Dr. Md. Shamsuzzoha Bayzid
Dr. Md. Shamsuzzoha Bayzid
ডঃ মোঃ সামসুজ্জোহা বায়েজীদ
Professor
  • shams DOT bayzid AT gmail DOT com, shams_bayzid AT cse DOT buet DOT ac DOT bd
  • 88029665650/7109
  • +8801841234464
  • shamsbayzid.github.io
  • Department of Computer Science and Engineering
    Bangladesh University of Engineering and Technology
    Dhaka 1000, Bangladesh
scholar.google sites.google
Biography
TBW
Education

PhD in Computer Science, 2016
University of Texas at Austin

M.Sc. in Computer Science and Engineering, 2010
Bangladesh University of Engineering and Technology

B.Sc. in Computer Science and Engineering, 2008
Bangladesh University of Engineering and Technology
Research Interest
Bioinformatics
Algorithms
Graph Theory
Machine Learning
Predictive Modeling Techniques
Publications
1. Anik Saha, Md Shamsuzzoha Bayzid, STELAR-X: Scaling Coalescent-Based Species Tree Inference to 100,000 Species and Beyond, International Conference on Research in Computational Molecular Biology (RECOMB), 2026. Conference
2. Abrar Rahman Abir, Md Toki Tahmid, and Md Shamsuzzoha Bayzid, BioLLMNet: enhancing RNA-interaction prediction with a specialized cross-LLM transformation network, Briefings in Bioinformatics, 26, bbaf549, 2025. Journal DOI
3. Tasfia Zahin, Md Hasin Abrar, Mizanur Rahman Jewel, Tahrina Tasnim, Md Shamsuzzoha Bayzid, and Atif Rahman, An alignment-free method for phylogeny estimation using maximum likelihood, BMC Bioinformatics, 26, 1-14, 2025. Journal
4. Tanjeem Azwad Zaman, Rabib Jahin, and Md. Shamsuzzoha Bayzid, On the robustness to gene tree rooting (or lack thereof) of triplet-based species tree estimation methods, RECOMB International Workshop on Comparative Genomics (RECOMB-CG), 2025. Conference
5. Md Toki Tahmid, Haz Sameen Shahgir, Sazan Mahbub, Yue Dong, Md. Shamsuzzoha Bayzid, BiRNA-BERT allows efficient RNA language modeling with adaptive tokenization, Nature Communications Biology, 8, 1621, 2025. Journal DOI
6. Navid Bin Hasan, Sohaib, and Md. Shamsuzzoha Bayzid, QT-WEAVER: Correcting quartet distribution improves phylogenomic analyses despite gene tree estimation error, RECOMB International Workshop on Comparative Genomics (RECOMB-CG), 2025. Conference
7. Abdur Rafi, Ahmed Mahir Sultan Rumi, Sheikh Azizul Hakim, Sohaib, Md Toki Tahmid, Rabib Jahin Ibn Momin, Tanjeem Azwad Zaman, Rezwana Reaz, and Md Shamsuzzoha Bayzid, wQFM-TREE: highly accurate and scalable quartet-based species tree inference from gene trees , Bioinformatics Advances, 5, vbaf053, 2025. Journal DOI
8. Nazmus Sakib, Tahmid Nafis, Shattik Islam Rhythm, Md Shamsuzzoha Bayzid, Amit Bhasin, Bitumen optical microscopy as a quality assurance tool through deployment of trained Siamese neural network model., Road Materials and Pavement Design, 26, 110-134, 2025. Journal DOI
9. Md Toki Tahmid, AKM Mehedi Hasan, and Md Shamsuzzoha Bayzid, TransBind allows precise detection of DNA-binding proteins and residues using language models and deep learning, Nature Communications Biology, 8, 568, 2025. Journal DOI
10. Navid Bin Hasan, Avijit Biswas, Zahin Wahab, Mahim Mahbub, Rezwana Reaz, Md Shamsuzzoha Bayzid, Leveraging weighted quartet distributions for enhanced species tree inference from genome-wide data, Genome Biology and Evolution, 1, evaf159, 2025. Journal DOI
11. Mursalin Habib, Kowshic Roy, Saem Hasan, Atif Hasan, Md Shamsuzzoha Bayzid, Terraces in species tree inference from gene trees, BMC Ecology and Evolution, 24, 135, 2024. Journal DOI
12. Ramisa Alam, Sazan Mahbub, Md Shamsuzzoha Bayzid, Pair-EGRET: enhancing the prediction of protein–protein interaction sites through graph attention networks and protein language models, Bioinformatics, 40, btae588, 2024. Journal DOI
13. Roy Nilanjan, Kabir Acramul Haque, Zahan Nourin, Mouna Shahba Tasmiya, Chakravarty Sakshar, Rahman Atif Hasan, Md Shamsuzzoha Bayzid, Genome wide association studies on seven yield-related traits of 183 rice varieties in Bangladesh, Plant Direct, 8, e593, 2024. Journal
14. Gourab Saha, Md Toki Tahmid, Md. Shamsuzzoha Bayzid, EmbedSimScore: Advancing Protein Similarity Analysis with Structural and Contextual Embeddings, NeurIPS Workshop on Self-Supervised Learning Theory and Practice , 2024. Conference
15. Sheikh Azizul Hakim, Md Rownok Zahan Ratul, Md Shamsuzzoha Bayzid, wQFM-DISCO: DISCO-enabled wQFM improves phylogenomic analyses despite the presence of paralogs, Bioinformatics Advances, 4, vbae189, 2024. Journal DOI
16. Md Toki Tahmid, Haz Sameen Shahgir, Sazan Mahbub,Yue Dong, and Md. Shamsuzzoha Bayzid, BiRNA-BERT allows efficient RNA language modeling with adaptive tokenization., Efficient Natural Language and Speech Processing (ENLSP) workshop at NeurIPS , 2024. Conference
17. Prottoy Saha, M Shamiul Islam, Tasnim Rahman, Adiba Shaira, Kazi Noshin, Rezwana Reaz, and Md Shamsuzzoha Bayzid, Gene Tree Parsimony in the Presence of Gene Duplication, Loss, and Incomplete Lineage Sorting, RECOMB International Workshop on Comparative Genomics (RECOMB-CG), 2024. Conference
18. Md Shamsuzzoha Bayzid, Inferring Optimal Species Trees in the Presence of Gene Duplication and Loss: Beyond Rooted Gene Trees, Journal of Computational Biology, 30, 161--175, 2023. Journal DOI
19. Nabil Ibtehaz, SM Shakhawat Hossain Sourav, Md Shamsuzzoha Bayzid, M Sohel Rahman, Align-gram: Rethinking the Skip-gram Model for Protein Sequence Analysis, The Protein Journal, 42, 135--146, 2023. Journal DOI
20. Mim Sharmin Akter, Md Zarif-Ul-Alam, Rezwana Reaz, Md Shamsuzzoha Bayzid, and Mohammad Saifur Rahman, Quartet Fiduccia–Mattheyses revisited for larger phylogenetic studies, Bioinformatics, 39, btad332, 2023. Journal DOI
21. A K M Mehedi Hasan, Ajmain Yasar Ahmed, Sazan Mahbub, M Saifur Rahman, Shamsuzzoha Bayzid, SAINT-Angle: self-attention augmented inception-inside-inception network and transfer learning improve protein backbone torsion angle prediction, Bioinformatics Advances, 3, vbad042, 2023. Journal DOI
22. Ramisa Alam, Sazan Mahbub, Md Shamsuzzoha Bayzid, Pair-EGRET: Enhancing the prediction of protein-protein interaction sites through graph attention networks and protein language models., Machine Learning in Structural Biology Workshop at the Conference on Neural Information Processing Systems (NeurIPS), 2023. Conference
23. Sazan Mahbub, Shashata Sawmya, Arpita Saha, Rezwana Reaz, M Sohel Rahman, Md Shamsuzzoha Bayzid, Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data, Journal of Computational Biology, 29, 1156--1172, 2022. Journal DOI
24. Navid Bin Hasan, Avijit Biswas, Metin Balaban, Siavash Mirarab, and Md. Shamsuzzoha Bayzid, Fast and accurate branch support calculation for distance-based phylogenetic placements, RECOMB International Workshop on Comparative Genomics (RECOMB-CG), 2022. Conference
25. Sazan Mahbub, Shashata Sawmya, Arpita Saha, Rezwana Reaz, M Sohel Rahman, Md Shamsuzzoha Bayzid, QT-GILD: Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data, International Conference on Research in Computational Molecular Biology (RECOMB), 159--176, 2022. Conference DOI
26. Sazan Mahbub, Md Shamsuzzoha Bayzid, EGRET: edge aggregated graph attention networks and transfer learning improve protein–protein interaction site prediction, Briefings in Bioinformatics, 23, bbab578, 2022. Journal DOI
27. Metin Balaban, Nishat Anjum Bristy, Ahnaf Faisal, Md Shamsuzzoha Bayzid, Siavash Mirarab, Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model, Bioinformatics Advances, 2, 1--11, 2022. Journal DOI
28. Navid Bin Hasan, Metin Balaban, Avijit Biswas, Md. Shamsuzzoha Bayzid, Siavash Mirarab, Distance-Based Phylogenetic Placement with Statistical Support, Biology, 11, 1212, 2022. Journal DOI
29. Md. Shamsuzzoha Bayzid, Inferring Optimal Species Trees in the Presence of Gene Duplication and Loss: Beyond Rooted Gene Trees., Mathematical Foundations in Bioinformatics (MatBio), 2021. Conference
30. Aniruddha Ganguly,Tasin Ishmam, Khandker Aftarul Islam, Md Zahidur Rahman, Md. Shamsuzzoha Bayzid, 3D-FFS: Faster 3D object detection with Focused Frustum Search in sensor fusion based networks, 2021 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), 6848-6853, 2021. Conference DOI
31. Anjum Naser and Nabil Raian Latif and Rafi Rakibul Islam and Bayzid Shamsuzzoha and Rahman M. Saifur, CD-MAWS: An Alignment-free Phylogeny Estimation Method Using Cosine Distance on Minimal Absent Word Sets, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Online, 2021. Journal DOI
32. Mahim Mahbub, and Zahin Wahab, Rezwana Reaz, M Saifur Rahman, and Md Shamsuzzoha Bayzid, wQFM: highly accurate genome-scale species tree estimation from weighted quartets, Bioinformatics, 37, 3734-3743, 2021. Journal DOI
33. Nabil Ibtehaz and Ishtiaque Ahmed and Md Sabbir Ahmed and M Sohel Rahman and Rajeev K Azad and Md Shamsuzzoha Bayzid, SSG-LUGIA: Single Sequence based Genome Level Unsupervised Genomic Island Prediction Algorithm, Briefings in Bioinformatics, 22, bbab116, 2021. Journal DOI
34. Zaineb Chelly Dagdia, Pavel Avdeyev, Md Shamsuzzoha Bayzid, Biological computation and computational biology: survey, challenges, and discussion, Artificial Intelligence Review, 54, 4169-4235, 2021. Journal DOI
35. Ishrat Tanzila Farah, Muktadirul Islam, Kazi Tasnim Zinat, Atif Hasan Rahman, Shamsuzzoha Bayzid, Species tree estimation from gene trees by minimizing deep coalescence and maximizing quartet consistency: a comparative study and the presence of pseudo species tree terraces, Systematic Biology, 70, 1213--1231, 2021. Journal DOI
36. Mostofa Rafid Uddin, Sazan Mahbub, Mohammad Saifur Rahman, Md. Shamsuzzoha Bayzid, SAINT: Self-Attention Augmented Inception-Inside-Inception Network Improves Protein Secondary Structure Prediction, Bioinformatics, 2020. Journal DOI
37. Nafis Irtiza Tripto, Mohimenul Kabir, Md. Shamsuzzoha Bayzid, Atif Rahman, Evaluation of classification and forecasting methods on time series gene expression data, PLoS ONE, 15, e0241686, 2020. Journal DOI
38. Mazharul Islam, Kowshika Sarker, Trisha Das, Rezwana Reaz, Md Shamsuzzoha Bayzid, STELAR: a statistically consistent coalescent-based species tree estimation method by maximizing triplet consistency, BMC genomics, 21, 1--13, 2020. Journal DOI
39. Ananya Bhattacharjee and Md. Shamsuzzoha Bayzid, Machine learning based imputation techniques for estimating phylogenetic trees from incomplete distance matrices, BMC genomics, 21, 1--14, 2020. Journal DOI
40. Nayeem Muhammad Ali and Bayzid Md Shamsuzzoha and Rahman Atif Hasan and Shahriyar Rifat and Rahman M Sohel, Multiobjective formulation of multiple sequence alignment for phylogeny inference (Can an application-aware measure guide towards better phylogeny estimation?), IEEE Transactions on Cybernetics, 52, 2775--2786, 2020. Journal
41. M. A. Nayeem and M. S. Bayzid and S. Chakravarty and M. S. Rahman and M. S. Rahman, A Multi-objective Metaheuristic Approach for Accurate Species Tree Estimation, IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE), 79-84, 2020. Conference DOI
42. Nazifa Ahmed Moumi, Badhan Das, Tasnim Zarin Promi, Nishat Anjum Bristy, and Md Shamsuzzoha Bayzid, Quartet-based inference of cell differentiation trees from chip-seq histone modification data, Plos one, 14, e0221270, 2019. Journal DOI
43. Md Shamsuzzoha Bayzid, Tandy Warnow, Gene tree parsimony for incomplete gene trees: addressing true biological loss, Algorithms for Molecular Biology, 13, 1--12, 2018. Journal DOI
44. Bayzid Md Shamsuzzoha and Warnow Tandy, Gene tree parsimony for incomplete gene trees, Workshop on Algorithms in Bioinformatics (WABI), 2017. Conference
45. Mirarab Siavash and Bayzid Md Shamsuzzoha and Boussau Bastien and Warnow Tandy, Statistical binning enables an accurate coalescent-based estimation of the avian tree, Science, 346, 1250463, 2014. Journal
46. Siavash Mirarab, Rezwana Reaz, Md. Shamsuzzoha Bayzid, Theo Zimmermann, Shel Swenson and Tandy Warnow, ASTRAL: Genome- Scale Coalescent-Based Species Tree, European Conference on Computational Biology (ECCB), 2014. Conference
47. Muhammad Nur Yanhaona, Md. Shamsuzzoha Bayzid, Md. Saidur Rahman, Discovering Pairwise Compatibility Graphs, International Computing and Combinatorics Conference (COCOON), 2010. Conference

Copyright © Department of Computer Science and Engineering, BUET, Dhaka-1000.