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Blue Waters Graduate Fellow: Paul Hime

The Blue Waters Graduate Fellowship was awarded to ten outstanding Ph.D. students in computational science. In this series we’re featuring brief introductions to who they are and what they’re trying to accomplish. This program serves to prepare the next generation of science researchers to solve the world’s problems. Follow along as we highlight these young researchers. Read more profiles here.

Tell me a little bit about yourself—where are you studying now, where did you do your undergrad, what was your major, etc.

I am a Ph.D. candidate at University of Kentucky in Lexington, Kentucky studying evolutionary biology and genomics of amphibians. As an undergraduate, I majored in Biology at Washington University in St. Louis, Missouri. And prior to coming to graduate school, I was an amphibian and reptile keeper at the St. Louis Zoo. I’ve been fascinated with the natural world, and amphibians in particular, for as long as I can remember.

Tell me about your research—what are you trying/hoping to accomplish? What made you want to pursue this topic?

I am an aspiring evolutionary biologist who is interested in understanding the remarkable diversity of life. One main feature of life on Earth is that all organisms trace their origins back to a single common ancestor nearly four billion years ago. Yet today, there are tens of millions of species. My research seeks to reconstruct these evolutionary relationships among organisms to better understand and conserve this biological diversity. A second feature of all life forms is that they each possess genetic material which orchestrates the ways in which they are constructed and which also evolves through time. I use these genome sequences to infer patterns of evolutionary relationships among living organisms, a field of evolutionary biology known as phylogenetics, and to understand the processes which have led to their present-day diversity.

Historically, the DNA sequence data that phylogeneticists use to reconstruct evolutionary relationships have been limited to a small portion of the genome. However, we now know that different regions of the genome may each tell different versions of this evolutionary history, and that relying on a small sampling of the genome may not accurately reflect the true evolutionary origins of organisms. More genetic data should, in theory, produce more reliable estimates of evolutionary relationships. Yet, DNA sequences have traditionally been very difficult to obtain en masse. But over the past 15 years, advances in genome sequencing technologies have opened up exciting new avenues for phylogeneticists to survey broad swaths of the genome and to untangle some of the difficult branches in the Tree of Life. This new flood of genetic data itself is necessary, but not sufficient, to answer some of the most thorny evolutionary questions. As the amount of data available to evolutionary biologists has expanded, so too have the computational challenges to appropriately modeling DNA evolution between organisms. For instance, for a set of just over 50 different organisms (a relatively small-scale evolutionary question), there are more potential evolutionary histories than there are atoms in the observable universe! Performing phylogenetic inference for large numbers of species and large numbers of genes is clearly a difficult question.

My doctoral research in the Weisrock Lab at University of Kentucky uses new computational and statistical approaches to reconstruct evolutionary relationships. I utilize amphibians (frogs, salamanders, and caecilians) as a model system in which to explore these exciting questions. Access to extremely powerful supercomputing resources is vital to this research, and the Blue Waters Fellowship through the NCSA provides unprecedented opportunities to advance this work. As one of the world’s most powerful computing systems, the NSF-funded Blue Waters supercomputer will allow me to probe aspects of phylogenetics which have previously been inaccessible due to computational constraints.

So what was your process like getting involved with Blue Waters? What made you want to apply for this fellowship?

I saw the previous two calls for applications come up and had set my targets on the Blue Waters fellowship for my final year in the PhD program here at UK. My work is highly computational and this aspect of my field has become a major bottleneck to research with the recent availability of genome-scale data in phylogenetics. This seemed like a perfect storm of sorts, for me to have a chance to use such a remarkable computing platform at a stage in my research where our ability to ask questions and to collect data were rapidly outpacing our ability to efficiently and appropriately analyze our data. The fellowship was very attractive because of the access to Blue Waters and the competitive stipend. But I assumed looking back over the past award recipients that I would not stand much of a chance, after seeing the amazing research in so many disparate fields that had been supported by this fellowship. I was very surprised to get notification of this award, and immediately knew that this could be a game-changer for my dissertation research.

How will the ability to use Blue Waters impact your research?

In a word, massively. Access to Blue Waters will totally redefine the types of analyses that I am able to perform and will make this work possible to finish within the next year. I am hopeful that this fellowship will provide opportunities to investigate aspects of my dissertation research that simply would not have been possible without access to this amazing computing system. Looking forward, I also anticipate that the computational skills I will gain from working with the NCSA researchers will be broadly applicable in my planned career as an academic researcher, given that computation is increasingly an important component of so many different fields of science.

Would you have been able to do this kind of research on any other machine? Why or why not?

Yes, in a sense, but it would have taken a ridiculously long time on other platforms and I would not be able to implement the scale of analyses which I intend to run on Blue Waters. Modeling DNA sequence evolution at the (more realistic) level of 64-state codons involves substantially more computation than for the standard four-state nucleotide models. But using high performance statistical libraries, these analyses can be spread across the large-scale GPU/CPU resources on Blue Waters and completed substantially faster.

What is the overall impact that your research will have on the science community and the world at large?

As genome-scale data permeate phylogenetics, computational challenges to appropriately analyzing this new generation of data sets are proving substantial. My research addresses long-standing questions in deep vertebrate evolution, but also seeks to address more general questions about how phylogeneticists can accurately reconstruct complex evolutionary relationships. I feel a great responsibility as a Blue Waters Fellow to attempt to make meaningful contributions to the intersecting fields of evolutionary biology and computational science.

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