Dong-Qing Wei

Publication Activity (10 Years)

Years Active: 2011-2024
Publications (10 Years): 63

Top Topics

Immune Response

Protein Interaction

Cancer Patients

Top Venues

Comput. Biol. Medicine

Briefings Bioinform.

J. Chem. Inf. Model.

Database J. Biol. Databases Curation

Publications

Yufang Zhang, Jiayi Li, Shenggeng Lin, Jianwei Zhao, Yi Xiong, Dong-Qing Wei
An end-to-end method for predicting compound-protein interactions based on simplified homogeneous graph convolutional network and pre-trained language model. J. Cheminformatics 16 (1) (2024)
Muhammad Shahab, Muhammad Waleed Iqbal, Abbas Ahmad, Fahad M. Alshabrmi, Dong-Qing Wei, Abbas Khan, Guojun Zheng
Immunoinformatics-driven In silico vaccine design for Nipah virus (NPV): Integrating machine learning and computational epitope prediction. Comput. Biol. Medicine 170 (2024)
Chen Zhang, Junhui Gao, Hong-Yu Chen, Lingxin Kong, Guangshuo Cao, Xiangyu Guo, Wei Liu, Bin Ren, Dong-Qing Wei
STGIC: A graph and image convolution-based method for spatial transcriptomic clustering. PLoS Comput. Biol. 20 (2) (2024)
Abdul Nasir, Abdus Samad, Sami Ullah, Arif Ali, Dong-Qing Wei, Bai Qian
Omicron variant (B.1.1.529) challenge the integrity of blood brain barrier: Evidence from protein structural analysis. Comput. Biol. Medicine 169 (2024)
Yifan Jin, Addeela Fayyaz, Ayesha Liaqat, Abbas Khan, Abdulrahman Alshammari, Yanjing Wang, Ruo-Xu Gu, Dong-Qing Wei
Proteomics-based vaccine targets annotation and design of subunit and mRNA-based vaccines for Monkeypox virus (MPXV) against the recent outbreak. Comput. Biol. Medicine 159 (2023)
Jing Zhao, Bowen Zhao, Xiaotong Song, Chujun Lyu, Weizhi Chen, Yi Xiong, Dong-Qing Wei
Subtype-DCC: decoupled contrastive clustering method for cancer subtype identification based on multi-omics data. Briefings Bioinform. 24 (2) (2023)
Yitian Fang, Fan Xu, Lesong Wei, Yi Jiang, Jie Chen, Leyi Wei, Dong-Qing Wei
AFP-MFL: accurate identification of antifungal peptides using multi-view feature learning. Briefings Bioinform. 24 (1) (2023)
Yitian Fang, Yi Jiang, Leyi Wei, Qin Ma, Zhixiang Ren, Qianmu Yuan, Dong-Qing Wei
DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model. Bioinform. 39 (12) (2023)
Abbas Khan, Shoaib Adil, Hafiza Ayesha Qudsia, Yasir Waheed, Fahad M. Alshabrmi, Dong-Qing Wei
Structure-based design of promising natural products to inhibit thymidylate kinase from Monkeypox virus and validation using free energy calculations. Comput. Biol. Medicine 158 (2023)
Asma Sindhoo Nangraj, Saima Sipy, Abbas Khan, Gurudeeban Selvaraj, Abdulrahman Alshammari, Mark E. Casida, Dong-Qing Wei
ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer. Database J. Biol. Databases Curation 2023 (2023)
Wenfeng Li, Farah Bano, Abbas Khan, Dong-Qing Wei, Abdulrahman Alshammari, Bin Xu, Yanjing Wang
Inhibition of cMYC-MAX transcription factors hetero-dimerization with structurally engineered omoMYC to downregulate oncogenic pathways in renal carcinoma. Comput. Biol. Medicine 164 (2023)
Heqi Sun, Jianmin Wang, Hongyan Wu, Shenggeng Lin, Junwei Chen, Jinghua Wei, Shuai Lv, Yi Xiong, Dong-Qing Wei
A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions. J. Chem. Inf. Model. 63 (23) (2023)
Tianyu Wang, Wenming Yang, Jie Chen, Yonghong Tian, Dong-Qing Wei
ConformerDTI: Local Features Coupling Global Representations for Drug-Target Interaction Prediction. BIBM (2022)
Aamir Mehmood, Sadia Nawab, Yanjing Wang, Aman Chandra Kaushik, Dong-Qing Wei
Discovering potent inhibitors against the Mpro of the SARS-CoV-2. A medicinal chemistry approach. Comput. Biol. Medicine 143 (2022)
Yanyi Chu, Yan Zhang, Qiankun Wang, Lingfeng Zhang, Xuhong Wang, Yanjing Wang, Dennis Russell Salahub, Qin Xu, Jianmin Wang, Xue Jiang, Yi Xiong, Dong-Qing Wei
A transformer-based model to predict peptide-HLA class I binding and optimize mutated peptides for vaccine design. Nat. Mach. Intell. 4 (3) (2022)
Athar Shafiq, Farrukh Zubair, Amna Ambreen, Muhammad Suleman, Qudsia Yousafi, Zahid Rasul Niazi, Zeeshan Anwar, Abbas Khan, Anwar Mohammad, Dong-Qing Wei
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 146 (2022)
Shenggeng Lin, Weizhi Chen, Gengwang Chen, Songchi Zhou, Dong-Qing Wei, Yi Xiong
MDDI-SCL: predicting multi-type drug-drug interactions via supervised contrastive learning. J. Cheminformatics 14 (1) (2022)
Yi Cao, Zhen-Qun Yang, Xu-Lu Zhang, Wenqi Fan, Yaowei Wang, Jiajun Shen, Dong-Qing Wei, Qing Li, Xiao-Yong Wei
Identifying the kind behind SMILES - anatomical therapeutic chemical classification using structure-only representations. Briefings Bioinform. 23 (5) (2022)
Taimoor Khan, Muhammad Suleman, Syed Shujait Ali, Muhammad Farhan Sarwar, Imtiaz Ali, Liaqat Ali, Abbas Khan, Bakht Rokhan, Yanjing Wang, Ruili Zhao, Dong-Qing Wei
for immune response induction. Comput. Biol. Medicine 145 (2022)
Abbas Khan, Wenfeng Li, Amna Ambreen, Dong-Qing Wei, Yanjing Wang, Yuanshen Mao
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 146 (2022)
Shenggeng Lin, Yanjing Wang, Lingfeng Zhang, Yanyi Chu, Yatong Liu, Yitian Fang, Mingming Jiang, Qiankun Wang, Bowen Zhao, Yi Xiong, Dong-Qing Wei
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. 23 (1) (2022)
Imtiaz Ali, Abbas Khan, Zhang Fa, Taimoor Khan, Dong-Qing Wei, Jianting Zheng
and biophysical investigations. Comput. Biol. Medicine 145 (2022)
Abdullah Shah, Saira Rehmat, Iqra Aslam, Muhmmad Suleman, Farah Batool, Abdul Aziz, Farooq Rashid, Midrarullah, Muhmmad Asif Nawaz, Syed Shujait Ali, Muhammad Junaid, Abbas Khan, Dong-Qing Wei
Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Comput. Biol. Medicine 141 (2022)
Muhammad Suleman, Uzair Asad, Shafia Arshad, Ayaz ur Rahman, Fazal Akbar, Haji Khan, Zahid Hussain, Syed Shujait Ali, Anwar Mohammad, Abbas Khan, Liaqat Ali, Dong-Qing Wei
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 148 (2022)
Yaning Yang, Xiaoqi Wang, Deshan Zhou, Dong-Qing Wei, Shaoliang Peng
SVPath: an accurate pipeline for predicting the pathogenicity of human exon structural variants. Briefings Bioinform. 23 (2) (2022)
Fahad Humayun, Abbas Khan, Sajjad Ahmad, Wang Yuchen, Guoshen Wei, N. Nizam-Uddin, Zahid Hussain, Wajid Khan, Nasib Zaman, Muhammad Rizwan, Muhammad Waseem, Dong-Qing Wei
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 141 (2022)
Ismail Shah, Sehrooz Jamil, Saira Rehmat, Hammad Ahmad Butt, Syed Shujait Ali, Muhammad Idrees, Yifei Zhan, Zahid Hussain, Shahid Ali, Muhammad Waseem, Arshad Iqbal, Sajjad Ahmad, Abbas Khan, Yanjing Wang, Dong-Qing Wei
for immune response instigation. Comput. Biol. Medicine 143 (2022)
Shenggeng Lin, Guangwei Zhang, Dong-Qing Wei, Yi Xiong
DeepPSE: Prediction of polypharmacy side effects by fusing deep representation of drug pairs and attention mechanism. Comput. Biol. Medicine 149 (2022)
Abbas Khan, Sarfaraz Hussain, Sajjad Ahmad, Muhammad Suleman, Imrana Bukhari, Taimoor Khan, Farooq Rashid, Abul Kalam Azad, Muhammad Waseem, Wajid Khan, Zahid Hussain, Asghar Khan, Syed Shujait Ali, Qiyao Qin, Dong-Qing Wei
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 141 (2022)
Taimoor Khan, Abbas Khan, Syed Nouman Nasir, Sajjad Ahmad, Syed Shujait Ali, Dong-Qing Wei
CytomegaloVirusDb: Multi-omics knowledge database for cytomegaloviruses. Comput. Biol. Medicine 135 (2021)
Muhammad Suleman, Qudsia Yousafi, Javaid Ali, Syed Shujait Ali, Zahid Hussain, Shahid Ali, Muhammad Waseem, Arshad Iqbal, Sajjad Ahmad, Abbas Khan, Yanjing Wang, Dong-Qing Wei
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 138 (2021)
Aman Chandra Kaushik, Yanjing Wang, Xiangeng Wang, Dong-Qing Wei
Irinotecan and vandetanib create synergies for treatment of pancreatic cancer patients with concomitant TP53 and KRAS mutations. Briefings Bioinform. 22 (3) (2021)
Nagina Inayat, Mukhtaj Khan, Nadeem Iqbal, Salman Khan, Mushtaq Raza, Dost Muhammad Khan, Abbas Khan, Dong-Qing Wei
iEnhancer-DHF: Identification of Enhancers and Their Strengths Using Optimize Deep Neural Network With Multiple Features Extraction Methods. IEEE Access 9 (2021)
Aman Chandra Kaushik, Aamir Mehmood, Ajay Kumar, Ankit Babu, Dong-Qing Wei, Zhongming Zhao
Pancreatic Adenocarcinoma Patients. BIBM (2021)
Wei Wang, Qiuying Dai, Fang Li, Yi Xiong, Dong-Qing Wei
MLCDForest: multi-label classification with deep forest in disease prediction for long non-coding RNAs. Briefings Bioinform. 22 (3) (2021)
Zhiwen Shi, Yanyi Chu, Yonghong Zhang, Yanjing Wang, Dong-Qing Wei
Prediction of Blood-Brain Barrier Permeability of Compounds by Fusing Resampling Strategies and eXtreme Gradient Boosting. IEEE Access 9 (2021)
Dong-Qing Wei, Aman Chandra Kaushik, Gurudeeban Selvaraj, Yi Pan
Editorial: Computational Genomics and Molecular Medicine for Emerging COVID-19. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (4) (2021)
Taimoor Khan, Abbas Khan, Dong-Qing Wei
MMV-db: vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses. Database J. Biol. Databases Curation 2021 (2021)
Qiuying Dai, Yanyi Chu, Zhiqi Li, Yusong Zhao, Xueying Mao, Yanjing Wang, Yi Xiong, Dong-Qing Wei
MDA-CF: Predicting MiRNA-Disease associations based on a cascade forest model by fusing multi-source information. Comput. Biol. Medicine 136 (2021)
Deshan Zhou, Shaoliang Peng, Dong-Qing Wei, Wu Zhong, Yutao Dou, Xiaolan Xie
LUNAR : Drug Screening for Novel Coronavirus Based on Representation Learning Graph Convolutional Network. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (4) (2021)
Yanyi Chu, Aman Chandra Kaushik, Xiangeng Wang, Wei Wang, Yufang Zhang, Xiaoqi Shan, Dennis Russell Salahub, Yi Xiong, Dong-Qing Wei
DTI-CDF: a cascade deep forest model towards the prediction of drug-target interactions based on hybrid features. Briefings Bioinform. 22 (1) (2021)
Abbas Khan, Shahzeb Khan, Shoaib Saleem, N. Nizam-Uddin, Anwar Mohammad, Taimoor Khan, Sajjad Ahmad, Muhammad Arshad, Syed Shujait Ali, Muhammad Suleman, Dong-Qing Wei
cloning and immune simulation. Comput. Biol. Medicine 133 (2021)
Adnan Zeb, Syed Shujait Ali, Abul Kalam Azad, Muhammad Safdar, Zeeshan Anwar, Muhammad Suleman, N. Nizam-Uddin, Abbas Khan, Dong-Qing Wei
. Comput. Biol. Medicine 133 (2021)
Abbas Khan, Taimoor Khan, Syed Nouman Nasir, Syed Shujait Ali, Muhammad Suleman, Muhammad Rizwan, Muhammad Waseem, Shahid Ali, Xia Zhao, Dong-Qing Wei
BC-TFdb: a database of transcription factor drivers in breast cancer. Database J. Biol. Databases Curation 2021 (2021)
Aman Chandra Kaushik, Aamir Mehmood, Gurudeeban Selvaraj, Xiaofeng Dai, Yi Pan, Dong-Qing Wei
CoronaPep: An Anti-Coronavirus Peptide Generation Tool. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (4) (2021)
Yanyi Chu, Xuhong Wang, Qiuying Dai, Yanjing Wang, Qiankun Wang, Shaoliang Peng, Xiaoyong Wei, Jingfei Qiu, Dennis Russell Salahub, Yi Xiong, Dong-Qing Wei
MDA-GCNFTG: identifying miRNA-disease associations based on graph convolutional networks via graph sampling through the feature and topology graph. Briefings Bioinform. 22 (6) (2021)
Mingming Jiang, Bowen Zhao, Shenggan Luo, Qiankun Wang, Yanyi Chu, Tianhang Chen, Xueying Mao, Yatong Liu, Yanjing Wang, Xue Jiang, Dong-Qing Wei, Yi Xiong
NeuroPpred-Fuse: an interpretable stacking model for prediction of neuropeptides by fusing sequence information and feature selection methods. Briefings Bioinform. 22 (6) (2021)
Muhammad Tahir Ul Qamar, Sajjad Ahmad, Abbas Khan, Muhammad Usman Mirza, Sarfraz Ahmad, Asma Abro, Ling-Ling Chen, Ahmad Almatroudi, Dong-Qing Wei
through integrated computational approaches. Comput. Biol. Medicine 138 (2021)
Aamir Mehmood, Aman Chandra Kaushik, Qiankun Wang, Cheng-Dong Li, Dong-Qing Wei
Bringing Structural Implications and Deep Learning-Based Drug Identification for KRAS Mutants. J. Chem. Inf. Model. 61 (2) (2021)
Yanyi Chu, Xiaoqi Shan, Tianhang Chen, Mingming Jiang, Yanjing Wang, Qiankun Wang, Dennis Russell Salahub, Yi Xiong, Dong-Qing Wei
DTI-MLCD: predicting drug-target interactions using multi-label learning with community detection method. Briefings Bioinform. 22 (3) (2021)
Nazia Azim, Nadeem Iqbal, Jamil Ahmad, Mukhtaj Khan, Amnah Siddiqa, Javaria Ashraf, Abbas Khan, Dong-Qing Wei
Biological Regulatory Networks for ARVC Using Automata Network Model. IEEE Access 9 (2021)
Xiaoyi Feng, Shaoliang Peng, Fei Li, Ying Xu, Xiangxiang Zeng, Dong-Qing Wei, Yunhao Liu
A drug information embedding method based on graph convolution neural network. HealthCom (2020)
Shaozhen Ding, Yu Tian, Pengli Cai, Dachuan Zhang, Xingxiang Cheng, Dandan Sun, Le Yuan, Junni Chen, Weizhong Tu, Dong-Qing Wei, Qian-Nan Hu
novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Wei Wang, Xiaoqing Guan, Muhammad Tahir Khan, Yi Xiong, Dong-Qing Wei
LMI-DForest: A deep forest model towards the prediction of lncRNA-miRNA interactions. Comput. Biol. Chem. 89 (2020)
Muhammad Junaid, Muhammad Tahir Khan, Shaukat Iqbal Malik, Dong-Qing Wei
Insights into the Mechanisms of the Pyrazinamide Resistance of Three Pyrazinamidase Mutants N11K, P69T, and D126N. J. Chem. Inf. Model. 59 (1) (2019)
Satyavani Kaliamurthi, Gurudeeban Selvaraj, Sathishkumar Chinnasamy, Qian Wang, Asma Sindhoo Nangraj, William C. S. Cho, Keren Gu, Dong-Qing Wei
Immunomics Datasets and Tools: To Identify Potential Epitope Segments for Designing Chimeric Vaccine Candidate to Cervix Papilloma. Data 4 (1) (2019)
Cheng-Dong Li, Muhammad Junaid, Hui Chen, Arif Ali, Dong-Qing Wei
Helix-Switch Enables C99 Dimer Transition between the Multiple Conformations. J. Chem. Inf. Model. 59 (1) (2019)
Xiaoqi Shan, Xiangeng Wang, Cheng-Dong Li, Yanyi Chu, Yufang Zhang, Yi Xiong, Dong-Qing Wei
Prediction of CYP450 Enzyme-Substrate Selectivity Based on the Network-Based Label Space Division Method. J. Chem. Inf. Model. 59 (11) (2019)
Ling Liu, Yi Xiong, Hongyun Gao, Dong-Qing Wei, Julie C. Mitchell, Xiaolei Zhu
dbAMEPNI: a database of alanine mutagenic effects for protein-nucleic acid interactions. Database J. Biol. Databases Curation 2018 (2018)
Gurudeeban Selvaraj, Satyavani Kaliamurthi, Aman Chandra Kaushik, Abbas Khan, Yong-Kai Wei, William C. S. Cho, Keren Gu, Dong-Qing Wei
Identification of target gene and prognostic evaluation for lung adenocarcinoma using gene expression meta-analysis, network analysis and neural network algorithms. J. Biomed. Informatics 86 (2018)
Abbas Khan, Arif Ali, Muhammad Junaid, Chang Liu, Aman Chandra Kaushik, William C. S. Cho, Dong-Qing Wei
Identification of novel drug targets for diamond-blackfan anemia based on RPS19 gene mutation using protein-protein interaction network. BMC Syst. Biol. 12 (4) (2018)
Weizhong Tu, Shaozhen Ding, Ling Wu, Zhe Deng, Hui Zhu, Xiaotong Xu, Chen Lin, Chaonan Ye, Minlu Han, Mengna Zhao, Juan Liu, Zixin Deng, Junni Chen, Dong-Qing Wei, Qian-Nan Hu
SynBioEcoli: a comprehensive metabolism network of engineered E. coli in three dimensional visualization. Quant. Biol. 5 (1) (2017)
Shuang Hou, Ruo-Xu Gu, Dong-Qing Wei
Inhibition of β-Amyloid Channels with a Drug Candidate wgx-50 Revealed by Molecular Dynamics Simulations. J. Chem. Inf. Model. 57 (11) (2017)
Ying Wang, Xiaolin Wu, Dong-Qing Wei, Yi-Xue Li, Jing-Fang Wang
Autoinhibitory Mechanism for the Mutation-Induced Impaired FGF9 Signaling. J. Chem. Inf. Model. 52 (9) (2012)
Jue Li, Dong-Qing Wei, Jing-Fang Wang, Yi-Xue Li
A Negative Cooperativity Mechanism of Human CYP2E1 Inferred from Molecular Dynamics Simulations and Free Energy Calculations. J. Chem. Inf. Model. 51 (12) (2011)
Tao Zhang, Limin Angela Liu, David F. V. Lewis, Dong-Qing Wei
Long-Range Effects of a Peripheral Mutation on the Enzymatic Activity of Cytochrome P450 1A2. J. Chem. Inf. Model. 51 (6) (2011)