Learning From the Fruit Fly

Diving deep into the functional elements of the fruit fly to grasp a better understanding of human biology may seem like a long shot, but that’s exactly what CSAIL Principal Investigator Manolis Kellis and his colleagues have done. In a paper released in the December 24 edition of Science, Kellis and members of the model organism ENCyclopedia Of DNA Elements Consortium (modENCODE) publish the integrative analysis of the Drosophila (fruitfly) project, which is funded by the National Human Genome Research Institute.

The paper details modENCODE’s research into the inner workings of the fruit fly, providing the basis for years of further study into the functional elements shared by both humans and fruit flies. The findings should provide scientists a better understanding of human biology, gene regulation and how the body reacts to disease, information which can be used in medical studies.

“This is everything a computational biologist would wish for for Christmas, but is too shy to ask. This is the first time this amount of data is available on a single organism across such a diverse range of phenotypes,” explained Kellis. “By probing the cell with dozens of different types of experiments, systematically and uniformly across different conditions, modENCODE has provided computational biologists a treasure trove of information, which is a dream come true for large-scale data mining.”

Kellis’ work could have an impact far beyond the confines of fruit fly research, as the biological lessons and principles learned are likely conserved between the human and fruit fly genomes. Additionally, the methodology used will likely guide researchers undertaking similar studies in other species, including humans. “Through the study of model organisms, such as fruit flies and worms, scientists can reach a better understanding of the human genome because many of the cellular mechanisms that lead to body plan formation, brain development, and even behavior, are deeply conserved across animal species,” said Kellis.

Kellis’ work provides a striking example of how computer science can have a deep impact in other fields, such as understanding the basic principles of biology. Kellis is an associate professor of Computational Science at MIT, and has helped train many students and postdocs in the field of computational biology in his group and through his course, “Computational Biology: Genomes, Networks, Evolution.”

“I could not be happier with the current direction of genomics - we are just scratching the envelope of what is possible. The questions are becoming richer, the data sets denser, the kinds of computational models coming more complex,” said Kellis. “The transformations genomics has gone through in recent years have made it an ideal field of study right now, and they are only accelerating the pace of genomics research.”

Kellis, the recent recipient of a Presidential Early Career Award, is thrilled to be immersed in such a breathtaking field and hopes to encourage other computer scientists to explore the field of computational biology. As for working at CSAIL, Kellis remarked that it is, “wonderful to be surrounded by all these computer science students and postdocs who can take this sort of complex data set to the next level.”

For more information on the modENCODE project, click here.

Abby Abazorius, CSAIL