Publications
Explore our latest research contributions in bioinformatics, machine learning, and computational biology
ResearchGate Publications list:
https://www.researchgate.net/profile/Xinqi_Gong
Filter by Year
Publication List
23 Publications
| Year | Title | Link | News Report |
|---|---|---|---|
| 2026 |
scHG: A supercell framework with high-order graph learning enables scalable multi-omics analysis
PLOS Computational Biology
doi: 10.1371/journal.pcbi.1013851
|
||
| 2026 |
Exogenous Epstein–Barr virus nuclear antigen 1 induces ADAR1-driven tumor resistance against immunotherapy
Signal Transduction and Targeted Therapy
doi: 10.1038/s41392-026-02574-y
| ||
| 2025 |
Evaluation Metrics and Quality Assessment Methods for Predicted Protein Complex Structures
Tsinghua Science and Technology
doi: 10.26599/TST.2025.9010068
|
||
| 2025 |
A pan-KRAS inhibitor and its derived degrader elicit multifaceted anti-tumor efficacy in KRAS-driven cancers
Cancer Cell
doi: 10.1016/j.ccell.2025.07.006
| ||
| 2025 |
Predicting interface residues for protein polymers based on module division
PHYSICAL REVIEW E
doi: 10.1103/pj5v-cdf4
|
||
| 2025 |
Multimeric protein interaction and complex prediction: Structure, dynamics and function
Computational and Structural Biotechnology Journal
doi: 10.1016/j.csbj.2025.05.009
|
||
| 2025 |
Sable: bridging the gap in protein structure understanding with an empowering and versatile pre-training paradigm
Briefings in Bioinformatics
doi: 10.1093/bib/bbaf120
| ||
| 2025 |
TopoQA: a topological deep learning-based approach for protein complex structure interface quality assessment
Briefings in Bioinformatics
doi: 10.1093/bib/bbaf083
|
||
| 2025 |
Unlocking hidden flaws in PPV and ACC: a step towards more reliable identification of protein complex
bioRxiv
doi: 10.1101/2025.03.03.641161
|
||
| 2025 |
Harnessing pre-trained models for accurate prediction of protein-ligand binding affinity
BMC Bioinformatics
doi: 10.1186/s12859-025-06064-w
|
||
| 2024 |
Review and Comparative Analysis of Methods and Advancements in Predicting Protein Complex Structure
Interdisciplinary Sciences Computational Life Sciences
doi: 10.1007/s12539-024-00626-x
| ||
| 2024 |
DCI: An Accurate Quality Assessment Criteria for Protein Complex Structure Models
arXiv
doi: 10.48550/arXiv.2407.00560
|
||
| 2024 |
Interferon-induced transmembrane protein-1 competitively blocks Ephrin receptor A2-mediated Epstein–Barr virus entry into epithelial cells
Nature Microbiology
doi: 10.1038/s41564-024-01659-0
|
||
| 2024 |
BDM: An Assessment Metric for Protein Complex Structure Models Based on Distance Difference Matrix
Interdisciplinary Sciences Computational Life Sciences
doi: 10.1007/s12539-024-00622-1
|
||
| 2024 |
ABAG-docking benchmark: a non-redundant structure benchmark dataset for antibody–antigen computational docking
Briefings in Bioinformatics
doi: 10.1093/bib/bbae048
| ||
| 2023 |
DSR: Dynamical Surface Representation as Implicit Neural Networks for Protein
Thirty-seventh Conference on Neural Information Processing Systems (NeurIPS 2023)
doi: 10.52202/075280-0611
| ||
| 2023 |
Computational Methods for Cryogenic Electron Tomography and in Situ Structural Studies
Frontiers in Cellular and Infection Microbiology
doi: 10.3389/fcimb.2023.1135013
|
||
| 2023 |
Computational methods for in situ structural studies with cryogenic electron tomography
Frontiers in Cellular and Infection Microbiology
doi: 10.3389/fcimb.2023.1135013
|
||
| 2023 |
The Application of Time Series Analysis in the Fiscal Budget Variance of China
Proceedings of the Second International Forum on Financial Mathematics and Financial Technology
doi: 10.1007/978-981-99-2366-3_12
|
||
| 2023 |
Conformational Dynamics of the D53-D3-D14 Complex in Strigolactone Signaling
Plant and Cell Physiology
doi: 10.1093/pcp/pcad067
|
||
| 2023 |
Computational Prediction of Protein Intrinsically Disordered Region Related Interactions and Functions
Genes
doi: 10.3390/genes14020432
|
||
| 2023 |
A review of computational models for predicting protein-protein interaction and non-interaction
Communications in Information and Systems
doi: 10.4310/CIS.2023.v23.n2.a1
|
||
| 2023 |
Quantitative anatomy of characteristics and influencing factors of PM2.5 and O3 in Liaoning province of China
Communications in Information and Systems
doi: 10.4310/CIS.2023.v23.n2.a2
|
||
| 2022 |
ACPred-BMF: bidirectional LSTM with multiple feature representations for explainable anticancer peptide prediction
Scientific Reports
doi: 10.1038/s41598-022-24404-1
|
||
| 2022 |
Inter-chain contact map prediction for protein complex based on graph attention network and triangular multiplication update
2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
doi: 10.1109/BIBM55620.2022.9995360
|
||
| 2022 |
An adaptive variational model for multireference alignment with mixed noise
2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
doi: 10.1109/BIBM55620.2022.9995092
|
||
| 2022 |
Nicking mechanism underlying the DNA phosphorothioate-sensing antiphage defense by SspE
Nature Communications
doi: 10.1038/s41467-022-34505-0
|
||
| 2022 |
Protein–protein interaction and non-interaction predictions using gene sequence natural vector
Communications Biology
doi: 10.1038/s42003-022-03617-0
|
||
| 2022 |
Polymeric coating lubricates nanocontainers to escape macrophage uptake for bioreceptor recognition
Bioactive Materials
doi: 10.1016/j.bioactmat.2021.12.035
|
||
| 2021 |
Inter-protein contact map generated only from intra-monomer by image inpainting
2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
doi: 10.1109/BIBM52615.2021.9669709
|
||
| 2020 |
Review of multimer protein–protein interaction complex topology and structure prediction
Chinese Physics B
doi: 10.1088/1674-1056/abb659
|
||
| 2020 |
A Two-Layer SVM Ensemble-Classifier to Predict Interface Residue Pairs of Protein Trimers
Molecules
doi: 10.3390/molecules25194353
|
||
| 2020 |
Tetramer protein complex interface residue pairs prediction with LSTM combined with graph representations
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
doi: 10.1016/j.bbapap.2020.140504
|
||
| 2020 |
The unidirectional causality influence of factors on PM2.5 in Shenyang city of China
Scientific Reports
doi: 10.1038/s41598-020-65391-5
|
||
| 2020 |
A Review of Protein Inter-residue Distance Prediction
Current Bioinformatics
doi: 10.2174/1574893615999200425230056
|
||
| 2020 |
Heterogeneous multiple kernel learning for breast cancer outcome evaluation
BMC Bioinformatics
doi: 10.1186/s12859-020-3483-0
|
||
| 2020 |
Protein Interface Complementarity and Gene Duplication Improve Link Prediction of Protein-Protein Interaction Network
Frontiers in Genetics
doi: 10.3389/fgene.2020.00291
|
||
| 2020 |
Modulation of BIN2 kinase activity by HY5 controls hypocotyl elongation in the light
Nature Communications
doi: 10.1038/s41467-020-15394-7
|
||
| 2020 |
A Novel Index of Contact Frequency from Noise Protein–Protein Interaction Data Help for Accurate Interface Residue Pair Prediction
Interdisciplinary Sciences Computational Life Sciences
doi: 10.1007/s12539-020-00364-w
|
||
| 2020 |
Maximizing multiple influences and fair seed allocation on multilayer social networks
PLOS One
doi: 10.1371/journal.pone.0229201
|
||
| 2020 |
Densely Dilated Spatial Pooling Convolutional Network using benign loss functions for imbalanced volumetric prostate segmentation DDSP network with benign loss for prostate segmentation
Current Bioinformatics
doi: 10.2174/1574893615666200127124145
|
||
| 2019 |
Attention mechanism enhanced LSTM with residual architecture and its application for protein-protein interaction residue pairs prediction
BMC Bioinformatics
doi: 10.1186/s12859-019-3199-1
|
||
| 2019 |
Trimer Protein-Protein Complex Interface Interacting Residue Pairs Prediction Using Deep Learning Approach
the 10th ACM International Conference
doi: 10.1145/3307339.3343864
|
||
| 2019 |
Noise Ｒeduction Algorithm on the Extremely Low Signal-noise Ｒatio CryoEM Images Based on Deep Learning Methods-DWT-CAE
|
||
| 2019 |
Cideb controls sterol‐regulated ER export of SREBP/SCAP by promoting cargo loading at ER exit sites
The EMBO Journal
doi: 10.15252/embj.2018100156
|
||
| 2019 |
An automatic particle picking method based on Generative Adversarial Network
Communications in Information and Systems
doi: 10.4310/CIS.2019.v19.n3.a5
|
||
| 2018 |
Natural distinct inter-preference between genetic codon and protein secondary structure combinations
Communications in Information and Systems
doi: 10.4310/CIS.2018.v18.n4.a6
|
||
| 2018 |
S-Nitrosylation Targets GSNO Reductase for Selective Autophagy during Hypoxia Responses in Plants
Molecular Cell
doi: 10.1016/j.molcel.2018.05.024
|
||
| 2018 |
Geometric and amino acid type determinants for protein-protein interaction interfaces
Quantitative Biology
doi: 10.1007/s40484-018-0138-5
|
||
| 2018 |
Hierarchical combinatorial deep learning architecture for pancreas segmentation of medical computed tomography cancer images
BMC Systems Biology
doi: 10.1186/s12918-018-0572-z
|
||
| 2018 |
Bi-clustering interpretation and prediction of correlation between gene expression and protein abundance
doi: 10.1101/270397
|
||
| 2018 |
Volumetric Densely Dilated Spatial Pooling ConNets for Prostate Segmentation
arXiv
doi: 10.48550/arXiv.1801.10517
|
||
| 2017 |
Five Dimensional Feature Space for Protein Binding Site Residue Prediction
Beijing Gongye Daxue Xuebao / Journal of Beijing University of Technology
doi: 10.11936/bjutxb2017070008
|
||
| 2017 |
Different protein-protein interface patterns predicted by different machine learning methods
Scientific Reports
doi: 10.1038/s41598-017-16397-z
|
||
| 2017 |
The E3 ubiquitin ligase SCF FBXL14 complex stimulates neuronal differentiation by targeting the Notch signaling factor HES1 for proteolysis
Journal of Biological Chemistry
doi: 10.1074/jbc.M117.815001
|
||
| 2017 |
Structural and mechanistic insights into the biosynthesis of CDP-archaeol in membranes
Cell Research
doi: 10.1038/cr.2017.122
|
||
| 2017 |
A new probability method to understand protein-protein interface formation mechanism at amino acid level
Journal of Theoretical Biology
doi: 10.1016/j.jtbi.2017.09.026
|
||
| 2017 |
CLE42 binding induces PXL2 interaction with SERK2
Protein & Cell
doi: 10.1007/s13238-017-0435-1
|
||
| 2017 |
Understanding Protein-Protein Interface Formation Mechanism in a New Probability Way at Amino Acid Level
International Symposium on Bioinformatics Research and Applications
doi: 10.1007/978-3-319-59575-7_36
|
||
| 2017 |
Protein-Protein Interaction Interface Residue Pair Prediction Based on Deep Learning Architecture
IEEE/ACM Transactions on Computational Biology and Bioinformatics
doi: 10.1109/TCBB.2017.2706682
|
||
| 2017 |
Structural insights into the γ-lactamase activity and substrate enantioselectivity of an isochorismatase-like hydrolase from Microbacterium hydrocarbonoxydans
Scientific Reports
doi: 10.1038/srep44542
|
||
| 2016 |
Multiple dimensional space for protein interface residue characterization
Computational and Mathematical Biophysics
doi: 10.1515/mlbmb-2016-0004
|
||
| 2016 |
Structural basis for specific self-incompatibility response in Brassica
Cell Research
doi: 10.1038/cr.2016.129
|
||
| 2016 |
Targeted next-generation sequencing of dedifferentiated chondrosarcoma in the skull base reveals combined TP53 and PTEN mutations with increased proliferation index, an implication for pathogenesis
Oncotarget
doi: 10.18632/oncotarget.9618
|
||
| 2016 |
Molecular Mechanism for Fungal Cell Wall Recognition by Rice Chitin Receptor OsCEBiP
Structure
doi: 10.1016/j.str.2016.04.014
|
||
| 2015 |
Phosphorylation of Atg31 is required for autophagy
Protein & Cell
doi: 10.1007/s13238-015-0138-4
|
||
| 2014 |
Structural basis for recognition of an endogenous peptide by the plant receptor kinase PEPR1
Cell Research
doi: 10.1038/cr.2014.161
|
||
| 2014 |
GdX/UBL4A specifically stabilizes the TC45/STAT3 association and promotes dephosphorylation of STAT3 to repress tumorigenesis
Molecular Cell
doi: 10.1016/j.molcel.2014.01.020
|
||
| 2014 |
Structure and mechanism of a eukaryotic transmembrane ascorbate-dependent oxidoreductase
Proceedings of the National Academy of Sciences
doi: 10.1073/pnas.1323931111
|