Yasamin Tabatabaee

I am a Computer Science PhD candidate at the University of Illinois Urbana-Champaign advised by Prof. Tandy Warnow. Prior to this, I received a B.S. degree in Computer Engineering from Sharif University of Technology in 2021 and an M.S. degree in Computer Science from UIUC in 2023. During summer 2024, I was a visiting scholar at UCSD working with Prof. Siavash Mirarab.

My main research is on algorithmic problems in computational biology. In particular, my PhD dissertation has been focused on developing algorithms and computational tools for estimating the evolutionary history of species from genome-scale datasets (phylogenomics). I have also worked on community detection and clustering on large networks.

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Publications
Preprints
  • Y. Tabatabaee, S. Claramunt, and S. Mirarab (2025). Coalescent-based branch length estimation improves dating of species trees. [preprint] [code and data]

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  • Y. Tabatabaee, C. Zhang, S. Arasti and S. Mirarab (2025). Species tree branch length estimation despite incomplete lineage sorting, duplication, and loss. [preprint] [code] [data]

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  • S. Arasti, P. Tabaghi, Y. Tabatabaee and S. Mirarab. (2025). Branch length transforms using optimal tree metric matching (extended version of RECOMB 2024 paper). [preprint] [code] [data]

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  • Y. Tabatabaee, E. Wedell, M. Park and T. Warnow (2025). Scalable ensemble clustering on large networks (extended version of CNA 2024 paper). [preprint] [code] [data]

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    Journal papers
  • T. Warnow, Y. Tabatabaee and S.N.Evans. (2025). Advances in Estimating Level-1 Phylogenetic Networks from Unrooted SNPs. Journal of Computational Biology, Vol. 32, No. 1. [paper]

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  • M. Park*, Y. Tabatabaee*, V. Ramavarapu*, B. Liu, V. Pailodi, R. Ramachandran, D. Korobskiy, F. Ayres, G. Chacko, and T. Warnow (2024). Well-Connectedness and Community Detection. PLOS Complex Systems. Vol. 1, No. 3: e0000009. [paper] [CM code] [LFR generation code] [data]

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  • Y. Tabatabaee, S. Roch and T. Warnow (2023). QR-STAR: A polynomial-time statistically consistent method for rooting species trees under the coalescent. Journal of Computational Biology. Vol. 30, No. 11 (extended version of RECOMB 2023 paper). [paper] [code] [data]

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  • Y. Tabatabaee, C. Zhang, T. Warnow and S. Mirarab. (2023). Phylogenomic branch length estimation using quartets. Bioinformatics, Vol. 39, Issue Supplement 1, pages i185-i193, special issue for Intelligent Systems for Molecular Biology and European Conference on Computational Biology (ISMB/ECCB). [paper] [code] [data] [slides] [talk]

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  • J. Willson, Y. Tabatabaee, B. Liu, and T. Warnow (2023). DISCO+QR: rooting species trees in the presence of GDL and ILS. Bioinformatics Advances, Vol. 3, Issue 1, vbad015, special issue for ISCB-Latin America Conference on Bioinformatics (ISCB-LA) 2022. [paper] [data]

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  • Y. Tabatabaee, K. Sarkar, and T. Warnow (2022). Quintet Rooting: rooting species trees under the multi-species coalescent model. Bioinformatics, Vol. 38, Supplement 1, pages i109-i117, special issue for Intelligent Systems for Molecular Biology (ISMB). [paper] [code] [data] [slides] [talk]

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    Conference Proceedings
  • Y. Tabatabaee, E. Wedell, M. Park and T. Warnow (2024). FastEnsemble: A new scalable ensemble clustering method. International Conference on Complex Networks and Their Applications (CNA 2024). [preprint] [code] [data]

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  • T. Warnow, Y. Tabatabaee and S.N. Evans (2024). Statistically consistent estimation of rooted and unrooted level-1 phylogenetic networks from SNP data. Proceedings of RECOMB Comparative Genomics (RECOMB-CG 2024). [paper]

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  • S. Arasti*, P. Tabaghi*, Y. Tabatabaee and S. Mirarab. (2024). Optimal tree metric matching enables phylogenomic branch length estimation. International Conference on Research in Computational Molecular Biology (RECOMB 2024), pages 462–465. [paper] [code] [data]

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  • Y. Tabatabaee, S. Roch and T. Warnow. (2023). Statistically consistent rooting of species trees under the multispecies coalescent model. International Conference on Research in Computational Molecular Biology (RECOMB 2023), pages 41-57. [paper] [code] [data] [slides] [talk]

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  • M. Park*, Y. Tabatabaee*, V. Ramavarapu*, B. Liu, V. Pailodi, R. Ramachandran, D. Korobskiy, F. Ayres, G. Chacko, and T. Warnow (2023). Identifying well connected communities in real-world and synthetic networks. International Conference on Complex Networks and Their Applications (CNA 2023). [paper] [CM code] [LFR generation code] [data]

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  • D. Lin, Y. Tabatabaee, Y. Pote and D. Jevdjic. (2022). Managing reliability skew in DNA storage. Proceedings of the 49th Annual International Symposium on Computer Architecture (ISCA 2022). pages 482–494. [paper]

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    Conference Talks
    Graduate Teaching

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