Fabian Theis
Principal investigator
Single-cell genomics · Perturbation responses · Bulk omics and genetics
Topics · Biology and medicine · Disease areas
Immunity and inflammation
Work on the immune system, infection and inflammatory disease, such as immune cells, cytokines, autoimmunity, allergy, asthma, chronic lung disease or inflammatory skin disease. Not for immune cells that only appear among other cell types.
In Biology and medicine › Disease areas142 works2 people2 tools
People2
Publications142
A Community-Driven Single-Cell PBMC Reference Integrating Landmark Datasets Spanning Health and Disease
Time-resolved predictability of end-of-therapy outcome and relapse after cure in Phase 3 tuberculosis trials
Multimodal discovery of a pathogenic B-cell-dependent T-cell state in multiple sclerosis
Designing antimicrobials with programmable mechanism and safety
Chemokine Landscapes of the Tumor Microenvironment
Plasticity of human microglia and brain perivascular macrophages in aging and Alzheimer’s disease
Multi-scale modeling of human tissues from spatial transcriptomics with TERRA
Multimodal temporal mapping of macrophage transcriptome remodeling during Salmonella infection
TNF alpha unmasks enteric malate aspartate shuttle dysfunction bridging Parkinson disease and intestinal inflammation
Large-scale proteomics across neurological disorders uncovers biomarker panel and targets in multiple sclerosis
A combinatorial transcription factor screening platform for immune cell reprogramming
Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers
A single-cell cytokine dictionary of human peripheral blood
DISCO-seq: 3D single-cell transcriptomics of intact biological systems
Spatial single-cell atlas reveals regional variations in healthy and diseased human lung
Toward a ToxAtlas of Carbon-Based Nanomaterials: Single-Cell RNA Sequencing Reveals Initiating Cell Circuits in Pulmonary Inflammation
Graph neural networks learn emergent tissue properties from spatial molecular profiles
Single-cell multiome and spatial profiling reveals pancreas cell type–specific gene regulatory programs of type 1 diabetes progression
Single cell decomposition of multicellular aging programs associated with impaired lung regeneration
Biologically Informed Variational Inference Enables Interpretable Cell Phenotyping and Discovery
HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma
Modulation of TCR stimulation and pifithrin-α improve the genomic safety profile of CRISPR-engineered human T cells
Mode of actions of nanomaterial-induced respiratory toxicity
An open-source framework for end-to-end analysis of electronic health record data
A liver immune rheostat regulates CD8 T cell immunity in chronic HBV infection
Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data
Machine learning integrative approaches to advance computational immunology
Shared inflammatory glial cell signature after stab wound injury, revealed by spatial, temporal, and cell-type-specific profiling of the murine cerebral cortex
Cell circuits underlying nanomaterial specific respiratory toxicology
Sfrp1 inhibits lung fibroblast invasion during transition to injury-induced myofibroblasts
Time-resolved single-cell transcriptomics defines immune trajectories in glioblastoma
Exploratory electronic health record analysis with ehrapy
Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis
Explainable machine learning for profiling the immunological synapse and functional characterization of therapeutic antibodies
Systematic analysis of drug combinations against Gram-positive bacteria
Identification of cell types, states and programs by learning gene set representations
Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multi-lineage cell circuit dynamics in human lung fibrogenesis
Distinct molecular profiles of skull bone marrow in health and neurological disorders
The neglected twin: Nummular eczema is a variant of atopic dermatitis with codominant TH2/TH17 immune response
Gene Expression–Based Molecular Test as Diagnostic Aid for the Differential Diagnosis of Psoriasis and Eczema in Formalin-Fixed and Paraffin-Embedded Tissue, Microbiopsies, and Tape Strips
Tolerance of repeated toxic injuries of murine livers is associated with steatosis and inflammation
Systemic alterations in neutrophils and their precursors in early-stage chronic obstructive pulmonary disease
An integrated cell atlas of the lung in health and disease
394 Gene expression based molecular test proves clinical validity as diagnostic aid for the differential diagnosis of psoriasis and eczema in formalin fixed and paraffin embedded tissue
Synthetic enforcement of STING signaling in cancer cells appropriates the immune microenvironment for checkpoint inhibitor therapy
HBV rewires liver cancer signaling by altering PP2A complexes
High-throughput profiling of drug interactions in Gram-positive bacteria
Spatial transcriptomics landscape of lesions from non-communicable inflammatory skin diseases
T cells modulate the microglial response to brain ischemia
Spatial proteomics in three-dimensional intact specimens
TDP-43 condensates and lipid droplets regulate the reactivity of microglia and regeneration after traumatic brain injury
Ex vivo modeling of human lung fibrogenesis and drug mode of action screens using single cell RNA-seq in precision-cut lung slices
Single cell transcriptomic dissection of virus induced immunopathology in interferon gamma receptor null mice
Early transcriptional responses of bronchial epithelial cells to whole cigarette smoke mirror those of in-vivo exposed human bronchial mucosa
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
Ly6D+Siglec-H+ precursors contribute to conventional dendritic cells via a Zbtb46+Ly6D+ intermediary stage
Mature neutrophils and a NF-κB-to-IFN transition determine the unifying disease recovery dynamics in COVID-19
Gene expression based molecular test proves clinical validity as diagnostic aid for the differential diagnosis of psoriasis and eczema in formalin fixed and paraffin embedded tissue
Effect of Atmospheric Aging on Soot Particle Toxicity in Lung Cell Models at the Air–Liquid Interface: Differential Toxicological Impacts of Biogenic and Anthropogenic Secondary Organic Aerosols (SOAs)
The discovAIR project: a roadmap towards the Human Lung Cell Atlas
Repeated toxic injuries of murine liver are tolerated through microsteatosis and mild inflammation
Multi-omics and 3D-imaging reveal bone heterogeneity and unique calvaria cells in neuroinflammation
SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis
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
Aged alveolar epithelium contributes to inflammaging and reduced stem cell function in the lung
Chronic WNT/ß-catenin signaling impairs mitochondrial function in lung epithelial cells
Group Testing for SARS-CoV-2 Allows for Up to 10-Fold Efficiency Increase Across Realistic Scenarios and Testing Strategies
Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through ‘reverse phenotyping’
Low numbers of cytokine transcripts drive inflammatory skin diseases by initiating amplification cascades in localized epidermal clusters
Swarm Learning for decentralized and confidential clinical machine learning
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?
Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis
CD23 Levels on B Cells Determine Long-Term Therapeutic Response in Patients with Atopic Eczema Treated with Selective IgE Immune Apheresis
Inhibition of LTβR signalling activates WNT-induced regeneration in lung
Asthma in farm children is more determined by genetic polymorphisms and in non‐farm children by environmental factors
Protocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19)
Predicting antigen specificity of single T cells based on TCR CDR3 regions
Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis
In vivo identification of apoptotic and extracellular vesicle‐bound live cells using image‐based deep learning
Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease
SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues
IL‐17C amplifies epithelial inflammation in human psoriasis and atopic eczema
Longitudinal single cell transcriptomics reveals Krt8+ alveolar epithelial progenitors in lung regeneration
scSLAM-seq reveals core features of transcription dynamics in single cells
Meeting the Challenges of High-Dimensional Single-Cell Data Analysis in Immunology
A cellular census of human lungs identifies novel cell states in health and in asthma
Altered relaxation times in MRI indicate bronchopulmonary dysplasia
Common patterns of gene regulation associated with Cesarean section and the development of islet autoimmunity – indications of immune cell activation
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
A cellular census of healthy lung and asthmatic airway wall identifies novel cell states in health and disease
Editorial: Integrative Computational Systems Biology Approaches in Immunology and Medicine
Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data
Type I Immune Response Induces Keratinocyte Necroptosis and Is Associated with Interface Dermatitis
Is the humoral immunity dispensable for the pathogenesis of psoriasis?
The role of humoral immunity in the pathogenesis of psoriasis
Mathematical concepts and their challenges in predicting severity of atopic eczema patients
Toll-like receptor 7/8 agonists stimulate plasmacytoid dendritic cells to initiate TH17-deviated acute contact dermatitis in human subjects
Early Identification of Bronchopulmonary Dysplasia Using Novel Biomarkers by Proteomic Screening
Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway
Model Based Targeting of IL-6-Induced Inflammatory Responses in Cultured Primary Hepatocytes to Improve Application of the JAK Inhibitor Ruxolitinib
360 Interface Dermatitis is characterized by a type I immune response and an epidermal reaction to IFN-γ and TNF-α
489 TLR7/8 agonists stimulate plasmacytoid dendritic cells to initiate a Th17-deviated acute contact dermatitis in humans
2D cross-omics integrated enrichment analysis reveals insights into COPD pathogenesis
Identification of a plasma miRNA biomarker signature for allergic asthma: A translational approach
Pulmonary microRNA profiles identify involvement of Creb1 and Sec14l3 in bronchial epithelial changes in allergic asthma
Label Free Identification of Peripheral Blood Eosinophils Using High-Throughput Imaging Flow Cytometry
Peptide serum markers in islet autoantibody-positive children
A computational model to predict severity of atopic eczema from 30 serum proteins
A novel molecular disease classifier for psoriasis and eczema
Dynamic landscape of pancreatic carcinogenesis reveals early molecular networks of malignancy
TALEN/CRISPR-mediated engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus
340 Interface dermatitis shows a distinctive molecular signature independent from individual disease background
LSC Abstract – Systemic and local metabolomics profiling reveals novel insights into the progression of emphysema
LSC Abstract – Systemic and local metabolomics profiling reveals novel insights into the progression of emphysema
LSC Abstract – Early biomarkers indicating the development of neonatal chronic lung disease defined by clinical and imaging parameters
Interleukin-4 and interferon-γ orchestrate an epithelial polarization in the airways
A novel molecular disease classifier for eczema and psoriasis
Metabolomics screening identifies reduced L-carnitine to be associated with progressive emphysema
Opposing effects of allogrooming on disease transmission in ant societies
Effects of High-Dose Oral Insulin on Immune Responses in Children at High Risk for Type 1 Diabetes
Metabolism gene signatures and surgical site infections in abdominal surgery
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
Allergic Contact Dermatitis in Psoriasis Patients: Typical, Delayed, and Non-Interacting
Intraindividual genome expression analysis reveals a specific molecular signature of psoriasis and eczema
Cytokine-Regulated GADD45G Induces Differentiation and Lineage Selection in Hematopoietic Stem Cells
A strategy to find gene combinations that identify children who progress rapidly to type 1 diabetes after islet autoantibody seroconversion
Integrative genetic and metabolite profiling analysis suggests altered phosphatidylcholine metabolism in asthma
Genome-wide association analyses identify 18 new loci associated with serum urate concentrations
Specific temperature-induced perturbations of secondary mRNA structures are associated with the cold-adapted temperature-sensitive phenotype of influenza A virus
A strategy for combining minor genetic susceptibility genes to improve prediction of disease in type 1 diabetes
Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies
Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling
Knowledge-based gene expression classification via matrix factorization
Analyzing M-CSF dependent monocyte/macrophage differentiation: Expression modes and meta-modes derived from an independent component analysis
Phase-specific differential gene expression of peripheral blood mononuclear cells in rapid cycling syndrome
Adaptive signal analysis of immunological data
Neural network signal analysis in immunology
Software2
tcellmatch
41Python
huCIRA
36v0.1.36 mo agoPython