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pyPESTO: A modular and scalable tool for parameter estimation for dynamic models
Multi-range ERK responses shape the proliferative trajectory of single cells following oncogene induction
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance
Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks
Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models
BioSimulators: a central registry of simulation engines and services for recommending specific tools
Combination treatment optimization using a pan-cancer pathway model
A protocol for dynamic model calibration
AMICI: high-performance sensitivity analysis for large ordinary differential equation models
PEtab—Interoperable specification of parameter estimation problems in systems biology
Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells
Efficient parameterization of large-scale dynamic models based on relative measurements
Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model
Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection
Benchmarking optimization methods for parameter estimation in large kinetic models
Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis
A Hierarchical, Data-Driven Approach to Modeling Single-Cell Populations Predicts Latent Causes of Cell-To-Cell Variability
GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models
PESTO: Parameter EStimation TOolbox
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
Parameter estimation for dynamical systems with discrete events and logical operations
Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion
CERENA: ChEmical REaction Network Analyzer - A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics
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Dynamics of Living Systems Lab
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Dynamics of Living Systems Lab
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Giacomo Fabrini
Marta Sadlej
Pierre de Metz
Fabian Fröhlich
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Pathways and Systems Dynamics
Software for Mathematical Modeling
System State to Molecular Processes
Structure Dynamics to Molecular Processes
The Francis Crick Institute
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