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• Journal Publications
  
  
• Sazan Mahbub and Md Shamsuzzoha Bayzid, EGRET: Edge Aggregated Graph Attention Networks and Transfer Learning Improve Protein-Protein Interaction Site Prediction, Briefings in Bioinformatics. (to appear)
  
  
• 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). (to appear)
  
  
• 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, 2021.
  
  
• 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.
  
  
• 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.
  
  
• 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.
  
  
• 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.
  
  
• 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.
  
  
• Ananya Bhattacharjee and Md. Shamsuzzoha Bayzid, Machine learning based imputation techniques for estimating phylogenetic trees from incomplete distance matrices, BMC Genomics, 21:497, 2020.
  
  
• Mostofa Rafid Uddin, Sazan Mahbub, M Saifur Rahman, Md. Shamsuzzoha Bayzid, SAINT: Self-Attention Augmented Inception-Inside-Inception Network Improves Protein Secondary Structure Prediction, Bioinformatics, btaa531, https://doi.org/10.1093/bioinformatics/btaa531, 2020.
  
  
• 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, 2020.
  
  
• 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.
  
  
• Md. Shamsuzzoha Bayzid and Tandy Warnow, Gene Tree Parsimony for Incomplete Gene Trees: addressing true biological loss, Algorithms for Molecular Biology, 13:1, 2018.
  
  
• 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. [pdf]
  
  
• 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. [pdf]
  
  
• 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.[pdf]
  
  
• 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.[pdf]
  
  
• 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.[pdf] [supplementary information]
  
  
• 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.[pdf] [supplementary information]
  
  
• 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. [pdf] [supplementary information]
  
  
• 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.[pdf]
  
  
• Md. Shamsuzzoha Bayzid and Tandy Warnow, Naive Binning Improves Phylogenomic Analyses, Bioinformatics, doi: 10.1093/bioinformatics/btt394, 2013. [pdf] [supplementary data]
  
  
• 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. [pdf]
  
  
• 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. [pdf]
  
  
• 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. [pdf]
  
  
• Conference Publications
  
  
• 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), King's College, London, UK.
  
  
• 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.
  
  
• 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 International Conference on Bioinformatics and Bioengineering (BIBE), Cincinnati, OH, pp. 79-84, doi: 10.1109/BIBE50027.2020.00021.2020, 2020.
  
  
• 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.
  
  
• Md Shamsuzzoha Bayzid and Tandy Warnow, Gene Tree Parsimony for Incomplete Gene Trees, Workshop on Algorithms in Bioinformatics (WABI), 2017.
  
  
• Md Shamsuzzoha Bayzid, Tyler Hunt and Tandy Warnow, Disk Covering Methods Improve Phylogenomic Analyses, RECOMB Comparative Genomics, 2014.[pdf] [supplementary information]
  
  
• 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. [pdf]
  
  
• 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. [pdf]
  
  
• Muhammad Nur Yanhaona, Md. Shamsuzzoha Bayzid and Md. Saidur Rahman, Discovering Pairwise Compatibility Graphs, COCOON 2010, pp. 399-408, 2010. [pdf]
  
  
• 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. [pdf]
  
  
• 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 (BMEI), IEEE Computer Society Press, pp. 792-796, 2008. [pdf]
  
  
• 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. [pdf]