Fabian Theis
Principal investigator
Single-cell genomics · Perturbation responses · Bulk omics and genetics
Topics · Biology and medicine · Cell biology
Gene regulation
Work on how the activity of genes is controlled, such as by transcription factors, microRNAs, chromatin, DNA methylation, splicing or regulatory networks. Not for gene expression measured without asking how it is regulated.
In Biology and medicine › Cell biology127 works1 person6 tools
People1
Publications127
Plasticity of human microglia and brain perivascular macrophages in aging and Alzheimer’s disease
Multimodal temporal mapping of macrophage transcriptome remodeling during Salmonella infection
Transcriptional repression by TGIF2 coordinates neurogenic priming and neural stem cell maintenance
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
Longitudinal modality prediction learns gene regulatory patterns: insights from a single-cell competition
Single-cell atlas of the transcriptome and chromatin accessibility in the human retina
Single-cell characterization of the adult male hippocampus suggests a prominent, and cell-type specific, role for Nrgn and Sgk1 in response to a social stressor
A combinatorial transcription factor screening platform for immune cell reprogramming
Protocol for Predicting Cell Fate Responses to in Silico Perturbation using RegVelo, from Code to Agentic Platform Analysis
A multimodal cross-species comparison of pancreas development
scooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution
Disentangling Transcription Factor Programs for Direct Reprogramming with Generative Modeling
Single-cell multiome and spatial profiling reveals pancreas cell type–specific gene regulatory programs of type 1 diabetes progression
Exon-variant interplay and multi-modal evidence identify endocrine dysregulation in severe psychiatric disorders impacting excitatory neurons
UniversalEPI: a generalized attention-based deep ensemble model to accurately predict enhancer-promoter interactions across diverse cell types and conditions
TGIF2 is a major regulator of neural stem cell fate and neurogenic priming
Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids
Heterogeneity-driven phenotypic plasticity and treatment response in branched-organoid models of pancreatic ductal adenocarcinoma
Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery
Endothelial regulatory circuits control cranial neural crest migration and plasticity
Polyploidisation pleiotropically buffers ageing in hepatocytes
A liver immune rheostat regulates CD8 T cell immunity in chronic HBV infection
CellRank 2: unified fate mapping in multiview single-cell data
Quantitative characterization of cell niches in spatial atlases
Human pluripotent stem cell fate trajectories toward lung and hepatocyte progenitors
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
Probing cell identity hierarchies by fate titration and collision during direct reprogramming
Association of bronchial steroid inducible methylation quantitative trait loci with asthma and chronic obstructive pulmonary disease treatment response
Alveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation
Ketamine exerts its sustained antidepressant effects via cell-type-specific regulation of Kcnq2
Mature neutrophils and a NF-κB-to-IFN transition determine the unifying disease recovery dynamics in COVID-19
Cell-Type-Specific Impact of Glucocorticoid Receptor Activation on the Developing Brain: A Cerebral Organoid Study
Parkinson's disease motor symptoms rescue by CRISPRa‐reprogramming astrocytes into GABAergic neurons
Integration of single-cell transcriptomes and chromatin landscapes reveals regulatory programs driving pharyngeal organ development
Determinants of expression of SARS‐CoV‐2 entry‐related genes in upper and lower airways
Current Smoking Alters Gene Expression and DNA Methylation in the Nasal Epithelium of Patients with Asthma
Chronic WNT/ß-catenin signaling impairs mitochondrial function in lung epithelial cells
EpiScanpy: integrated single-cell epigenomic analysis
Epithelial cell plasticity drives endoderm formation during gastrulation
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis
Single cell trajectory analysis of human pluripotent stem cells differentiating towards lung and hepatocyte progenitors
Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis
SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues
The single-cell eQTLGen consortium
Epithelial Planar Bipolarity Emerges from Notch-Mediated Asymmetric Inhibition of Emx2
DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning
MPRAnalyze: statistical framework for massively parallel reporter assays
Longitudinal single cell transcriptomics reveals Krt8+ alveolar epithelial progenitors in lung regeneration
scSLAM-seq reveals core features of transcription dynamics in single cells
Integrated analysis of environmental and genetic influences on cord blood DNA methylation in new-borns
Dynamic modelling of an ACADS genotype in fatty acid oxidation – Application of cellular models for the analysis of common genetic variants
Common patterns of gene regulation associated with Cesarean section and the development of islet autoimmunity – indications of immune cell activation
Deep learning: new computational modelling techniques for genomics
IRE1α-XBP1s pathway promotes prostate cancer by activating c-MYC signaling
WHAT SHAPES THE CHILD'S EPIGENOME: GENOTYPE, PRENATAL ENVIRONMENT OR BOTH?
GENOTYPE, PRENATAL ENVIRONMENT OR BOTH–WHAT SHAPES THE NEWBORN'S EPIGENOME?
Metabolic regulation of pluripotency and germ cell fate through α‐ketoglutarate
Lineage marker synchrony in hematopoietic genealogies refutes the PU.1/GATA1 toggle switch paradigm
Inductive and Selective Effects of GSK3 and MEK Inhibition on Nanog Heterogeneity in Embryonic Stem Cells
Epigenetically Regulated Chromosome 14q32 miRNA Cluster Induces Metastasis and Predicts Poor Prognosis in Lung Adenocarcinoma Patients
Maternal whole blood cell miRNA-340 is elevated in gestational diabetes and inversely regulated by glucose and insulin
GATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency
Model Based Targeting of IL-6-Induced Inflammatory Responses in Cultured Primary Hepatocytes to Improve Application of the JAK Inhibitor Ruxolitinib
MicroRNA as an Integral Part of Cell Communication: Regularized Target Prediction and Network Prediction
Pulmonary microRNA profiles identify involvement of Creb1 and Sec14l3 in bronchial epithelial changes in allergic asthma
Analysis of Cell Lineage Trees by Exact Bayesian Inference Identifies Negative Autoregulation of Nanog in Mouse Embryonic Stem Cells
TALEN/CRISPR-mediated engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus
Abstract 1945: Identification of a miRNA/mRNA network driving non-small cell lung cancer (NSCLC) dissemination
Interleukin-4 and interferon-γ orchestrate an epithelial polarization in the airways
Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios
miTALOS v2: Analyzing Tissue Specific microRNA Function
Epigenetic germline inheritance of diet-induced obesity and insulin resistance
Pitchfork and Gprasp2 Target Smoothened to the Primary Cilium for Hedgehog Pathway Activation
MicroRNA-138 promotes acquired alkylator resistance in glioblastoma by targeting the Bcl-2-interacting mediator BIM
The global gene expression profile of the secondary transition during pancreatic development
Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions
MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma
Network plasticity of pluripotency transcription factors in embryonic stem cells
SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins
Integrative Analysis of MicroRNA and mRNA Data Reveals an Orchestrated Function of MicroRNAs in Skeletal Myocyte Differentiation in Response to TNF-α or IGF1
Transcriptional Mechanisms of Proneural Factors and REST in Regulating Neuronal Reprogramming of Astrocytes
Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data
Atrx promotes heterochromatin formation at retrotransposons
Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer
Decoding the regulatory network of early blood development from single-cell gene expression measurements
miR-23a-3p Causes Cellular Senescence by Targeting Hyaluronan Synthase 2: Possible Implication for Skin Aging
Stem-Cell-like Properties and Epithelial Plasticity Arise as Stable Traits after Transient Twist1 Activation
Proteome-wide analysis reveals an age-associated cellular phenotype of in situ aged human fibroblasts
Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain
Hypothalamic miR-103 Protects from Hyperphagic Obesity in Mice
MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression 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
Posttranscriptional Regulatory Networks: From Expression Profiling to Integrative Analysis of mRNA and MicroRNA Data
A modular framework for gene set analysis integrating multilevel omics data
The cytokine-induced microrna193b modulates ckit expression and STAT5 signaling
Myeloid lineage choice is not controlled by the PU.1 - Gata1 switch
The human transcriptome is enriched for miRNA-binding sites located in cooperativity-permitting distance
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 Unilateral Negative Feedback Loop Between miR-200 microRNAs and Sox2/E2F3 Controls Neural Progenitor Cell-Cycle Exit and Differentiation
Multi‐scale modeling of GMP differentiation based on single‐cell genealogies
Stability and Multiattractor Dynamics of a Toggle Switch Based on a Two-Stage Model of Stochastic Gene Expression
Bayesian Inference of Latent Causes in Gene Regulatory Dynamics
PhenomiR: MicroRNAs in Human Diseases and Biological Processes
An Ensemble Approach for Inferring Semi-quantitative Regulatory Dynamics for the Differentiation of Mouse Embryonic Stem Cells Using Prior Knowledge
MicroRNAs coordinately regulate protein complexes
Hierarchical Differentiation of Myeloid Progenitors Is Encoded in the Transcription Factor Network
Steady‐state robustness of qualitative gene regulation networks
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
MicroRNA Loss Enhances Learning and Memory in Mice
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
Tissue-Specific Target Analysis of Disease-Associated MicroRNAs in Human Signaling Pathways
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
Intronic microRNAs support their host genes by mediating synergistic and antagonistic regulatory effects
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
Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine
Estimating Hidden Influences in Metabolic and Gene Regulatory Networks
Gene regulatory networks simplified by nonlinear balanced truncation
Software6
regvelo
inferring regulatory cellular dynamics
200v0.4.210 mo agoPython
mubind
Learning motif contributions to cell transitions using sequence features and graphs.
270.2.12 y agoPython
cellink
Scalable framework for integrating single-cell omics with genetic data using AnnData.
25Python
greatpy
GREAT algorithm in Python
170.1.04 y agoJupyter Notebook
bindome
Assembling of biomolecule binding data (TF/RNA) from genomics databases for ML-downstream.
3pre-release4 y agoPython
transcription_factor_activity
1Jupyter Notebook