Model selection in systems and synthetic biology

P Kirk, T Thorne, MPH Stumpf - Current opinion in biotechnology, 2013 - Elsevier
Develo** mechanistic models has become an integral aspect of systems biology, as has
the need to differentiate between alternative models. Parameterizing mathematical models …

A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation

J Liepe, P Kirk, S Filippi, T Toni, CP Barnes… - Nature protocols, 2014 - nature.com
As modeling becomes a more widespread practice in the life sciences and biomedical
sciences, researchers need reliable tools to calibrate models against ever more complex …

Scalable inference of ordinary differential equation models of biochemical processes

F Fröhlich, C Loos, J Hasenauer - Gene regulatory networks: methods and …, 2019 - Springer
Ordinary differential equation models have become a standard tool for the mechanistic
description of biochemical processes. If parameters are inferred from experimental data …

Robustness of MEK-ERK dynamics and origins of cell-to-cell variability in MAPK signaling

S Filippi, CP Barnes, PDW Kirk, T Kudo, K Kunida… - Cell reports, 2016 - cell.com
Cellular signaling processes can exhibit pronounced cell-to-cell variability in genetically
identical cells. This affects how individual cells respond differentially to the same …

A general moment expansion method for stochastic kinetic models

A Ale, P Kirk, MPH Stumpf - The Journal of chemical physics, 2013 - pubs.aip.org
Moment approximation methods are gaining increasing attention for their use in the
approximation of the stochastic kinetics of chemical reaction systems. In this paper we derive …

The signal within the noise: efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations

G Lillacci, M Khammash - Bioinformatics, 2013 - academic.oup.com
Motivation: In the noisy cellular environment, stochastic fluctuations at the molecular level
manifest as cell–cell variability at the population level that is quantifiable using high …

Simulation-based estimation of mean and standard deviation for meta-analysis via Approximate Bayesian Computation (ABC)

D Kwon, IM Reis - BMC medical research methodology, 2015 - Springer
Background When conducting a meta-analysis of a continuous outcome, estimated means
and standard deviations from the selected studies are required in order to obtain an overall …

Multi-model and network inference based on ensemble estimates: avoiding the madness of crowds

MPH Stumpf - Journal of the Royal Society Interface, 2020 - royalsocietypublishing.org
Recent progress in theoretical systems biology, applied mathematics and computational
statistics allows us to compare the performance of different candidate models at describing a …

[PDF][PDF] Therapeutic agents for the management of atherosclerosis from herbal sources: A computational approach

EA Huwait - Jour. Bas. Sci, 2024 - jbsciences.com
One of the most prevalent illnesses in the world, atherosclerosis has a significant role in the
development of hypertension, stroke, myocardial localised necrosis, and several other …

Sensitive targeted quantification of ERK phosphorylation dynamics and stoichiometry in human cells without affinity enrichment

T Shi, Y Gao, MJ Gaffrey, CD Nicora… - Analytical …, 2015 - ACS Publications
Targeted mass spectrometry is a promising technology for site-specific quantification of
posttranslational modifications. However, a major constraint is the limited sensitivity for …