Fabian Theis
Principal investigator
Single-cell genomics · Perturbation responses · Bulk omics and genetics
Topics · Methods · Modelling and inference
Mechanistic modelling
Work that builds models of how a biological system works, such as differential equations, stochastic reaction networks or logical models, and fits or analyses them, for example by parameter estimation. Not for models learned from data alone.
In Methods › Modelling and inference65 works1 person1 toolMathematical foundations
People1
Publications65
RegVelo: Gene-regulatory-informed dynamics of single cells
Pseudodynamics+: Reconstructing Population Dynamics from Time-Resolved Single Cell Landscapes with Physics Informed Neural Networks
MISATO: machine learning dataset of protein–ligand complexes for structure-based drug discovery
Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells
Progressive disruption of hematopoietic architecture from clonal hematopoiesis to MDS
Toward modeling metabolic state from single-cell transcriptomics
RNA velocity—current challenges and future perspectives
Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines
Inferring population dynamics from single-cell RNA-sequencing time series data
Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection
Increasing Neural Stem Cell Division Asymmetry and Quiescence Are Predicted to Contribute to the Age-Related Decline in Neurogenesis
Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model
Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data
Data Driven Computational Modeling of Hematopoiesis in Myelodysplastic Syndromes Unveils Differences in Hematopoietic Stem Cell Kinetics Compared to Age-Matched Healthy Controls
Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering
Model Based Targeting of IL-6-Induced Inflammatory Responses in Cultured Primary Hepatocytes to Improve Application of the JAK Inhibitor Ruxolitinib
A scalable moment-closure approximation for large-scale biochemical reaction networks
Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems
cgCorrect: a method to correct for confounding cell–cell variation due to cell growth in single-cell transcriptomics
Parallelization and High-Performance Computing Enables Automated Statistical Inference of Multi-scale Models
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
Parameter estimation for dynamical systems with discrete events and logical operations
Large-scale modeling of cancer signaling: Mechanistic modeling meets Big Data
Inferring catalysis in biological systems
Analysis of Cell Lineage Trees by Exact Bayesian Inference Identifies Negative Autoregulation of Nanog in Mouse Embryonic Stem Cells
Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints
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
Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions
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.
Bayesian Model Selection Methods and Their Application to Biological ODE Systems
Identifying latent dynamic components in biological systems
Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems
Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data
Data-Driven Modelling of Biological Multi-Scale Processes
Opposing effects of allogrooming on disease transmission in ant societies
Decoding the regulatory network of early blood development from single-cell gene expression measurements
ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics
miR-335 promotes mesendodermal lineage segregation and shapes a transcription factor gradient in the endoderm
High-dimensional Bayesian parameter estimation: Case study for a model of JAK2/STAT5 signaling
iVUN: interactive Visualization of Uncertain biochemical reaction Networks
Lessons Learned from Quantitative Dynamical Modeling in Systems Biology
Method of conditional moments (MCM) for the Chemical Master Equation
Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis
Sharpening of expression domains induced by transcription and microRNA regulationwithin a spatio-temporal model of mid-hindbrain boundary formation
A Vine-copula Based Adaptive MCMC Sampler for Efficient Inference of Dynamical Systems
Truth-Content and Phase Transitions of Random Boolean Networks with Generic Logics
Bayesian model selection validates a biokinetic model for zirconium processing in humans
Multi‐scale modeling of GMP differentiation based on single‐cell genealogies
Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies
Stability and Multiattractor Dynamics of a Toggle Switch Based on a Two-Stage Model of Stochastic Gene Expression
Systematic Complexity Reduction of Signaling Models and Application to a CD95 Signaling Model for Apoptosis
An Ensemble Approach for Inferring Semi-quantitative Regulatory Dynamics for the Differentiation of Mouse Embryonic Stem Cells Using Prior Knowledge
Hierarchical Differentiation of Myeloid Progenitors Is Encoded in the Transcription Factor Network
Steady‐state robustness of qualitative gene regulation networks
Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets
Effective Parameters Determining the Information Flow in Hierarchical Biological Systems
Biologically meaningful update rules increase the critical connectivity of generalized Kauffman networks
Theoretical Analysis of Time-to-Peak Responses in Biological Reaction Networks
Odefy - From discrete to continuous models
Robust Stability Analysis and Design Under Consideration of Multiple Feedback Loops of the Tryptophan Regulatory Network of Escherichia coli
From Binary to Multivalued to Continuous Models: The lac Operon as a Case Study
Spatial Analysis of Expression Patterns Predicts Genetic Interactions at the Mid-Hindbrain Boundary
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling
Gene regulatory networks simplified by nonlinear balanced truncation
Software1
pseudodynamics
Dynamic models for single-cell RNA-seq time series.
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