Workshop on Constraint Based Methods for Bioinformatics

September 12, 2011 University of Perugia, Italy

Workshop OrganizersAlessandro Dal PalùUniversità degli Studi di Parma, ItalyAgostino Dovier Università degli Studi di Udine, ItalyAndrea FormisanoUniversità degli Studi di Perugia, Italy

Programme CommitteeRolf Backofen (Germany)Pedro Barahona (Portugal) Alexander Bockmayr (Germany)Mats Carlsson (Sweden)Alessandro Dal Palù (Italy)Simon de Givry (France)Agostino Dovier (Italy)Esra Erdem (Turkey)

François Fages (France)Andrea Formisano (Italy) Inês Lynce (Portugal) Neil Moore (Scotland)Enrico Pontelli (USA)Sven Thiele (Germany)Sebastian Will (Germany)

09:00 Invited Talk

Alessandro BrozziInferring Gene Pathways Controlling Clonal Outgrowth by High-throughput Insertional Mutagenesis Screens

09:55 Aljoscha Palinkas and Alexander Bockmayr.Petri Nets for Integrated Models of Metabolic and Gene Regulatory Networks

10:25 Coffee Break

10:55 Jimmy Vandel and Simon De Givry.A New Local Move Operator for Reconstructing Gene Regulatory networks

11:25 Steven Gay, Francois Fages, Thierry Martinez, and Sylvain Soliman.A Constraint Program for Subgraph Epimorphisms

with Application to Identifying Model Reductions in Systems Biology

11:55 Thomas Eiter, Thomas Krennwallner, and Christoph Redl.Declarative Merging of and Reasoning about Decision Diagrams

12:35 Lunch Break

14:00 Christian Theil Have.Constraints and Global Optimization for Gene Prediction Overlap Resolution

14:30 Marco Correia, Fabio Madeira, Pedro Barahona, and Ludwig Krippahl.Improving Multiple Sequence Alignments with Constraint Programming and Local Search

15:00 Michael Best, Kabi Bhattarai, Federico Campeotto, Alessandro Dal Palu', Hung Dang,Agostino Dovier, Ferdinando Fioretto, Federico Fogolari, Trung Le, and Enrico Pontelli.

Introducing FIASCO: Fragment-based Interactive Assembly for protein Structure prediction with COnstraints

15:40 Coffee Break

16:10 Panel & Discussion

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