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Computational Phylogenetics

Peer-reviewed Journal Publications

  1. Zhang, C., C. Scornavacca, E.K. Molloy, S. Mirarab, "ASTRAL-Pro: quartet-based species tree inference despite paralogy," Molecular Biology and Evolution, In press. [html] [code] [data]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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 2019] [html] [code] [data]
  7. 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]
  8. 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]
  9. 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]
  10. 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. Legried, B., E.K. Molloy, T. Warnow,and S. Roch, "Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss," in 24th International Conference on Research in Computational Molecular Biology. [RECOMB 2020] [html] [data]
  3. 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]
  4. 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]
  5. 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]
  6. 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. Under revision. [Edited by Drs. Lacey Knowles and Laura Kubatko] [html]

Moral Judgement / Decision Making

Peer-reviewed Journal Publications

  1. 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

  1. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]