Categories

• papers 23
• misc 4
• home 1
• team 4
• tools 4
• blog 1
• news 12
• research 4

papers

• 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

misc

• Research
• Join
• Dynamics of Living Systems Lab
• About

home

• Dynamics of Living Systems Lab

team

• Giacomo Fabrini
• Marta Sadlej
• Pierre de Metz
• Fabian Fröhlich

tools

• pyPESTO
• Fides
• AMICI
• PEtab

blog

• Hello World

news

• Giacomo joins the group
• We're Hiring (PostDoc, closed)
• Marta joins the group
• We're Hiring (PhD, closed)
• Conference Talk
• Symposium Talk
• We're Hiring (PostDoc, closed)
• Workshop Talk
• We're Hiring (PhD, closed)
• Symposium Talk
• Conference Talk
• We're Hiring (PostDoc, closed)

research

• Pathways and Systems Dynamics
• Software for Mathematical Modeling
• System State to Molecular Processes
• Structure Dynamics to Molecular Processes