You can find me on Google Scholar, Research Gate, and ORCiD.
Population Structure and Admixture Graphs
Preprints
- 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
- 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
- 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
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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
- 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]
- 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]
- 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]
- 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]
- 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
- Molloy, E.K. and T. Warnow. 2019. Large-scale Species Tree Estimation. Accepted. [Edited by Drs. Lacey Knowles and Laura Kubatko] [html]
Moral Judgement / Decision Making
Peer-reviewed Journal Publications
- Kruepke, M., E.K. Molloy, K.W. Bresin, A.K. Barbey, and E. Verona, "A Brief Assessment Tool for Investigating Facets of Moral Judgment from Realistic Moral Vignettes," Behavior Research Methods, 2018. [html] [code] [data]
Functional Neuroimaging
Peer-reviewed Journal Publications
- Patriat, R., E.K. Molloy, and R.M. Birn, "Using Edge Voxel Information to Improve Motion Regression for rs-fMRI Connectivity Studies," Brain Connectivity, 2015. [html]
- Molloy, E.K. , M.E. Meyerand, and R.M. Birn, "The influence of spatial resolution and smoothing on the detectability of resting-state and task fMRI," Neuroimage, 2014. [html]
- Birn, R.M., M.D. Cornejo, E.K. Molloy, R. Patriat, T.B. Meier, G.R. Kirk, V.A. Nair, M.E. Meyerand, and V. Prabhakran, "The Influence of Physiological Noise Correction on Test-Retest Reliability of Resting-State Functional Connectivity," Brain Connectivity, 2014. [html]
- Birn, R.M., E.K. Molloy, R. Patriat, T. Parker, T.B. Meier, G.R. Kirk, V.A. Nair, M.E. Meyerand, and V. Prabhakran, "The effect of scan length on the reliability of resting-state fMRI connectivity estimates," Neuroimage, 2013. [html] [code]
- Patriat, R. E.K. Molloy, T.B. Meier, G.R. Kirk, V.A. Nair, M.E. Meyerand, V. Prabhakran, and R.M. Birn, "The effect of resting condition on resting-state fMRI reliability and consistency: A comparison between resting with eyes open, closed, and fixated," Neuroimage, 2013. [html] [code]
- Burghy, C.A., D.E. Stodola, P.L. Ruttle, E.K. Molloy, J.M. Armstrong, J.A. Oler, M.E. Fox, A.S. Hayes, N.H. Kalin, M.J. Essex, R.J. Davidson, and R.M. Birn, "Developmental pathways to amygdala-prefrontal function and internalizing symptoms in adolescence," Nature Neuroscience, 2012. [html]