title: Comparison of reverse-engineering methods using an in silico network.
abstract: The reverse engineering of biochemical networks is a central problem in systems biology. In recent years several methods have been developed for this purpose, using techniques from a variety of fields. A systematic comparison of the different methods is complicated by their widely varying data requirements, making benchmarking difficult. Also, because of the lack of detailed knowledge about most real networks, it is not easy to use experimental data for this purpose. This paper contains a comparison of four reverse-engineering methods using data from a simulated network. The network is sufficiently realistic and complex to include many of the challenges that data from real networks pose. Our results indicate that the two methods based on genetic perturbations of the network outperform the other methods, including dynamic Bayesian networks and a partial correlation method.
authors.affiliation: Applied Biodynamics Lab, Biomedical Engineering Department, Boston University, MA, USA.
authors.forename: Diogo
authors.initials: D
authors.lastname: Camacho
authors.forename: Paola
authors.initials: P
authors.lastname: Vera Licona
authors.forename: Pedro
authors.initials: P
authors.lastname: Mendes
authors.forename: Reinhard
authors.initials: R
authors.lastname: Laubenbacher
mesh_terms: D000465:Algorithms; D001698:Biomedical Engineering / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D015870:Gene Expression / Q000502:physiology*; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000502:physiology*; D008954:Models, Biological; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D020543:Proteome