Fabian Theis
Principal investigator
Single-cell genomics · Perturbation responses · Bulk omics and genetics
Topics · Methods · Modelling and inference
Networks and graphs
Work that studies networks or graphs as such, such as their structure, clustering, reconstruction from data or dynamics, including Boolean networks and graph theory. Not for a regulatory network studied only for its biology, or for neural networks in machine learning.
In Methods › Modelling and inference69 works1 person4 toolsMathematical foundations
People1
Publications69
IDTrack: Time- and Namespace-Aware Identifier Harmonization for Reproducible Workflows
A single-cell cytokine dictionary of human peripheral blood
Language may be all omics needs: Harmonizing multimodal data for omics understanding with CellHermes
GraphCompass: spatial metrics for differential analyses of cell organization across conditions
Multi-omics regulatory network inference in the presence of missing data
Tolerance of repeated toxic injuries of murine livers is associated with steatosis and inflammation
HBV rewires liver cancer signaling by altering PP2A complexes
Network reconstruction for trans acting genetic loci using multi-omics data and prior information
Squidpy: a scalable framework for spatial omics analysis
Repeated toxic injuries of murine liver are tolerated through microsteatosis and mild inflammation
Graph representation learning for single-cell biology
Cellular connectomes as arbiters of local circuit models in the cerebral cortex
Inferring Interaction Networks From Multi-Omics Data
PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells
Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway
MicroRNA as an Integral Part of Cell Communication: Regularized Target Prediction and Network Prediction
A scalable moment-closure approximation for large-scale biochemical reaction networks
Inferring catalysis in biological systems
Lactation is associated with altered metabolomic signatures in women with gestational diabetes
Computational approaches for systems metabolomics
MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma
Identifying latent dynamic components in biological systems
Gender-specific pathway differences in the human serum metabolome
The Human Blood Metabolome-Transcriptome Interface
Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data
Multi-omic signature of body weight change: results from a population-based cohort study
Decoding the regulatory network of early blood development from single-cell gene expression measurements
Network-Based Approach for Analyzing Intra- and Interfluid Metabolite Associations in Human Blood, Urine, and Saliva
Bayesian Blind Source Separation for Data with Network Structure
iVUN: interactive Visualization of Uncertain biochemical reaction Networks
Metabolite profiling reveals new insights into the regulation of serum urate in humans
Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis
Visualizing edge-edge relations in graphs
Truth-Content and Phase Transitions of Random Boolean Networks with Generic Logics
STATISTICAL METHODS FOR THE ANALYSIS OF HIGH-THROUGHPUT METABOLOMICS DATA
Mining the Unknown: A Systems Approach to Metabolite Identification Combining Genetic and Metabolic Information
Body Fat Free Mass Is Associated with the Serum Metabolite Profile in a Population-Based Study
Bayesian Fuzzy Clustering of Colored Graphs
An Ensemble Approach for Inferring Semi-quantitative Regulatory Dynamics for the Differentiation of Mouse Embryonic Stem Cells Using Prior Knowledge
Modularity Maximization and Tree Clustering: Novel Ways to Determine Effective Geographic Borders
Hierarchical Differentiation of Myeloid Progenitors Is Encoded in the Transcription Factor Network
Steady‐state robustness of qualitative gene regulation networks
Gaussian graphical modeling reveals specific lipid correlations in glioblastoma cells
Vertex centralities in input-output networks reveal the structure of modern economies
The Heckscher–Ohlin model and the network structure of international trade
miTALOS: Analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs
Huge Splicing Frequency in Human Y Chromosomal UTY Gene
Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data
Dynamic regimes of random fuzzy logic networks
Effective Parameters Determining the Information Flow in Hierarchical Biological Systems
Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation
The Structure of Borders in a Small World
Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs
Biologically meaningful update rules increase the critical connectivity of generalized Kauffman networks
Patterns of Subnet Usage Reveal Distinct Scales of Regulation in the Transcriptional Regulatory Network of Escherichia coli
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
Second-Order Source Separation Based on Prior Knowledge Realized in a Graph Model
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
Reconstruction of graphs based on random walks
Hypergraphs and Cellular Networks
Estimating Hidden Influences in Metabolic and Gene Regulatory Networks
An evolutionary and structural characterization of mammalian protein complex organization
Money Circulation, Trackable Items, and the Emergence of Universal Human Mobility Patterns
Gene regulatory networks simplified by nonlinear balanced truncation
Topological Constructions in the o–Graph Calculus
Software4
Squidpy
Spatial Single Cell Analysis in Python
612v1.8.49 d agoPython
graphcompass
GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems
39Jupyter Notebook
huCIRA
36v0.1.36 mo agoPython
geome
17v0.0.38 mo agoPython