GAMES: A Dynamic Model Development Workflow for Rigorous Characterization of Synthetic Genetic Systems

Reproducibility in systems biology modelling

(2021) Krishna Tiwari et al.   Molecular Systems Biology

Benchmarking of numerical integration methods for ODE models of biological systems

(2021) Philipp Städter et al.   Scientific Reports

Model-guided design of mammalian genetic programs

(2021) J. J. Muldoon et al.   Science Advances

The COMET toolkit for composing customizable genetic programs in mammalian cells

(2020) Patrick S. Donahue et al.   Nature Communications

An efficient procedure to assist in the re-parametrization of structurally unidentifiable models

(2020) D. Joubert et al.   MATHEMATICAL BIOSCIENCES

Genetic circuit design automation for yeast

(2020) Ye Chen et al.   Nature Microbiology

SINDy-PI: a robust algorithm for parallel implicit sparse identification of nonlinear dynamics

(2020) Kadierdan Kaheman et al.   PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Characterization and mitigation of gene expression burden in mammalian cells

(2020) Timothy Frei et al.   Nature Communications

Best Practices for Making Reproducible Biochemical Models

(2020) Veronica L. Porubsky et al.   Cell Systems

Reactive SINDy: Discovering governing reactions from concentration data

(2019) Moritz Hoffmann et al.   JOURNAL OF CHEMICAL PHYSICS

An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs

(2019) Jing Wui Yeoh et al.   ACS Synthetic Biology

An easy and efficient approach for testing identifiability

(2018) Clemens Kreutz   BIOINFORMATICS

Mathematical Modeling of RNA-Based Architectures for Closed Loop Control of Gene Expression

(2018) Deepak K. Agrawal et al.   ACS Synthetic Biology

Synthetic control systems for high performance gene expression in mammalian cells

(2018) Gabriele Lillacci et al.   NUCLEIC ACIDS RESEARCH

A quasi-integral controller for adaptation of genetic modules to variable ribosome demand

(2018) Hsin-Ho Huang et al.   Nature Communications

Control theory meets synthetic biology

(2016) Domitilla Del Vecchio et al.   Journal of the Royal Society Interface

On the relationship between sloppiness and identifiability

(2016) Oana-Teodora Chis et al.   MATHEMATICAL BIOSCIENCES

Complex transcriptional modulation with orthogonal and inducible dCas9 regulators

(2016) Yuchen Gao et al.   NATURE METHODS

Genetic circuit design automation

(2016) A. A. K. Nielsen et al.   SCIENCE

Driving the Model to Its Limit: Profile Likelihood Based Model Reduction

(2016) Tim Maiwald et al.   PLoS One

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems: Fig. 1.

(2015) A. Raue et al.   BIOINFORMATICS

A unified framework for estimating parameters of kinetic biological models

(2015) Syed Murtuza Baker et al.   BMC BIOINFORMATICS

Robust and efficient parameter estimation in dynamic models of biological systems

(2015) Attila Gábor et al.   BMC Systems Biology

Designing Genetic Feedback Controllers

(2015) Andreas W. K. Harris et al.   IEEE Transactions on Biomedical Circuits and Systems

Comparison of approaches for parameter identifiability analysis of biological systems

(2014) A. Raue et al.   BIOINFORMATICS

Model Reduction by Manifold Boundaries

(2014) Mark K. Transtrum et al.   PHYSICAL REVIEW LETTERS

Model selection in systems and synthetic biology

(2013) Paul Kirk et al.   CURRENT OPINION IN BIOTECHNOLOGY

Lessons Learned from Quantitative Dynamical Modeling in Systems Biology

(2013) Andreas Raue et al.   PLoS One

Convergence in parameters and predictions using computational experimental design

(2013) D. R. Hagen et al.   Interface Focus

Optimal experiment selection for parameter estimation in biological differential equation models

(2012) Mark K Transtrum et al.   BMC BIOINFORMATICS

Likelihood based observability analysis and confidence intervals for predictions of dynamic models

(2012) Clemens Kreutz et al.   BMC Systems Biology

Identifiability and observability analysis for experimental design in nonlinear dynamical models

(2011) A. Raue et al.   CHAOS

Addressing parameter identifiability by model-based experimentation

(2011) A. Raue et al.   IET Systems Biology

Sloppy models, parameter uncertainty, and the role of experimental design

(2010) Joshua F. Apgar et al.   Molecular BioSystems

Why are Nonlinear Fits to Data so Challenging?

(2010) Mark K. Transtrum et al.   PHYSICAL REVIEW LETTERS

Parameter Estimation and Model Selection in Computational Biology

(2010) Gabriele Lillacci et al.   PLoS Computational Biology

Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood

(2009) A. Raue et al.   BIOINFORMATICS

Systems biology: model based evaluation and comparison of potential explanations for given biological data

(2009) Gunnar Cedersund et al.   FEBS Journal

Systems biology: parameter estimation for biochemical models

(2009) Maksat Ashyraliyev et al.   FEBS Journal

Designing and encoding models for synthetic biology

(2009) L. Endler et al.   Journal of the Royal Society Interface

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

Dynamical modeling and multi-experiment fitting with PottersWheel

(2008) Thomas Maiwald et al.   BIOINFORMATICS