Ryan Kennedy, Computer Science & Engineering

Ryan Kennedy

“Interdisciplinarity” is the buzz word of modern education. What does it actually mean? A careful definition would state it to be drawing on disciplinary perspectives and integrating their insights through construction of a more comprehensive perspective.*/ The research and work of Ryan Kennedy, who received his doctorate in Computer Science and Engineering in 2011 and is now a postdoctoral scholar at the University of California, San Francisco, fits this definition perfectly.

Ryan grew up in Niles, Michigan—a child who aspired to one day attend Notre Dame and who thrived at one of Michigan’s excellent public school math and science centers. As an undergraduate at Notre Dame, Ryan found his way to computer science sophomore year and also participated in a summer Research Experiences for Undergraduates (REU) program with Prof. Gregory Madey, who introduced him to the concept of agent-based modeling. That term describes computer simulations of complex physical phenomena—from molecules to societies to entire ecosystems. Basically, explains Prof. Madey, who became Ryan’s dissertation advisor: “We study large numbers of diverse things and how they interact. Rather than developing a lot of equations and trying to predict what’s going to happen—which is difficult mathematically when the items to be studied are all different—we build a model of the system and let it behave as it would in real life.”

In graduate school, Ryan’s research focused on two major areas—bioinformatics and agent-based modeling and simulation—bound together with the common thread of global health. “A major component of my dissertation work involved the discovery and annotation of transposable elements within genomes, a work co-advised by Prof. Frank Collins of the Biological Sciences Department. Transposable elements are sequences of DNA found throughout most genomes that have the ability to move about the genome, playing a major role in genome evolution. My research focused on a pipeline for the automatic discovery of transposable elements as well as implementing a community annotation pipeline for them. This work was included at VectorBase, a bioinformatics resource center for vectors of human pathogens. The broad goal of my work was to combat the explosion of available genomic data with new automated analysis techniques.

“The agent-based modeling and simulation aspect of my research explored pathogen spread among long-tailed macaque monkeys in Bali, Indonesia," Ryan further explains. "Together with Biological Sciences professor Hope Hollocher and fellow doctoral student Kelly Lane ND ’11, as well as Anthropology professor Agustín Fuentes, we developed a computer simulation model that studied the impact of landscape—for example, forests, rivers, and rice fields—on pathogen spread. On Bali, macaques have coexisted with humans for at least 2,000 years. Changing land-use patterns have resulted in increased contact between the macaques and humans. In fact, the macaques have been implicated as hosts and reservoirs in the emergence of several diseases in humans.”

Ryan’s interdisciplinary work continues as a postdoctoral researcher at the University of California, San Francisco within the Department of Bioengineering and Therapeutic Sciences under the supervision of C. Anthony Hunt. His current projects involve developing a cell-centered method aimed to increase the understanding of cell behavior through a 2- and 3D perspective, as well as implementing plausible mechanisms for in silico cyst-size regulation.

“My graduate education at the University of Notre Dame more than adequately prepared me for postgraduate research,” Ryan says. "I was fortunate to participate in a number of interdisciplinary projects while at Notre Dame. These projects helped me learn how to work effectively with those in other disciplines, as well as how to quickly develop knowledge outside my area of expertise. Each of these skills has helped me immeasurably in my current position, as I am better able to contribute my computer science knowledge to solve problems within other disciplines.

“At Notre Dame, my advisors were always available and willing to help, which is emblematic of the University as a whole. I thoroughly enjoyed my experience at Notre Dame- I was welcomed into the family and was able to pursue my research interests in a supportive and friendly environment.”

*/ See Julie T. Klein and William H. Newell, Chapter 19, “Advancing Interdisciplinary Studies,” in Jerry Gaff & James Ratcliff, Handbook of the Undergraduate Curriculum (San Francisco: Jossey-Bass, 1997), 393-394.

Last updated: January 16, 2014