Jörg Stelling

BMC Bioinform., December, 2023

Assumptions on decision making and environment can yield multiple steady states in microbial community models.

[BibT_eX]

[DOI]

Axel Theorell

BMC Bioinform., December, 2023

2022

Metabolic Networks, Microbial Consortia, and Analogies to Smart Grids.

[BibT_eX]

[DOI]

Axel Theorell

Proc. IEEE, 2022

Systems and Synthetic Biology.

[BibT_eX]

[DOI]

Mustafa Hani Khammash

Proc. IEEE, 2022

PolyRound: polytope rounding for random sampling in metabolic networks.

[BibT_eX]

[DOI]

Bioinform., 2022

2021

Probabilistic thermodynamic analysis of metabolic networks.

[BibT_eX]

[DOI]

Mattia G. Gollub

Bioinform., 2021

Population Design for Synthetic Gene Circuits.

[BibT_eX]

[DOI]

Baptiste Turpin

Eline Y. Bijman

Proceedings of the Computational Methods in Systems Biology, 2021

Microbial Community Decision Making Models in Batch and Chemostat Cultures.

[BibT_eX]

[DOI]

Axel Theorell

Proceedings of the Computational Methods in Systems Biology, 2021

2020

TopoFilter: a MATLAB package for mechanistic model identification in systems biology.

[BibT_eX]

[DOI]

BMC Bioinform., 2020

BioSwitch: a tool for the detection of bistability and multi-steady state behaviour in signalling and gene regulatory networks.

[BibT_eX]

[DOI]

Pencho Yordanov

Irene Otero-Muras

Bioinform., 2020

2017

Chemical Reaction Network Theory elucidates sources of multistability in interferon signaling.

[BibT_eX]

[DOI]

Irene Otero-Muras

Pencho Yordanov

PLoS Comput. Biol., 2017

2016

Modular Parameter Identification of Biomolecular Networks.

[BibT_eX]

[DOI]

Moritz Lang

Vítor A. P. Martins dos Santos

SIAM J. Sci. Comput., 2016

Efficient Reconstruction of Predictive Consensus Metabolic Network Models.

[BibT_eX]

[DOI]

Ruben G. A. van Heck

Mathias Ganter

PLoS Comput. Biol., 2016

2015

Deterministic Description of Biochemical Networks.

[BibT_eX]

[DOI]

Proceedings of the Encyclopedia of Systems and Control, 2015

Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks.

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2015

2014

A method for inverse bifurcation of biochemical switches: inferring parameters from dose response curves.

[BibT_eX]

[DOI]

Irene Otero-Muras

Pencho Yordanov

Adrián López García de Lomana

BMC Syst. Biol., 2014

Topological augmentation to infer hidden processes in biological systems.

[BibT_eX]

[DOI]

Mikael Sunnåker

Elías Zamora-Sillero

Bioinform., 2014

Accurate cell segmentation in microscopy images using membrane patterns.

[BibT_eX]

[DOI]

Bioinform., 2014

2013

Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits.

[BibT_eX]

[DOI]

BMC Syst. Biol., 2013

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks.

[BibT_eX]

[DOI]

Bioinform., 2013

Near-optimal experimental design for model selection in systems biology.

[BibT_eX]

[DOI]

Alberto Giovanni Busetto

Bioinform., 2013

2012

System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes.

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2012

A specialized ODE integrator for the efficient computation of parameter sensitivities.

[BibT_eX]

[DOI]

BMC Syst. Biol., 2012

2011

Automatic Design of Digital Synthetic Gene Circuits.

[BibT_eX]

[DOI]

Mario A. Marchisio

PLoS Comput. Biol., 2011

Efficient characterization of high-dimensional parameter spaces for systems biology.

[BibT_eX]

[DOI]

BMC Syst. Biol., 2011

Graph-Based Decomposition of Biochemical Reaction Networks into Monotone Subsystems.

[BibT_eX]

[DOI]

Simona Constantinescu

Justin Feigelman

Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

2009

Automatic Control in Systems Biology.

[BibT_eX]

[DOI]

Proceedings of the Springer Handbook of Automation, 2009

Precise Regulation of Gene Expression Dynamics Favors Complex Promoter Architectures.

[BibT_eX]

[DOI]

Dirk Müller

PLoS Comput. Biol., 2009

Parallel Extreme Ray and Pathway Computation.

[BibT_eX]

[DOI]

Proceedings of the Parallel Processing and Applied Mathematics, 2009

Synthetic Gene Network Computational Design.

[BibT_eX]

[DOI]

Mario A. Marchisio

Proceedings of the International Symposium on Circuits and Systems (ISCAS 2009), 2009

2008

Circadian Phase Resetting via Single and Multiple Control Targets.

[BibT_eX]

[DOI]

Neda Bagheri

Francis J. Doyle III

PLoS Comput. Biol., 2008

Large-scale computation of elementary flux modes with bit pattern trees.

[BibT_eX]

[DOI]

Bioinform., 2008

Computational design of synthetic gene circuits with composable parts.

[BibT_eX]

[DOI]

Mario A. Marchisio

Bioinform., 2008

2007

Elementary flux modes - state-of-the-art implementation and scope of application.

[BibT_eX]

[DOI]

BMC Syst. Biol., 2007

Quantitative performance metrics for robustness in circadian rhythms.

[BibT_eX]

[DOI]

Neda Bagheri

Francis J. Doyle III

Bioinform., 2007

2006

Accelerating the Computation of Elementary Modes Using Pattern Trees.

[BibT_eX]

[DOI]

Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

2005

Sensitivity analysis of oscillatory (bio)chemical systems.

[BibT_eX]

[DOI]

Daniel E. Zak

Francis J. Doyle III

Comput. Chem. Eng., 2005

Optimal phase-tracking of the nonlinear circadian oscillator.

[BibT_eX]

[DOI]

Neda Bagheri

Francis J. Doyle

Proceedings of the American Control Conference, 2005

2003

FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps.

[BibT_eX]

[DOI]

Bioinform., 2003

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

[BibT_eX]

[DOI]

Bioinform., 2003

Making predictions about robustness and flexibility from metabolic network structure.

[BibT_eX]

Stefan Schuster

Steffen Klamt