skip to main content
Department of Computer Science University of Colorado Boulder
cu: home | engineering | mycuinfo | about | cu a-z | search cu | contact cu cs: about | calendar | directory | catalog | schedules | mobile | contact cs
home · events · colloquia · 2009-2010 · 

Colloquium - Goldberg

ECCR 265

Mining Protein Interaction Networks
Department of Computer Science

In recent years, high-throughput assays for interactions between proteins have provided researchers with abundant graph represented data. Though error-prone, these protein interaction networks (PINs) nevertheless provide deep insights into the function and evolution of proteins.

Debra Goldberg photo

In this talk I'll describe some of the work we have done to make inferences from PIN data in order to reach a better understanding of protein evolution. First, we found that the prevalence of the de novo acquisition of function by a duplicate gene has been significantly overestimated. Second, we identified putative interaction dynamics (topological trends) for yeast across 300 million years of evolution and mapped the interaction dynamics to biological processes. Third, we identified additional features of evolution absent in current models which contribute to higher clustering, and substantial differences between a model's parameters and the measurements observed as the model runs. This work has led to a new model of protein interaction network evolution which features protein evolution at the domain level. This is joint work with Todd Gibson.

Next, I'll present work that investigates our ability to discover protein complexes from PIN data. We performed a systematic survey of known complexes to better understand which properties are good indicators for protein complexes and what parameter values we can expect to see in complexes within the incomplete data. As part of this survey, we created an algorithm to find the most highly connected subgraph of a graph, a topological property that has not previously been examined within PINs. This is joint work with Suzanne Gallagher.

Finally, I'll briefly describe my efforts to broaden participation in computer science. Together with Dirk Grunwald, Clayton Lewis, Katie Siek, Michael Eisenberg, Alexander Repenning, Roger (Buzz) King, and Shivakant Mishra, we have initiated ECSITE (Engaging Computer Science In Traditional Education), an NSF-funded program that will incorporate computing into existing high school and middle school courses, such as biology, physics, civics, health education, and animation.

The Department holds colloquia throughout the Fall and Spring semesters. These colloquia, open to the public, are typically held on Thursday afternoons, but sometimes occur at other times as well. If you would like to receive email notification of upcoming colloquia, subscribe to our Colloquia Mailing List. If you would like to schedule a colloquium, see Colloquium Scheduling.

Sign language interpreters are available upon request. Please contact Stephanie Morris at least five days prior to the colloquium.

See also:
Department of Computer Science
College of Engineering and Applied Science
University of Colorado Boulder
Boulder, CO 80309-0430 USA
Send email to

Engineering Center Office Tower
ECOT 717
FAX +1-303-492-2844
XHTML 1.0/CSS2 ©2012 Regents of the University of Colorado
Privacy · Legal · Trademarks
May 5, 2012 (13:29)