Biological networks: Challenges, Solutions and Opportunities

Date(s) - 09/28/2015
3:00 pm

Tamer Kahveci, Ph.D., Professor, Department of Computer and Information Science and Engineering


Biological networks of an organism show how different bio-chemical entities, such as enzymes or genes interact with each other to perform vital functions for that organism. Dr. Kahveci’s lab is focusing on developing computational methods that will help in understanding the functions of large-scale biological networks. In this talk, we will discuss some of the recent research activities at Dr. Kahveci’s lab. In the first part of the talk, we will focus on the scalability issues resulting from growing size of biological network databases and describe an indexing method aimed at tackling this problem. In the second part, we will shift the focus on the computational challenges centered on uncertainty in the topology of biological networks. We will discuss our new mathematical model, which represent probabilistic networks as collections of polynomials. We show that this is a powerful model that enables solving seemingly very tough computational problems on probabilistic networks efficiently and precisely. We will demonstrate the expressive power of this model on the signal reachability problem, which computes whether an extracellular signal reaches from a membrane receptor to a reporter gene. Finally, we will briefly discuss a set of possible future applications of our polynomial model for probabilistic biological networks and the challenges arising from dynamically evolving network topologies.

Short Bio:

Tamer Kahveci received his Ph.D. degree in Computer Science from University of California at Santa Barbara in 2004. He is currently a Professor in the Computer and Information Science and Engineering Department at the University of Florida, serving as the Associate Chair of Academic affairs. Dr. Kahveci received the Ralph E. Powe Junior Faculty Enhancement award in 2006, CSB best paper award in 2008, the NSF Career award in 2009, the ACM-BCB (Bioinformatics and Computational Biology) best student paper award in 2010 and the ACM-BCB honorary best paper award in 2011.  His main research interests are bioinformatics and databases. He has worked on indexing sequence and protein structure databases, sequence alignment and computational analysis of biological pathways.

Dr. Kahveci has served as the PC co-chair of the ACM BCB conference, the BioKDD workshop and the International Workshop on Robustness and Stability of Biological Systems and Computational Solutions in 2012. He served as the PC co-chair of the Workshop on Epigenomics and Cell Function in 2013 and the Workshop on Computational Network Analysis, the Workshops Chair of the ACM-BCB conference in 2014. He is the tutorials chair of the ACM BCB and the IEEE BIBM conferences in 2015. He is a member of the governing board of the ACM SIGBIO and a steering committee member of the ACM-BCB. He is a member of the editorial review board for of the journal International Journal of Knowledge Discovery in Bioinformatics (IJKDB). He is the lead guest editor of the Journal of Advances in Bioinformatics, special issue on “Computational analysis of biological networks” and associate editor in IEEE/ACM Transactions on Computational Biology and Bioinformatics.  In addition to these, he has served on the program committees of numerous computational biology and database conferences.