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Publications about 'stoichiometry'
Articles in journal or book chapters
  1. S. Wang, J.-R. Lin, E.D. Sontag, and P.K. Sorger. Inferring reaction network structure from single-cell, multiplex data, using toric systems theory. PLoS Computational Biology, 15:e1007311, 2019. [WWW] [PDF] Keyword(s): chemical reaction networks, stoichiometry, complex balancing, toric varieties, systems biology.
    Abstract:
    The goal of many single-cell studies on eukaryotic cells is to gain insight into the biochemical reactions that control cell fate and state. This paper introduces the concept of effective stoichiometric space (ESS) to guide the reconstruction of biochemical networks from multiplexed, fixed time-point, single-cell data. In contrast to methods based solely on statistical models of data, the ESS method leverages the power of the geometric theory of toric varieties to begin unraveling the structure of chemical reaction networks (CRN). This application of toric theory enables a data-driven mapping of covariance relationships in single cell measurements into stoichiometric information, one in which each cell subpopulation has its associated ESS interpreted in terms of CRN theory. In the development of ESS we reframe certain aspects of the theory of CRN to better match data analysis. As an application of our approach we process cytomery- and image-based single-cell datasets and identify differences in cells treated with kinase inhibitors. Our approach is directly applicable to data acquired using readily accessible experimental methods such as Fluorescence Activated Cell Sorting (FACS) and multiplex immunofluorescence.


  2. S. Prabakaran, J. Gunawardena, and E.D. Sontag. Paradoxical results in perturbation-based signaling network reconstruction. Biophysical Journal, 106:2720-2728, 2014. [PDF] Keyword(s): stoichiometry, MAPK cascades, systems biology, biochemical networks, gene and protein networks, reverse engineering, systems identification, retroactivity.
    Abstract:
    This paper describes a potential pitfall of perturbation-based approaches to network inference It is shows experimentally, and then explained mathematically, how even in the simplest signaling systems, perturbation methods may lead to paradoxical conclusions: for any given pair of two components X and Y, and depending upon the specific intervention on Y, either an activation or a repression of X could be inferred. The experiments are performed in an in vitro minimal system, thus isolating the effect and showing that it cannot be explained by feedbacks due to unknown intermediates; this system utilizes proteins from a pathway in mammalian (and other eukaryotic) cells that play a central role in proliferation, gene expression, differentiation, mitosis, cell survival, and apoptosis and is a perturbation target of contemporary therapies for various types of cancers. The results show that the simplistic view of intracellular signaling networks being made up of activation and repression links is seriously misleading, and call for a fundamental rethinking of signaling network analysis and inference methods.


  3. E.D. Sontag. A technique for determining the signs of sensitivities of steady states in chemical reaction networks. IET Systems Biology, 8:251-267, 2014. Note: Code is here: https://github.com/sontaglab/CRNSeSi. [PDF] Keyword(s): sensitivity, retroactivity, biomolecular networks, systems biology, stoichiometry, biochemical networks, systems biology.
    Abstract:
    This paper studies the direction of change of steady states to parameter perturbations in chemical reaction networks, and, in particular, to changes in conserved quantities. Theoretical considerations lead to the formulation of a computational procedure that provides a set of possible signs of such sensitivities. The procedure is purely algebraic and combinatorial, only using information on stoichiometry, and is independent of the values of kinetic constants. Two examples of important intracellular signal transduction models are worked out as an illustration. In these examples, the set of signs found is minimal, but there is no general guarantee that the set found will always be minimal in other examples. The paper also briefly discusses the relationship of the sign problem to the question of uniqueness of steady states in stoichiometry classes.


  4. L. Bleris, Z. Xie, D. Glass, A. Adadey, E.D. Sontag, and Y. Benenson. Synthetic incoherent feed-forward circuits show adaptation to the amount of their genetic template. Molecular Systems Biology, 7:519-, 2011. [PDF] Keyword(s): adaptation, feedforward loops, systems biology, synthetic biology, incoherent feedforward loop, feedforward, IFFL.
    Abstract:
    Natural and synthetic biological networks must function reliably in the face of fluctuating stoichiometry of their molecular components. These fluctuations are caused in part by changes in relative expression efficiency and the DNA template amount of the network-coding genes. Gene product levels could potentially be decoupled from these changes via built-in adaptation mechanisms, thereby boosting network reliability. Here we show that a mechanism based on an incoherent feed-forward motif enables adaptive gene expression in mammalian cells. We modeled, synthesized, and tested transcriptional and post-transcriptional incoherent loops and found that in all cases the gene product adapts to changes in DNA template abundance. We also observed that the post-transcriptional form results in superior adaptation behavior, higher absolute expression levels, and lower intrinsic fluctuations. Our results support a previously-hypothesized endogenous role in gene dosage compensation for such motifs and suggest that their incorporation in synthetic networks will improve their robustness and reliability.



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Last modified: Wed Aug 17 10:22:07 2022
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