Xuefeng Cui

According to our database, Xuefeng Cui authored at least 44 papers between 2007 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

ContactLib-ATT: A Structure-Based Search Engine for Homologous Proteins.

Cheng Chen, Yuguo Zha, Daming Zhu, Kang Ning, Xuefeng Cui

IEEE ACM Trans. Comput. Biol. Bioinform., 2023

Learned Fingerprint Embedding for Large-Scale Peptide Mass Spectra Retrieval.

Yongshuai Wang, Xiaojun Cai, Defeng Li, Shiwei Sun, Cheng Chen, Xuefeng Cui

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

De Novo Molecular Structure Generation from Mass Spectra.

Yanmin Liu, Xuan Zhang, Wei Zhao, Daming Zhu, Xuefeng Cui

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

Variational Clustering and Denoising of Spatial Transcriptomics.

Cuiyuan Li, Fa Zhang, Kai Hu, Xuefeng Cui

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

Using Deep Learning to Classify Full-Length Transcriptome Sequences.

Weiguo Li, Junchi Ma, Cuiyuan Li, Ting Yu, Xuefeng Cui

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

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, Zhiyong Liu, Jintao Li, Shihua Zhang, Xuefeng Cui, Fa Zhang

Comput. Methods Programs Biomed., 2022

CoAtGIN: Marrying Convolution and Attention for Graph-based Molecule Property Prediction.

Xuan Zhang, Cheng Chen, Zhaoxu Meng, Zhenghe Yang, Haitao Jiang, Xuefeng Cui

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

Graph-based Reaction Classification by Contrasting between Precursors and Products.

Zhengwei Wang, Yuxiao Wang, Xuan Zhang, Zhaoxu Meng, Zhenghe Yang, Wei Zhao, Xuefeng Cui

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

Boosting Deep Learning-based Docking with Cross-attention and Centrality Embedding.

Jingxuan Wang, Zongzhao Qiu, Xuan Zhang, Zhenghe Yang, Wei Zhao, Xuefeng Cui

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

Pretraining Transformers for TCR-pMHC Binding Prediction.

Jinsheng Shang, Qihong Jiao, Cheng Chen, Daming Zhu, Xuefeng Cui

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

Longest k-tuple Common Sub-Strings.

Tiantian Li, Daming Zhu, Haitao Jiang, Haodi Feng, Xuefeng Cui

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

Hexagonal Convolutional Neural Network for Spatial Transcriptomics Classification.

Jing Gao, Fa Zhang, Kai Hu, Xuefeng Cui

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

2021

SVLR: Genome Structural Variant Detection Using Long-Read Sequencing Data.

Wenyan Gu, Aizhong Zhou, Lusheng Wang, Shiwei Sun, Xuefeng Cui, Daming Zhu

J. Comput. Biol., 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

Comput. Biol. Medicine, 2021

Structure-Based Protein-Drug Affinity Prediction with Spatial Attention Mechanisms.

Yuxiao Wang, Zongzhao Qiu, Qihong Jiao, Cheng Chen, Zhaoxu Meng, Xuefeng Cui

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

rzMLP-DTA: gMLP network with ReZero for sequence-based drug-target affinity prediction.

Zongzhao Qiu, Qihong Jiao, Yuxiao Wang, Cheng Chen, Daming Zhu, Xuefeng Cui

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

Edge-Gated Graph Neural Network for Predicting Protein-Ligand Binding Affinities.

Qihong Jiao, Zongzhao Qiu, Yuxiao Wang, Cheng Chen, Zhenghe Yang, Xuefeng Cui

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

Hydrogen bonds meet self-attention: all you need for protein structure embedding.

Cheng Chen, Yuguo Zha, Daming Zhu, Kang Ning, Xuefeng Cui

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 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, Xuefeng Cui

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

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, 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

Proceedings of the 14th Eurographics Workshop on 3D Object Retrieval, 2021

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, Xuefeng Cui, Fa Zhang, Emmanuel Moebel, Xiao Wang, Daisuke Kihara, Xiangrui Zeng, Min Xu, Nguyen P. Nguyen, Tommi A. White, Filiz Bunyak

Comput. Graph., 2020

MIMO Radar Imaging With Multiple Probing Pulses for 2D Off-Grid Targets via Variational Sparse Bayesian Learning.

Chao Wen, Lu Chen, Pengting Duan, Xuefeng Cui

IEEE Access, 2020

SVLR: Genome Structure Variant Detection Using Long Read Sequencing Data.

Wenyan Gu, Aizhong Zhou, Lusheng Wang, Shiwei Sun, Xuefeng Cui, Daming Zhu

Proceedings of the Bioinformatics Research and Applications - 16th International Symposium, 2020

Dilated-DenseNet for Macromolecule Classification in Cryo-electron Tomography.

Shan Gao, Renmin Han, Xiangrui Zeng, Xuefeng Cui, Zhiyong Liu, Min Xu, Fa Zhang

Proceedings of the Bioinformatics Research and Applications - 16th International Symposium, 2020

2019

Homologous Protein Detection.

Xuefeng Cui, Yaosen Min

Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 3, 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

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

Neural Comput. Appl., 2019

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, 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

Proceedings of the 12th Eurographics Workshop on 3D Object Retrieval, 2019

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, Xiaohua Wan, Zhiyong Liu, Fa Zhang, Xuefeng Cui

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

Learning Protein Structural Fingerprints under the Label-Free Supervision of Domain Knowledge.

Yaosen Min, Shang Liu, Chenyao Lou, Xuefeng Cui

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

2017

Multi-instance dictionary learning via multivariate performance measure optimization.

Jim Jing-Yan Wang, Ivor Wai-Hung Tsang, Xuefeng Cui, Zhiwu Lu, Xin Gao

Pattern Recognit., 2017

K-nearest uphill clustering in the protein structure space.

Xuefeng Cui, Xin Gao

Neurocomputing, 2017

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

Nucleic Acids Res., 2016

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, Sheng Wang, Jim Jing-Yan Wang, Xin Gao

Bioinform., 2016

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

Finding optimal interaction interface alignments between biological complexes.

Xuefeng Cui, Hammad Naveed, Xin Gao

Bioinform., 2015

Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces.

Xuefeng Cui, Hammad Naveed, Xin Gao

Proceedings of the 6th ACM Conference on Bioinformatics, 2015

Compare local pocket and global protein structure models by small structure patterns.

Xuefeng Cui, Hiroyuki Kuwahara, Shuai Cheng Li, Xin Gao

Proceedings of the 6th ACM Conference on Bioinformatics, 2015

2014

Fingerprinting protein structures effectively and efficiently.

Xuefeng Cui, Shuai Cheng Li, Lin He, Ming Li

Bioinform., 2014

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

Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles?

Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi, Ming Li

Algorithms Mol. Biol., 2013

Towards Reliable Automatic Protein Structure Alignment.

Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Ming Li

Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

2012

How Accurately Can We Model Protein Structures with Dihedral Angles?

Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi Ramandi, Ming Li

Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

2007

Homology search for genes.

Xuefeng Cui, Tomás Vinar, Brona Brejová, Dennis E. Shasha, Ming Li

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007