Xuefeng Cui

Publication Activity (10 Years)

Years Active: 2007-2024
Publications (10 Years): 40

Top Topics

Protein Structure

Learning To Classify

Top Venues

Publications

Lijuan Miao, Yangfeng Zou, Xuefeng Cui, Giri Raj Kattel, Yi Shang, Jingwen Zhu
Predicting China's Maize Yield Using Multi-Source Datasets and Machine Learning Algorithms. Remote. Sens. 16 (13) (2024)
Yaoyu Wang, Xiaohua Wan, Cheng Chen, Fa Zhang, Xuefeng Cui
Central Feature Network Enables Accurate Detection of Both Small and Large Particles in Cryo-Electron Tomography. ISBRA (1) (2024)
Weiguo Li, Junchi Ma, Cuiyuan Li, Ting Yu, Xuefeng Cui
Using Deep Learning to Classify Full-Length Transcriptome Sequences. BIBM (2023)
Cheng Chen, Yuguo Zha, Daming Zhu, Kang Ning, Xuefeng Cui
ContactLib-ATT: A Structure-Based Search Engine for Homologous Proteins. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (6) (2023)
Yongshuai Wang, Xiaojun Cai, Defeng Li, Shiwei Sun, Cheng Chen, Xuefeng Cui
Learned Fingerprint Embedding for Large-Scale Peptide Mass Spectra Retrieval. BIBM (2023)
Cuiyuan Li, Fa Zhang, Kai Hu, Xuefeng Cui
Variational Clustering and Denoising of Spatial Transcriptomics. BIBM (2023)
Yanmin Liu, Xuan Zhang, Wei Zhao, Daming Zhu, Xuefeng Cui
De Novo Molecular Structure Generation from Mass Spectra. BIBM (2023)
Zhengwei Wang, Yuxiao Wang, Xuan Zhang, Zhaoxu Meng, Zhenghe Yang, Wei Zhao, Xuefeng Cui
Graph-based Reaction Classification by Contrasting between Precursors and Products. BIBM (2022)
Jing Gao, Fa Zhang, Kai Hu, Xuefeng Cui
Hexagonal Convolutional Neural Network for Spatial Transcriptomics Classification. BIBM (2022)
Ilja Gubins, Marten L. Chaillet, Gijs van der Schot, M. Cristina Trueba, Remco C. Veltkamp, Friedrich Förster, Xiao Wang, Daisuke Kihara, Emmanuel Moebel, Nguyen P. Nguyen, Tommi A. White, Filiz Bunyak, Giorgos Papoulias, Stavros Gerolymatos, Evangelia I. Zacharaki, Konstantinos Moustakas, Xiangrui Zeng, Sinuo Liu, Min Xu, Yaoyu Wang, Cheng Chen, Xuefeng Cui, Fa Zhang
SHREC 2021: Classification in cryo-electron tomograms. CoRR (2022)
Jingxuan Wang, Zongzhao Qiu, Xuan Zhang, Zhenghe Yang, Wei Zhao, Xuefeng Cui
Boosting Deep Learning-based Docking with Cross-attention and Centrality Embedding. BIBM (2022)
Xuan Zhang, Cheng Chen, Zhaoxu Meng, Zhenghe Yang, Haitao Jiang, Xuefeng Cui
CoAtGIN: Marrying Convolution and Attention for Graph-based Molecule Property Prediction. BIBM (2022)
Tiantian Li, Daming Zhu, Haitao Jiang, Haodi Feng, Xuefeng Cui
Longest k-tuple Common Sub-Strings. BIBM (2022)
Jinsheng Shang, Qihong Jiao, Cheng Chen, Daming Zhu, Xuefeng Cui
Pretraining Transformers for TCR-pMHC Binding Prediction. BIBM (2022)
Yu Hao, Xiaohua Wan, Rui Yan, Zhiyong Liu, Jintao Li, Shihua Zhang, Xuefeng Cui, Fa Zhang
VP-Detector: A 3D multi-scale dense convolutional neural network for macromolecule localization and classification in cryo-electron tomograms. Comput. Methods Programs Biomed. 221 (2022)
Cheng Chen, Han Shi, Zhiwen Jiang, Adil Salhi, Ruixin Chen, Xuefeng Cui, Bin Yu
DNN-DTIs: Improved drug-target interactions prediction using XGBoost feature selection and deep neural network. Comput. Biol. Medicine 136 (2021)
Wenyan Gu, Aizhong Zhou, Lusheng Wang, Shiwei Sun, Xuefeng Cui, Daming Zhu
SVLR: Genome Structural Variant Detection Using Long-Read Sequencing Data. J. Comput. Biol. 28 (8) (2021)
Zongzhao Qiu, Qihong Jiao, Yuxiao Wang, Cheng Chen, Daming Zhu, Xuefeng Cui
rzMLP-DTA: gMLP network with ReZero for sequence-based drug-target affinity prediction. BIBM (2021)
Yuxiao Wang, Zongzhao Qiu, Qihong Jiao, Cheng Chen, Zhaoxu Meng, Xuefeng Cui
Structure-Based Protein-Drug Affinity Prediction with Spatial Attention Mechanisms. BIBM (2021)
Cheng Chen, Zongzhao Qiu, Zhenghe Yang, Bin Yu, Xuefeng Cui
Jointly Learning to Align and Aggregate with Cross Attention Pooling for Peptide-MHC Class I Binding Prediction. BIBM (2021)
Ilja Gubins, Marten L. Chaillet, Gijs van der Schot, M. Cristina Trueba, Remco C. Veltkamp, Friedrich Förster, Xiao Wang, Daisuke Kihara, Emmanuel Moebel, Nguyen P. Nguyen, Tommi A. White, Filiz Bunyak, Giorgos Papoulias, Stavros Gerolymatos, Evangelia I. Zacharaki, Konstantinos Moustakas, Xiangrui Zeng, Sinuo Liu, Min Xu, Yaoyu Wang, Cheng Chen, Xuefeng Cui, Fa Zhang
SHREC 2021: Classification in Cryo-electron Tomograms. 3DOR (2021)
Qihong Jiao, Zongzhao Qiu, Yuxiao Wang, Cheng Chen, Zhenghe Yang, Xuefeng Cui
Edge-Gated Graph Neural Network for Predicting Protein-Ligand Binding Affinities. BIBM (2021)
Cheng Chen, Yuguo Zha, Daming Zhu, Kang Ning, Xuefeng Cui
Hydrogen bonds meet self-attention: all you need for protein structure embedding. BIBM (2021)
Shan Gao, Renmin Han, Xiangrui Zeng, Xuefeng Cui, Zhiyong Liu, Min Xu, Fa Zhang
Dilated-DenseNet for Macromolecule Classification in Cryo-electron Tomography. ISBRA (2020)
Chao Wen, Lu Chen, Pengting Duan, Xuefeng Cui
MIMO Radar Imaging With Multiple Probing Pulses for 2D Off-Grid Targets via Variational Sparse Bayesian Learning. IEEE Access 8 (2020)
Ilja Gubins, Marten L. Chaillet, Gijs van der Schot, Remco C. Veltkamp, Friedrich Förster, Yu Hao, Xiaohua Wan, Xuefeng Cui, Fa Zhang, Emmanuel Moebel, Xiao Wang, Daisuke Kihara, Xiangrui Zeng, Min Xu, Nguyen P. Nguyen, Tommi A. White, Filiz Bunyak
SHREC 2020: Classification in cryo-electron tomograms. Comput. Graph. 91 (2020)
Wenyan Gu, Aizhong Zhou, Lusheng Wang, Shiwei Sun, Xuefeng Cui, Daming Zhu
SVLR: Genome Structure Variant Detection Using Long Read Sequencing Data. ISBRA (2020)
Jim Jing-Yan Wang, Xuefeng Cui, Ge Yu, Lili Guo, Xin Gao
When sparse coding meets ranking: a joint framework for learning sparse codes and ranking scores. Neural Comput. Appl. 31 (3) (2019)
Ilja Gubins, Gijs van der Schot, Remco C. Veltkamp, Friedrich Förster, Xuefeng Du, Xiangrui Zeng, Zhenxi Zhu, Lufan Chang, Min Xu, Emmanuel Moebel, Antonio Martínez-Sánchez, Charles Kervrann, Tuan Manh Lai, Xusi Han, Genki Terashi, Daisuke Kihara, Benjamin A. Himes, Xiaohua Wan, Jingrong Zhang, Shan Gao, Yu Hao, Zhilong Lv, Xiaohua Wan, Zhidong Yang, Zijun Ding, Xuefeng Cui, Fa Zhang
Classification in Cryo-Electron Tomograms. 3DOR@Eurographics (2019)
Guanghui Zheng, Dongryeol Ryu, Caixia Jiao, Xianli Xie, Xuefeng Cui, Gang Shang
Visible and Near-Infrared Reflectance Spectroscopy Analysis of a Coastal Soil Chronosequence. Remote. Sens. 11 (20) (2019)
Zihao Wang, Mingzhe Zhang, Jingrong Zhang, Rui Yan, Xiaohua Wan, Zhiyong Liu, Fa Zhang, Xuefeng Cui
Mmalloc: A Dynamic Memory Management on Many-core Coprocessor for the Acceleration of Storage-intensive Bioinformatics Application. BIBM (2018)
Yaosen Min, Shang Liu, Chenyao Lou, Xuefeng Cui
Learning Protein Structural Fingerprints under the Label-Free Supervision of Domain Knowledge. BIBM (2018)
Xuefeng Cui, Xin Gao
K-nearest uphill clustering in the protein structure space. Neurocomputing 220 (2017)
Jim Jing-Yan Wang, Ivor Wai-Hung Tsang, Xuefeng Cui, Zhiwu Lu, Xin Gao
Multi-instance dictionary learning via multivariate performance measure optimization. Pattern Recognit. 66 (2017)
Hiroyuki Kuwahara, Meshari Alazmi, Xuefeng Cui, Xin Gao
MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Xuefeng Cui, Zhiwu Lu, Sheng Wang, Jim Jing-Yan Wang, Xin Gao
CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction. Bioinform. 32 (12) (2016)
Xuefeng Cui, Hammad Naveed, Xin Gao
Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces. BCB (2015)
Xuefeng Cui, Hammad Naveed, Xin Gao
Finding optimal interaction interface alignments between biological complexes. Bioinform. 31 (12) (2015)
Lijuan Miao, Peilong Ye, Bin He, Lizi Chen, Xuefeng Cui
Future Climate Impact on the Desertification in the Dry Land Asia Using AVHRR GIMMS NDVI3g Data. Remote. Sens. 7 (4) (2015)
Xuefeng Cui, Hiroyuki Kuwahara, Shuai Cheng Li, Xin Gao
Compare local pocket and global protein structure models by small structure patterns. BCB (2015)
Xuefeng Cui, Shuai Cheng Li, Lin He, Ming Li
Fingerprinting protein structures effectively and efficiently. Bioinform. 30 (7) (2014)
Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi, Ming Li
Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles? Algorithms Mol. Biol. 8 (2013)
Lijuan Miao, Yibo Luan, Xiangzhong Luo, Qiang Liu, John C. Moore, Reshmita Nath, Bin He, Feng Zhu, Xuefeng Cui
Analysis of the Phenology in the Mongolian Plateau by Inter-Comparison of Global Vegetation Datasets. Remote. Sens. 5 (10) (2013)
Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Ming Li
Towards Reliable Automatic Protein Structure Alignment. WABI (2013)
Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi Ramandi, Ming Li
How Accurately Can We Model Protein Structures with Dihedral Angles? WABI (2012)
Xuefeng Cui, Tomás Vinar, Brona Brejová, Dennis E. Shasha, Ming Li
Homology search for genes. ISMB/ECCB (Supplement of Bioinformatics) (2007)