Fabian Theis
Principal investigator
Single-cell genomics · Perturbation responses · Bulk omics and genetics
Topics · Methods · Modelling and inference
Statistical inference
Work that develops a statistical model, test or inference method, such as Bayesian inference, mixed models, network inference or experimental design, as a main contribution. Not for standard statistics or clustering applied to answer a biological question.
In Methods › Modelling and inference99 works1 person10 toolsMathematical foundations
People1
Publications99
NetworkVI: Biologically Guided Variational Inference for Interpretable Multimodal Single-Cell Integration and Discovery
UniversalEPI: robust prediction of cell type-specific and differential chromatin interactions from DNA sequence and chromatin accessibility
Continuous multi-omics pathway enrichment analysis resolves hidden functional heterogeneity
CellRank: consistent and data view agnostic fate mapping for single-cell genomics
Automated evaluation of single-cell reference atlas mappings enables the identification of disease-associated cell states
Causal machine learning for single-cell genomics
GraphCompass: spatial metrics for differential analyses of cell organization across conditions
CellRank 2: unified fate mapping in multiview single-cell data
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
Unified fate mapping in multiview single-cell data
Network reconstruction for trans acting genetic loci using multi-omics data and prior information
Modeling Single-Cell Dynamics Using Unbalanced Parameterized Monge Maps
A Python library for probabilistic analysis of single-cell omics data
CellRank for directed single-cell fate mapping
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
Cellular connectomes as arbiters of local circuit models in the cerebral cortex
Deep Learning-based Propensity Scores for Confounding Control in Comparative Effectiveness Research
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
A strategy for high‐dimensional multivariable analysis classifies childhood asthma phenotypes from genetic, immunological, and environmental factors
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
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
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
pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms
Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems
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
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
Computational approaches for systems metabolomics
MEMO: multi-experiment mixture model analysis of censored data
Unbiased Prediction and Feature Selection in High-Dimensional Survival Regression
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
Model selection using limiting distributions of second-order blind source separation algorithms
Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems
Data-Driven Modelling of Biological Multi-Scale Processes
Anatomic-landmark detection using graphical context modelling
An adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson’s rule
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
Approximate Bayesian Computation for Stochastic Single-Cell Time-Lapse Data Using Multivariate Test Statistics
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
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
A modular framework for gene set analysis integrating multilevel omics data
Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability 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
STATISTICAL METHODS FOR THE ANALYSIS OF HIGH-THROUGHPUT METABOLOMICS DATA
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
Bayesian Independent Component Analysis Recovers Pathway Signatures from Blood Metabolomics Data
Multi‐scale modeling of GMP differentiation based on single‐cell genealogies
On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies
Bayesian Inference of Latent Causes in Gene Regulatory Dynamics
Bayesian Fuzzy Clustering of Colored Graphs
Uniqueness of Non-Gaussianity-Based Dimension Reduction
Gaussian graphical modeling reveals specific lipid correlations in glioblastoma cells
Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data
Colored Subspace Analysis: Dimension Reduction Based on a Signal's Autocorrelation Structure
The a d coefficient as a descriptive measure of the within‐group agreement of ratings
Information-Theoretic Model Selection for Independent Components
Median-based clustering for underdetermined blind signal processing
Estimating Non-Gaussian Subspaces by Characteristic Functions
Bispectrum-Based Statistical Tests for VAD
Software10
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
diffxpy
Differential expression analysis for single-cell RNA-seq data.
204v0.6.27 y agoPythonArchived
kBET
An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
181First_minor7 y agoHTML
batchglm
Fit generalized linear models in python.
28v0.1.08 y agoPython
LabCompass
28Python
scRatio
18Jupyter Notebook
greatpy
GREAT algorithm in Python
170.1.04 y agoJupyter Notebook
superexacttestpy
Python implementation of the SuperExactTest package
100.1.04 y agoJupyter Notebook
kbranches
Finding branching events and tips in single cell differentiation trajectories
6R