Publications

Journals:

24. Xuan Tran-Thi, Nguyen Thi-Tuyen, Nguyen Quoc Khanh Le and Van-Nui Nguyen*, "KD_MultiSucc: Incorporating Multi-Teacher Knowledge Distillation and Word Embeddings for Cross-Species Prediction of Protein Succinylation Sites", Biology Methods & Protocols. ISSN: 2396-8923, (WoS/Scopus (ESCI); IF 2023: 2.5; SCImago SJR 2024 0.795 - Q1)

23. Van-Nui Nguyen, Nguyen Quoc Khanh Le*, "Data-driven proteomics for post-translational modification discovery", Proteomics, 2025, Volume 25, Issue 9-10 (SCIE Q2, IF 2025: 3.4). 

22. Xuan Tran-Thi, Nguyen Quoc Khanh Le and Van-Nui Nguyen*, 01/2025, "Integrating CNN and Bi-LSTM for Protein Succinylation Sites Prediction based on Natural Language Procesing Technique",  Computers in Biology and Medicine, Volume 186, March 2025, 109664 (ISI, Q1, IF 2025: 7.0)

21. Van-Nui Nguyen, Xuan Tran-Thi*, Thi-Tuyen Nguyen, Nguyen Quoc Khanh Le* , 10/2024, "Enhancing Arabidopsis thaliana ubiquitination site prediction through knowledge distillation and natural language processing",  Methods (ISI, Q1, IF 2024: 4.2).

20. Xuan Tran-Thi, Thi-Thu-Huong Tran, Le-Nguyen-Quoc Khanh Le, Van-Nui Nguyen* 9/2024, "CLW_SUMO: A hybrid Deep Learning model for predicting protein SUMOylation sites", Journal of Computer Science and Cybernetics. V.40, N.4 (2024),1-.

21. Van-Nui Nguyen*, Trang-Thi Ho, Thu-Dung Doan, Nguyen Quoc Khanh Le*, 5/2024, "Using a hybrid neural network architecture for DNA sequence representation: A study on 𝑁4-methylcytosine sites", Computers in Biology and Medicine, (ISI, Q1, IF 2025: 7.0)

19. Nguyen Quoc Khanh Le*, Thi-Xuan Tran, Phung-Anh Nguyen, Trang-Thi Ho & Van-Nui Nguyen*, 5/2024, "Recent progress in machine learning approaches for predicting carcinogenicity in drug development", Expert Opinion on Drug Metabolism & Toxicology, DOI: https://doi.org/10.1080/17425255.2024.2356162. (ISI, Q1, IF 2022: 4.3)

18. Thi-Tuyen Nguyen, Van-Nui Nguyen*, Thi-Xuan Tran, Nguyen-Quoc-Khanh Le*, 12/2023, "Enhanced Prediction of mRNA Subcellular Localization Using a Novel Ensemble Learning and Hybrid Approach", Lecture Notes in Networks and Systems book series (LNNS, volume 847), pp 60-68. (Scopus Q4)

17. Tran Thi Xuan, Nguyễn Văn Núi*, Le Nguyen Quoc Khanh, 12/2022, "Predict human phosphorylation sites using XGBoost and protein sequence-based characterization",  TNU Journal of Science and Technology, ISSN 1859-2171, e-ISSN 2615-9562. 227(18): 66 - 73

16. Nguyễn Văn Núi*, Nguyễn Thị Hằng, 12/2022, "Phương pháp quy hoạch động sử dụng kỹ thuật lập hệ thức giải một số bài toán tiêu biểu trong lý thuyết đồ thị",  Tạp chí Khoa học và Công nghệ Đại học Thái Nguyên, ISSN 1859-2171, e-ISSN 2615-9562. 228(02): 70 - 77

15. Quang-Hien Kha, Trinh-Trung-Duong Nguyen, Van-Nui Nguyen, Khoat Than, Nguyen Quoc Khanh Le, 9/2022, "An interpretable deep learning model for classifying adaptor protein complexes from sequence information",  Methods (ISI, Q1, IF 2022: 4.647).

14. Nguyen Quoc Khanh Le, Quang-Thai Ho, Van-Nui Nguyen and Jung-Su Chang, 7/2022, "BERT-Promoter: an improved sequence-based predictor of DNA promoter using BERT pre-trained model and SHAP feature selection",  Computational Biology and Chemistry (ISI, Q2, IF 2022: 3.737).

13. Trần Thị Xuân*, Nguyễn Văn Núi, 11/2021, "Khai phá luật kết hợp sử dụng thuật toán Apriori, hỗ trợ cho hoạt động bán hàng tại siêu thị",  Tạp chí Khoa học và Công nghệ Đại học Thái Nguyên, ISSN 1859-2171, e-ISSN 2615-9562. 226(16): 212-217.

12. Trần Thị Xuân, Nguyễn Văn Núi*, 11/2021, "Phân lớp khách hàng dựa trên hành vi, sử dụng kỹ thuật khai phá dữ liệu",  Tạp chí Khoa học và Công nghệ Đại học Thái Nguyên, ISSN 1859-2171, e-ISSN 2615-9562. 226(16): 134-141.

11. Nguyễn Văn Núi*, 7/2021, "Phân lớp dữ liệu hoa IRIS sử dụng các thuật toán Naive Bayes, Random Forest và KNN",  Tạp chí Khoa học và Công nghệ Đại học Thái Nguyên, ISSN 1859-2171, e-ISSN 2615-9562. 226(11): 79-84.

10. Hui-Ju Kao+, Van-Nui Nguyen+ (+ joint first author), Kai-Yao Huang, Wen-Chi Chang, Tzong-Yi Lee, 4/2020, "SuccSite: Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites", Genomics, Proteomics & Bioinformatics (ISI, Q1,  IF 2024: 11.5)

9. Thu-Ha Le, Thi-Xuan Tran and Van-Nui Nguyen*, 3/2020, "Factors influencing satisfaction on the e-learning and traditional training method of students at Thai Nguyen University of Economics and Business Administration", IOSR Journal of Business and Management (IOSR-JBM), e-ISSN: 2278-487X, p-ISSN: 2319-7668. Volume 22, Issue 3. Ser. II (March. 2020), PP 01-07.

8. Van-Nui Nguyen, Hong-Tan Nguyen, “Identifying Protein SUMOylation Sites based on the Combination of Amino Acid Composition and k-Spaced Amino Acid Pairs”, International Journal of Science and Research (IJSR), Volume 8 Issue 11, June 2019. ISSN: 2319-7064

7. Trần Thị Xuân, Nguyễn Văn Núi*, 8/2019, "Phân lớp vị trí protein Farnesylation với máy vector hỗ trợ (SVM) và cây quyết định",  Tạp chí Khoa học và Công nghệ Đại học Thái Nguyên, ISSN 1859-2171, e-ISSN 2615-9562. 204(11): 149-154.

6. Nguyen Quoc Khanh Le, Van-Nui Nguyen, 02/2019, "SNARE-CNN: a 2D convolutional neural network architecture to identify SNARE proteins from high-throughput sequencing data", PeerJ Computer Science (2017/Q1 ISI/Scopus)

5. Van-Nui Nguyen*, Kai-Yao Huang, Chien-Hsun Huang, K. Robert Lai* and Tzong-Yi Lee*, 2017, "A new scheme to characterize and identify protein ubiquitination sites," IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume: 14, Issue: 2, March-April 1 2017 (ISI, Q2; IF 2025: 3.6;). Link: http://ieeexplore.ieee.org/abstract/document/7400980/

4. Van-Nui Nguyen*, Kai-Yao Huang, Julia Tzu-Ya Weng, K. Robert Lai* and Tzong-Yi Lee*, 2016, "UbiNet: an online resource for exploring functional associations and regulatory networks of protein ubiquitylation," DATABASE: The Journal of Biological Databases and Curation, (ISI, Q1;  2016/2017 IF: 3.29; 7/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

3. Van-Nui Nguyen*, Kai-Yao Huang, Chien-Hsun Huang, Tzu-Hao Chang, Neil Arvin Bretaña, K. Robert Lai, Julia Tzu-Ya Weng* and Tzong-Yi Lee*, 2015, "Characterization and Identification of Ubiquitin Conjugation Sites with E3 Ligase Recognition Specificities," BMC Bioinformatics, Vo. 16 (Suppl. 1), S1. (ISI, Q1; 2016/2017 IF:2.448; 10/56 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)

2. Than Quang Khoat, Trần Thị Ngân, Bùi Thị Thanh Xuân, Van-Nui Nguyen, “Về một cách tiếp cận mới giải bài toán Quy hoạch tuyến tính nguyên”. Thai Nguyen Journal of Science and Technology, vol. 56(8), pages 51-59, 2009.

1. Than Quang Khoat, Nguyễn Hồng Tân and Van-Nui Nguyen, “Chứng minh độ khó NP-hard của một số bài toán Lưới”. Vietnam Journal on Information Technologies and Communications, No. 19(2), pages 124-133, 2008.

Conferences:

18. Nguyen Thi-Tuyen, Nguyen Van-Nui*, Tran Thi-Xuan and Nguyen Quoc Khanh Le*, “Improved Linear B-Cell Epitope Prediction Using CNN and BiLSTM", The 3rd International Conference on Advances in Information and Communication Technology (ICTA2024), November 16-17, 2024, Phu Tho, Viet Nam. (Scopus Q4).

17. Tran Thi-Xuan, Nguyen Thi-Tuyen, Nguyen Quoc Khanh Le and Nguyen Van-Nui*, “A Hybrid Deep Learning and Natural Language Processing Model for Plant Ubiquitination Site Prediction", The 3rd International Conference on Advances in Information and Communication Technology (ICTA2024), November 16-17, 2024, Phu Tho, Viet Nam. (Scopus Q4).

16. Nguyen Quoc Khanh Le, Van-Nui Nguyen, Thi-Tuyen Nguyen, Tran Thi-Xuan, Trang-Thi Ho, Van-Lam Ho “Deep Learning-Based Identification of Rab Proteins: A Convolutional Neural Network Approach with Evolutionary Information Integration", The Third International Conference on Intelligence of Things (ICIT2024), September 12-14, 2024, Da Nang, Vietnam. (Scopus Q3)

15. Nguyen Quoc Khanh Le, Van-Nui Nguyen, Thi-Tuyen Nguyen, Tran Thi-Xuan, Trang-Thi Ho, “Enhancing Protein Sequence Classification with a Fuzzy Neural Network: A Study in Anticancer Peptide Identification", 2024 International Conference on Fuzzy Theory and Its Applications (iFUZZY), August 10-13, 2024, Kagawa, Japan. DOI: 10.1109/iFUZZY63051.2024.10662887; (IEEE indexed).

14. Tran Thi-Xuan, Nguyen Thi-Tuyen, Le Nguyen Quoc Khanh, Hong-Hai Nguyen and Nguyen Van-Nui*, “A Novel Deep Learning Approach for the Prediction of  Arabidopsis Thaliana Ubiquitination Sites", The 13th Conference on Information Technology and Its Application (CITA2024), July 19-20, 2024, Da Nang City, Viet Nam.

13. Nguyen Thi-Tuyen, Nguyen Van-Nui*, Tran Thi-Xuan and Nguyen-Quoc-Khanh Le*, “A Machine Learning Approach for Predictive Insights into Tight Junction Protein Functions", The 13th Conference on Information Technology and Its Application (CITA2024), July 19-20, 2024, Da Nang City, Viet Nam.

12. Thi-Xuan Tran, Van-Nui Nguyen*, Nguyen Quoc Khanh Le, 7/2023, "Incorporating Natural Language-Based and Sequence-Based Features to Predict Protein SUMOylation Sites",  Lecture Notes in Networks and Systems book series (LNNS, volume 734), pp 74-88. DOI: https://link.springer.com/chapter/10.1007/978-3-031-36886-8_7 (Scopus Q4)

11. Nguyen Le Quoc Khanh, Quang-Thai Ho, Van-Nui Nguyen and Jung-Su Chang, “BERT-Promoter: an improved sequence-based predictor of DNA promoter using BERT pre-trained model and SHAP feature selection", 20th Asia Pacific Bioinformatics Conference, 04/2022, ISBN 978-629-96723.

10. Van-Nui Nguyen, Thi-Xuan Tran, Le Nguyen Quoc Khanh, Khoat Than, “Sequence-based machine learning model for phage virion proteins: a wrapper subset evaluation approach", The 24th National Symposium of Selected ICT problems, 13-14, December, 2021, Thai Nguyen, Viet Nam.

9. Trần Quang Qúy, Nguyễn Hải Minh, Nguyễn Văn Núi, Lê Anh Tú; Ứng dụng mô hình toán học SIR và ngôn ngữ R trong phân tích dịch tễ; The 24th National Symposium of Selected ICT problems, 13-14, December, 2021, Thai Nguyen, Viet Nam, 591-597.

8. Quang-Quy Tran, Van-Nui Nguyen, Duc-Binh Nguyen, Kirpishnikov Alexandr Petrovich, “Probale characteristics of multi-channel queuing system with "impatient" claims", The 23th National Symposium of Selected ICT problems, 05-06, November, 2020, Quang Ninh, Viet Nam.

7. Van-Nui Nguyen*, Huy-Khoi Do, Thi-Xuan Tran, Nguyen-Quoc-Khanh Le, Anh-Tu Le and Tzong-Yi Lee , “ Exploiting two-layer support vector machine to predict protein SUMOylation sites", ICERA 2018 International Conference on Engineering Research and Applications, 1-2 December 2018, Thai Nguyen, Viet Nam. Springer Indexed.

6. Van-Nui Nguyen*, Thi-Xuan Tran and Huy-Khoi Do, “Towards more accurate prediction of protein SUMOylation sites by exploiting the maximal dependence decomposition method” The 21th National Symposium of Selected ICT problems, 27-28, July, 2018, Thanh Hoa, Viet Nam. pages 338-343.
5. Van-Nui Nguyen*, Hai-Minh Nguyen and Thi-Xuan Tran, “An approach by exploiting support vector machine to characterize and identify protein SUMOylation sites” The 20th National Symposium of Selected ICT problems, 23-24, November, 2017, Quy Nhon, Viet Nam.

4. Hai-Minh Nguyen, Van-Nui Nguyen, and Quang-Minh Le,  “Flexible Render Medical Data in a CDA Document on Mobile Browsers”, Fair 10, 17-18, August, 2017, Da Nang, Viet Nam.

3. Van-Nui Nguyen*, Thi-Xuan Tran, Hai-Minh Nguyen, Hong-Tan Nguyen and Tzong-Yi Lee*, 2017, “A new schema to identify S-farnesyl cysteine prenylation sites with substrate motifs” In: Akagi M., Nguyen TT., Vu DT., Phung TN., Huynh VN. (eds) Advances in Information and Communication Technology. ICTA 2016. Advances in Intelligent Systems and Computing, vol 538. Springer, Cham. ISBN: 9783319490731; ISSN: 2194-5365; DOI: 10.1007/978-3-319-49073-1.

2. Van-Minh Bui and Van-Nui Nguyen*, "The prediction of Succinylation site in protein by analyzing amino acid composition" In: Akagi M., Nguyen TT., Vu DT., Phung TN., Huynh VN. (eds) Advances in Information and Communication Technology. ICTA 2016. Advances in Intelligent Systems and Computing, vol 538. Springer, Cham. ISBN: 9783319490731; ISSN: 2194-5365; DOI: 10.1007/978-3-319-49073-1.

1. Van-Nui Nguyen*, Kai-Yao Huang, Chien-Hsun Huang, Tzu-Hao Chang, Neil Arvin Bretaña, K. Robert Lai, Julia Tzu-Ya Weng andTzong-Yi Lee, “Characterization and Identification of Ubiquitin Conjugation Sites with E3 Ligase Recognition Specificities” The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015), 21-23 January 2015, HsinChu, Taiwan.

Books:

1. Lê Hoàng Hiệp, Trần Duy Minh, Nguyễn Thu Huyền, Phạm Thị Liên, Phùng Thế Huân, Đỗ Đình Lực, Nguyễn Văn Núi, “Công nghệ và thiết bị mạng", Nhà xuất bản Giao thông vận tải, 2018.

2. Nguyễn Văn Núi, Trần Thị Xuân, Vũ Văn Huy, Nguyễn Thị Hạnh, Đào Thị Phương Anh, "Characterization of protein ubiquitination sites and E3 Ligase regulatory networks", Nhà xuất bản Hồng Đức, 2020.

3. Nguyễn Hiền Trinh, Dương Thị Mai Thương, Nguyễn Thị Tuyển, Đào Thị Thu, Nguyễn Văn Núi, "Toán rời rạc", Nhà xuất bản Đại học Thái Nguyên, 2022.