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
  • Department of Computer Science and Engineering
    Bangladesh University of Engineering and Technology
    Dhaka 1000, Bangladesh
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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 and Computational Biology
Algorithms
Graph Theory
Machine Learning
Publications
1. Abdur Rafi, Ahmed Mahir Sultan Rumi, Sheikh Azizul Hakim, Md. Shamsuzzoha Bayzid, QFM-GDL Enables Accurate Quartet-based Genome-scale Species Tree Inference Under Gene Duplication and Loss, RECOMB International Workshop on Comparative Genomics (RECOMB-CG), 2026. Conference
2. 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
3. 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
4. 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
5. 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
6. 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
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. 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
9. 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
10. 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
11. 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
12. 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
13. 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
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. 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
16. 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
17. 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
18. 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
19. 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
20. Md Ashiqur Rahman, Abdullah Aman Tutul, Mahfuza Sharmin, Md Shamsuzzoha Bayzid, BEENE: deep learning-based nonlinear embedding improves batch effect estimation, Bioinformatics, 39.000000, btad479, 2023. Journal DOI
21. 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
22. 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
23. 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
24. 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
25. 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
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. Md. Ashiqur Rahman, Abdullah Aman Tutul, Sifat Muhammad Abdullah, and Md. Shamsuzzoha Bayzid, CHAPAO: likelihood and hierarchical reference based representation of biomolecular sequences and applications to compressing multiple sequence alignments, PLoS ONE, 17.000000, e0265360, 2022. Journal DOI
29. 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
30. 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
31. 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
32. 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
33. 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
34. Anjum Naser, Raian Latif Nabil, Rakibul Islam Rafi, Shamsuzzoha Bayzid, M. Saifur Rahman, 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
35. 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
36. Mahim Mahbub, 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
37. 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
38. 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
39. 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
40. 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
41. 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
42. 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
43. 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
44. 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
45. Muhammad Ali Nayeem, Md Shamsuzzoha Bayzid, Atif Hasan Rahman, Rifat Shahriyar, and M Sohel Rahman, A 'phylogeny-aware' multi-objective optimization approach for computing MSA, Proceedings of the Genetic and Evolutionary Computation Conference, 577--585, 2019. Conference DOI
46. 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
47. 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
48. Bayzid Md Shamsuzzoha and Warnow Tandy, Gene tree parsimony for incomplete gene trees, Workshop on Algorithms in Bioinformatics (WABI), 2017. Conference
49. Siavash Mirarab, Md. Shamsuzzoha Bayzid, and Tandy Warnow, Evaluating summary methods for multi-locus species tree estimation in the presence of incomplete lineage sorting, Systematic Biology, 65.000000, 366--380, 2016. Journal DOI
50. Md. Shamsuzzoha Bayzid, Vojtech Huser, Joydeep Ghosh, Conversion of MIMIC to OHDSI CDM, OHDSI Symposium, 2016. Conference
51. Md. Shamsuzzoha Bayzid, Siavash Mirarab, Bastien Boussau and Tandy Warnow, Weighted Statistical Binning: enabling statistically consistent genome-scale phylogenetic analyses, PLoS ONE, 10.000000, e0129183, 2015. Journal DOI
52. Siavash Mirarab, Md. Shamsuzzoha Bayzid, Bastien Boussau and Tandy Warnow, Response to Comment on “Statistical binning enables an accurate coalescent-based estimation of the avian tree”, Science, 350.000000, 171--171, 2015. Journal DOI
53. E. D. Jarvis, S. Mirarab, A. J. Aberer, B. Li, P. Houde, C. Li, S. Y. W. Ho, B. C. Faircloth, B. Nabholz, J. T. Howard, A. Suh, C. C. Weber, R. R. da Fonseca, J. Li, F. Zhang, H. Li, L. Zhou, N. Narula, L. Liu, G. Ganapathy, B. Boussau, Md. S. Bayzid, V. , Whole-genome analyses resolve early branches in the tree of life of modern birds, SCIENCE, 346.000000, 1320--1331, 2014. Journal DOI
54. S. Mirarab, R. Reaz, M. S. Bayzid, T. Zimmermann, S. Swenson and T. Warnow, ASTRAL: genome-scale coalescent-based species tree estimation, Bioinformatics, 30.000000, i541--i548, 2014. Journal DOI
55. Md Shamsuzzoha Bayzid, Tyler Hunt and Tandy Warnow, Disk Covering Methods Improve Phylogenomic Analyses, BMC genomics, 15.000000, 1--11, 2014. Journal DOI
56. Rezwana Reaz, Md. Shamsuzzoha Bayzid, and M. Sohel Rahman, Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach, PloS one, 9.000000, e104008, 2014. Journal DOI
57. 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
58. Md Shamsuzzoha Bayzid, Tandy Warnow, Disk Covering Methods Improve Phylogenomic Analyses, RECOMB International Workshop on Comparative Genomics (RECOMB-CG), 2014. Conference
59. 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
60. Md. Shamsuzzoha Bayzid and Tandy Warnow, Naive Binning Improves Phylogenomic Analyses, Bioinformatics, 29.000000, 2277–2284, 2013. Journal DOI
61. Md. Shamsuzzoha Bayzid, Md. Maksudul Alam, Abdullah Mueen and Md. Saidur Rahman, HMEC: A Heuristic Algorithm for Individual Haplotyping with Minimum Error Correction, International Scholarly Research Notices, 2013.000000, 2013. Journal
62. Md. Shamsuzzoha Bayzid, Siavash Mirarab and Tandy Warnow, Inferring optimal species trees under gene duplication and loss, Biocomputing 2013, 250--261, 2013. Conference DOI
63. Md. Shamsuzzoha Bayzid and Tandy Warnow, Estimating Optimal Species Trees from Incomplete Gene Trees under Deep Coalescence, Journal of Computational Biology, 19.000000, 591--605, 2012. Journal DOI
64. Md. Shamsuzzoha Bayzid, Md. Maksudul Alam and Md. Saidur Rahman, A heuristic algorithm for Minimum Conflict Individual Haplotyping, 2010 3rd International Conference on Biomedical Engineering and Informatics, 2145--2149, 2010. Conference DOI
65. Muhammad Nur Yanhaona, Md. Shamsuzzoha Bayzid and Md. Saidur Rahman, Discovering pairwise compatibility graphs, Discrete Mathematics, Algorithms and Applications, 2.000000, 607--623, 2010. Journal DOI
66. Muhammad Nur Yanhaona, Md. Shamsuzzoha Bayzid, Md. Saidur Rahman, Discovering Pairwise Compatibility Graphs, International Computing and Combinatorics Conference (COCOON), 2010. Conference
67. Muhammad Nur Yanhaona, Md. Shamsuzzoha Bayzid, Md. Saidur Rahman, Not All Graphs are Pairwise Compatibility Graphs, 3rd Annual Meeting of the Asian Association for Algorithms and Computation, 2010. Conference
68. Abdullah Al Mueen, Md. Shamsuzzoha Bayzid, Md. Maksudul Alam, Md. Saidur Rahman, A Heuristic Algorithm for Individual Haplotyping with Minimum Error Correction, International Conference on Biomedical Engineering and Informatics (BMEI), 2008. Conference
69. Md. Shamsuzzoha Bayzid, Anindya Iqbal, Chowdhury Sayeed Hyder and Mohammad Tanvir Irfan, Application of artificial neural network in social computing in the context of third world countries, 2008 International Conference on Electrical and Computer Engineering, 648--653, 2008. Conference DOI

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