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

Professor

Research Area:

Bioinformatics and Computational Biology

Research Interest:

Bioinformatics
Algorithms
Graph Theory
Machine Learning
Predictive Modeling Techniques

Academic Background:

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

Selected Publications:

Google Scholar Profile

55. 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(10), btae588, 2024.

54. Nilanjan Roy, Acramul Haque Kabir, Nourin Zahan, Shahba Tasmiya Mouna, Sakshar Chakravarty, Atif Hasan Rahman, and Md Shamsuzzoha Bayzid, Genome wide association studies on seven yield-related traits of 183 rice varieties in Bangladesh, Plant Direct, Vol 8(6), e593, 2024.

53. Prottoy Saha, M Shamiul Islam, Tasnim Rahman, Adiba Shaira, Kazi Noshin, Rezwana Reaz, 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), Boston, MA, USA, 2024.

52. Ramisa Alam, Sazan Mahbub, and 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.

51. Md Ashiqur Rahman, Abdullah Aman Tutul, Mahfuza Sharmin, and Md Shamsuzzoha Bayzid, BEENE: Deep Learning based Nonlinear Embedding Improves Batch Effect Estimation, Bioinformatics, btad479, https://doi.org/10.1093/bioinformatics/btad479, 2023.

50. Sharmin Akter Mim, Md Zarif-Ul-Alam, Rezwana Reaz, Md Shamsuzzoha Bayzid, and Mohammad Saifur Rahman, Quartet Fiduccia–Mattheyses revisited for larger phylogenetic studies, Bioinformatics, Vol. 39(6), btad332, 2023.

49. A K M Mehedi Hasan, Ajmain Yasar Ahmed, Sazan Mahbub, M Saifur Rahman, and Md Shamsuzzoha Bayzid, SAINT-Angle: self-attention augmented inception-inside-inception network and transfer learning improve protein backbone torsion angle prediction, Bioinformatics Advances, Vol. 3(1): vbad042, https://doi.org/10.1093/bioadv/vbad042, 2023.

48. Nabil Ibtehaz, S. M. Shakhawat Hossain Sourav, Md. Shamsuzzoha Bayzid, and M. Sohel Rahman, Align-gram: Rethinking the Skip-gram Model for Protein Sequence Analysis, The Protein Journal, 42:135–146. https://doi.org/10.1007/s10930-023-10096-7, 2023.

47. Md. Shamsuzzoha Bayzid, Inferring Optimal Species Trees in the Presence of Gene Duplication and Loss: Beyond Rooted Gene Trees, Journal of Computational Biology, Vol. 30(2), pp. 161-175, 2023.

46. Sazan Mahbub, Shashata Sawmya, Arptia Saha, Rezwana Reaz, M. Sohel Rahman, and Md. Shamsuzzoha Bayzid, Quartet based gene tree imputation using deep learning improves phylogenomic analyses despite missing data, Journal of Computational Biology (RECOMB 2022 special issue), Vol. 29(0), pp. 1-17, 2022.

45. Navid Bin Hasan, Metin Balaban, Avijit Biswas, Md. Shamsuzzoha Bayzid, and Siavash Mirarab, Distance-Based Phylogenetic Placement with Statistical Support, Biology, 11(8):1212, https://doi.org/10.3390/biology11081212, 2022.

44. Metin Balaban, Nishat Anjum Bristy, Ahnaf Faisal, Md. Shamsuzzoha Bayzid, and Siavash Mirarab, Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model, Bioinformatics Advances, 2(1):vbac055, https://doi.org/10.1093/bioadv/vbac055, 2022.

43. 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-CG, 2022.

42. 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(4): e0265360, https://doi.org/10.1371/journal.pone.0265360, 2022.

41. Muhammad Ali Nayeem, Md. Shamsuzzoha Bayzid, Naser Anjum Samudro, Mohammad Saifur Rahman, and M. Sohel Rahman, PASTA with many application-aware optimization criteria for alignment based phylogeny inference, Computational Biology and Chemistry, Vol. 22:107661, https://doi.org/10.1016/j.compbiolchem.2022.107661, 2022.

40. Sazan Mahbub, Shashata Sawmya, Arptia Saha, Rezwana Reaz, M. Sohel Rahman, and 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) 2022.

39. Sazan Mahbub and Md. Shamsuzzoha Bayzid, EGRET: Edge Aggregated Graph Attention Networks and Transfer Learning Improve Protein-Protein Interaction Site Prediction, Briefings in Bioinformatics, https://doi.org/10.1093/bib/bbab578, 2022.

38. Naser Anjum, Raian Latif Nabil, Rakibul Islam Rafi, Md. Shamsuzzoha Bayzid, and 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 (TCBB), doi: 10.1109/TCBB.2021.3136792, 2021.

37. 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), September 25, King's College, London, UK.

36. Aniruddha Ganguly, Tasin Ishmam, Khandker Aftarul Islam, Md Zahidur Rahman and Md. Shamsuzzoha Bayzid, 3D-FFS: Faster 3D object detection with Focused Frustum Search in sensor fusion based networks, Accepted for presentation at the 2021 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2021), September 27-October 1, Prague, Czech Republic.

35. 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, btab428, https://doi.org/10.1093/bioinformatics/btab428, 2021.

34. Ishrat Tanzila Farah, Md Muktadirul Islam, Kazi Tasnim Zinat, Atif Hasan Rahman, and Md 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, https://doi.org/10.1093/sysbio/syab026, 2021.

33. Nabil Ibtehaz, Ishtiaque Ahmed, Md. Sabbir Ahmed, M. Sohel Rahman, Rajeev K. Azad, and Md. Shamsuzzoha Bayzid, SSG-LUGIA: Single Sequence based Genome Level Unsupervised Genomic Island Prediction Algorithm, Briefings in Bioinformatics, bbab116, https://doi.org/10.1093/bib/bbab116, 2021.

32. Zaineb Chelly, Pavel Avdeyev, and Md. Shamsuzzoha Bayzid, Biological Computation and Computational Biology: Survey, Challenges, and Discussion, Artificial Intelligence Review, https://doi.org/10.1007/s10462-020-09951-1, 2021.

31. Nafis Irtiza Tripto, Mohimenul Kabir, Md. Shamsuzzoha Bayzid, and Atif Hasan Rahman, Evaluation of classification and forecasting methods on time series gene expression data, PLoS ONE, 15(11): e0241686, 2020.

30. Muhammad Ali Nayeem, Md. Shamsuzzoha Bayzid, Sakshar Chakravarty, M. Saifur Rahman, and M. Sohel Rahman, A multi-objective metaheuristic approach for accurate species tree estimation, IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE), Cincinnati, OH, pp. 79-84, doi: 10.1109/BIBE50027.2020.00021.2020, 2020.

29. Muhammad Ali Nayeem, Md. Shamsuzzoha Bayzid, Atif Hasan Rahman, Rifat Shahriyar, and M. Sohel Rahman, Multi-objective formulation of MSA for phylogeny estimation (Do application-aware measures guide towards better phylogenetic tree?), IEEE Transactions on Cybernetics, doi: 10.1109/TCYB.2020.3020308, 2020.

28. Ananya Bhattacharjee and Md. Shamsuzzoha Bayzid, Machine learning based imputation techniques for estimating phylogenetic trees from incomplete distance matrices, BMC Genomics, 21:497, https://doi.org/10.1186/s12864-020-06892-5, 2020.

27. Mostofa Rafid Uddin, Sazan Mahbub, M Saifur Rahman, and Md. Shamsuzzoha Bayzid, SAINT: Self-Attention Augmented Inception-Inside-Inception Network Improves Protein Secondary Structure Prediction, Bioinformatics, doi:10.1093/bioinformatics/btaa531, 2020.

26. Mazharul Islam, Kowshika Sarker, Trisha Das, Rezwana Reaz, and Md. Shamsuzzoha Bayzid, STELAR: A statistically consistent coalescent-based species tree estimation method by maximizing triplet consistency, BMC Genomics, 21:136, https://doi.org/10.1186/s12864-020-6519-y, 2020.

25. Nazifa Ahmed Moumi, Badhan Das, Zarin Tasnim Promi, Nishat Anjum Bristy, and Md. Shamsuzzoha Bayzid, Quartet-based inference of cell differentiation trees from ChIP-Seq histone modification data, PLoS ONE, doi.org/10.1371/journal.pone.0221270, 2019.

24. 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, The Genetic and Evolutionary Computation Conference (GECCO), pp. 577-585. ACM, 2019.

23. Md Shamsuzzoha Bayzid and Tandy Warnow, Gene Tree Parsimony for Incomplete Gene Trees: addressing true biological loss, Algorithms for Molecular Biology, 13:1, 2018.

22. Md Shamsuzzoha Bayzid and Tandy Warnow, Gene Tree Parsimony for Incomplete Gene Trees, Workshop on Algorithms in Bioinformatics (WABI), Lecture Notes in Computer Science, 2017.

21. Md. Shamsuzzoha Bayzid, Vojtech Huser, and, Joydeep Ghosh, Conversion of MIMIC to OHDSI CDM, OHDSI Symposium, 2016.

20. 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, October 9, 2015, Vol. 350 no. 6257 p. 171, doi: 10.1126/science.aaa7719.

19. Md. Shamsuzzoha Bayzid, Siavash Mirarab, Bastien Boussau and Tandy Warnow, Weighted Statistical Binning: enabling statistically consistent genome-scale phylogenetic analyses, PLoS ONE 10(6): e0129183. doi:10.1371/ journal.pone.0129183, 2015.

18. Siavash Mirarab, Md. Shamsuzzoha Bayzid, Bastien Boussau and Tandy Warnow, Statistical binning enables an accurate coalescent-based estimation of the avian tree, Science, December 12, 2014, vol. 346 (6215 ), doi:10.1126/science.1250463.

17. 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. Zavidovych, S. Subramanian, T. Gabaldon, S. Capella-Gutierrez, J. Huerta-Cepas, B. Rekepalli, K. Munch, M. Schierup, B. Lindow, W. C. Warren, D. Ray, R. E. Green, M. W. Bruford, X. Zhan, A. Dixon, S. Li, N. Li, Y. Huang, E. P. Derryberry, M. F. Bertelsen, F. H. Sheldon, R. T. Brumfield, C. V. Mello, P. V. Lovell, M. Wirthlin, M. P. C. Schneider, F. Prosdocimi, J. A. Samaniego, A. M. V. Velazquez, A. Alfaro-Nunez, P. F. Campos, B. Petersen, T. Sicheritz-Ponten, A. Pas, T. Bailey, P. Scofield, M. Bunce, D. M. Lambert, Q. Zhou, P. Perelman, A. C. Driskell, B. Shapiro, Z. Xiong, Y. Zeng, S. Liu, Z. Li, B. Liu, K. Wu, J. Xiao, X. Yinqi, Q. Zheng, Y. Zhang, H. Yang, J. Wang, L. Smeds, F. E. Rheindt, M. Braun, J. Fjeldsa, L. Orlando, F. K. Barker, K. A. Jonsson, W. Johnson, K.-P. Koepfli, S. O'Brien, D. Haussler, O. A. Ryder, C. Rahbek, E. Willerslev, G. R. Graves, T. C. Glenn, J. McCormack, D. Burt, H. Ellegren, P. Alstrom, S. V. Edwards, A. Stamatakis, D. P. Mindell, J. Cracraft, E. L. Braun, T. Warnow, W. Jun, M. T. P. Gilbert, and G. Zhang, Whole-genome analyses resolve early branches in the tree of life of modern birds, Science, December 12, 2014, vol. 346 (6215 ), pp. 1320-1331, doi:10.1126/science.1253451.

16. Md Shamsuzzoha Bayzid, Tyler Hunt and Tandy Warnow, Disk Covering Methods Improve Phylogenomic Analyses, BMC Genomics (accepted papers from RECOMB Comparative Genomics), 15(Suppl 6):S7, doi:10.1186/1471-2164-15-S6-S7, 2014.

15. S. Mirarab, R. Reaz, M. S. Bayzid, T. Zimmermann, S. Swenson and T. Warnow, ASTRAL: Genome-scale coalescent-based species tree estimation, Bioinformatics, 30 (17): i541--i548., doi: 10.1093/bioinformatics/btu462, 2014. (Special Issue, ECCB 2014)

14. S. Mirarab, R. Reaz, M. S. Bayzid, T. Zimmermann, S. Swenson and T. Warnow, ASTRAL: Genome-scale coalescent-based species tree estimation, Proceedings, ECCB (European Conference on Computational Biology), 2014.

13. Rezwana Reaz, Md. Shamsuzzoha Bayzid, and M. Sohel Rahman, Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach, PLoS ONE, 9 (8): e104008, doi:10.1371/journal.pone.0104008, 2014.

12. 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, doi: 10.1093/sysbio/syu063, 2014.

11. Md Shamsuzzoha Bayzid, Tyler Hunt and Tandy Warnow, Disk Covering Methods Improve Phylogenomic Analyses, RECOMB Comparative Genomics, 2014.

10. Md. Shamsuzzoha Bayzid, Siavash Mirarab and Tandy Warnow, Inferring Optimal Species Trees under Gene Duplication and Loss, Pacific Symposium on Biocomputing (PSB), 18:250-261, Hawaii, January 3 - 7, 2013.

9. Md. Shamsuzzoha Bayzid and Tandy Warnow, Naive Binning Improves Phylogenomic Analyses, Bioinformatics, doi: 10.1093/bioinformatics/btt394, 2013.

8. Md. Shamsuzzoha Bayzid, Md. Maksudul Alam, Abdullah Mueen and Md. Saidur Rahman, HMEC: A Heuristic Algorithm for Individual Haplotyping with Minimum Error Correction, ISRN Bioinformatics, Vol. 2013, Article ID 291741, doi:10.1155/2013/291741, 2013.

7. Md. Shamsuzzoha Bayzid and Tandy Warnow, Estimating Optimal Species Trees from Incomplete Gene Trees under Deep Coalescence, Journal of Computational Biology, Vol. 19(6), pp. 591-605, 2012.

6. Md. Shamsuzzoha Bayzid, Md. Maksudul Alam and Md. Saidur Rahman, A Heuristic Algorithm for Minimum Conflict Individual Haplotyping, Proc. of International Conference on Biomedical Engineering and Informatics (BMEI), IEEE Computer Society Press,Vol. 5, pp. 2145--2149, 2010.

5. Muhammad Nur Yanhaona, Md. Shamsuzzoha Bayzid and Md. Saidur Rahman, Discovering Pairwise Compatibility Graphs, Discrete Mathematics, Algorithms and Applications, Vol. 2(4), pp. 607-623, 2010.

4. Muhammad Nur Yanhaona, Md. Shamsuzzoha Bayzid and Md. Saidur Rahman, Discovering Pairwise Compatibility Graphs, COCOON 2010, pp. 399-408, 2010.

3. Muhammad Nur Yanhaona, Md. Shamsuzzoha Bayzid and Md. Saidur Rahman, Not All Graphs are Pairwise Compatibility Graphs, Proc. of 3rd Annual Meeting of the Asian Association for Algorithms and Computation, 2010.

2. Abdullah Al Mueen, Md. Shamsuzzoha Bayzid, Md. Maksudul Alam and Md. Saidur Rahman, "A Heuristic Algorithm for Individual Haplotyping with Minimum Error Correction", Proc. of International Conference on BioMedical Engineering and Informatics 2008 (BMEI 2008), IEEE Computer Society, pp. 792-796, 2008.

1. 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, Proc. of International Conference on Electrical and Computer Engineering (ICECE), pp. 648-653, 2008

Journal Papers:

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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
10.	Navid Bin Hasan, Metin Balaban, Avijit Biswas, Md. Shamsuzzoha Bayzid, Siavash Mirarab, Distance-Based Phylogenetic Placement with Statistical Support, Biology, 11, 1212, 2022. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
32.	Md Shamsuzzoha Bayzid, Tyler Hunt and Tandy Warnow, Disk Covering Methods Improve Phylogenomic Analyses, BMC genomics, 15.000000, 1--11, 2014. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]

Conference Papers:

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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]
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. [paper link]