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Publications of Eduardo D. Sontag jointly with Y. Zhang
Articles in journal or book chapters
  1. M. Ali Al-Radhawi, S. Tripathi, Y. Zhang, E.D. Sontag, and H. Levine. Epigenetic factor competition reshapes the EMT landscape. Proc Natl Acad Sci USA, 2022. Note: Submitted.Keyword(s): gene networks, Epithelial-Mesenchymal Transition, EMT, epigenetics, systems biology, cancer.
    Abstract:
    The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene regulatory elements. These elements include chromatin remodelers, histone modifiers, transcription factors, and regulatory RNAs. Mathematical models known as Gene Regulatory Networks (GRNs) are an increasingly important tool to unravel the workings of such complex networks. In such models, epigenetic factors are usually proposed to act on the chromatin regions directly involved in the expression of relevant genes. However, it has been well-established that these factors operate globally and compete with each other for targets genome-wide. Therefore, a perturbation of the activity of a regulator can redistribute epigenetic marks across the genome and modulate the levels of competing regulators. In this paper, we propose a conceptual and mathematical modeling framework that incorporates both local and global competition effects between antagonistic epigenetic regulators in addition to local transcription factors, and show the counter-intuitive consequences of such interactions. We apply our approach to recent experimental findings on the Epithelial-Mesenchymal Transition (EMT). We show that it can explain the puzzling experimental data as well provide new verifiable predictions.


  2. B. DasGupta, G.A. Enciso, E.D. Sontag, and Y. Zhang. Algorithmic and complexity aspects of decompositions of biological networks into monotone subsystems. BioSystems, 90:161-178, 2007. [PDF] Keyword(s): monotone systems, systems biology, biochemical networks.
    Abstract:
    A useful approach to the mathematical analysis of large-scale biological networks is based upon their decompositions into monotone dynamical systems. This paper deals with two computational problems associated to finding decompositions which are optimal in an appropriate sense. In graph-theoretic language, the problems can be recast in terms of maximal sign-consistent subgraphs. The theoretical results include polynomial-time approximation algorithms as well as constant-ratio inapproximability results. One of the algorithms, which has a worst-case guarantee of 87.9% from optimality, is based on the semidefinite programming relaxation approach of Goemans-Williamson. The algorithm was implemented and tested on a Drosophila segmentation network and an Epidermal Growth Factor Receptor pathway model.


  3. B. Dasgupta, G.A. Enciso, E.D. Sontag, and Y. Zhang. Algorithmic and complexity results for decompositions of biological networks into monotone subsystems. In C. Ālvarez and M. Serna, editors, Lecture Notes in Computer Science: Experimental Algorithms: 5th International Workshop, WEA 2006, pages 253-264. Springer-Verlag, 2006. Note: (Cala Galdana, Menorca, Spain, May 24-27, 2006). Keyword(s): systems biology, biochemical networks, monotone systems, theory of computing and complexity.



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Last modified: Wed Aug 17 10:22:06 2022
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