Dongqing Wei

This page is a disambiguation page, it actually contains mutiple papers from persons of the same or a similar name.

Bibliography

2024
An end-to-end method for predicting compound-protein interactions based on simplified homogeneous graph convolutional network and pre-trained language model.
J. Cheminformatics, December, 2024

Immunoinformatics-driven In silico vaccine design for Nipah virus (NPV): Integrating machine learning and computational epitope prediction.
Comput. Biol. Medicine, March, 2024

STGIC: A graph and image convolution-based method for spatial transcriptomic clustering.
PLoS Comput. Biol., February, 2024

Omicron variant (B.1.1.529) challenge the integrity of blood brain barrier: Evidence from protein structural analysis.
Comput. Biol. Medicine, February, 2024

DDSBC: A Stacking Ensemble Classifier-Based Approach for Breast Cancer Drug-Pair Cell Synergy Prediction.
J. Chem. Inf. Model., 2024

2023
A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions.
J. Chem. Inf. Model., December, 2023

DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model.
Bioinform., December, 2023

Running ahead of evolution - AI-based simulation for predicting future high-risk SARS-CoV-2 variants.
Int. J. High Perform. Comput. Appl., November, 2023

Inhibition of cMYC-MAX transcription factors hetero-dimerization with structurally engineered omoMYC to downregulate oncogenic pathways in renal carcinoma.
Comput. Biol. Medicine, September, 2023

Proteomics-based vaccine targets annotation and design of subunit and mRNA-based vaccines for Monkeypox virus (MPXV) against the recent outbreak.
Comput. Biol. Medicine, June, 2023

Structure-based design of promising natural products to inhibit thymidylate kinase from Monkeypox virus and validation using free energy calculations.
Comput. Biol. Medicine, May, 2023

Subtype-DCC: decoupled contrastive clustering method for cancer subtype identification based on multi-omics data.
Briefings Bioinform., March, 2023

More or less deadly? A mathematical model that predicts SARS-CoV-2 evolutionary direction.
Comput. Biol. Medicine, February, 2023

AFP-MFL: accurate identification of antifungal peptides using multi-view feature learning.
Briefings Bioinform., January, 2023

AdaPPI: identification of novel protein functional modules via adaptive graph convolution networks in a protein-protein interaction network.
Briefings Bioinform., January, 2023

ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer.
Database J. Biol. Databases Curation, 2023

A Novel Deep Learning Approach Featuring Graph-Based Algorithm for Cell Segmentation and Tracking.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

2022
A transformer-based model to predict peptide-HLA class I binding and optimize mutated peptides for vaccine design.
Nat. Mach. Intell., 2022

MDDI-SCL: predicting multi-type drug-drug interactions via supervised contrastive learning.
J. Cheminformatics, 2022

Screening of immune epitope in the proteome of the Dabie bandavirus, SFTS, to design a protein-specific and proteome-wide vaccine for immune response instigation using an immunoinformatics approaches.
Comput. Biol. Medicine, 2022

Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches.
Comput. Biol. Medicine, 2022

Evaluation and identification of essential therapeutic proteins and vaccinomics approach towards multi-epitopes vaccine designing against <i>Legionella pneumophila</i> for immune response instigation.
Comput. Biol. Medicine, 2022

Investigation of the binding and dynamic features of A.30 variant revealed higher binding of RBD for hACE2 and escapes the neutralizing antibody: A molecular simulation approach.
Comput. Biol. Medicine, 2022

Discovering potent inhibitors against the Mpro of the SARS-CoV-2. A medicinal chemistry approach.
Comput. Biol. Medicine, 2022

DeepPSE: Prediction of polypharmacy side effects by fusing deep representation of drug pairs and attention mechanism.
Comput. Biol. Medicine, 2022

Subtractive proteomics assisted therapeutic targets mining and designing ensemble vaccine against <i>Candida auris</i> for immune response induction.
Comput. Biol. Medicine, 2022

A protein coupling and molecular simulation analysis of the clinical mutants of androgen receptor revealed a higher binding for Leupaxin, to increase the prostate cancer invasion and motility.
Comput. Biol. Medicine, 2022

Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study.
Comput. Biol. Medicine, 2022

Abrogation of SARS-CoV-2 interaction with host (NRP1) neuropilin-1 receptor through high-affinity marine natural compounds to curtail the infectivity: A structural-dynamics data.
Comput. Biol. Medicine, 2022

Structure-guided design of multi-epitopes vaccine against variants of concern (VOCs) of SARS-CoV-2 and validation through In silico cloning and immune simulations.
Comput. Biol. Medicine, 2022

Crystal structure of Acetyl-CoA carboxylase (AccB) from <i>Streptomyces antibioticus</i> and insights into the substrate-binding through <i>in silico mutagenesis</i> and biophysical investigations.
Comput. Biol. Medicine, 2022

SVPath: an accurate pipeline for predicting the pathogenicity of human exon structural variants.
Briefings Bioinform., 2022

MDF-SA-DDI: predicting drug-drug interaction events based on multi-source drug fusion, multi-source feature fusion and transformer self-attention mechanism.
Briefings Bioinform., 2022

Identifying the kind behind SMILES - anatomical therapeutic chemical classification using structure-only representations.
Briefings Bioinform., 2022

ConformerDTI: Local Features Coupling Global Representations for Drug-Target Interaction Prediction.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

2021
LUNAR : Drug Screening for Novel Coronavirus Based on Representation Learning Graph Convolutional Network.
IEEE ACM Trans. Comput. Biol. Bioinform., 2021

Editorial: Computational Genomics and Molecular Medicine for Emerging COVID-19.
IEEE ACM Trans. Comput. Biol. Bioinform., 2021

CoronaPep: An Anti-Coronavirus Peptide Generation Tool.
IEEE ACM Trans. Comput. Biol. Bioinform., 2021

Bringing Structural Implications and Deep Learning-Based Drug Identification for KRAS Mutants.
J. Chem. Inf. Model., 2021

Genome-wide screening of vaccine targets prioritization and reverse vaccinology aided design of peptides vaccine to enforce humoral immune response against <i>Campylobacter jejuni</i>.
Comput. Biol. Medicine, 2021

Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor.
Comput. Biol. Medicine, 2021

Structural probing of HapR to identify potent phytochemicals to control <i>Vibrio cholera</i> through integrated computational approaches.
Comput. Biol. Medicine, 2021

Immunogenomics guided design of immunomodulatory multi-epitope subunit vaccine against the SARS-CoV-2 new variants, and its validation through <i>in silico</i> cloning and immune simulation.
Comput. Biol. Medicine, 2021

CytomegaloVirusDb: Multi-omics knowledge database for cytomegaloviruses.
Comput. Biol. Medicine, 2021

MDA-CF: Predicting MiRNA-Disease associations based on a cascade forest model by fusing multi-source information.
Comput. Biol. Medicine, 2021

MMV-db: vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses.
Database J. Biol. Databases Curation, 2021

BC-TFdb: a database of transcription factor drivers in breast cancer.
Database J. Biol. Databases Curation, 2021

MLCDForest: multi-label classification with deep forest in disease prediction for long non-coding RNAs.
Briefings Bioinform., 2021

Irinotecan and vandetanib create synergies for treatment of pancreatic cancer patients with concomitant TP53 and KRAS mutations.
Briefings Bioinform., 2021

Exosomal ncRNAs profiling of mycobacterial infection identified miRNA-185-5p as a novel biomarker for tuberculosis.
Briefings Bioinform., 2021

NeuroPpred-Fuse: an interpretable stacking model for prediction of neuropeptides by fusing sequence information and feature selection methods.
Briefings Bioinform., 2021

MDA-GCNFTG: identifying miRNA-disease associations based on graph convolutional networks via graph sampling through the feature and topology graph.
Briefings Bioinform., 2021

DTI-MLCD: predicting drug-target interactions using multi-label learning with community detection method.
Briefings Bioinform., 2021

DTI-CDF: a cascade deep forest model towards the prediction of drug-target interactions based on hybrid features.
Briefings Bioinform., 2021

Prediction of Blood-Brain Barrier Permeability of Compounds by Fusing Resampling Strategies and eXtreme Gradient Boosting.
IEEE Access, 2021

iEnhancer-DHF: Identification of Enhancers and Their Strengths Using Optimize Deep Neural Network With Multiple Features Extraction Methods.
IEEE Access, 2021

A Static Analysis of Wnt/β-Catenin and Wnt/Ca<sup>2+</sup> Biological Regulatory Networks for ARVC Using Automata Network Model.
IEEE Access, 2021

CFCN: A Multi-scale Fully Convolutional Network with Dilated Convolution for Nuclei Classification and Localization.
Proceedings of the Bioinformatics Research and Applications - 17th International Symposium, 2021

Mining Cancer Cell Line-Based Drugs to Benefit KRAS<sup>(G12D)</sup> Pancreatic Adenocarcinoma Patients.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

2020
High-Scalable Collaborated Parallel Framework for Large-Scale Molecular Dynamic Simulation on Tianhe-2 Supercomputer.
IEEE ACM Trans. Comput. Biol. Bioinform., 2020

novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model.
Nucleic Acids Res., 2020

LMI-DForest: A deep forest model towards the prediction of lncRNA-miRNA interactions.
Comput. Biol. Chem., 2020

A drug information embedding method based on graph convolution neural network.
Proceedings of the 22nd IEEE International Conference on E-health Networking, 2020

2019
Prediction of CYP450 Enzyme-Substrate Selectivity Based on the Network-Based Label Space Division Method.
J. Chem. Inf. Model., 2019

Helix-Switch Enables C99 Dimer Transition between the Multiple Conformations.
J. Chem. Inf. Model., 2019

Insights into the Mechanisms of the Pyrazinamide Resistance of Three Pyrazinamidase Mutants N11K, P69T, and D126N.
J. Chem. Inf. Model., 2019

Immunomics Datasets and Tools: To Identify Potential Epitope Segments for Designing Chimeric Vaccine Candidate to Cervix Papilloma.
Data, 2019

2018
Identification of target gene and prognostic evaluation for lung adenocarcinoma using gene expression meta-analysis, network analysis and neural network algorithms.
J. Biomed. Informatics, 2018

Identification of novel drug targets for diamond-blackfan anemia based on RPS19 gene mutation using protein-protein interaction network.
BMC Syst. Biol., 2018

dbAMEPNI: a database of alanine mutagenic effects for protein-nucleic acid interactions.
Database J. Biol. Databases Curation, 2018

2017
Inhibition of β-Amyloid Channels with a Drug Candidate wgx-50 Revealed by Molecular Dynamics Simulations.
J. Chem. Inf. Model., November, 2017

SynBioEcoli: a comprehensive metabolism network of engineered E. coli in three dimensional visualization.
Quant. Biol., 2017

2016
mAMBER: A CPU/MIC collaborated parallel framework for AMBER on Tianhe-2 supercomputer.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015
Personalized clinical data screening: Special issue on health informatics.
Comput. Biol. Medicine, 2015

2013
Impact of Resistance Mutations on Inhibitor Binding to HIV-1 Integrase.
J. Chem. Inf. Model., 2013

2012
Adaptive Visual and Auditory Map Alignment in Barn Owl Superior Colliculus and Its Neuromorphic Implementation.
IEEE Trans. Neural Networks Learn. Syst., 2012

Autoinhibitory Mechanism for the Mutation-Induced Impaired FGF9 Signaling.
J. Chem. Inf. Model., 2012

2011
Long-Range Effects of a Peripheral Mutation on the Enzymatic Activity of Cytochrome P450 1A2.
J. Chem. Inf. Model., 2011

A Negative Cooperativity Mechanism of Human CYP2E1 Inferred from Molecular Dynamics Simulations and Free Energy Calculations.
J. Chem. Inf. Model., 2011

2010
Molecular Dynamics Studies on T1 Lipase: Insight into a Double-Flap Mechanism.
J. Chem. Inf. Model., 2010

The computational model to predict accurately inhibitory activity for inhibitors towardsCYP3A4.
Comput. Biol. Medicine, 2010

2005
Assessment of chemical libraries for their druggability.
Comput. Biol. Chem., 2005

2004
Virtual Screening for SARS-CoV Protease Based on KZ7088 Pharmacophore Points.
J. Chem. Inf. Model., 2004


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