You can find me on Google Scholar, Research Gate, and ORCiD.

Population Structure and Admixture Graphs

Preprints

1. Chiu, A.M., E.K. Molloy, Z. Tan, A. Talwalkar, S. Sankararaman, "Inferring population structure in biobank-scale genomic data," 2021. [html]

Peer-reviewed Journal Publications

1. Molloy, E.K., A. Durvasula, S. Sankararaman, "Advancing admixture graph estimation via maximum likelihood network orientation," Bioinformatics, 2021. [Special issue for ISMB/ECCB 2021] [html] [code] [data]

Metagenomics

Peer-reviewed Journal Publications

1. Shah, N., E.K. Molloy, M. Pop, T. Warnow, "TIPP2: metagenomic taxonomic profiling using phylogenetic markers," Bioinformatics, 2020. [html] [code] [data]

Computational Phylogenetics

Peer-reviewed Journal Publications

1. Molloy, E.K., J. Gatesy, M.S. Springer, "Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone," Systematic Biology, Accepted. [html]
2. Yu, X., T. Le, S. Christensen, E.K. Molloy, and T. Warnow, "Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation," Algorithms for Molecular Biology, 2021. [Journal version of WABI 2020 paper] [html]
3. Legried, B., E.K. Molloy, T. Warnow, and S. Roch, "Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss," Journal of Computational Biology, 2020. [Journal version of RECOMB 2020 paper] [html] [data]
4. Zhang, C., C. Scornavacca, E.K. Molloy, and S. Mirarab, "ASTRAL-Pro: quartet-based species tree inference despite paralogy," Molecular Biology and Evolution, 2020. [html] [code] [data]
5. Molloy, E.K. and T. Warnow, "FastMulRFS: Fast and highly accurate species tree estimation under generic gene duplication and loss models," Bioinformatics, 2020. [Special issue for ISMB 2020] [html] [code] [data]
6. Le, T., A. Sy, E.K. Molloy, Q. Zhang, S. Rao, and T. Warnow, "Using Constrained-INC for Large-scale Gene Tree and Species Tree Estimation," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2020. [Extended version of AlCoB 2019 paper] [html] [code]
7. Springer, M.S., E.K. Molloy, D.B. Sloan, M.P. Simmons, and J. Gatesy, "ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets," Journal of Heredity, 2020. [Editor's Choice] [html]
8. Christensen, S., E.K. Molloy, P. Vachaspati, A. Yammanuru, and T. Warnow, "Non-parametric correction of estimated gene trees using TRACTION," Algorithms for Molecular Biology, 2020. [Extended version of WABI 2019 paper] [html]
9. Molloy, E.K. and T. Warnow, "TreeMerge: A new method for improving the scalability of species tree estimation methods," Bioinformatics, 2019. [Special issue for ISMB/ECCB 2019] [html] [code] [data]
10. Molloy, E.K. and T. Warnow, "Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge," Algorithms for Molecular Biology, 2019. [Extended version of RECOMB-CG 2018 paper] [html] [code] [data]
11. Nute, M., J. Chou, E.K. Molloy, and T. Warnow, "The Performance of Coalescent-Based Species Tree Estimation Methods under Models of Missing Data," BMC Genomics, 2018. [Extended version of RECOMB-CG 2017 paper] [html] [data]
12. Molloy, E.K. and T. Warnow, "To include or not to include: The Impact of Gene Filtering on Species Tree Estimation Methods," Systematic Biology, 2018. [html] [data]
13. Christensen, S., E.K. Molloy, P. Vachaspati, and T. Warnow, "OCTAL: Optimal completion of gene trees in polynomial time," Algorithms for Molecular Biology, 2018. [Extended version of WABI 2017 paper] [html] [code] [data]

Peer-reviewed Conference Proceedings

1. Yu, X., T. Le, S. Christensen, E.K. Molloy, and T. Warnow, "Advancing Divide-And-Conquer Phylogeny Estimation Using Robinson-Foulds Supertrees," in 20th International Workshop on Algorithms and Bioinformatics. [WABI 2020] [html] [code]
2. Christensen, S., E.K. Molloy, P. Vachaspati, and T. Warnow, "TRACTION: Fast non-parametric improvement of estimated gene trees," in 19th International Workshop on Algorithms and Bioinformatics. [WABI 2019] [html] [code] [data]
3. Le, T., A. Sy, E.K. Molloy, Q. Zhang, S. Rao, and T. Warnow, "Using INC within Divide-and-Conquer Phylogeny Estimation," in 6th International Conference on Algorithms for Computational Biology. [AlCoB 2019] [html] [code] [data]
4. Molloy, E.K. and T. Warnow, "NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees," in 16th RECOMB International Conference on Comparative Genomics. [RECOMB-CG 2018] [html] [code] [data]
5. Christensen, S., E.K. Molloy, P. Vachaspati, and T. Warnow, "Optimal completion of incomplete gene trees in polynomial time using OCTAL," in 17th International Workshop on Algorithms and Bioinformatics. [WABI 2017] [html] [code] [data]

Book Chapters

1. Molloy, E.K. and T. Warnow. 2019. Large-scale Species Tree Estimation. Accepted. [Edited by Drs. Lacey Knowles and Laura Kubatko] [html]