Browsing Harvard Medical School by Keyword "Biochemical Simulations"
Now showing items 1-7 of 7
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Exploring the Contextual Sensitivity of Factors that Determine Cell-to-Cell Variability in Receptor-Mediated Apoptosis
(Public Library of Science, 2012)Stochastic fluctuations in gene expression give rise to cell-to-cell variability in protein levels which can potentially cause variability in cellular phenotype. For TRAIL (TNF-related apoptosis-inducing ligand) variability ... -
Gene Networks of Fully Connected Triads with Complete Auto-Activation Enable Multistability and Stepwise Stochastic Transitions
(Public Library of Science, 2014)Fully-connected triads (FCTs), such as the Oct4-Sox2-Nanog triad, have been implicated as recurring transcriptional motifs embedded within the regulatory networks that specify and maintain cellular states. To explore the ... -
Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models
(Public Library of Science, 2012)Background: Bacteria have evolved the ability to efficiently and resourcefully adapt to changing environments. A key means by which they optimize their use of available nutrients is through adjustments in gene expression ... -
A Linear Framework for Time-Scale Separation in Nonlinear Biochemical Systems
(Public Library of Science, 2012)Cellular physiology is implemented by formidably complex biochemical systems with highly nonlinear dynamics, presenting a challenge for both experiment and theory. Time-scale separation has been one of the few theoretical ... -
Pharmacointeraction Network Models Predict Unknown Drug-Drug Interactions
(Public Library of Science, 2013)Drug-drug interactions (DDIs) can lead to serious and potentially lethal adverse events. In recent years, several drugs have been withdrawn from the market due to interaction-related adverse events (AEs). Current methods ... -
Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM
(Public Library of Science, 2013)The filamentous fungus Neurospora crassa played a central role in the development of twentieth-century genetics, biochemistry and molecular biology, and continues to serve as a model organism for eukaryotic biology. Here, ... -
Synergistic and Antagonistic Drug Combinations Depend on Network Topology
(Public Library of Science, 2014)Drug combinations may exhibit synergistic or antagonistic effects. Rational design of synergistic drug combinations remains a challenge despite active experimental and computational efforts. Because drugs manifest their ...