kboolnet: a toolkit for the verification, validation, and visualization of reaction-contingency (rxncon) models.
BMC Bioinform., December, 2023
Identification of periodic attractors in Boolean networks using a priori information.
PLoS Comput. Biol., 2022
Sperm migration in the genital tract - In silico experiments identify key factors for reproductive success.
PLoS Comput. Biol., 2021
Moonlighting proteins - an approach to systematize the concept.
Silico Biol., 2020
Chemical Reaction Networks Possess Intrinsic, Temperature-Dependent Functionality.
Entropy, 2020
Information Thermodynamics for Time Series of Signal-Response Models.
Entropy, 2019
Spatial modeling of the membrane-cytosolic interface in protein kinase signal transduction.
PLoS Comput. Biol., 2018
Differential T cell response against BK virus regulatory and structural antigens: A viral dynamics modelling approach.
,
,
,
,
,
,
,
,
,
,
PLoS Comput. Biol., 2018
Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency.
PLoS Comput. Biol., 2016
A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast <i>Saccharomyces cerevisiae</i>.
PLoS Comput. Biol., 2016
Computational Lipidomics and Lipid Bioinformatics: Filling In the Blanks.
J. Integr. Bioinform., 2016
The game theory of <i>Candida albicans</i> colonization dynamics reveals host status-responsive gene expression.
BMC Syst. Biol., 2016
SBtab: a flexible table format for data exchange in systems biology.
Bioinform., 2016
Bud-Localization of <i>CLB2</i> mRNA Can Constitute a Growth Rate Dependent Daughter Sizer.
PLoS Comput. Biol., 2015
Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks.
BMC Syst. Biol., 2015
Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems.
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
Bioinform., 2015
Yeast Mating and Image-Based Quantification of Spatial Pattern Formation.
PLoS Comput. Biol., 2014
Global dynamic optimization approach to predict activation in metabolic pathways.
BMC Syst. Biol., 2014
SensA: web-based sensitivity analysis of SBML models.
Bioinform., 2014
BooleSim: an interactive Boolean network simulator.
Bioinform., 2014
Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress.
,
,
,
,
,
,
,
,
,
,
PLoS Comput. Biol., 2013
Reaction-contingency based bipartite Boolean modelling.
BMC Syst. Biol., 2013
Biographer: web-based editing and rendering of SBGN compliant biochemical networks.
Bioinform., 2013
Propagating semantic information in biochemical network models.
BMC Bioinform., 2012
Modeling mechanistic biological networks: An advanced Boolean approach.
Bioinform., 2012
STSE: Spatio-Temporal Simulation Environment Dedicated to Biology.
BMC Bioinform., 2011
Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation.
Bioinform., 2010
Annotation and merging of SBML models with semanticSBML.
Bioinform., 2010
Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network.
BMC Syst. Biol., 2009
TIde: a software for the systematic scanning of drug targets in kinetic network models.
BMC Bioinform., 2009
Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation.
BMC Bioinform., 2009
Systems Biology - a Textbook.
Wiley, ISBN: 978-3-527-31874-2, 2009
SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool.
BMC Bioinform., 2008
Cell Size at S Phase Initiation: An Emergent Property of the G<sub>1</sub>/S Network.
PLoS Comput. Biol., 2007
SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.
Bioinform., 2006