List of works by Jan Hasenauer

A Hierarchical, Data-Driven Approach to Modeling Single-Cell Populations Predicts Latent Causes of Cell-To-Cell Variability

scientific article published on 02 May 2018

A maximum likelihood estimator for parameter distributions in heterogeneous cell populations

article by Jan Hasenauer et al published May 2010 in Procedia Computer Science

A protocol for dynamic model calibration

scientific article published on 08 September 2021

A scalable moment-closure approximation for large-scale biochemical reaction networks

scientific article published on July 2017

A visual analytics approach for models of heterogeneous cell populations

scientific article

AMICI: high-performance sensitivity analysis for large ordinary differential equation models

scientific article published in 2021

An adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson’s rule

Analysis and simulation of division- and label-structured population models : a new tool to analyze proliferation assays

scientific article published on 20 October 2012

Analysis of CFSE time-series data using division-, age- and label-structured population models

scientific article

Analysis of heterogeneous cell populations: A density-based modeling and identification framework

article

Approximate Bayesian Computation for Stochastic Single-Cell Time-Lapse Data Using Multivariate Test Statistics

Approximative classification of regions in parameter spaces of nonlinear ODEs yielding different qualitative behavior

AsthmaMap: an interactive knowledge repository for mechanisms of asthma

scientific article published on 09 December 2020

Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

scientific article published on 17 July 2020

Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering.

scientific article published in July 2018

Benchmark Problems for Dynamic Modeling of Intracellular Processes

scientific article published on 01 September 2019

Benchmarking optimization methods for parameter estimation in large kinetic models.

scientific article published in March 2019

Beyond pseudotime: Following T-cell maturation in single-cell RNAseq time series

scholarly article published 14 November 2017

CERENA: ChEmical REaction Network Analyzer--A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics

scientific article

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

scientific article published on 05 May 2020

COVID-19 outbreak in Wuhan demonstrates the limitations of publicly available case numbers for epidemiological modelling.

scientific article published on 23 April 2020

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms ⬇️

journal article from 'Molecular Systems Biology' published in 2021

Cell differentiation modeled via a coupled two-switch regulatory network

scientific article published on December 2010

Characterization of Rare, Dormant, and Therapy-Resistant Cells in Acute Lymphoblastic Leukemia

scientific article published on 18 November 2016

Closing the gap between formats for storing layout information in systems biology

scientific article published on 21 February 2020

Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions

scientific article

Community-driven roadmap for integrated disease maps.

scientific article published on 23 April 2018

Comparison of null models for combination drug therapy reveals Hand model as biochemically most plausible

scientific article published on 28 February 2019

Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems

scientific article

Computation of the posterior entropy in a Bayesian framework for parameter estimation in biological networks

Continuous analogue to iterative optimization for PDE-constrained inverse problems

scientific article published on 10 July 2018

Convex Optimization

article in Encyclopedia of Systems Biology 2013 edition

Correction to: Determining the effects of trastuzumab, cetuximab and afatinib by phosphoprotein, gene expression and phenotypic analysis in gastric cancer cell lines

scientific article published on 23 November 2020

Data-Driven Modelling of Biological Multi-Scale Processes

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

scientific article

Density-based modeling and identification of biochemical networks in cell populations

Determinants of robustness in spindle assembly checkpoint signalling

scientific article

Determining the effects of trastuzumab, cetuximab and afatinib by phosphoprotein, gene expression and phenotypic analysis in gastric cancer cell lines

scientific article published on 28 October 2020

Domain Model Explains Propagation Dynamics and Stability of Histone H3K27 and H3K36 Methylation Landscapes

scientific article published on 01 January 2020

Dominant negative effects of tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) receptor 4 on TRAIL receptor 1 signaling by formation of heteromeric complexes

scientific article published on 24 April 2014

Dynamical optimization using reduced order models: A method to guarantee performance

Effects of trastuzumab and afatinib on kinase activity in gastric cancer cell lines.

scientific article published on 11 January 2018

Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model

scientific article published on 28 November 2018

Efficient exact inference for dynamical systems with noisy measurements using sequential approximate Bayesian computation

scientific article published on 01 July 2020

Efficient gradient-based parameter estimation for dynamic models using qualitative data

scientific article published in 2021

Efficient parameterization of large-scale dynamic models based on relative measurements

scientific article published on 01 January 2020

Erratum: Publisher Correction: Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection

scientific article published on 07 March 2019

Evaluation of epidermal growth factor receptor signaling effects in gastric cancer cell lines by detailed motility-focused phenotypic characterization linked with molecular analysis

scientific article published on 13 December 2017

Feasibility

scientific article published in 2013

GenSSI 2.0: Multi-experiment structural identifiability analysis of SBML models.

scientific article published on 30 November 2017

Global Uncertainty Analysis for a Model of TNF-Induced NF-κB Signalling

Guaranteed Steady-State Bounds for Uncertain Chemical Processes

Guaranteed steady state bounds for uncertain (bio-)chemical processes using infeasibility certificates

Hierarchical optimization for the efficient parametrization of ODE models

scientific article published on 01 December 2018

High-dimensional Bayesian parameter estimation: case study for a model of JAK2/STAT5 signaling

scientific article published on 16 April 2013

Identifiability analysis for models of the translation kinetics after mRNA transfection

scientific article published in 2022

Identification of models of heterogeneous cell populations from population snapshot data

scientific article

Increasing Neural Stem Cell Division Asymmetry and Quiescence Are Predicted to Contribute to the Age-Related Decline in Neurogenesis

scientific article published on 01 December 2018

Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion

scientific article

Inference of finite mixture models and the effect of binning

scientific article published on 26 July 2019

Inferring population dynamics from single-cell RNA-sequencing time series data

scientific article published on 01 April 2019

Integration based profile likelihood calculation for PDE constrained parameter estimation problems ⬇️

article by R Boiger et al published 18 November 2016 in Inverse Problems

MEMO: multi-experiment mixture model analysis of censored data

scientific article

Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data

Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data

scientific article published on 01 December 2018

Mechanistic hierarchical population model identifies latent causes of cell-to-cell variability

Method of conditional moments (MCM) for the Chemical Master Equation: a unified framework for the method of moments and hybrid stochastic-deterministic models

scientific article

Mini-batch optimization enables training of ODE models on large-scale datasets

scientific article published in 2022

Model Falsification, Semidefinite Programming

article

Model predictive control using reduced order models: Guaranteed stability for constrained linear systems

article by Martin Löhning et al published November 2014 in Journal of Process Control

Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines

scientific article published on 02 March 2020

Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis

scientific article

Modeling of stochastic biological processes with non-polynomial propensities using non-central conditional moment equation

Multi-Experiment Nonlinear Mixed Effect Modeling of Single-Cell Translation Kinetics after Transfection

Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection

Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection.

scientific article published on 10 December 2018

Network plasticity of pluripotency transcription factors in embryonic stem cells

scientific article published on 21 September 2015

ODE constrained mixture modelling: a method for unraveling subpopulation structures and dynamics

scientific article

Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis.

scientific article published in July 2018

PESTO: Parameter EStimation TOolbox

scientific article published on 23 October 2017

PKA-RII subunit phosphorylation precedes activation by cAMP and regulates activity termination.

scientific article published on 3 April 2018

Pain modulators regulate the dynamics of PKA-RII phosphorylation in subgroups of sensory neurons

scientific article published on 4 November 2013

Parallelization and High-Performance Computing Enables Automated Statistical Inference of Multi-scale Models

scientific article published on 10 January 2017

Parameter Estimation and Identifiability of Biological Networks Using Relative Data

Parameter estimation for dynamical systems with discrete events and logical operations

scientific article published on 31 December 2016

Parameter identification, experimental design and model falsification for biological network models using semidefinite programming

scientific article

Parameterization of mechanistic models from qualitative data using an efficient optimal scaling approach

scientific article published on 21 July 2020

Quadratic Decomposition

Quantitative comparison of competing PDE models for Pomlp dynamics in fission yeast * *The authors acknowledge financial support from the Postdoctoral Fellowship Program (PFP) of the Helmholtz Zentrum Munchen

Radial Basis Function Approximations of Bayesian Parameter Posterior Densities for Uncertainty Analysis

Robust calibration of hierarchical population models for heterogeneous cell populations

scientific article published on 19 December 2019

Robust parameter estimation for dynamical systems from outlier-corrupted data

scientific article

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

scientific article (publication date: 2017)

Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation

scientific article

Steady state stability preserving nonlinear model reduction using sequential convex optimization

Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints

scientific article

Threshold-free population analysis identifies larger DRG neurons to respond stronger to NGF stimulation.

scientific article

Trajectory-based model reduction of nonlinear biochemical networks employing the observability normal form*

Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More

article by Fabian Fröhlich et al published 2014 in Lecture Notes in Computer Science

Uncertainty-aware visual analysis of biochemical reaction networks

Visualizing edge-edge relations in graphs

scholarly article published February 2013

Whither systems medicine?

scientific article published on 2 March 2018

Wound-healing growth factor, basic FGF, induces Erk1/2-dependent mechanical hyperalgesia.

scientific article published on 16 July 2013

iVUN: interactive Visualization of Uncertain biochemical reaction Networks

scientific article

pyABC: distributed, likelihood-free inference

scientific article published on 01 October 2018

yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML

scientific article published on 27 May 2021

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