Laboratory for Control, Learning, and Systems Biology

Papers by A. de la Fuente and E.D. Sontag

2015
  1. ▪P. Bastiaens, M. R. Birtwistle, N. Bluthgen, F. J. Bruggeman, K.-H. Cho, C. Cosentino, A. de la Fuente, J. B. Hoek, A. Kiyatkin, S. Klamt, W. Kolch, S. Legewie, P. Mendes, T. Naka, T. Santra, E.D. Sontag, H. V. Westerhoff, B. N. Kholodenko, "Silence on the relevant literature and errors in implementation", Nature Biotech, vol. 33, pp. 336-339, 2015. pdf
    modular response analysis · systems biology · reaction networks · reverse engineering · gene and protein networks · protein networks · gene networks · systems identification
    Abstract

    This letter discusses a paper in the same journal which reported a method for reconstructing network topologies. Here we show that the method is a variant of a previously published method, modular response analysis. We also demonstrate that the implementation of the algorithm in that paper using statistical similarity measures as a proxy for global network responses to perturbations is erroneous and its performance is overestimated.