Home » AI Researchs » Research Team » Bioinformatics

Introduction

In recent years, with the rapid development of modern gene sequencing and protein analysis techniques, the amount of digitized biological data has increased rapidly. Given the great complexity of DNA such as the number of up to about 3 billion nucleotides in the DNA of human cells, understanding the mechanism that controls the action of genes will require the assistance of computational algorithms which are capable of running on powerful computer systems. Therefore, bioinformatics is an interdisciplinary research field that is receiving great attention in order to apply information technology to solve important problems in biology, medicine, especially in biology molecular.

Our research group focuses on the study and development of machine learning methods to explore factors affecting transcription, translation as well as post-translational modification of proteins, to determine functions of proteins, and apply to supporting the treatment of human diseases such as cancer as well as reducing and removing the harmful effects of viruses and bacteria to humans. See the slides here for more detail.

Contact: Dr. Nguyen Hong Quang, Email: hauld@soict.hust.edu.vn

Research Directions

  • Molecular biology research: Develop machine learning methods to predict gene expression as well as protein function.
  • Researching viruses and bacteria: Develop machine learning methods to predict the biological mechanisms of viruses and bacteria, thereby proposing solutions for each type.

Research Problems

  • Gene expression prediction: in humans as well as in plants and animals, different gene expression regulators allow different types of cells in the body to perform their specific functions. These control mechanisms include transcription, translation, and post-translation modification.
  • Protein structure and function prediction: Protein structure prediction is a technique that assigns biological or biochemical roles to proteins in relation to their genome sequence. The need to understand protein function has attracted the attention of researchers in studies with the aim of improving predictive efficiency.
  • Antibiotic-resistant bacteria prediction: Predict the types of bacteria that are resistant to current antibiotics and determine the concentrations of current antibiotics for these bacteria.
  • Predict the evolution of viruses: Predict the mutation of pathogenic viruses such as influenza A or corona virus as well as the expression of these viruses to the body’s immune system.
  • Support cancer treatment: Identify factors in the molecule that affect the transformation and growth of cancer cells.

Team Members

Assoc. Prof. Le Duc Hau
Team Leader

Dr. Nguyen Hong Quang
Member

Dr. Nguyen Duc Anh
Member

Dr. Nguyen Phu Binh
Collaborator

Tools and Open Sources

Identifying antioxidant using Deep Learning
iProDNA-CapsNet: Identifying Protein-DNA Binding Residues using Capsule Neural Networks
iPseU-NCP: Identifying RNA Pseudouridine sites using Random Forest and NCP-encoded features
Minimum Inhibitory Concentration Prediction for Antibiotics towards Klebsiella Pneumoniae

Latest Publications

Publications in 2025

  1. Quang Duc Nguyen, Tung Nguyen, Duc Anh Nguyen, Linh Ngo Van, Sang Dinh, Thien Huu Nguyen. GloCOM: A Short Text Neural Topic Model via Global Clustering Context. Proceedings of the 2025 Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics: Human Language Technologies. 1109–1124. Albuquerque, New Mexico. 29/04/2025
  2. Tran Thi Thanh Hoa1, Le Tuan Phuc1, Pham Ngoc Hung1, Lai Quoc Dat2, Hoang Quoc Tuan1, Cung Thi To Quynh1, Nguyen Hoang Dzung2*. Development of Odor Lexicons for Black Pepper Grown in Some Provinces in Vietnam. Tạp chị KHCN ĐH BKHN. Volume 35, Issue 1, March 2025, 032-043. 25/01/2024
  3. Tung Nguyen, Tue Le, Hoang Tran Vuong, Quang Duc Nguyen, Duc Anh Nguyen, Linh Ngo Van, Sang Dinh, Thien Huu Nguyen. Sharpness-Aware Minimization for Topic Models with High-Quality Document Representations. Proceedings of the 2025 Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics: Human Language Technologies. 4507–4524. Albuquerque, New Mexico. 29/04/2025
  4. Peter Petschner, Sahel Kumar, Duc A. Nguyen, Dora Torok, Zsofia Gal, Daniel Baksa, Kinga Gecse, Gyongyi Kokonyei, Hiroshi Mamitsuka & Gabriella Juhasz. The interictal transcriptomic map of migraine without aura. The Journal of Headache and Pain. 1-17. 11/04/2025
  5. Khoi N.P. Dang, Thu Thuy Tran, Ta Cong Son, Tran Tien Anh, Duc Anh Nguyen, Nguyen Van Son. CoreNet: Leveraging context-aware representations via MLP networks for CTR prediction. Knowledge-based systems. 1-10. 15/02/2025
  6. Duc-Hau Le, Hung-Cuong Trinh, Tran Duc Quynh, Truong Cong Doan. The interplay of assortativity, centrality, and robustness in human signaling networks: Implications for drug discovery. Chaos, Solitons & Fractals. 02/03/2025
  7. Tran Thi Thanh Hoa, Le Tuan Phuc, Pham Ngoc Hung, Lai Quoc Dat, Hoang Quoc Tuan, Cung Thi To Quynh, Nguyen Hoang Dzung. Development of Odor Lexicons for Black Pepper Grown in Some Provinces in Vietnam. Journal of Science and Technology. 25/09/2024
  8. Tran Thi Thanh Hoa1, Le Tuan Phuc1, Pham Ngoc Hung1, Lai Quoc Dat2, Hoang Quoc Tuan1, Cung Thi To Quynh1, Nguyen Hoang Dzung. Development of Odor Lexicons for Black Pepper Grown in Some Provinces in Vietnam. Tạp chí KHCN ĐH BKHN. 32-43. 25/09/2024

Publications in 2024

  1. Hoa Thi Phuong Bui,Duong Huy Do,Ha Thi Thanh Ly,Kien Trung Tran,Huong Thi Thanh Le,Kien Trung Nguyen,Linh Thi Dieu Pham,Hau Duc Le,Vinh Sy Le,Arijit Mukhopadhyay ,Liem Thanh Nguyen. De novo copy number variations in candidate genomic regions in patients of severe autism spectrum disorder in Vietnam. PLoS ONE. 09/12/2023
  2. Giang T.T. Nguyen, Kien T. Phuong, Khanh Nguyen-Trong, Duc-Hau Le. A hybrid model integrating multi-omic and topological information of PPI network for synergism prediction. RIVF 2023. Hanoi, Vietnam. 23/12/2023
  3. T. K. Lai, and I. L. Ngo. An investigation on the thermo-electrohydraulic performance of novel ECF micro-pump.. International Journal of Heat and Mass Transfer. 29/09/2024
  4. Nguyễn Thị Trang, Lê Tú Linh, Đinh Văn Lượng, Nguyễn Xuân Đại, Nguyễn Hồng Quang, Lê Thị Minh Phương. Nghiên cứu phát triển bảng gen liên quan điều trị đích ở bệnh nhân ung thư phổi người Việt Nam. Tạp chí nghiên cứu Y học, Trường Đại học Y Hà Nội. 56-67. 30/05/2024
  5. Le Tuan Phuc1*, Tran Thi Thanh Hoa1,Pham Ngoc Hung1, , Nguyen Ngoc Vien1,Cung Thi To Quynh1, Le Thanh Nhan2, Hoang Quoc Tuan1*,. Beer Type Classification Based on Electromagnetic Waves Using Vector Network Analyzer with Machine Learning Model. The International Conference on Smart Cities for ASEAN: Experience and Innovation (ISSCEI 2023). 30-32. Đà nẵng. 12/04/2024
  6. Sikandar Ali Qalati, MengMeng Jiang, Samuel Gyedu, and Emmanuel Kwaku Manu. Do Strong Innovation Capability and Environmental Turbulence Influence the Nexus Between Customer Relationship Management and Business Performance?. Business Strategy and the Environment. 02/07/2024
  7. T. K. Lai, K. D. Tran, and I. L. Ngo. A numerical study on the thermo-electrohydrodynamic performance of ECF micro-pumps. Sustainability and Emerging Technologies for Smart Manufacturing. 29/04/2024
  8. Le Tuan Phuc, Nguyen Mai Anh, Le Kim Oanh, Tran Xuan Tien, Tran Thi Thanh Hoa, Nguyen Thi Thao, Cung Thi To Quynh, Pham Ngoc Hung, Nguyen Hoang Dzung, and Hoang Quoc Tuan. Rapid sensory profiling of rice milk using natural language processing on free description. SPISE 2024. 22/07/2024
  9. Duy-Tung Pham, Thien Trang Nguyen Vu, Tung Nguyen, Linh Ngo Van, Duc Anh Nguyen, Thien Huu Nguyen. NeuroMax: Enhancing Neural Topic Modeling via Maximizing Mutual Information and Group Topic Regularization. the 2024 Conference on Empirical Methods in Natural Language Processing. 7758–7772. 11/11/2024
  10. Le Tuan Phuc1*, Tran Thi Thanh Hoa1,Pham Ngoc Hung1, , Bui Uyen Diem1,Cung Thi To Quynh1, Le Thanh Nhan2, Hoang Quoc Tuan1*,. Determination of Pol Content in Molasses Using Near-Infrared Spectroscopy and Partial Least Squares Regression. The International Conference on Smart Cities for ASEAN: Experience and Innovation (ISSCEI 2023). 48-50. Đà Nẵng. 12/01/2024
  11. Long D. Nguyen, Quang H. Nguyen, Quang H. Trinh, Binh P. Nguyen. From SMILES to Enhanced Molecular Property Prediction: A Unified Multimodal Framework with Predicted 3D Conformers and Contrastive Learning Techniques. Journal of Chemical Information and Modeling. 9173-9195. 22/12/2024
  12. Ha An Le , Trinh Van Chien , Van Duc Nguyen†,Wan Choi. Channel Analysis and End-to-End Design for Double RIS-Aided Communication Systems with Spatial Correlation and Finite Scatterers. IEEE Conference on Global Communications (GLOBECOM). 1561-1566. Kuala Lumpur, Malaysia. 03/08/2023
  13. JYE Tin, WW Tan, AA Bakar, MS Mahali, FF Lothai, NF Mohammad, SSA Hassan & KF Chin. A Conceptual Design of Sustainable Solar Photovoltaic (PV) Powered Corridor Lighting System with IoT Application. ICREEM 2022. 09/03/2024
  14. Quang H. Nguyen, Thanh-Hoang Nguyen-Vo, Trang T. T. Do, Binh P. Nguyen. An Efficient Hybrid Deep Learning Architecture for Predicting Short Antimicrobial Peptides. Proteomics. 1-8. 07/05/2024
  15. Sikandar Ali Qalati, Domitilla Magni, and Faiza Siddiqui. Senior Management's Sustainability Commitment and Environmental Performance: Revealing the Role of Green Human Resource Management Practices.. Business Strategy and the Environment. 02/08/2024
  16. T. K. Lai, and I. L. Ngo. A new design and optimization of VD-ECF micro-pump: Advancements in electrohydraulic performance. Physics of Fluids. 29/07/2024
  17. Le Tuan Phuca*, Nguyen Mai Anha, Le Kim Oanha, Tran Xuan Tiena, Tran Thi Thanh Hoaa, Nguyen Thi Thaoa, Cung Thi To Quynha, Pham Ngoc Hunga, Nguyen Hoang Dzungb, and Hoang Quoc Tuana. Rapid sensory profiling of rice milk using natural language processing on free description. PROCEEDINGS OF SPISE 2024 The New Diverse Facets of Sensory Evaluation: Exploring its Intersection with Modern Technologies. 39-50. TP Hồ Chí Minh. 26/07/2024
  18. T. K. Lai, and I. L. Ngo. An investigation on the electrohydraulic performance of novel ECF micro-pump with NACAshaped electrodes. Theoretical and Computational Fluid Dynamics. 29/02/2024
  19. Nguyễn Duy Long, Nguyen Hồng Quang, Trịnh Huy Quang, Nguyễn Phú Bình. From SMILES to Enhanced Molecular Property Prediction: A Unified Multimodal Framework with Predicted 3D Conformers and Contrastive Learning Techniques. Journal of Chemical Information and Modeling. 23/11/2024
  20. • Emilia Leszkowicz, Hung Ngoc Pham, Minh Tu Thi Nguyen, Hong Son Vu, Son Chu Ky, Artur Hugo Świergiel. Deprivation of visual stimuli increases sensitivity to sweet taste in a Vietnamese Kinh population. Food Quality and Preference. 30/01/2024
  21. Tran, X.T, Nguyen, T.T, Le Tuan.P, Tran, T.T.H, Nguyen, T.T, Cung, T.T.Q, Pham, N.H, Nguyen, H.D and Hoang, Q.T. Application of a free JAR sensory assessment method in evaluating consumer preferences for beer products. PROCEEDINGS OF SPISE 2024The New Diverse Facets of Sensory Evaluation: Exploring its Intersection with Modern Technologies. 7-20. 26/07/2024
  22. Thi-Thao Nguyen, Thi Minh-Tu Nguyen, Tien-Cuong Nguyen, Phu-Ha Ho, Quoc-Tuan Hoang, Thu-Trang Vu, Ngoc-Hung Pham, Tuan-Phuc Le, Van-Hung Nguyen, Chinh-Nghia Nguyen, Tuan-Anh Pham, Lan-Huong Nguyen, Tien-Thanh Nguyen, Thi Thu-Huong Hoang, Thi Anh Tuyet Nguyen, Nguyen-Thanh Vu, Quang-Thuat Bui, Anh-Duong Cao, Quyet-Tien Phi, Anh-Tuan Pham, Thanh-Khiem Nguyen & Son Chu-Ky. Adding Values to Sugar Industry in Vietnam Toward Net-zero and Digitalization Trend. Sugar Tech. 992-1004. 13/07/2024

Publications in 2023

  1. Nguyễn Đức Ca, Phan Thị Thu, Hoàng Thị Minh Anh, Phạm Ngọc Dương, Nguyễn Hoàng Giang, Nguyễn Lệ Hằng. Nâng cao hiệu quả quản trị đại học trong bối cảnh đổi mới giáo dục tại Việt Nam. Tạp chí khoa học giáo dục Việt Nam. 14/03/2023
  2. Le Tuan Phuc, Tran Thi Thanh Hoa, Cung Thi To Quynh, Nguyen Hoang Dzung, Pham Ngoc Hung. Rapid Identification of the Geographical Origin of Black Pepper in Vietnam Using Near-Infrared Spectroscopy and Chemometrics. JST: Engineering and Technology for Sustainable Development. 001-008. 02/02/2023
  3. Ha An Le, Trinh Van Chien, Van Duc Nguyen, Wan Choi. Double RIS-Assisted MIMO Systems Over Spatially Correlated Rician Fading Channels and Finite Scatterers. IEEE Transactions on Communications. 4941-4956. 13/05/2023
  4. Sikandar Ali Qalati, Belem Barbosa, and Blend Ibrahim. Factors influencing employees’ eco-friendly innovation capabilities and behavior: the role of green culture and employees’ motivations. Environment, Development and Sustainability. 02/10/2023
  5. Phạm Ngọc Hưng, Phạm Duy Tự, Nguyễn Thị Dung, Bùi Uyển Diễm, Hoàng Quốc Tuấn1, Nguyễn Thị Thảo, Phùng Đức Định, Phùng Đức Long.. Nghiên cứu tối ưu công nghệ sấy nấm đùi gà bằng phương pháp sấy lạnh. Tạp chí Nông nghiệp & Phát triển nông thôn. 207-215. 25/04/2023
  6. Tran Xuan Bach, Nguyen Duc Anh, Ngo Van Linh, Khoat Than. Dynamic Transformation of Prior Knowledge Into Bayesian Models for Data Streams. IEEE Transactions on Knowledge and Data Engineering. 3742-3750. 23/12/2021
  7. Duc Anh Nguyen, Canh Hao Nguyen, Hiroshi Mamitsuka. Central-Smoothing Hypergraph Neural Networks for Predicting Drug-Drug Interactions. IEEE Transactions on Neural Networks and Learning Systems. 1-6. 10/03/2023
  8. Pham Ngoc Hung, Le Tuan Phuc, Hoang Quoc Tuan, Cung Thi To Quynh. Modeling the Effect of Temperature on Brix Concentration of Tomato Juice during Vacuum Concentration. JST: Engineering and Technology for Sustainable Development. 001-008. 17/03/2023
  9. Thu Trang Vu, Thi Trang Nguyen, Hong Quan Duong, Van Hung Nguyen, Viet Hung Le, Viet Hung Nguyen, Xuan Lam Nguyen, Van Tan Le, Giang Hoang, Quoc Tuan Hoang, Thi Thao Nguyen, Tien Cuong Nguyen, Ngoc Hung Pham, Hong Son Vu, Thi Hanh Nguyen, Ky Son Chu. Quality assessment of japonica brown rice J02 (Oryza sativa L. J02) and its hydrolysis ability for the production of a rice-based drink containing an abundance of dextrin. Vietnam Journal of Science, Technology and Engineering. 37-41. 28/10/2022
  10. Sikandar Ali Qalati, Sonia Kumari, Kayhan Tajeddini, Namarta Kumari Bajaj, and Rajib Ali. Innocent devils: The varying impacts of trade, renewable energy and financial development on environmental damage: Nonlinearly exploring the disparity between developed and developing nations. Journal of Cleaner Production. 02/02/2023
  11. Wu Qinqin, Sikandar Ali Qalati, Rana Yassir Hussain, Hira Irshad, Kayhan Tajeddini, Faiza Siddique, Thilini Chathurika Gamage. The effects of enterprises' attention to digital economy on innovation and cost control: Evidence from A-stock market of China. Journal of Innovation & Knowledge. 02/12/2023
  12. Nga Nguyen Thi Thanh, Quang H. Nguyen. Detection of abnormal network traffic using bidirectional long short-term memory. Computer Systems Science and Engineering. 491–504. 28/10/2022
  13. Sikandar Ali Qalati , Belem Barbosa & Shuja Iqbal. The effect of firms’ environmentally sustainable practices on economic performance. Economic. Economic Research-Ekonomska Istraživanja. 02/06/2023