Fang-Xiang Wu; Min Li 007 (Bioinform., 2023)

A review of enzyme design in catalytic stability by artificial intelligence. - Yongfan Ming; Wenkang Wang; Rui Yin 002; Min Zeng; Li Tang; Shizhe Tang; Min Li 007 (Briefings Bioinform., 2023)

A comprehensive assessment and comparison of tools for HLA class I peptide-binding prediction. - Meng Wang; Lukasz A. Kurgan; Min Li 007 (Briefings Bioinform., 2023)

Medical Knowledge Graph: Data Sources, Construction, Reasoning, and Applications. - Xuehong Wu; Junwen Duan; Yi Pan 001; Min Li 007 (Big Data Min. Anal., 2023)

ViPal: A framework for virulence prediction of influenza viruses with prior viral knowledge using genomic sequences. - Rui Yin 002; Zihan Luo 001; Pei Zhuang; Min Zeng; Min Li 007; Zhuoyi Lin; Chee Keong Kwoh 001 (J. Biomed. Informatics, 2023)

DKADE: a novel framework based on deep learning and knowledge graph for identifying adverse drug events and related medications. - Ze-Ying Feng; Xue-Hong Wu; Jun-Long Ma; Min Li 007; Ge-Fei He; Dong-Sheng Cao 001; Guo-Ping Yang (Briefings Bioinform., 2023)

CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. - Alessio Del Conte; Adel Bouhraoua; Mahta Mehdiabadi; Damiano Clementel; Alexander Miguel Monzon; Alex S. Holehouse; Daniel A. Griffith; Ryan J. Emenecker; Ashwini Patil; Ronesh Sharma; Tatsuhiko Tsunoda; Alok Sharma; et al. (Nucleic Acids Res., 2023)

scNCL: transferring labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization. - Xuhua Yan; Ruiqing Zheng; Jinmiao Chen; Min Li 007 (Bioinform., 2023)

Inferring single-cell gene regulatory network by non-redundant mutual information. - Yanping Zeng; Yongxin He; Ruiqing Zheng; Min Li 007 (Briefings Bioinform., 2023)

StackCPA: A stacking model for compound-protein binding affinity prediction based on pocket multi-scale features. - Chuqi Lei; Zhangli Lu; Meng Wang; Min Li 007 (Comput. Biol. Medicine, 2023)

CACO: A Core-Attachment Method With Cross-Species Functional Ortholog Information to Detect Human Protein Complexes. - Wenkang Wang; Xiangmao Meng; Ju Xiang; Yunyan Shuai; Hayat Dino Bedru; Min Li 007 (IEEE J. Biomed. Health Informatics, 2023)

The Impact of Computational Drug Discovery on Society. - Jianxin Wang 001; Min Li 007; Edwin Wang; Jing Tang 002; Bin Hu 001 (IEEE Trans. Comput. Soc. Syst., 2023)

LncLocFormer: a Transformer-based deep learning model for multi-label lncRNA subcellular localization prediction by using localization-specific attention mechanism. - Min Zeng; Yifan Wu 008; Yiming Li; Rui Yin 002; Chengqian Lu; Junwen Duan; Min Li 007 (Bioinform., 2023)

Fusion-Based Deep Learning Architecture for Detecting Drug-Target Binding Affinity Using Target and Drug Sequence and Structure. - Kaili Wang; Min Li 007 (IEEE J. Biomed. Health Informatics, 2023)

AutoCAP: Towards Automatic Cross-lingual Alignment Planning for Zero-shot Chain-of-Thought. - Yongheng Zhang 001; Qiguang Chen; Min Li 007; Wanxiang Che; Libo Qin 001 (ACL (Findings), 2024)

RBVS: Database of the Receptor-Based Virtual Screening. - Senbiao Fang; Huimin Zhu; Yongfan Ming; Kunying Niu; Baoying Zhao; Min Li 007 (BCB, 2024)

CellCom: A web server for prediction, visualization, and evaluation of cell-cell communication mediated by ligand-receptor pairs. - Jianing Wang; Jin A; Hanjun Pan; Ruiqing Zheng; Chaojin Wu; Min Li 007 (BCB, 2024)

Aligning Multimodal Biomedical Images and Language via One Large Vision-Language Model. - Haojie Zhang; Min Zeng; Jinfeng Ding; Yixiong Liang; Ruiqing Zheng; Zhe Qu; Min Li 007; Shichao Kan (BIBM, 2024)

An Effective Tool for Differential Interaction Analysis in Single-Cell Hi-C Data. - Yichao Zhao; Ruiqing Zheng; Li Tang; Pengzhen Jia; Min Li 007 (BIBM, 2024)

LabCLIP: Label-Enhanced Clip for Improving Zero-Shot Text Classification. - Yongheng Zhang 001; Peng Wang 168; Qiguang Chen; Jingxuan Zhou; Yongmei Wang; Min Li 007; Libo Qin 001 (ICASSP, 2024)

scCoRR: A Data-Driven Self-correction Framework for Labeled scRNA-Seq Data. - Yongxin He; Jin Liu 012; Min Li 007; Ruiqing Zheng (ISBRA (2), 2024)

MSMK: Multiscale Module Kernel for Identifying Disease-Related Genes. - Ju Xiang; Shengkai Chen; Xiangmao Meng; Ruiqing Zheng; Ying Zheng; Min Li 007 (ISBRA (1), 2024)

What Factors Affect Multi-Modal In-Context Learning? An In-Depth Exploration. - Libo Qin 001; Qiguang Chen; Hao Fei 003; Zhi Chen 006; Min Li 007; Wanxiang Che (NeurIPS, 2024)

Leveraging Visual Tokens for Extended Text Contexts in Multi-Modal Learning. - Alex Jinpeng Wang; Linjie Li; Yiqi Lin; Min Li 007; Lijuan Wang; Mike Zheng Shou (NeurIPS, 2024)

scMLC: an accurate and robust multiplex community detection method for single-cell multi-omics data. - Yuxuan Chen; Ruiqing Zheng; Jin Liu 012; Min Li 007 (Briefings Bioinform., 2024)

stAA: adversarial graph autoencoder for spatial clustering task of spatially resolved transcriptomics. - Zhaoyu Fang; Teng Liu; Ruiqing Zheng; Jin A; Mingzhu Yin; Min Li 007 (Briefings Bioinform., 2024)

A comprehensive review of protein-centric predictors for biomolecular interactions: from proteins to nucleic acids and beyond. - Pengzhen Jia; Fuhao Zhang; Chaojin Wu; Min Li 007 (Briefings Bioinform., 2024)

CAKE: a flexible self-supervised framework for enhancing cell visualization, clustering and rare cell identification. - Jin Liu 012; Weixing Zeng; Shichao Kan; Min Li 007; Ruiqing Zheng (Briefings Bioinform., 2024)

TripHLApan: predicting HLA molecules binding peptides based on triple coding matrix and transfer learning. - Meng Wang; Chuqi Lei; Jianxin Wang 001; Yaohang Li; Min Li 007 (Briefings Bioinform., 2024)

A comprehensive computational benchmark for evaluating deep learning-based protein function prediction approaches. - Wenkang Wang; Yunyan Shuai; Qiurong Yang; Fuhao Zhang; Min Zeng; Min Li 007 (Briefings Bioinform., 2024)

Multiplex Networks and Pan-Cancer Multiomics-Based Driver Gene Identification Using Graph Neural Networks. - Xingyi Li; Junming Li; Jun Hao; Xingyu Liao; Min Li 007; Xuequn Shang 001 (Big Data Min. Anal., 2024)

SGCL-LncLoc: An Interpretable Deep Learning Model for Improving IncRNA Subcellular Localization Prediction with Supervised Graph Contrastive Learning. - Min Li 007; Baoying Zhao; Yiming Li; Pingjian Ding; Rui Yin 002; Shichao Kan; Min Zeng (Big Data Min. Anal., 2024)

Editorial: The 21st Asian Pacific Bioinformatics Conference 2023. - Min Li 007; Yi-Ping Phoebe Chen (Comput. Biol. Chem., 2024)

Multilingual Large Language Model: A Survey of Resources, Taxonomy and Frontiers. - Libo Qin 001; Qiguang Chen; Yuhang Zhou; Zhi Chen 006; Yinghui Li; Lizi Liao; Min Li 007; Wanxiang Che; Philip S. Yu (CoRR, 2024)

Large Language Models Meet NLP: A Survey. - Libo Qin 001; Qiguang Chen; Xiachong Feng; Yang Wu 010; Yongheng Zhang 001; Yinghui Li; Min Li 007; Wanxiang Che; Philip S. Yu (CoRR, 2024)

IR2QSM: Quantitative Susceptibility Mapping via Deep Neural Networks with Iterative Reverse Concatenations and Recurrent Modules. - Min Li 007; Chen Chen; Zhuang Xiong; Ying Liu; Pengfei Rong; Shanshan Shan; Feng Liu 005; Hongfu Sun; Yang Gao 030 (CoRR, 2024)

Knowledge Graph Convolutional Network with Heuristic Search for Drug Repositioning. - Xiang Du; Xinliang Sun; Min Li 007 (J. Chem. Inf. Model., 2024)

LGGA-MPP: Local Geometry-Guided Graph Attention for Molecular Property Prediction. - Lei Song; Huimin Zhu; Kaili Wang; Min Li 007 (J. Chem. Inf. Model., 2024)

Plug-and-Play latent feature editing for orientation-adaptive quantitative susceptibility mapping neural networks. - Yang Gao 030; Zhuang Xiong; Shanshan Shan; Yin Liu; Pengfei Rong; Min Li 007; Alan H. Wilman; G. Bruce Pike; Feng Liu 005; Hongfu Sun (Medical Image Anal., 2024)

scMoMtF: An interpretable multitask learning framework for single-cell multi-omics data analysis. - Wei Lan; Tongsheng Ling; Qingfeng Chen; Ruiqing Zheng; Min Li 007; Yi Pan 001 (PLoS Comput. Biol., 2024)

Dopcc: Detecting Overlapping Protein Complexes via Multi-Metrics and Co-Core Attachment Method. - Wenkang Wang; Xiangmao Meng; Ju Xiang; Hayat Dino Bedru; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

MDDOmics: multi-omics resource of major depressive disorder. - Yichao Zhao; Ju Xiang; Xingyuan Shi; Pengzhen Jia; Yan Zhang; Min Li 007 (Database J. Biol. Databases Curation, 2024)

Divide-Solve-Combine: An Interpretable and Accurate Prompting Framework for Zero-shot Multi-Intent Detection. - Libo Qin 001; Qiguang Chen; Jingxuan Zhou; Jin Wang; Hao Fei 003; Wanxiang Che; Min Li 007 (AAAI, 2025)

CoMT: A Novel Benchmark for Chain of Multi-modal Thought on Large Vision-Language Models. - Zihui Cheng; Qiguang Chen; Jin Zhang; Hao Fei 003; Xiaocheng Feng; Wanxiang Che; Min Li 007; Libo Qin 001 (AAAI, 2025)

MLDebugging: Towards Benchmarking Code Debugging Across Multi-Library Scenarios. - Jinyang Huang; Xiachong Feng; Qiguang Chen; Hanjie Zhao; Zihui Cheng; Jiesong Bai; Jingxuan Zhou; Min Li 007; Libo Qin 001 (ACL (Findings), 2025)

DDLB: Using the Protein Language Model and Hierarchical Architecture to Improve Disordered Lipid-Binding Residues Prediction. - Chaojin Wu; Fuhao Zhang; Pengzhen Jia; Min Zeng; Min Li 007 (ISBRA (1), 2025)

Towards Multi-resolution Spatiotemporal Graph Learning for Medical Time Series Classification. - Wei Fan 010; Jingru Fei; Dingyu Guo; Kun Yi 001; Xiaozhuang Song; Haolong Xiang; Hangting Ye; Min Li 007 (WWW, 2025)

Large Language Model for Medical Images: A Survey of Taxonomy, Systematic Review, and Future Trends. - Peng Wang 168; Wenpeng Lu; Chunlin Lu; Ruoxi Zhou; Min Li 007; Libo Qin 001 (Big Data Min. Anal., 2025)

A survey of multilingual large language models. - Libo Qin 001; Qiguang Chen; Yuhang Zhou; Zhi Chen 006; Yinghui Li; Lizi Liao; Min Li 007; Wanxiang Che; Philip S. Yu (Patterns, 2025)

MedGNN: Towards Multi-resolution Spatiotemporal Graph Learning for Medical Time Series Classification. - Wei Fan 010; Jingru Fei; Dingyu Guo; Kun Yi 001; Xiaozhuang Song; Haolong Xiang; Hangting Ye; Min Li 007 (CoRR, 2025)

TextAtlas5M: A Large-scale Dataset for Dense Text Image Generation. - Alex Jinpeng Wang; Dongxing Mao; Jiawei Zhang; Weiming Han; Zhuobai Dong; Linjie Li; Yiqi Lin; Zhengyuan Yang; Libo Qin 001; Fuwei Zhang; Lijuan Wang; Min Li 007 (CoRR, 2025)

CellCircLoc: Deep Neural Network for Predicting and Explaining Cell Line-Specific CircRNA Subcellular Localization. - Min Zeng; Jingwei Lu; Yiming Li; Chengqian Lu; Shichao Kan; Fei Guo 001; Min Li 007 (IEEE J. Biomed. Health Informatics, 2025)

Beyond Words: Advancing Long-Text Image Generation via Multimodal Autoregressive Models. - Alex Jinpeng Wang; Linjie Li; Zhengyuan Yang; Lijuan Wang; Min Li 007 (CoRR, 2025)

PathActMarker: an R package for inferring pathway activity of complex diseases. - Xingyi Li; Jun Hao; Zhelin Zhao; Junming Li; Xingyu Liao; Min Li 007; Xuequn Shang 001 (Frontiers Comput. Sci., 2025)

DRGCL: Drug Repositioning via Semantic-Enriched Graph Contrastive Learning. - Xiao Jia 020; Xinliang Sun; Kaili Wang; Min Li 007 (IEEE J. Biomed. Health Informatics, 2025)

ActivityDiff: A diffusion model with Positive and Negative Activity Guidance for De Novo Drug Design. - Renyi Zhou; Huimin Zhu; Jing Tang 002; Min Li 007 (CoRR, 2025)