Fabian Theis
Principal investigator
Single-cell genomics · Perturbation responses · Bulk omics and genetics
Topics · Data · Molecular data
Bulk omics and genetics
Work that measures or analyses the molecules of whole tissue, blood or serum samples, such as gene expression profiles, microRNAs, proteins, metabolites or genotypes. Not for single-cell measurements.
In Data › Molecular data155 works1 person5 tools
People1
Publications155
Pregestational maternal diabetes primes neonatal beta cell dysfunction with structural remodelling, impaired calcium buffering and altered mTORC2–Gαq–PKCα signalling in a pig model
An interpretable omnigenic neural network architecture for the human genome
Learning the shared structure of human health across diseases, modalities, and time
Rectangle: robust and scalable multiscale deconvolution informed by single-cell RNA sequencing data
Transcriptional repression by TGIF2 coordinates neurogenic priming and neural stem cell maintenance
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
Non-destructive transcriptomics via vesicular export
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
Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers
QuiCAT: a scalable and flexible framework for mapping synthetic sequences
Exon-variant interplay and multi-modal evidence identify endocrine dysregulation in severe psychiatric disorders impacting excitatory neurons
TGIF2 is a major regulator of neural stem cell fate and neurogenic priming
ProCyon: A multimodal foundation model for protein phenotypes
HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma
A reversible state of hypometabolism in a human cellular model of sporadic Parkinson’s disease
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
Longitudinal Effects of 1-Year Smoking Cessation on Human Bronchial Epithelial Transcriptome
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
HBV rewires liver cancer signaling by altering PP2A complexes
Network reconstruction for trans acting genetic loci using multi-omics data and prior information
Ex vivo modeling of human lung fibrogenesis and drug mode of action screens using single cell RNA-seq in precision-cut lung slices
Early transcriptional responses of bronchial epithelial cells to whole cigarette smoke mirror those of in-vivo exposed human bronchial mucosa
Variant-risk-exon interplay impacts circadian rhythm and dopamine signaling pathway in severe psychiatric disorders
Association of bronchial steroid inducible methylation quantitative trait loci with asthma and chronic obstructive pulmonary disease treatment response
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
Repeated toxic injuries of murine liver are tolerated through microsteatosis and mild inflammation
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
AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution
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
Posterior subcapsular cataracts are a late effect after acute exposure to 0.5 Gy ionizing radiation in mice
Deep learning the collisional cross sections of the peptide universe from a million experimental values
Single-cell molecular profiling of all three components of the HPA axis reveals adrenal ABCB1 as a regulator of stress adaptation
Asthma in farm children is more determined by genetic polymorphisms and in non‐farm children by environmental factors
The proteome landscape of the kingdoms of life
DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning
IL‐17C amplifies epithelial inflammation in human psoriasis and atopic eczema
Pheno-seq – linking visual features and gene expression in 3D cell culture systems
BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis
Inferring Interaction Networks From Multi-Omics Data
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
A strategy for high‐dimensional multivariable analysis classifies childhood asthma phenotypes from genetic, immunological, and environmental factors
An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics
IRE1α-XBP1s pathway promotes prostate cancer by activating c-MYC signaling
Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model
Data Driven Computational Modeling of Hematopoiesis in Myelodysplastic Syndromes Unveils Differences in Hematopoietic Stem Cell Kinetics Compared to Age-Matched Healthy Controls
Copy number aberrations from Affymetrix SNP 6.0 genotyping data—how accurate are commonly used prediction approaches?
MetaMap, an interactive webtool for the exploration of metatranscriptomic reads in human disease-related RNA-seq data
Characterization of missing values in untargeted MS-based metabolomics data and evaluation of missing data handling strategies
Impulse model-based differential expression analysis of time course sequencing data
Type I Immune Response Induces Keratinocyte Necroptosis and Is Associated with Interface Dermatitis
Is the humoral immunity dispensable for the pathogenesis of psoriasis?
MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data
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
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
Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway
GATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency
pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms
2D cross-omics integrated enrichment analysis reveals insights into COPD pathogenesis
Prediction of type 1 diabetes using a genetic risk model in the Diabetes Autoimmunity Study in the Young
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
AURKA, DLGAP5, TPX2, KIF11 and CKAP5: Five specific mitosis-associated genes correlate with poor prognosis for non-small cell lung cancer patients
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
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
Lactation is associated with altered metabolomic signatures in women with gestational diabetes
Abstract 1945: Identification of a miRNA/mRNA network driving non-small cell lung cancer (NSCLC) dissemination
Clinical impact of GATA2 mutations in acute myeloid leukemia patients harboring CEBPA mutations: a study of the AML study group
Interleukin-4 and interferon-γ orchestrate an epithelial polarization in the airways
Computational approaches for systems metabolomics
Unbiased Prediction and Feature Selection in High-Dimensional Survival Regression
miTALOS v2: Analyzing Tissue Specific microRNA Function
Metabolomics reveals effects of maternal smoking on endogenous metabolites from lipid metabolism in cord blood of newborns
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
Metabolomics screening identifies reduced L-carnitine to be associated with progressive emphysema
MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma
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
Gender-specific pathway differences in the human serum metabolome
The Human Blood Metabolome-Transcriptome Interface
Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer
Multi-omic signature of body weight change: results from a population-based cohort study
Metabolism gene signatures and surgical site infections in abdominal surgery
miR-23a-3p Causes Cellular Senescence by Targeting Hyaluronan Synthase 2: Possible Implication for Skin Aging
A subset of metastatic pancreatic ductal adenocarcinomas depends quantitatively on oncogenic Kras/Mek/Erk-induced hyperactive mTOR signalling
Network-Based Approach for Analyzing Intra- and Interfluid Metabolite Associations in Human Blood, Urine, and Saliva
Proteome-wide analysis reveals an age-associated cellular phenotype of in situ aged human fibroblasts
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
Allergic Contact Dermatitis in Psoriasis Patients: Typical, Delayed, and Non-Interacting
Intraindividual genome expression analysis reveals a specific molecular signature of psoriasis and eczema
Novel genetic associations with serum level metabolites identified by phenotype set enrichment analyses
An atlas of genetic influences on human blood metabolites
Posttranscriptional Regulatory Networks: From Expression Profiling to Integrative Analysis of mRNA and MicroRNA Data
A strategy to find gene combinations that identify children who progress rapidly to type 1 diabetes after islet autoantibody seroconversion
A modular framework for gene set analysis integrating multilevel omics data
Metabolomic profiles in individuals with negative affectivity and social inhibition: A population-based study of Type D personality
Metabolite profiling reveals new insights into the regulation of serum urate in humans
The human transcriptome is enriched for miRNA-binding sites located in cooperativity-permitting distance
Effects of smoking and smoking cessation on human serum metabolite profile: results from the KORA cohort study
Integrative genetic and metabolite profiling analysis suggests altered phosphatidylcholine metabolism in asthma
STATISTICAL METHODS FOR THE ANALYSIS OF HIGH-THROUGHPUT METABOLOMICS DATA
Genome-wide association analyses identify 18 new loci associated with serum urate concentrations
Mining the Unknown: A Systems Approach to Metabolite Identification Combining Genetic and Metabolic Information
A strategy for combining minor genetic susceptibility genes to improve prediction of disease in type 1 diabetes
Identification and Quantification of 1-Hydroxybutene-2-yl Mercapturic Acid in Human Urine by UPLC- HILIC-MS/MS as a Novel Biomarker for 1,3-Butadiene Exposure
Bayesian Independent Component Analysis Recovers Pathway Signatures from Blood Metabolomics Data
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
The dynamic range of the human metabolome revealed by challenges
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
Discovery of Sexual Dimorphisms in Metabolic and Genetic Biomarkers
Gaussian graphical modeling reveals specific lipid correlations in glioblastoma cells
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
Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation
MIPS: curated databases and comprehensive secondary data resources in 2010
Patterns of Subnet Usage Reveal Distinct Scales of Regulation in the Transcriptional Regulatory Network of Escherichia coli
PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes
Intronic microRNAs support their host genes by mediating synergistic and antagonistic regulatory effects
Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine
Knowledge-based gene expression classification via matrix factorization
Episode-Specific Differential Gene Expression of Peripheral Blood Mononuclear Cells in Rapid Cycling Supports Novel Treatment Approaches
Hybridizing sparse component analysis with genetic algorithms for microarray analysis
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
How to extract marker genes from microarray data sets
Sparse Nonnegative Matrix Factorization with Genetic Algorithms for Microarray Analysis
Blind Matrix Decomposition Techniques to Identify Marker Genes from Microarrays
Sparse Nonnegative Matrix Factorization Applied to Microarray Data Sets
Software5
AutoGeneS
64Jupyter Notebook
prophet
42Python
cellink
Scalable framework for integrating single-cell omics with genetic data using AnnData.
25Python
quicat
2v0.1.215 mo agoPython
chem-perturbridge_lpm
1Python