Advances in Computational Protein-Protein Interaction Prediction

Dr. Sylvain Pitre

NSERC Postdoctoral Fellow, School of Computer Science, Carleton University

January 23, 2014 12:00 - 13:00

311 Southam Hall, Carleton University

Registration not required.

 

abstract

Protein-protein interactions (PPI) are the corner-stone of most biological processes taking place in cells. Recent advances in high throughput interaction detection techniques have led to the elucidation of substantial parts of the entire protein interaction maps for several species.

While these large-scale experimental approaches are critical to our understanding of the inner workings of the living cell, they have significant technical limitations. The last decade or so has seen the development of numerous computational methods to characterize unknown proteins and predict PPIs. Although computational predictions can avoid some of the issues with experimental approaches they have their own weaknesses, mainly their accuracy and also the amount of data required to make a prediction. PIPE (Protein-protein Interaction Prediction Engine) was developed as an accurate predictor of PPIs by analysing the amino-acid sequence of proteins. PIPE has been used to evaluate the PPI network of several model organisms and as a source of information for many exciting projects.

This talk will give an overview of PPIs and examine the characteristics of existing experimental and computational PPI detection techniques. PIPE, as well as some projects it made possible, will be presented as an example of a sequence-based predictor and its applications.

biography

Sylvain Pitre received his Bachelor of Applied Computer Science (BCS, 2001) from the Université de Moncton (NB, Canada) then moved to Ottawa to complete his Master of Computer Science (MCS, 2003) at Carleton University. He continued his studies at Carleton to obtain his Ph.D in Computer Science (2010) working on computational protein-protein interaction prediction. In 2010, he was one of the few recipients of the Mitacs Elevate Industrial Fellowship sponsored in part by industry partner Goldak Technologies, Inc., working in the field of computational weld mechanics (2010-2012). He is currently an NSERC postdoctoral fellow at Carleton University in the School of Computer Science working on topics including biological networks (analysis, comparison and evolution) and high-performance weld pool simulation using Smoothed-particle hydrodynamics (SPH). His research interests are bioinformatics, computational biology, high-performance computing (multi-core, multi-processor, GPGPU), parallel algorithms, scientific computing and computer simulation.