Xuefeng Cui

发表

Understanding the core of RNA interference: The dynamic aspects of Argonaute-mediated processes.

Xuhui Huang, Yanli Wang, Xin Gao, 2017, Progress in biophysics and molecular biology.

A Flexible Domain-Domain Hinge Promotes an Induced-fit Dominant Mechanism for the Loading of Guide-DNA into Argonaute Protein in Thermus thermophilus.

Xuhui Huang, Yanli Wang, Xin Gao, 2016, The journal of physical chemistry. B.

H-NS uses an autoinhibitory conformational switch for environment-controlled gene silencing

Yu Li, Xin Gao, S. Arold, 2018, Nucleic acids research.

Yaosen Min, Xuefeng Cui, Shang Liu, .

Homologous Gene Finding with a Hidden Markov Model

Xuefeng Cui, 2007 .

Ontology-aware deep learning enables ultrafast and interpretable source tracking among sub-million microbial community samples from hundreds of niches

K. Ning, Yuguo Zha, Xuefeng Cui, 2022, Genome Medicine.

Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology

K. Ning, Maozhen Han, Pengshuo Yang, 2020, NAR genomics and bioinformatics.

Fingerprinting protein structures effectively and efficiently

Shuai Cheng Li, Lin He, Ming Li, 2014, Bioinform..

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

Daming Zhu, K. Ning, Yuguo Zha, 2021, bioRxiv.

Ontology-aware deep learning for antibiotic resistance gene prediction: novel function discovery and comprehensive profiling from metagenomic data

K. Ning, Xuefeng Cui, Cheng Chen, 2022, bioRxiv.

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

Wei Zhao, Xuefeng Cui, Wei Zhao, 2022, 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Hexagonal Convolutional Neural Network for Spatial Transcriptomics Classification

Kai Hu, Xuefeng Cui, Fa Zhang, 2022, 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

SHREC 2020: Classification in cryo-electron tomograms

Daisuke Kihara, Remco C. Veltkamp, Xiao Wang, 2020, Comput. Graph..

MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind

Xin Gao, Xuefeng Cui, Hiroyuki Kuwahara, 2016, Nucleic Acids Res..

Pretraining Transformers for TCR-pMHC Binding Prediction

Daming Zhu, Xuefeng Cui, Cheng Chen, 2022, 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

SVLR: Genome Structure Variant Detection Using Long Read Sequencing Data

Daming Zhu, Lusheng Wang, Wenyan Gu, 2020, ISBRA.

Homology search for genes

Dennis Shasha, Ming Li, Xuefeng Cui, 2007, ISMB/ECCB.

Homology Search for Genes Using Biased HMMs

Dennis Shasha, Xuefeng Cui, D. Shasha, 2007 .

SHREC’19 Track: Classification in Cryo-Electron Tomograms

Min Xu, Genki Terashi, Daisuke Kihara, 2019 .

CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

Zhiwu Lu, Jim Jing-Yan Wang, Xin Gao, 2016, Bioinform..

Homologous Protein Detection

Yaosen Min, Xuefeng Cui, Yaosen Min, 2019, Encyclopedia of Bioinformatics and Computational Biology.

Ontology-aware deep learning enables ultrafast and interpretable source tracking among sub-million microbial community samples from hundreds of niches

Kang Ning, Kai Kang, Hao Qiu, 2020, Genome Medicine.

Ontology-Aware Deep Learning Enables Novel Antibiotic Resistance Gene Discovery Towards Comprehensive Profiling of ARGs

K. Ning, Xuefeng Cui, Cheng Chen, 2021 .

K-nearest uphill clustering in the protein structure space

Xin Gao, Xuefeng Cui, Xin Gao, 2017, Neurocomputing.

Xuefeng Cui, Xuefeng Cui, 2014 .

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

Shuai Cheng Li, Babak Alipanahi, Ming Li, 2013, Algorithms for Molecular Biology.

VP-Detector: A 3D multi-scale dense convolutional neural network for macromolecule localization and classification in cryo-electron tomograms

Fa Zhang, Rui Yan, Xiaohua Wan, 2022, Comput. Methods Programs Biomed..

Classification in Cryo-Electron Tomograms

Genki Terashi, Daisuke Kihara, Charles Kervrann, 2019, 3DOR@Eurographics.

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

Shuai Cheng Li, Xin Gao, Xuefeng Cui, 2015, BCB.

Finding optimal interaction interface alignments between biological complexes

Xin Gao, Xuefeng Cui, Hammad Naveed, 2015, Bioinform..

SHREC 2021: Classification in Cryo-electron Tomograms

Daisuke Kihara, Remco C. Veltkamp, Konstantinos Moustakas, 2022, 3DOR.

DNN-DTIs: improved drug-target interactions prediction using XGBoost feature selection and deep neural network

Bin Yu, Yu Han, Cheng Chen, 2020, bioRxiv.

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

Xuan Zhang, Haitao Jiang, Xuefeng Cui, 2022, bioRxiv.

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

Yuxiao Wang, Xuefeng Cui, Zongzhao Qiu, 2021, 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

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

Xuefeng Cui, Cheng Chen, Zhenghe Yang, 2021, 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

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

Yuxiao Wang, Xuefeng Cui, Zongzhao Qiu, 2021, 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Towards Reliable Automatic Protein Structure Alignment

Shuai Cheng Li, Ming Li, Xuefeng Cui, 2013, WABI.

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

Yaosen Min, Xuefeng Cui, Shang Liu, 2018, bioRxiv.

How Accurately Can We Model Protein Structures with Dihedral Angles?

Shuai Cheng Li, Babak Alipanahi, Ming Li, 2012, WABI.

MetaGIN: A Lightweight Framework for Molecular Property Prediction

Xuefeng Cui, Xiao-Tian Wang, Cheng Chen, 2023, bioRxiv.

Longest k-tuple Common Sub-Strings

Haodi Feng, Daming Zhu, Haitao Jiang, 2022, IEEE International Conference on Bioinformatics and Biomedicine.

Graph-based Reaction Classification by Contrasting between Precursors and Products

Zheng Wang, Wei Zhao, Xuefeng Cui, 2022, 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

SHREC 2021: CryoET Track

Marten L. Chaillet, Min Xu, D. Kihara, 2022 .