Fields of Interest

Computational Biology, RNA structure, Systems Biology

Academic Profile

There are many computational problems in Biology that can be represented as Combinatorial Optimization Problems. Many tools and algorithms available to solve these problems are not effective or efficient enough, sometimes because they do not produce optimal solutions or because they are only capable of solving a high level abstraction of the real problem.

Using Artificial Intelligence methods such as Constraint Programming, Local Search, Large Neighborhood Search, etc., these approaches can be greatly improved.We have applied these techniques with considerable success to problems such as protein structure prediction, riboswitch energy barrier calculation, RNA segmentation and Between Pathway Models discovery.

Representative Publications

Ivan Dotu, William A. Lorenz, Pascal Van Hentenryck and Peter Clote, " RNA structural segmentation". In PSB'10 Proceedings, 2010.

Ivan Dotu, William A. Lorenz, Pascal Van Hentenryck and Peter Clote, "Computing folding pathways between RNA secondary structures". In Nucleic Acids Research Journal, December 2009.

Manuel Cebrián, Iván Dotú, Pascal Van Hentenryck, Peter Clote: Protein Structure Prediction on the Face Centered Cubic Lattice by Local Search. AAAI 2008: 241-246

Iván Dotú, Manuel Cebrián, Pascal Van Hentenryck, Peter Clote: Protein Structure Prediction with Large Neighborhood Constraint Programming Search. CP 2008: 82-96