Homology search for genes. - Xuefeng Cui; Tomás Vinar; Brona Brejová; Dennis E. Shasha; Ming Li 001 (ISMB/ECCB (Supplement of Bioinformatics), 2007)

How Accurately Can We Model Protein Structures with Dihedral Angles? - Xuefeng Cui; Shuai Cheng Li 001; Dongbo Bu; Babak Alipanahi Ramandi; Ming Li 001 (WABI, 2012)

Towards Reliable Automatic Protein Structure Alignment. - Xuefeng Cui; Shuai Cheng Li 001; Dongbo Bu; Ming Li 001 (WABI, 2013)

Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles? - Xuefeng Cui; Shuai Cheng Li 001; Dongbo Bu; Babak Alipanahi; Ming Li 001 (Algorithms Mol. Biol., 2013)

Analysis of the Phenology in the Mongolian Plateau by Inter-Comparison of Global Vegetation Datasets. - Lijuan Miao; Yibo Luan; Xiangzhong Luo; Qiang Liu; John C. Moore; Reshmita Nath; Bin He; Feng Zhu; Xuefeng Cui (Remote. Sens., 2013)

Fingerprinting protein structures effectively and efficiently. - Xuefeng Cui; Shuai Cheng Li 001; Lin He 002; Ming Li 001 (Bioinform., 2014)

Compare local pocket and global protein structure models by small structure patterns. - Xuefeng Cui; Hiroyuki Kuwahara; Shuai Cheng Li 001; Xin Gao 001 (BCB, 2015)

Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces. - Xuefeng Cui; Hammad Naveed; Xin Gao 001 (BCB, 2015)

Finding optimal interaction interface alignments between biological complexes. - Xuefeng Cui; Hammad Naveed; Xin Gao 001 (Bioinform., 2015)

Future Climate Impact on the Desertification in the Dry Land Asia Using AVHRR GIMMS NDVI3g Data. - Lijuan Miao; Peilong Ye; Bin He; Lizi Chen; Xuefeng Cui (Remote. Sens., 2015)

CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction. - Xuefeng Cui; Zhiwu Lu 001; Sheng Wang 001; Jim Jing-Yan Wang; Xin Gao 001 (Bioinform., 2016)

MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind. - Hiroyuki Kuwahara; Meshari Alazmi; Xuefeng Cui; Xin Gao 001 (Nucleic Acids Res., 2016)

K-nearest uphill clustering in the protein structure space. - Xuefeng Cui; Xin Gao 001 (Neurocomputing, 2017)

Multi-instance dictionary learning via multivariate performance measure optimization. - Jim Jing-Yan Wang; Ivor Wai-Hung Tsang; Xuefeng Cui; Zhiwu Lu 001; Xin Gao 001 (Pattern Recognit., 2017)

Learning Protein Structural Fingerprints under the Label-Free Supervision of Domain Knowledge. - Yaosen Min; Shang Liu; Chenyao Lou; Xuefeng Cui (BIBM, 2018)

Mmalloc: A Dynamic Memory Management on Many-core Coprocessor for the Acceleration of Storage-intensive Bioinformatics Application. - Zihao Wang; Mingzhe Zhang; Jingrong Zhang; Rui Yan 009; Xiaohua Wan; Zhiyong Liu 002; Fa Zhang 001; Xuefeng Cui (BIBM, 2018)

Classification in Cryo-Electron Tomograms. - Ilja Gubins; Gijs van der Schot; Remco C. Veltkamp; Friedrich Förster; Xuefeng Du; Xiangrui Zeng; Zhenxi Zhu; Lufan Chang; Min Xu 009; Emmanuel Moebel; Antonio Martínez-Sánchez; Charles Kervrann; et al. (3DOR@Eurographics, 2019)

When sparse coding meets ranking: a joint framework for learning sparse codes and ranking scores. - Jim Jing-Yan Wang; Xuefeng Cui; Ge Yu; Lili Guo; Xin Gao 001 (Neural Comput. Appl., 2019)

Visible and Near-Infrared Reflectance Spectroscopy Analysis of a Coastal Soil Chronosequence. - Guanghui Zheng; Dongryeol Ryu; Caixia Jiao; Xianli Xie; Xuefeng Cui; Gang Shang (Remote. Sens., 2019)

Homologous Protein Detection. - Xuefeng Cui; Yaosen Min (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

Dilated-DenseNet for Macromolecule Classification in Cryo-electron Tomography. - Shan Gao; Renmin Han; Xiangrui Zeng; Xuefeng Cui; Zhiyong Liu 002; Min Xu 009; Fa Zhang 001 (ISBRA, 2020)

SVLR: Genome Structure Variant Detection Using Long Read Sequencing Data. - Wenyan Gu; Aizhong Zhou; Lusheng Wang 001; Shiwei Sun; Xuefeng Cui; Daming Zhu (ISBRA, 2020)

MIMO Radar Imaging With Multiple Probing Pulses for 2D Off-Grid Targets via Variational Sparse Bayesian Learning. - Chao Wen; Lu Chen 003; Pengting Duan; Xuefeng Cui (IEEE Access, 2020)

SHREC 2020: Classification in cryo-electron tomograms. - Ilja Gubins; Marten L. Chaillet; Gijs van der Schot; Remco C. Veltkamp; Friedrich Förster; Yu Hao; Xiaohua Wan 001; Xuefeng Cui; Fa Zhang 001; Emmanuel Moebel; Xiao Wang 004; Daisuke Kihara; et al. (Comput. Graph., 2020)

SHREC 2021: Classification in Cryo-electron Tomograms. - Ilja Gubins; Marten L. Chaillet; Gijs van der Schot; M. Cristina Trueba; Remco C. Veltkamp; Friedrich Förster; Xiao Wang 004; Daisuke Kihara; Emmanuel Moebel; Nguyen P. Nguyen; Tommi A. White; Filiz Bunyak; et al. (3DOR, 2021)

Jointly Learning to Align and Aggregate with Cross Attention Pooling for Peptide-MHC Class I Binding Prediction. - Cheng Chen; Zongzhao Qiu; Zhenghe Yang; Bin Yu 007; Xuefeng Cui (BIBM, 2021)

Hydrogen bonds meet self-attention: all you need for protein structure embedding. - Cheng Chen; Yuguo Zha; Daming Zhu; Kang Ning 001; Xuefeng Cui (BIBM, 2021)

Edge-Gated Graph Neural Network for Predicting Protein-Ligand Binding Affinities. - Qihong Jiao; Zongzhao Qiu; Yuxiao Wang 002; Cheng Chen; Zhenghe Yang; Xuefeng Cui (BIBM, 2021)

rzMLP-DTA: gMLP network with ReZero for sequence-based drug-target affinity prediction. - Zongzhao Qiu; Qihong Jiao; Yuxiao Wang 002; Cheng Chen; Daming Zhu; Xuefeng Cui (BIBM, 2021)

Structure-Based Protein-Drug Affinity Prediction with Spatial Attention Mechanisms. - Yuxiao Wang 002; Zongzhao Qiu; Qihong Jiao; Cheng Chen; Zhaoxu Meng; Xuefeng Cui (BIBM, 2021)

DNN-DTIs: Improved drug-target interactions prediction using XGBoost feature selection and deep neural network. - Cheng Chen; Han Shi; Zhiwen Jiang; Adil Salhi; Ruixin Chen; Xuefeng Cui; Bin Yu 007 (Comput. Biol. Medicine, 2021)

SVLR: Genome Structural Variant Detection Using Long-Read Sequencing Data. - Wenyan Gu; Aizhong Zhou; Lusheng Wang 001; Shiwei Sun; Xuefeng Cui; Daming Zhu (J. Comput. Biol., 2021)

Hexagonal Convolutional Neural Network for Spatial Transcriptomics Classification. - Jing Gao; Fa Zhang 001; Kai Hu 002; Xuefeng Cui (BIBM, 2022)

Longest k-tuple Common Sub-Strings. - Tiantian Li; Daming Zhu; Haitao Jiang; Haodi Feng; Xuefeng Cui (BIBM, 2022)

Pretraining Transformers for TCR-pMHC Binding Prediction. - Jinsheng Shang; Qihong Jiao; Cheng Chen; Daming Zhu; Xuefeng Cui (BIBM, 2022)

Boosting Deep Learning-based Docking with Cross-attention and Centrality Embedding. - Jingxuan Wang; Zongzhao Qiu; Xuan Zhang; Zhenghe Yang; Wei Zhao; Xuefeng Cui (BIBM, 2022)

Graph-based Reaction Classification by Contrasting between Precursors and Products. - Zhengwei Wang; Yuxiao Wang 002; Xuan Zhang; Zhaoxu Meng; Zhenghe Yang; Wei Zhao; Xuefeng Cui (BIBM, 2022)

CoAtGIN: Marrying Convolution and Attention for Graph-based Molecule Property Prediction. - Xuan Zhang; Cheng Chen; Zhaoxu Meng; Zhenghe Yang; Haitao Jiang; Xuefeng Cui (BIBM, 2022)

VP-Detector: A 3D multi-scale dense convolutional neural network for macromolecule localization and classification in cryo-electron tomograms. - Yu Hao; Xiaohua Wan; Rui Yan 009; Zhiyong Liu 002; Jintao Li 001; Shihua Zhang; Xuefeng Cui; Fa Zhang 001 (Comput. Methods Programs Biomed., 2022)

Using Deep Learning to Classify Full-Length Transcriptome Sequences. - Weiguo Li; Junchi Ma; Cuiyuan Li; Ting Yu; Xuefeng Cui (BIBM, 2023)

Variational Clustering and Denoising of Spatial Transcriptomics. - Cuiyuan Li; Fa Zhang 001; Kai Hu 002; Xuefeng Cui (BIBM, 2023)

De Novo Molecular Structure Generation from Mass Spectra. - Yanmin Liu; Xuan Zhang; Wei Zhao; Daming Zhu; Xuefeng Cui (BIBM, 2023)

Learned Fingerprint Embedding for Large-Scale Peptide Mass Spectra Retrieval. - Yongshuai Wang; Xiaojun Cai; Defeng Li; Shiwei Sun; Cheng Chen; Xuefeng Cui (BIBM, 2023)

ContactLib-ATT: A Structure-Based Search Engine for Homologous Proteins. - Cheng Chen; Yuguo Zha; Daming Zhu; Kang Ning 001; Xuefeng Cui (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Cutting-Edge Algorithms in Genomics: From Theory to Practice. - Xuefeng Cui (BCB, 2024)

Revolutionizing Enzyme Turnover Predictions with Non-Binary Reaction Fingerprints and AI. - Jibin Cheng; Cheng Chen; Guishan Cui; Haitao Jiang; Xuefeng Cui (BIBM, 2024)

Enhanced Protein-Ligand Affinity Prediction with Conditional Updating and Proximity Embedding. - Shuai Cui; Xuan Zhang; Zizheng Nie; Haitao Jiang; Guishan Cui; Xuefeng Cui (BIBM, 2024)

Advancing Template-Based Flexible Docking of P450-Heme Complexes via JAX MD. - Rongxu Guo; Cheng Chen; Jiaheng Sang; Guishan Cui; Fa Zhang 001; Xuefeng Cui; Shengying Li (BIBM, 2024)

Iterative Glycan Structure Generation by Component Localization and Classification from Mass Spectra. - Defeng Li; Zizheng Nie; Yanmin Liu; Xiaojun Cai; Yong Zhang; Xuefeng Cui (BIBM, 2024)

Deep Representation Learning for Electron Ionization Mass Spectra Retrieval. - Shibo Liu; Xuan Zhang; Anlei Jiao; Shiwei Sun; Longyang Dian; Xuefeng Cui (BIBM, 2024)

How to Integrate Non-Sequence Features for Peptide Collision Cross Section Prediction with Deep Learning? - Zhimeng Tian; Zizheng Nie; Yong Zhang; Daming Zhu; Xuefeng Cui (BIBM, 2024)

How to Train Your Neural Network for Molecular Structure Generation from Mass Spectra? - Kai Zhao; Yanmin Liu; Longyang Dian; Shiwei Sun; Xuefeng Cui (BIBM, 2024)

DTMIReID: Person Re-identification Based on Deformable Transformer to Incorporate Mutual Information Between Images. - Han Yang; Haodi Feng; Xuefeng Cui (ICPR (14), 2024)

Exploring Trial-and-Error in Deep Learning: Initial Application to Isotope Detection in Mass Spectrometry. - Qihong Jiao; Yuxiao Wang; Yongshuai Wang; Shiwei Sun; Xuefeng Cui (Big Data Min. Anal., 2024)

Exploring Fragment Adding Strategies to Enhance Molecule Pretraining in AI-Driven Drug Discovery. - Zhaoxu Meng; Cheng Chen; Xuan Zhang; Wei Zhao; Xuefeng Cui (Big Data Min. Anal., 2024)

Predicting China's Maize Yield Using Multi-Source Datasets and Machine Learning Algorithms. - Lijuan Miao; Yangfeng Zou; Xuefeng Cui; Giri Raj Kattel; Yi Shang; Jingwen Zhu (Remote. Sens., 2024)

Enough Consecutive Matches in k-Tuple Common Substrings. - Tiantian Li; Siqi Jiang; Haitao Jiang; Lianrong Pu; Haodi Feng; Xuefeng Cui; Lizhen Cui; Daming Zhu (ICIC (26), 2025)

MambaST: Hexagonal State Space Modeling for Spatial Domain Identification. - Xianglong Meng; Kai Hu 002; Xuefeng Cui; Fa Zhang 001 (ISBRA (1), 2025)

MetaGIN: a lightweight framework for molecular property prediction. - Xuan Zhang; Cheng Chen; Xiaoting Wang; Haitao Jiang; Wei Zhao; Xuefeng Cui (Frontiers Comput. Sci., 2025)

Central Feature Network Enables Accurate Detection of Both Small and Large Particles in Cryo-Electron Tomography. - Yaoyu Wang; Xiaohua Wan; Cheng Chen; Fa Zhang 001; Xuefeng Cui (J. Comput. Sci. Technol., 2025)