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 2026

  1. Thi Thanh Hoa Tran, Tuan Phuc Le, Ngoc Hung Pham, Quoc Dat Lai, Quoc Tuan Hoang, Thi To Quynh Cung, Hoang Dzung Nguyen. Can you taste the place? Building regional sensory standards for black pepper with GC-MS and sensory perception. Frontiers in Food Science and Technology. 1-17. 02/12/2025

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. 28/04/2025
  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. 28/04/2025
  4. Cui Wei, Ullah Ismat, Lin Weiming, Zhang Jupei, Chen Zhaowei, Yang Shuyi, Peng Wei, Zhuang Yin, Chen Wenjin, Cao Yi, Zhang Shujun, Jin Shengyang, Yang Liang. Multifunctional Sr2+/Zn2+ Co‐Doped Mesoporous Silica Nanoparticles in Injectable Hydrogel for Ameliorating Osteoporotic Osseointegration. Advanced Healthcare Materials. 15/06/2025
  5. Le Duc-Hau. Integrating multiple microRNA functional similarity networks for improved disease–microRNA association prediction. Biology Methods and Protocols. 06/08/2025
  6. Tran Thu Ha1, Hoang Quoc Tuan1, Pham Ngoc Hung1, Lại Quoc Dat2, Nguyen Hoang Dung2, Cung Thi To Quynh1*. Evaluation of Some Physicochemical Indicators of Black Pepper Purchased from Main Growing Areas in Vietnam. JST: Engineering and Technology for Sustainable Development. 18-24. 01/10/2024
  7. Nguyen Quang H., Tran Hoang V., Nguyen Huu Tien, Le Phuong T. M., Nguyen Phi Le, Nguyen Binh P.. AIM: an accurate and explainable model for ATAC to GEX translation and pathway analysis. Memetic Computing. 1-12. 22/02/2025
  8. Lê Tuấn Phúc, Bùi Uyển Diễm, Hoàng Quốc Tuấn, Phạm Ngọc Hưng, Lợi Quốc Đạt, Nguyễn Hoàng Dũng, Cung Thị Tố Quỳnh. Bước Đầu Xây Dựng Các Dấu Hiệu Nhận Diện Về Thành Phần Hóa Học Của Hạt Tiêu Đen Ở Một Số Vùng Trồng Tiêu Chính Tại Việt Nam. Tạp chí Nông nghiệp và Môi trường. 70-78. 15/08/2025
  9. Tiền Tiến Nam, Nguyễn Chính Nghĩa, Nguyễn Tiến Cường, Phạm Tuấn Anh, Phạm Ngọc Hưng, Chu Kỳ Sơn. Tiền xử lý nguyên liệu bằng sóng siêu âm và sự hình thành sản phẩm phụ trong quá trình sản xuất ethanol không gia nhiệt ở nồng độ chất khô cao từ bột gạo. Kỷ yếu Hội nghị Hóa học toàn quốc lần thứ 9. 233-236. 29/11/2025
  10. Nguyen Tung, Pham Duy-Tung, Nguyen Quang Duc, Ngo Van Linh, Nguyen Duc Anh, Dinh Viet Sang. TopiCOT: Neural topic model aligning with pre-trained clustering and optimal transport. Neurocomputing. 131268. 13/08/2025
  11. 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. 09/04/2025
  12. Le Duc-Hau. Unified Scour Depth Prediction for Culverts and Sluices Using Random Forest and Model-based Sensitivity Analysis. Environmental Research Communications. 23/12/2025
  13. 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
  14. 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
  15. Phạm Ngọc Hưng, Nguyễn Chính Nghĩa, Chu Kỳ Sơn. ĐÁNH GIÁ VÒNG ĐỜI SẢN PHẨM (LCA) CỦA QUY TRÌNH SẢN XUẤT CỒN THỰC PHẨM TỪ GẠO THEO CÔNG NGHỆ KHÔNG GIA NHIỆT Ở QUY MÔ 1 TẤN NGUYÊN LIỆU/MẺ. Tạp chí Nông nghiệp và Môi trường. 88-96. 08/08/2025
  16. Petschner Peter, Nguyen Anh Duc, Nguyen Canh Hao, Mamitsuka Hiroshi. Machine learning for predicting drug–drug interactions: Graph neural networks and beyond. Current Opinion in Systems Biology. 100551. 13/06/2025
  17. Duy-Long Nguyen, Duc-Luong Ho-Viet, Anh-Thu Ngo-Tran, Quang H. Nguyen, Binh P. Nguyen. MolHFCNet: Enhancing Molecular Graph Representations with Hierarchical Feature Combining and Hybrid Pretraining. The Thirty-Fourth International Joint Conference on Artificial Intelligence (IJCAI 2025). 9313-9321. Montreal, Canada. 16/08/2025
  18. Quang H. Nguyen, Duc A. Hoang, Hai Van Pham. Combination of 2D and 3D nnU-Net for ground glass opacity segmentation in CT images of Post-COVID-19 patients. Computers in Biology and Medicine. 110376. 09/05/2025
  19. Le Duc-Hau. Improving computational drug repositioning through multi-source disease similarity networks. Scientific Reports. 29/05/2025
  20. Tien Phat Nguyen, Vu Minh Ngo, Tung Nguyen, Linh Van Ngo, Duc Anh Nguyen, Sang Dinh, Trung Le. XTRA: Cross-Lingual Topic Modeling with Topic and Representation Alignments. Findings of the Association for Computational Linguistics: EMNLP 2025. 5561–5575. 04/11/2025
  21. Hoang Quoc Tuan*,a, Le Tuan Phuca, Pham Ngoc Hunga, Lai Quoc Datb, Nguyen Hoang Dungb, Do Van Longc, Cung Thi To Quynha. A Proposed Framework for Blockchain Technology in Vietnamese Domestic Pepper Supply Chain Regarding Authenticity and Traceability. Economia agro-alimentare / Food Economy An International Journal on Agricultural and Food Systems. 1-21. 16/09/2025

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. 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. 39-50. TP Hồ Chí Minh. 22/07/2024
  8. 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
  9. 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
  10. 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
  11. 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
  12. Trinh Thi Ha, Nguyen Trung Dung, Nguyen Thanh Huong, Tran Trong An, Pham Van Tuan, Vu Ngoc Hung, Chu Manh Hoang. Investigating the coupling length of two triangle hybrid gap plasmonic waveguides. The International Conference on Advanced Materials and Technology (ICAMT 2024). 10-13. Hanoi. 09/10/2024
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. • 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
  19. 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
  20. 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