Marco Avila-Elchiver's research while affiliated with Harvard Medical School and other places
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Publications (5)
In general, the invention relates to a method for designing a biological circuit. The method includes obtaining a target circuit objective for the biological circuit, determining an objective function corresponding to the target circuit objective, obtaining a number of nodes for the biological circuit, obtaining a set of possible circuit subgraphs...
Transcriptional motifs are small regulatory interaction patterns that regulate biological functions in highly-interacting cellular networks. Recently, attempts have been made to explain the significance of transcriptional motifs through dynamic function. However, fundamental questions remain unanswered. Why are certain transcriptional motifs with s...
The current state of the art for linear optimization in Flux Balance Analysis has been limited to single objective functions. Since mammalian systems perform various functions, a multiobjective approach is needed when seeking optimal flux distributions in these systems. In most of the available multiobjective optimization methods, there is a lack o...
Flux balance analysis (FBA) provides a framework for the estimation of intracellular fluxes and energy balance analysis (EBA) ensures the thermodynamic feasibility of the computed optimal fluxes. Previously, these techniques have been used to obtain optimal fluxes that maximize a single objective. Because mammalian systems perform various functions...
Citations
... Such metabolic contributions should be considered in the future, for improving the experimental and modeling paradigm of Exo-MFA. Additionally, algorithmic improvements like implementing the EMU technique (Antoniewicz et al., 2007) may further improve computational efficiency and enable development of dynamic Exo-MFA that can be applied to more complex metabolic models that consider multifold cell-specific functions and thermodynamic constraints (Avila-Elchiver et al., 2012;Nagrath et al., 2010Nagrath et al., , 2007Wang et al., 2012). Despite the caveats, Exo-MFA has the potential to improve our understanding of tumor development in the context of the TME and advance the field of cancer metabolism. ...
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... An extension with l 1 or l 2 regularization is often used to avoid degeneracy in the FBA solutions (Bonarius et al., 1996;Lewis et al., 2010). Moreover, a variation that considers multi-objective optimization via a weighted combination of common objectives has proven to better describe the fluxes in some organisms (Lee et al., 2004;Schuetz et al., 2012;García Sánchez et al., 2012); however, the weights are often arbitrarily assigned (Nagrath et al., 2010). The goal of this IOP is to learn the weight vector in multi-objective FBA from the synthetic datasets. ...
... Since reduced glutathione has been reported as a crucial metabolite related to embryogenesis, pluripotency, and differentiation (Hansen and Harris 2015; Ufer and Wang 2011), we investigated how glutathione influences metabolic tasks during the two transitions with Pareto analysis. According to the theory of optimality, tradeoffs in objectives can lead to optimal conditions lying on Pareto fronts, which represents the best solutions for optimizing multiple objectives (Nagrath et al. 2007;Schuetz et al. 2012). Any points inside the region formed by Pareto fronts are feasible but not optimal solutions; outside the region, however, the points are not biologically feasible. ...
