Dr. Md. Shamsuzzoha Bayzid (ডঃ মোঃ সামসুজ্জোহা বায়েজীদ)

Professor

shams.bayzid@gmail.com, shams_bayzid@cse.buet.ac.bd
88029665650/7109
+8801841234464
https://shamsbayzid.github.io/

Department of Computer Science and Engineering
Bangladesh University of Engineering and Technology
Dhaka 1000, Bangladesh

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

Journal Article

1. 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, 2024.
2. Mursalin Habib* and Kowshic Roy* and Saem Hasan* and Atif Hasan Rahman and Md Shamsuzzoha Bayzid, Terraces in species tree inference from gene trees, BMC Ecology and Evolution, 24, 135, 2024. DOI
3. 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. DOI
4. 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.
5. 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. DOI
6. 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. DOI
7. 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. DOI
8. 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, 2023. DOI
9. 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, 2023. DOI
10. Navid Bin Hasan, Metin Balaban, Avijit Biswas, Md. Shamsuzzoha Bayzid, Siavash Mirarab, Distance-Based Phylogenetic Placement with Statistical Support, Biology, 11, 1212, 2022. DOI
11. 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. DOI
12. 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. DOI
13. 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. DOI
14. 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. DOI
15. 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. DOI
16. Zaineb Chelly Dagdia, Pavel Avdeyev, Md Shamsuzzoha Bayzid, Biological computation and computational biology: survey, challenges, and discussion, Artificial Intelligence Review, 54, 4169-4235, 2021. DOI
17. 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. DOI
18. 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. DOI
19. 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. DOI
20. 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.
21. 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. DOI
22. 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. DOI
23. 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. DOI
24. 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. DOI
25. Naifa 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.
26. Md Shamsuzzoha Bayzid, Tandy Warnow, Gene tree parsimony for incomplete gene trees: addressing true biological loss, Algorithms for Molecular Biology, 13, 1--12, 2018. DOI
27. 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. DOI
28. 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. DOI
29. 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. DOI
30. 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.
31. Rezwana Reaz, Md. Shamsuzzoha Bayzid, and M. Sohel Rahman, Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach, PloS one, 9.000000, e104008, 2014. DOI
32. Md Shamsuzzoha Bayzid, Tyler Hunt and Tandy Warnow, Disk Covering Methods Improve Phylogenomic Analyses, BMC genomics, 15.000000, 1--11, 2014. DOI
33. 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. DOI
34. 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. DOI
35. 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.
36. Md. Shamsuzzoha Bayzid and Tandy Warnow, Naive Binning Improves Phylogenomic Analyses, Bioinformatics, 29.000000, 2277–2284, 2013. DOI
37. 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. DOI
38. Muhammad Nur Yanhaona, Md. Shamsuzzoha Bayzid and Md. Saidur Rahman, Discovering pairwise compatibility graphs, Discrete Mathematics, Algorithms and Applications, 2.000000, 607--623, 2010. DOI

Conference Article

1. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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. DOI
7. 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.
8. 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. DOI
9. 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. DOI
10. 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. DOI
11. Bayzid Md Shamsuzzoha and Warnow Tandy, Gene tree parsimony for incomplete gene trees, Workshop on Algorithms in Bioinformatics (WABI), 2017.
12. 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.
13. Md. Shamsuzzoha Bayzid, Siavash Mirarab and Tandy Warnow, Inferring optimal species trees under gene duplication and loss, Biocomputing 2013, 250--261, 2013. DOI
14. 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. DOI
15. 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. DOI

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