I currently a visiting scholar at UCLA for the IPAM Long Program: Science at Extreme Scales.


I am a PhD student at the University of Illinois at Urbana-Champaign. My current research, which lies in the intersection of computational phylogenetics and high performance parallel computing, is advised by Professors Tandy Warnow and William Gropp. I took the PhD Qualifying Exam in the Scientific Computing aka Numerical Analysis research area, see the reading list here. I am an NSF IGERT Fellow (2013), a Siebel Fellow (2014), an NSF Graduate Research Fellow (2015), and a Cohen Fellow (2017).

Before Illinois, I worked as a neuroimaging researcher supervised by Professor Rasmus Birn at the Health Emotions Research Institute at the University of Wisconsin-Madison. There I focused on evaluating and addressing critical methodological problems in resting-state functional MRI, including systematic image artifacts (head motion, physiological noise, etc.) and subject test-retest reliability. I have contributed both statistical analyses and writing to three publications each netting over 100 citations. If you are interested in test-retest reliability of functional connectivity maps, see my documentation on GitHub.

My bachelor's degree is in Physics from the University of Chicago.

Peer-Reviewed Publications

Conference Proceedings

2. Molloy E.K. & Warnow T. (2018). NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees. In: Blanchette M., Ouangraoua A. (eds) Comparative Genomics. RECOMB-CG 2018. Lecture Notes in Computer Science, vol 11183. Springer, Cham. doi:10.1007/978-3-030-00834-5_15

1. Christensen S., Molloy E.K., Vachaspati P. & Warnow T. (2017). Optimal completion of incomplete gene trees in polynomial time using OCTAL. In: Schwartz R., Reinert K. (eds) 17th International Workshop on Algorithms and Bioinformatics (WABI). Leibniz International Proceedings in Informatics (LIPIcs), vol 88. Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik, Dagstuhl. doi:10.4230/LIPIcs.WABI.2017.27

Journal Articles

11. Molloy E.K. & Warnow T. (2018). Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. Under review for a special issue in Algorithms for Molecular Biology; Pre-print available on bioRxiv.

10. Nute M., Chou J., Molloy E.K. & Warnow T. (2018). The Performance of Coalescent-Based Species Tree Estimation Methods under Models of Missing Data. BMC Genomics. 19(Suppl 5):286 doi:10.1186/s12864-018-4619-8.     Portions of this work were presented at the 2016 Evolution Meeting in the talk, "To include or not to include: The impact of missing data on summary methods for species tree estimation."

9. Christensen S., Molloy E.K., Vachaspati P. & Warnow T. (2018). OCTAL: Optimal completion of gene trees in polynomial time. Algorithms for Molecular Biology 13:6. doi:10.1186/s13015-018-0124-5

8. Molloy E.K. & Warnow T. (2018). To include or not to include: The Impact of Gene Filtering on Species Tree Estimation Methods. Systematic Biology 67(2):285-303. doi:10.1093/sysbio/syx077

7. Kruepke M., Molloy E.K., Bresin K.W., Barbey A. K. & Verona E. (2017). A Brief Assessment Tool for Investigating Facets of Moral Judgment from Realistic Moral Vignettes. Behavior Research Methods. doi:10.3758/s13428-017-0917-3

6. Patriat R., Molloy E.K. & Birn R.M. (2015). Using Edge Voxel Information to Improve Motion Regression for rs-fMRI Connectivity Studies. Brain Connectivity 5:582-595. doi:10.1089/brain.2014.0321

5. Molloy E.K., Meyerand M.E. & Birn R.M. (2014). The influence of spatial resolution and smoothing on the detectability of resting-state and task fMRI. Neuroimage 86:221-230. doi:10.1016/j.neuroimage.2013.09.001

4. Birn R.M., Cornejo M.D., Molloy E.K., Patriat R., Meier T.B., Kirk G.R., Nair V.A., Meyerand M.E. & Prabhakran V. (2014). The Influence of Physiological Noise Correction on Test-Retest Reliability of Resting-State Functional Connectivity. Brain Connectivity 4:511-522. doi:10.1089/brain.2014.0284

3. Birn R.M., Molloy E.K., Patriat R., Parker T., Meier T.B., Kirk G.R., Nair V.A., Meyerand M.E. & Prabhakran V. (2013). The effect of scan length on the reliability of resting-state fMRI connectivity estimates. Neuroimage 83:550-558. doi:10.1016/j.neuroimage.2013.05.099

2. Patriat R., Molloy E.K., Meier T.B., Kirk G.R., Nair V.A., Meyerand M.E., Prabhakran V. & Birn R.M. (2013). The effect of resting condition on resting-state fMRI reliability and consistency: A comparison between resting with eyes open, closed, and fixated. Neuroimage 78:463-473. doi:10.1016/j.neuroimage.2013.04.013

1. Burghy C.A., Stodola D.E., Ruttle P.L., Molloy E.K., Armstrong J.M., Oler J.A., Fox M.E., Hayes A.S., Kalin N.H., Essex M.J., Davidson R.J. & Birn R.M. (2012). Developmental pathways to amygdala-prefrontal function and internalizing symptoms in adolescence. Nature Neuroscience 15:1736-1741. doi:10.1038/nn.3257


I have TA'd two courses (see below) at the University of Illinois and was named to the "List of Teachers Ranked as Excellent by their Students" both semesters: Spring 2015 and Spring 2017. My teaching responsibilities included preparing and leading weekly recitation sections, holding weekly office hours, and writing homework solutions. I have also served as an instructor for the CITL's Graduate Academy for College Teaching.

CS 450: Numerical Analysis

This course covers numerical methods for solving linear and nonlinear systems of equations, least squares problems, eigenvalue problems, optimization problems, and ordinary and partial differential equations.

Learn more about CS450 and other courses in Scientific Computing.

CS 466: Introduction to Bioinformatics

This course covers algorithmic techniques (e.g., dynamic programming) with applications in biology: genome assembly, multiple sequence alignment, and phylogeny estimation.

Check out the CS466 course materials.


Engineering Graduate Student Advisory Committee (EGSAC)

While an EGSAC member, I initated and led a collaboration with Michael Krupeke (from the Department of Clinical and Community Psychology) to design a research study on the impact of department and research group communities as well as advisor-advisee relationships on graduate student wellbeing. Findings will be used by future EGSAC members to advocate for changes in the College of Engineering. I also served as Secretary (2014-15) and Chair (2015-16) of the committee.

Learn more about EGSAC.

Graduate Society of Women Engineers (GradSWE)

I served on the organizing committee, as Publicity Coordinator in 2017 and as Attendee Relations Coordinator in 2018, for the Women Empowered in STEM (weSTEM) conference organized by GradSWE at the University of Illinois.

Learn more about GradSWE and weSTEM.