Goutsias, John

Jenkinson, Garrett

Zhong, Xiaogang

English

PubMed

Garrett Jenkinson

Xiaogang Zhong

John Goutsias

Springer - Publisher Connector

Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems

A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat Protoc

A review of algorithms and trends in kinetic model identification for chemical and biochemical systems.

A: Assessing reproducibility of a protein dynamics study using in vivo labeling and liquid chromatography tandem mass spectrometry. Anal Chem

An empirical Bayesian approach for model-based inference of cellular signaling networks.

Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics. P Natl Acad Sci USA

C: Hybrid optimization method with general switching strategy for parameter estimation.

d’AlchéBuc F: Estimating parameters and hidden variables in non-linear state-space models based on ODEs for biological networks inference. Bioinformatics

DB: Bayesian Data Analysis. 2 edition. Boca Raton, Florida: Chapman and Hall/CRC;

Emili A: Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics

FJ: Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: Insights from an identifiability analysis of an in silico network. Genome Res

Hoijtink H: The Bayes factor for inequality and about equality constrained models. Comput Stat Data An

Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science

Introduction to Stochastic Search and Optimization: Estimation, Simulation and Control.

JR: A hybrid approach for efficient and robust parameter estimation in biochemical pathways. BioSystems

JR: Parameter estimation in biochemical pathways: A comparison of global optimization methods. Genome Res

Klipp E: Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theor Biol Med Model

Klipp E: Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data. Theor Biol Med Model

Laibe C: BioModels database: An enhanced, curated and annotated resource for published quantitative kinetic models.

Monte Carlo Strategies in Scientific Computing

Müller G: Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat Biotechnol

On imposing detailed balance in complex reaction mechanisms.

On the asymptotic behaviour of posterior distributions.

PE: Mathematical and computational techniques to deduce complex biochemical reaction mechanisms. Prog Biophys Mol Bio

Probabilistic sensitivity analysis of biochemical reaction systems. J Chem Phys

Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum. Bioinf

Rabitz H: Optimal identification of biochemical reaction networks.

Reconstructing nonlinear dynamic models of gene regulation using stochastic sampling.

Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling.

Schuster S: The Regulation of Cellular Systems

Sethna JP: Universally sloppy parameter sensitivities in systems biology models.

Statistical analysis of high-density oligonucleotide arrays: a multiplicative noise model. Bioinf

Statistical Decision Theory and Bayesian Analysis. 2 edition.

Subramaniam S: Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Bio

Thermodynamic constraints in kinetic modeling: Thermodynamic-kinetic modeling in comparison to other approaches. Eng Life Sci

Thermodynamically based constraints for rate coefficients of large biochemical networks. WIREs Syst Biol Med

Thermodynamically feasible kinetic models of reaction networks.

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3248051

Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems

Abstract

Similar works

Full text

Available Versions

Springer - Publisher Connector

Springer - Publisher Connector