Adithya Sagar

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With the rapid growth of structural genomics, numerous protein crystal structures have become available. However, the parallel increase in knowledge of the functional principles underlying biological processes, and more specifically the underlying molecular mechanisms of disease, has been less dramatic. This notwithstanding, the study of complex cellular(More)
In this study, we present a novel modeling approach which combines ordinary differential equation (ODE) modeling with logical rules to simulate an archetype biochemical network, the human coagulation cascade. The model consisted of five differential equations augmented with several logical rules describing regulatory connections between model components,(More)
In this study, we present an effective model All-Trans Retinoic Acid (ATRA)-induced differentiation of HL-60 cells. The model describes reinforcing feedback between an ATRA-inducible signalsome complex involving many proteins including Vav1, a guanine nucleotide exchange factor, and the activation of the mitogen activated protein kinase (MAPK) cascade. We(More)
Dynamic Modeling of the Human Coagulation Cascade Using Reduced Order Effective Kinetic Models Report Title Cell-free systems offer many advantages for the study, manipulation and modeling of metabolism compared to in vivo processes. Many of the challenges confronting genome-scale kinetic modeling can potentially be overcome in a cell-free system. For(More)
Cancer therapies require classification of cancers to target specific cancers with specific treatments. Thus the improvements in cancer therapies have been linked to improvements in cancer classification. To enhance the efficiency of the treatment it is important to identify the specific markers that are to be targeted in a treatment. Apart from enhancing(More)
Complement is an important pathway in innate immunity, inflammation, and many disease processes. However, despite its importance, there have been few validated mathematical models of complement activation. In this study, we developed an ensemble of experimentally validated reduced order complement models. We combined ordinary differential equations with(More)
Dynamic Modeling of Cell-Free Biochemical Networks Using Effective Kinetic Models Report Title In this study, we present a novel modeling approach which combines ordinary differential equation (ODE) modeling with logical rules to simulate an archetype biochemical network, the human coagulation cascade. The model consisted of five differential equations(More)
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