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Publications about 'modular response analysis'
Articles in journal or book chapters
  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, and B. N. Kholodenko. Silence on the relevant literature and errors in implementation. Nature Biotech, 33:336-339, 2015. [PDF] Keyword(s): reverse engineering, systems biology, 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.


  2. T. Kang, R. Moore, Y. Li, E.D. Sontag, and L. Bleris. Discriminating direct and indirect connectivities in biological networks. Proc Natl Acad Sci USA, 112:12893-12898, 2015. [PDF] Keyword(s): modular response analysis, stochastic systems, reverse engineering, gene networks, synthetic biology.
    Abstract:
    Reverse engineering of biological pathways involves an iterative process between experiments, data processing, and theoretical analysis. In this work, we engineer synthetic circuits, subject them to perturbations, and then infer network connections using a combination of nonparametric single-cell data resampling and modular response analysis. Intriguingly, we discover that recovered weights of specific network edges undergo divergent shifts under differential perturbations, and that the particular behavior is markedly different between different topologies. Investigating topological changes under differential perturbations may address the longstanding problem of discriminating direct and indirect connectivities in biological networks.


  3. E.D. Sontag. Network reconstruction based on steady-state data. Essays in Biochemistry, 45:161-176, 2008. [PDF] Keyword(s): systems biology, biochemical networks, gene and protein networks, reverse engineering, systems identification.
    Abstract:
    The ``reverse engineering problem'' in systems biology is that of unraveling of the web of interactions among the components of protein and gene regulatory networks, so as to map out the direct or local interactions among components. These direct interactions capture the topology of the functional network. An intrinsic difficulty in capturing these direct interactions, at least in intact cells, is that any perturbation to a particular gene or signaling component may rapidly propagate throughout the network, thus causing global changes which cannot be easily distinguished from direct effects. Thus, a major goal in reverse engineering is to use these observed global responses - such as steady-state changes in concentrations of active proteins, mRNA levels, or transcription rates - in order to infer the local interactions between individual nodes. One approach to solving this global-to-local problem is the ``Modular Response Analysis'' (MRA) method proposed in work of the author with Kholodenko et. al. (PNAS, 2002) and further elaborated in other papers. The basic method deals only with steady-state data. However, recently, quasi-steady state MRA has been used by Santos et. al. (Nature Cell Biology, 2007) for quantifying positive and negative feedback effects in the Raf/Mek/Erk MAPK network in rat adrenal pheochromocytoma (PC-12) cells. This paper presents an overview of the MRA technique, as well as a generalization of the algorithm to that quasi-steady state case.


  4. P. Berman, B. Dasgupta, and E.D. Sontag. Algorithmic issues in reverse engineering of protein and gene networks via the modular response analysis method. Annals of the NY Academy of Sciences, 1115:132-141, 2007. [PDF] Keyword(s): systems biology, biochemical networks, gene and protein networks, reverse engineering, systems identification, graph algorithms.
    Abstract:
    This paper studies a computational problem motivated by the modular response analysis method for reverse engineering of protein and gene networks. This set-cover problem is hard to solve exactly for large networks, but efficient approximation algorithms are given and their complexity is analyzed.


Conference articles
  1. Q. Tyles, T. Kang, E.D. Sontag, and L. Bleris. Exploring the impact of resource limitations on gene network reconstruction. In Proc. IEEE Conf. Decision and Control, Dec. 2016, pages 3350-3355, 2016. [PDF] Keyword(s): Biological systems, Genetic regulatory systems, Systems biology.
    Abstract:
    Applying Modular Response Analysis to a synthetic gene circuit, which was introduced in a recent paper by the authors, leads to the inference of a nontrivial "ghost" regulation edge which was not explicitly engineered into the network and which is, in fact, not immediately apparent from experimental measurements. One may thus hypothesize that this ghost regulatory effect is due to competition for resources. A mathematical model is proposed, and analyzed in closed form, that lends validation to this hypothesis.



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Last modified: Thu Nov 23 10:40:56 2017
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