Quantifying the propagation of parametric uncertainty on flux balance analysis
Flux balance analysis (FBA) and associated techniques operating on stoichiometric genome-
scale metabolic models play a central role in quantifying metabolic flows and constraining …
scale metabolic models play a central role in quantifying metabolic flows and constraining …
Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks
Dynamical models in the form of systems of ordinary differential equations have become a
standard tool in systems biology. Many parameters of such models are usually unknown and …
standard tool in systems biology. Many parameters of such models are usually unknown and …
PCA-based synthetic sensitivity coefficients for chemical reaction network in cancer
Chemical reaction networks are powerful tools for modeling cell signaling and its disruptions
in diseases like cancer. Realistic chemical reaction networks involve hundreds of proteins …
in diseases like cancer. Realistic chemical reaction networks involve hundreds of proteins …
Identification of conserved moieties in metabolic networks by graph theoretical analysis of atom transition networks
Conserved moieties are groups of atoms that remain intact in all reactions of a metabolic
network. Identification of conserved moieties gives insight into the structure and function of …
network. Identification of conserved moieties gives insight into the structure and function of …
Computational quantification of global effects induced by mutations and drugs in signaling networks of colorectal cancer cells
Colorectal cancer (CRC) is one of the most deadly and commonly diagnosed tumors
worldwide. Several genes are involved in its development and progression. The most …
worldwide. Several genes are involved in its development and progression. The most …
Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm
Stochasticity from gene expression in single cells is known to drive metabolic heterogeneity
at the level of cellular populations, which is understood to have important consequences for …
at the level of cellular populations, which is understood to have important consequences for …
Benchmarking methods for computing local sensitivities in ordinary differential equation models at dynamic and steady states
Estimating parameters of dynamic models from experimental data is a challenging, and
often computationally-demanding task. It requires a large number of model simulations and …
often computationally-demanding task. It requires a large number of model simulations and …
Thermodynamic and stoichiometric laws ruling the fates of growing systems
We delve into growing open chemical reaction systems (CRSs) characterized by
autocatalytic reactions within a variable volume, which changes in response to these …
autocatalytic reactions within a variable volume, which changes in response to these …
Gain and loss of function mutations in biological chemical reaction networks: a mathematical model with application to colorectal cancer cells
This paper studies a system of Ordinary Differential Equations modeling a chemical reaction
network and derives from it a simulation tool mimicking Loss of Function and Gain of …
network and derives from it a simulation tool mimicking Loss of Function and Gain of …
A UHPLC-QE-MS-based metabolomics approach for the evaluation of fermented lipase by an engineered Escherichia coli
J Zhang, Y Zhang, W Luo, Z Wang, P Lv… - Preparative …, 2024 - Taylor & Francis
Using an engineered Escherichia coli to produce lipase and can easily achieve high-level
expression. The investigation of biochemical processes during lipase fermentation …
expression. The investigation of biochemical processes during lipase fermentation …