Design principles of biological circuits
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Fold-Change Detection in Biological Systems
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Optimal Regulatory Circuit Topologies For Fold-Change Detection
- Out of a million possible circuits, only very few show optimal fold change detection - possibly explaining why only a few circuit designs recur across biology.
- Cell Systems preview
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Optimality and Sub-Optimality in a Bacterial Growth Law
Bacteria use a rule of thumb to optimize growth rate, which often works but sometimes fails
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Biphasic Response as a Mechanism Against Mutant Takeover in Tissue Homeostasis Circuits
Biphasic control, where a signal is toxic at both high and low levels, eliminates mis-sensing mutants at the cost of decreased resilience to dynamic perturbations, with implications for different diseases.
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Dynamical Compensation in Physiological Circuits
Dynamical compensation provides robustness of the entire output trace robust to variation in key parameters and appears in endocrine and neuronal circuits
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Linear Superposition and Prediction of Bacterial Promoter Activity Dynamics in Complex Conditions
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Paradoxical Signaling by a Secreted Molecule Leads to Homeostasis of Cell Levels
See preview by Hyun Youk and Wendell A. Lim
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Logarithmic and Power Law Input-Output Relations in Sensory Systems With Fold-Change Detection
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Hierarchy of Non-Glucose Sugars in Escherichia Coli
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The Last Generation of Bacterial Growth in Limiting Nutrient
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Comparing Apples and Oranges: Fold-Change Detection of Multiple Simultaneous Inputs
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The Utility of Paradoxical Components in Biological Circuits
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Promoters Maintain their Relative Activity Levels Under Different Growth Conditions
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Promoter Activity Dynamics in the Lag Phase of Escherichia Coli
Commentary by Daniel Schultz and Roy Kishony
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Design Principles of Cell Circuits With Paradoxical Components
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Mode of Regulation and the Insulation of Bacterial Gene Expression
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A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia Coli
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Robust Control of Nitrogen Assimilation by a Bifunctional Enzyme in E. Coli
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Robust Control of Nitrogen Assimilation by a Bifunctional Enzyme in e. Coli
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Symmetry Invariance For Adapting Biological Systems
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Robust Control of Pep Formation Rate in the Carbon Fixation Pathway of c-4 Plants by a Bifunctional Enzyme
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Structural Sources of Robustness in Biochemical Reaction Networks
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Cost of Unneeded Proteins in e. Coil is Reduced After Several Generations in Exponential Growth
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Fold-Change Detection and Scalar Symmetry of Sensory Input Fields
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Central Carbon Metabolism as a Minimal Biochemical Walk Between Precursors For Biomass and Energy
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Sensitivity and Robustness in Chemical Reaction Networks
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Robustness in Glyoxylate Bypass Regulation
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Invariant Distribution of Promoter Activities in Escherichia Coli
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The Incoherent Feedforward Loop Can Provide Fold-Change Detection in Gene Regulation
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Input-Output Robustness in Simple Bacterial Signaling Systems
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A Comprehensive Library of Fluorescent Transcriptional Reporters For Escherichia Coli
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Rules For Biological Regulation Based on Error Minimization
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Using a Quantitative Blueprint to Reprogram the Dynamics of the Flagella Gene Network
- See also cover page: URL.
- See also Preview article: [PDF]
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Just-in-Time Transcription Program in Metabolic Pathways
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Response Delays and the Structure of Transcription Networks
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Detailed Map of a Cis-Regulatory Input Function
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Negative Autoregulation Speeds the Response Times of Transcription Networks
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Assigning Numbers to the Arrows: Parameterizing a Gene Regulation Network by Using Accurate Expression Kinetics
See also JCB news: [PDF]
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Ordering Genes in a Flagella Pathway by Analysis of Expression Kinetics From Living Bacteria
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Robustness in Bacterial Chemotaxis