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


Associate Professor

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

  •  Telephone:
  • Office: 88029665650/7109
    Cell: +8801841234464, +8801937881293
    Residence:

  •  Email: shams.bayzid@gmail.com, shams_bayzid@cse.buet.ac.bd

  •  Homepage: https://shamsbayzid.github.io/

  •  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:

  • 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. Mostofa Rafid Uddin, Sazan Mahbub, Mohammad Saifur Rahman, and Md. Shamsuzzoha Bayzid, SAINT: Self-Attention Augmented Inception-Inside-Inception Network Improves Protein Secondary Structure Prediction. Bioinformatics, Oxford University Press, 2020 [paper link].

  •  Conference Papers:
  • Department of Computer Science and Engineering, ECE building, Palashi, Dhaka, Bangladesh. The Department is part of the Faculty of Electrical and Electronic Engineering at the Bangladesh University of Engineering & Technology. No part or content of this website may be copied or reproduced without permission of the department authority. Contact info@grad.cse.buet.ac.bd with questions or comments on this page.  [Development Credits]