Fabian Theis
Principal investigator
Single-cell genomics · Perturbation responses · Bulk omics and genetics
Mathematical foundations
Placeholder summary about the lab's work on signal separation, mechanistic models, networks and statistical inference.
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The theme
Theme 08
Placeholder narrative. This paragraph stands in for the description of the lab’s mathematical work, from component analysis and blind source separation to mechanistic models of biological systems, networks and statistical inference. The lab writes the real text before launch.
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People1
Publications272
272 works tagged with these topics since 2002
Rectangle: robust and scalable multiscale deconvolution informed by single-cell RNA sequencing data
NetworkVI: Biologically Guided Variational Inference for Interpretable Multimodal Single-Cell Integration and Discovery
RegVelo: Gene-regulatory-informed dynamics of single cells
UniversalEPI: robust prediction of cell type-specific and differential chromatin interactions from DNA sequence and chromatin accessibility
TarDis: Achieving robust and structured disentanglement of multiple covariates
Continuous multi-omics pathway enrichment analysis resolves hidden functional heterogeneity
IDTrack: Time- and Namespace-Aware Identifier Harmonization for Reproducible Workflows
CellRank: consistent and data view agnostic fate mapping for single-cell genomics
A single-cell cytokine dictionary of human peripheral blood
Pseudodynamics+: Reconstructing Population Dynamics from Time-Resolved Single Cell Landscapes with Physics Informed Neural Networks
Language may be all omics needs: Harmonizing multimodal data for omics understanding with CellHermes
Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data
Automated evaluation of single-cell reference atlas mappings enables the identification of disease-associated cell states
Causal machine learning for single-cell genomics
Disentangling cellular heterogeneity into interpretable biological factors through structured latent representations
GraphCompass: spatial metrics for differential analyses of cell organization across conditions
CellRank 2: unified fate mapping in multiview single-cell data
MISATO: machine learning dataset of protein–ligand complexes for structure-based drug discovery
longmixr: a tool for robust clustering of high-dimensional cross-sectional and longitudinal variables of mixed data types
Reconstructing disease dynamics for mechanistic insights and clinical benefit
Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells
Identification of cell types, states and programs by learning gene set representations
Multi-omics regulatory network inference in the presence of missing data
Progressive disruption of hematopoietic architecture from clonal hematopoiesis to MDS
Unified fate mapping in multiview single-cell 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
Modeling Single-Cell Dynamics Using Unbalanced Parameterized Monge Maps
Toward modeling metabolic state from single-cell transcriptomics
A Python library for probabilistic analysis of single-cell omics data
Squidpy: a scalable framework for spatial omics analysis
CellRank for directed single-cell fate mapping
Repeated toxic injuries of murine liver are tolerated through microsteatosis and mild inflammation
Graph representation learning for single-cell biology
scCODA is a Bayesian model for compositional single-cell data analysis
scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies
Group Testing for SARS-CoV-2 Allows for Up to 10-Fold Efficiency Increase Across Realistic Scenarios and Testing Strategies
RNA velocity—current challenges and future perspectives
AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution
Cellular connectomes as arbiters of local circuit models in the cerebral cortex
Comparison of genome-wide gene expression profiling by RNA Sequencing versus microarray in bronchial biopsies of COPD patients before and after inhaled corticosteroid treatment: does it provide new insights?
Deep Learning-based Propensity Scores for Confounding Control in Comparative Effectiveness Research
Learning interpretable latent autoencoder representations with annotations of feature sets
Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data
Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines
DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning
MPRAnalyze: statistical framework for massively parallel reporter assays
Faculty Opinions recommendation of Deep generative modeling for single-cell transcriptomics.
Inferring Interaction Networks From Multi-Omics Data
Inferring population dynamics from single-cell RNA-sequencing time series data
A strategy for high‐dimensional multivariable analysis classifies childhood asthma phenotypes from genetic, immunological, and environmental factors
PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells
Single-cell RNA-seq denoising using a deep count autoencoder
A test metric for assessing single-cell RNA-seq batch correction
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
Impulse model-based differential expression analysis of time course sequencing data
Lineage marker synchrony in hematopoietic genealogies refutes the PU.1/GATA1 toggle switch paradigm
Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering
Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway
netReg: network-regularized linear models for biological association studies
Model Based Targeting of IL-6-Induced Inflammatory Responses in Cultured Primary Hepatocytes to Improve Application of the JAK Inhibitor Ruxolitinib
pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms
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
Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems
A BaSiC tool for background and shading correction of optical microscopy images
Model-based branching point detection in single-cell data by K-branches clustering
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
Correcting Classifiers for Sample Selection Bias in Two-Phase Case-Control Studies
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
Diffusion pseudotime robustly reconstructs lineage branching
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
Lactation is associated with altered metabolomic signatures in women with gestational diabetes
Computational approaches for systems metabolomics
MEMO: multi-experiment mixture model analysis of censored data
Unbiased Prediction and Feature Selection in High-Dimensional Survival Regression
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.
MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma
destiny: diffusion maps for large-scale single-cell data in R
Bayesian Model Selection Methods and Their Application to Biological ODE Systems
Identifying latent dynamic components in biological systems
Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy
Separation of Uncorrelated Stationary time series using Autocovariance Matrices
Gender-specific pathway differences in the human serum metabolome
Model selection using limiting distributions of second-order blind source separation algorithms
Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems
The Human Blood Metabolome-Transcriptome Interface
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
Diffusion maps for high-dimensional single-cell analysis of differentiation data
Anatomic-landmark detection using graphical context modelling
Multi-omic signature of body weight change: results from a population-based cohort study
An adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson’s rule
Decoding the regulatory network of early blood development from single-cell gene expression measurements
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
An Affine Equivariant Robust Second-Order BSS Method
Approximate Bayesian Computation for Stochastic Single-Cell Time-Lapse Data Using Multivariate Test Statistics
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
RAMONA: a Web application for gene set analysis on multilevel omics data
Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes
MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data
ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics
Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data
miR-335 promotes mesendodermal lineage segregation and shapes a transcription factor gradient in the endoderm
Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles
Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More
High-dimensional Bayesian parameter estimation: Case study for a model of JAK2/STAT5 signaling
Dependent component analysis
iVUN: interactive Visualization of Uncertain biochemical reaction Networks
Lessons Learned from Quantitative Dynamical Modeling in Systems Biology
A modular framework for gene set analysis integrating multilevel omics data
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
Metabolite profiling reveals new insights into the regulation of serum urate in humans
Sharpening of expression domains induced by transcription and microRNA regulationwithin a spatio-temporal model of mid-hindbrain boundary formation
Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis
A Vine-copula Based Adaptive MCMC Sampler for Efficient Inference of Dynamical Systems
Rejoinder
Joining forces of Bayesian and frequentist methodology: a study for inference in the presence of non-identifiability
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
Uniqueness of linear factorizations into independent subspaces
Mining the Unknown: A Systems Approach to Metabolite Identification Combining Genetic and Metabolic Information
A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst
Bayesian model selection validates a biokinetic model for zirconium processing in humans
ICA over finite fields—Separability and algorithms
The signal separation evaluation campaign (2007–2010): Achievements and remaining challenges
Bayesian Independent Component Analysis Recovers Pathway Signatures from Blood Metabolomics Data
Multi‐scale modeling of GMP differentiation based on single‐cell genealogies
Body Fat Free Mass Is Associated with the Serum Metabolite Profile in a Population-Based Study
On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies
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
Joint Diagonalization of Several Scatter Matrices for ICA
To Infinity and Beyond: On ICA over Hilbert Spaces
Bayesian Inference of Latent Causes in Gene Regulatory Dynamics
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
Uniqueness of Non-Gaussianity-Based Dimension Reduction
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
Complex Principal Component and Correlation Structure of 16 Yeast Genomic Variables
miTALOS: Analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs
Huge Splicing Frequency in Human Y Chromosomal UTY Gene
Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets
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
Colored Subspace Analysis: Dimension Reduction Based on a Signal's Autocorrelation Structure
Theoretical Analysis of Time-to-Peak Responses in Biological Reaction Networks
Odefy - From discrete to continuous models
The a d coefficient as a descriptive measure of the within‐group agreement of ratings
Robust Stability Analysis and Design Under Consideration of Multiple Feedback Loops of the Tryptophan Regulatory Network of Escherichia coli
The 2010 Signal Separation Evaluation Campaign (SiSEC2010): Audio Source Separation
The 2010 Signal Separation Evaluation Campaign (SiSEC2010): Biomedical Source Separation
Information-Theoretic Model Selection for Independent Components
Second Order Subspace Analysis and Simple Decompositions
Second-Order Source Separation Based on Prior Knowledge Realized in a Graph Model
Robust Second-Order Source Separation Identifies Experimental Responses in Biomedical Imaging
ICA over Finite Fields
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
ICA, kernel methods and nonnegativity: New paradigms for dynamical component analysis of fMRI data
Hypergraphs and Cellular Networks
Blind Source Separation Techniques for the Decomposition of Multiply Labeled Fluorescence Images
Blind Source Separation Techniques For The Decomposition Of Multiply Labeled Fluorescence Images
Hierarchical Extraction of Independent Subspaces of Unknown Dimensions
Soft Dimension Reduction for ICA by Joint Diagonalization on the Stiefel Manifold
Estimating Hidden Influences in Metabolic and Gene Regulatory Networks
Blind Decomposition of Spectral Imaging Microscopy: A Study on Artificial and Real Test Data
An evolutionary and structural characterization of mammalian protein complex organization
Money Circulation, Trackable Items, and the Emergence of Universal Human Mobility Patterns
Knowledge-based gene expression classification via matrix factorization
Hybridizing sparse component analysis with genetic algorithms for microarray analysis
Gene regulatory networks simplified by nonlinear balanced truncation
Analyzing M-CSF dependent monocyte/macrophage differentiation: Expression modes and meta-modes derived from an independent component analysis
Joint low-rank approximation for extracting non-Gaussian subspaces
How to extract marker genes from microarray data sets
Sparse Nonnegative Matrix Factorization with Genetic Algorithms for Microarray Analysis
A bilinear algorithm for sparse representations
Sparse Component Analysis: a New Tool for Data Mining
Colored Subspace Analysis
Pivot Selection Strategies in Jacobi Joint Block-Diagonalization
Identifiability Conditions and Subspace Clustering in Sparse BSS
Independent Subspace Analysis Is Unique, Given Irreducibility
Blind Matrix Decomposition Techniques to Identify Marker Genes from Microarrays
Blind Matrix Decomposition Via Genetic Optimization of Sparseness and Nonnegativity Constraints
Exploiting Blind Matrix Decomposition Techniques to Identify Diagnostic Marker Genes
Statistical Analysis of Sample-Size Effects in ICA
Robust Sparse Component Analysis Based on a Generalized Hough Transform
Denoising using local projective subspace methods
On the use of simulated annealing to automatically assign decorrelated components in second-order blind source separation
Blind source separation based on self-organizing neural network
On the use of sparse signal decomposition in the analysis of multi-channel surface electromyograms
Median-based clustering for underdetermined blind signal processing
Separation of water artifacts in 2D NOESY protein spectra using congruent matrix pencils
Optimization Algorithms for Sparse Representations and Applications
Uniqueness of Non-Gaussian Subspace Analysis
Estimating Non-Gaussian Subspaces by Characteristic Functions
Sparse Nonnegative Matrix Factorization Applied to Microarray Data Sets
Region of Interest Based Independent Component Analysis
On the use of joint diagonalization in blind signal processing
New Riemannian metrics for speeding-up the convergence of over- and underdetermined ICA
Sparse Component Analysis and Blind Source Separation of Underdetermined Mixtures
On model identifiability in analytic postnonlinear ICA
A Hybridization of Simulated Annealing and Local PCA for Automatic Component Assignment Within ICA
Extended Sparse Nonnegative Matrix Factorization
Functional MRI Analysis by a Novel Spatiotemporal ICA Algorithm
Bispectrum-Based Statistical Tests for VAD
Hybridizing Sparse Component Analysis with Genetic Algorithms for Blind Source Separation
An algorithm for automatic assignment of artifact-related independent components in biomedical signal analysis
Blind signal separation into groups of dependent signals using joint block diagonalization
A New Concept for Separability Problems in Blind Source Separation
Uniqueness of complex and multidimensional independent component analysis
Tree-dependent and topographic independent component analysis for fMRI analysis
A geometric algorithm for overcomplete linear ICA
Denoising Using Local ICA and a Generalized Eigendecomposition with Time-Delayed Signals
Blind Source Separation of Linear Mixtures with Singular Matrices
Postnonlinear Overcomplete Blind Source Separation Using Sparse Sources
Second-Order Blind Source Separation Based on Multi-dimensional Autocovariances
Spatial ICA of fMRI data in time windows
Blind source recovery: algorithm comparison and fusion
Blind source separation and sparse component analysis of overcomplete mixtures
Clustering of dependent components: a new paradigm for fMRI signal detection
Kernel-PCA denoising of artifact-free protein NMR spectra
Denoising using local ICA and kernel-PCA
Postnonlinear blind source separation via linearization identification
3D spatial analysis of fMRI data: a comparison of ICA and GLM analysis on a word perception task
Blind Sensor Characteristics Estimation in a Multi-Sensor Network Applied to fMRI Analysis
Linear Geometric ICA: Fundamentals and Algorithms
An improved geometric overcomplete blind source separation algorithm
A Generalized Eigendecomposition Approach using Matrix Pencils to remove artefacts from 2D NMR Spectra
Generalizing Geometric ICA to Nonlinear Settings
An Adaptive Approach to Blind Source Separation Using a Self-Organzing Map and a Neural Gas
New Geometric ICA Approach for Blind Source Separation
Adaptive signal analysis of immunological data
A new ica method based on a lattice of the observation space
SOMICA and geometric ICA
Local features in biomedical image clusters extracted with independent component analysis
SOMICA - an application of self-organizing maps to geometric independent component analysis
Removing water artefacts from 2D protein NMR spectra using GEVD with congruent matrix pencils
Mathematics in independent component analysis
Topological Constructions in the o–Graph Calculus
Overcomplete ICA with a Geometric Algorithm
Software18
Squidpy
Spatial Single Cell Analysis in Python
612v1.8.49 d agoPython
CellRank
CellRank: dynamics from multi-view single-cell data
459v2.3.352 d agoPython
scCODA
A Bayesian model for compositional single-cell data analysis
205v0.1.94 y agoJupyter Notebook
kBET
An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
181First_minor7 y agoHTML
destiny
R package for single cell and other data analysis using diffusion maps
114R
DRVI
Unsupervised Deep Disentangled Representation of Single-Cell Omics
83v0.2.824 d agoPython
AutoGeneS
64Jupyter Notebook
pseudodynamics
Dynamic models for single-cell RNA-seq time series.
40Jupyter Notebook
graphcompass
GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems
39Jupyter Notebook
huCIRA
36v0.1.36 mo agoPython
batchglm
Fit generalized linear models in python.
28v0.1.08 y agoPython
LabCompass
28Python
scRatio
18Jupyter Notebook
geome
17v0.0.38 mo agoPython
greatpy
GREAT algorithm in Python
170.1.04 y agoJupyter Notebook
superexacttestpy
Python implementation of the SuperExactTest package
100.1.04 y agoJupyter Notebook
deconvATAC
Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data
6Jupyter Notebook
kbranches
Finding branching events and tips in single cell differentiation trajectories
6R