Building Predictive Models of Genetic Circuits Using the Principle of Maximum Caliber.

No abstract is available for this paper.

• Publication year

  2017

• Venue

  Biophysical Journal

• Publication date

  2017-11-07

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1016/j.bpj.2017.08.057PMID 29117534PMCID PMC5685677
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Engineering of a synthetic quadrastable gene network to approach Waddington landscape and cell fate determination

  2017cited by this paper
• Characterizing the Non-Normal Distribution of Flow Cytometry Measurements from Transiently Expressed Constructs in Mammalian Cells

  2016cited by this paper
• A Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to Mutations.

  2016cited by this paper
• Distinguishing between resistance, tolerance and persistence to antibiotic treatment

  2016cited by this paper
• A novel method to accurately locate and count large numbers of steps by photobleaching

  2016cited by this paper
• Build to understand: synthetic approaches to biology.

  2016cited by this paper
• Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes.

  2015cited by this paper
• Applications of Synthetic Gene Networks

  2015cited by this paper
• Inferring Microscopic Kinetic Rates from Stationary State Distributions

  2014cited by this paper
• Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems

  2014cited by this paper
• Gene Networks of Fully Connected Triads with Complete Auto-Activation Enable Multistability and Stepwise Stochastic Transitions

  2014cited by this paper
• Physical Biology of the Cell

  2014cited by this paper
• Single Molecule Conformational Memory Extraction: P5ab RNA Hairpin

  2014cited by this paper
• AMPA receptor/TARP stoichiometry visualized by single-molecule subunit counting

  2013cited by this paper
• Dissecting non-coding RNA mechanisms in cellulo by Single-molecule High-Resolution Localization and Counting.

  2013cited by this paper
• Designing experiments to understand the variability in biochemical reaction networks

  2013cited by this paper
• Engineering of regulated stochastic cell fate determination

  2013cited by this paper
• Principles of maximum entropy and maximum caliber in statistical physics

  2013cited by this paper
• The signal within the noise: efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations

  2013cited by this paper
• Asymmetric Stochastic Switching Driven by Intrinsic Molecular Noise

  2012cited by this paper
• Moment-based inference predicts bimodality in transient gene expression

  2012cited by this paper
• Bet Hedging in Yeast by Heterogeneous, Age-Correlated Expression of a Stress Protectant

  2012cited by this paper
• Counting protein molecules using quantitative fluorescence microscopy.

  2012cited by this paper
• A distribution‐matching method for parameter estimation and model selection in computational biology

  2012cited by this paper
• Intracellular single molecule microscopy reveals two kinetically distinct pathways for microRNA assembly

  2012cited by this paper
• Genetic programs constructed from layered logic gates in single cells

  2012cited by this paper
• Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit

  2012influential reference
• Modeling stochastic dynamics in biochemical systems with feedback using maximum caliber.

  2011influential reference
• Point centromeres contain more than a single centromere-specific Cse4 (CENP-A) nucleosome

  2011cited by this paper
• Subunit stoichiometry of human Orai1 and Orai3 channels in closed and open states

  2011cited by this paper
• Markov processes follow from the principle of maximum caliber.

  2011cited by this paper
• Stochastic dynamics of complexation reaction in the limit of small numbers.

  2011cited by this paper
• CENP-A exceeds microtubule attachment sites in centromere clusters of both budding and fission yeast

  2011cited by this paper
• Signal-dependent turnover of the bacterial flagellar switch protein FliM

  2010cited by this paper
• Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

  2010cited by this paper
• Maximum caliber inference of nonequilibrium processes.

  2010cited by this paper
• Biological role of noise encoded in a genetic network motif

  2010cited by this paper
• Parameter Estimation and Model Selection in Computational Biology

  2010cited by this paper
• Synthetic biology: applications come of age

  2010cited by this paper
• Stochastic bistability and bifurcation in a mesoscopic signaling system with autocatalytic kinase.

  2010cited by this paper
• Dynamical fluctuations in biochemical reactions and cycles.

  2010cited by this paper
• Intraflagellar transport particle size scales inversely with flagellar length: revisiting the balance-point length control model

  2009cited by this paper
• Synthetic biology: understanding biological design from synthetic circuits

  2009cited by this paper
• DIVERSITY-BASED, MODEL-GUIDED CONSTRUCTION OF SYNTHETIC GENE NETWORKS WITH PREDICTED FUNCTIONS

  2009cited by this paper
• Listening to the noise: random fluctuations reveal gene network parameters

  2009cited by this paper
• Investigation of Stoichiometry of T4 Bacteriophage Helicase Loader Protein (gp59)*

  2009cited by this paper
• Synthetic biology: The yin and yang of nature

  2009cited by this paper
• Robust, Tunable Biological Oscillations from Interlinked Positive and Negative Feedback Loops

  2008cited by this paper
• Chemical Biophysics: Quantitative Analysis of Cellular Systems

  2008cited by this paper
• A fast, robust, and tunable synthetic gene oscillator

  2008cited by this paper
• Transcriptional control of noise in gene expression

  2008cited by this paper
• Trajectory approach to two-state kinetics of single particles on sculpted energy landscapes.

  2008cited by this paper
• The stochastic nature of biochemical networks.

  2008cited by this paper
• Robustness analysis of cellular memory in an autoactivating positive feedback system

  2008cited by this paper
• Membrane Protein Stoichiometry Determined from the Step‐Wise Photobleaching of Dye‐Labelled Subunits

  2007cited by this paper
• Network motifs: theory and experimental approaches

  2007cited by this paper
• Measuring flux distributions for diffusion in the small-numbers limit.

  2007cited by this paper
• Counting of six pRNAs of phi29 DNA‐packaging motor with customized single‐molecule dual‐view system

  2007cited by this paper
• Subunit counting in membrane-bound proteins

  2007cited by this paper
• Stoichiometry and turnover in single, functioning membrane protein complexes

  2006cited by this paper
• Linking stochastic dynamics to population distribution: an analytical framework of gene expression.

  2006cited by this paper
• Genetic toggle switch without cooperative binding.

  2006cited by this paper
• The finite state projection algorithm for the solution of the chemical master equation.

  2006cited by this paper
• Weak pairwise correlations imply strongly correlated network states in a neural population

  2005cited by this paper
• Teaching the principles of statistical dynamics.

  2005cited by this paper
• Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations.

  2005cited by this paper
• Stochasticity in gene expression: from theories to phenotypes

  2005cited by this paper
• A proposal for using the ensemble approach to understand genetic regulatory networks.

  2004cited by this paper
• Bacterial Persistence as a Phenotypic Switch

  2004cited by this paper
• Summing up the noise in gene networks

  2004cited by this paper
• Intrinsic and external noise in an auto-regulatory genetic network.

  2004cited by this paper
• Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell.

  2003cited by this paper
• Stochastic Gene Expression in a Single Cell

  2002cited by this paper
• Regulation of noise in the expression of a single gene

  2002cited by this paper
• Synthetic gene network for entraining and amplifying cellular oscillations.

  2002cited by this paper
• Combinatorial Synthesis of Genetic Networks

  2002cited by this paper
• Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations.

  2001cited by this paper
• Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion

  2001cited by this paper
• A synthetic oscillatory network of transcriptional regulators

  2000cited by this paper
• Construction of a genetic toggle switch in Escherichia coli

  2000cited by this paper
• Frequency selectivity, multistability, and oscillations emerge from models of genetic regulatory systems.

  1998cited by this paper
• Model genetic circuits encoding autoregulatory transcription factors.

  1995cited by this paper
• Exact Stochastic Simulation of Coupled Chemical Reactions

  1977influential reference
• Stochastic Gene Expression in a Single Cell

  year unknowncited by this paper
• Molecular Systems Biology Peer Review Process File Stress-response Balance Drives the Evolution of a Network Module and Its Host Genome Transaction Report

  year unknowncited by this paper

• Modeling and Inferring Metacommunity Dynamics with Maximum Caliber

  2025cites this paper
• Inferring potential landscapes: A Schrödinger bridge approach to maximum caliber

  2024cites this paper
• Maximum entropy inference of reaction-diffusion models.

  2024cites this paper
• Entropy, irreversibility and inference at the foundations of statistical physics

  2024cites this paper
• Advances in automated and reactive flow cytometry for synthetic biotechnology.

  2023cites this paper
• The calculus of codes - From entropy, complexity, and information to life

  2023cites this paper
• Probabilistic and maximum entropy modeling of chemical reaction systems: Characteristics and comparisons to mass action kinetic models.

  2023influential citation
• MaxCal can infer models from coupled stochastic trajectories of gene expression and cell division.

  2023cites this paper
• Critical Comparison of MaxCal and Other Stochastic Modeling Approaches in Analysis of Gene Networks

  2021cites this paper
• On Conditional Tsallis Entropy

  2021cites this paper
• Use and Abuse of Entropy in Biology: A Case for Caliber

  2020cites this paper
• Inferring a network from dynamical signals at its nodes

  2020cites this paper
• The Maximum Caliber Variational Principle for Nonequilibria.

  2020cites this paper
• Optimal parameter identification of synthetic gene networks using harmony search algorithm

  2019cites this paper
• Quantitative Kinetic Models from Intravital Microcopy: A Case Study Using Hepatic Transport.

  2019cites this paper
• Screening by changes in stereotypical behavior during cell motility

  2019cites this paper
• Maximum Caliber Can Characterize Genetic Switches with Multiple Hidden Species.

  2018cites this paper
• Maximum Caliber can build and infer models of oscillation in a three-gene feedback network

  2018cites this paper
• Maximum Caliber Can Build and Infer Models of Oscillation in a Three-Gene Feedback Network.

  2018cites this paper