Plate III.6
Fabian Theis
0h2h4h6h8h10h12h14h16h18h20h22hMagnitude · works1 · 200 or more2 · 50 to 1993 · 10 to 494 · 3 to 95 · 1 to 26 · none yetmemberalumniguest
| Name | works | Linked to |
|---|---|---|
| Fabian Theis | 733 | Alex Example, Ilan Gold, Kemal Inecik, Philipp Angerer |
| Kemal Inecik | 12 | Fabian Theis |
| Philipp Angerer | 12 | Fabian Theis, Ilan Gold |
| Ilan Gold | 5 | Fabian Theis, Philipp Angerer |
| Alex Example | 0 | Dana Demo, Fabian Theis, Gray Placeholder |
| Dana Demo | 0 | Alex Example |
| Gray Placeholder | 0 | Alex Example |
Works per year7331992199720022007201220172022
| Series | Total works | By step from 1992 |
|---|---|---|
| Works per year | 733 | 1, 0, 0, 0, 0, 0, 1, 0, 1, 1, 3, 14, 19, 10, 16, 15, 11, 12, 24, 20, 25, 27, 22, 37, 41, 34, 31, 40, 33, 41, 46, 50, 44, 58, 56 |
Pl. III.6 Fabian Theis's medallion, and their constellation: the people they share works, software or declared connections with, and theirs in turn; brighter stars have more works. Below, their works per year.
7 people, 7 links of the collaboration graph; 733 works from 1992 to 2026 · data synced 6 Nov 2026
Publications733
Filter the lab's list202656 publications
Research area: Brain, Neurons, Reprogramming The Human Gut Cell Atlas v1.0: A Unified, Community-Built Reference of Cellular Diversity Across the Gut
Generative inverse design steers human hematopoietic cell fate in vitro
ArchMap is a web-based platform for reference-based analysis of single-cell datasets
A Community-Driven Single-Cell PBMC Reference Integrating Landmark Datasets Spanning Health and Disease
ConvexGating infers gating strategies from clusters in single cell cytometry data
AI Scientists for Building Virtual-Cell Models
Time-resolved predictability of end-of-therapy outcome and relapse after cure in Phase 3 tuberculosis trials
AlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics
Multimodal discovery of a pathogenic B-cell-dependent T-cell state in multiple sclerosis
Towards 3D-oid models that integrate molecular, morphological and spatial cellular features
Creating bottom-up RNA transfer vehicles from synthetic protein assemblies
Designing antimicrobials with programmable mechanism and safety
G2T: Tissue Reconstruction from Gene Expression via Embedding-Distance Flow Matching
Learning Discrete Cell and Niche Codes from Spatial Transcriptomics Using Dual Residual Vector Quantization
ArchMap
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
Building optimized single-cell reference atlases with scAtlasTb
Type 2 diabetes prevention across the life course
An interpretable omnigenic neural network architecture for the human genome
SpatioTemporal Omics Consortium: a global effort for biological discovery across species, space and time
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
NetworkVI: Biologically Guided Variational Inference for Interpretable Multimodal Single-Cell Integration and Discovery
Multimodal temporal mapping of macrophage transcriptome remodeling during Salmonella infection
Transcriptional repression by TGIF2 coordinates neurogenic priming and neural stem cell maintenance
Benchmarking gene expression reconstruction from single-cell latent representations
Cellpin enables reference-based imputation and denoising of spatial transcriptomes
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
Source Data Li et al Science Advances 2026
InterScale reveals multi-scale cellular interaction programs in spatial transcriptomics
TarDis: Achieving robust and structured disentanglement of multiple covariates
Continuous multi-omics pathway enrichment analysis resolves hidden functional heterogeneity
Pan-cancer virtual spatial transcriptomics from routine histology with Phoenix
Non-destructive transcriptomics via vesicular export
TNF alpha unmasks enteric malate aspartate shuttle dysfunction bridging Parkinson disease and intestinal inflammation
An integrated single cell and spatial omics atlas of human prenatal development
Large-scale proteomics across neurological disorders uncovers biomarker panel and targets in multiple sclerosis
Perturbation-guided mapping of colorectal cancer cell states to causal mechanisms
CP-BG-1M: A CONTROLLED MULTI-VIEW BENCH- MARK FOR DENSITY AND BACKGROUND SHORTCUTS IN MORPHOLOGY PROFILING
Generative models of cell dynamics: from Neural ODEs to flow matching
Longitudinal modality prediction learns gene regulatory patterns: insights from a single-cell competition
Beyond alignment: synergistic integration is required for multimodal cell foundation models
Identifying 3D signal overlaps in spatial transcriptomics data with ovrlpy
IDTrack: Time- and Namespace-Aware Identifier Harmonization for Reproducible Workflows
From modality-specific to compositional foundation models for cell biology
CellRank: consistent and data view agnostic fate mapping for single-cell genomics
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
Brain Region-Specific Oligodendrocyte States Highlight Mitochondrial Gene Upregulation and Loss of Canonical Identity Signatures in Alzheimer’s Disease
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
Protocol for Predicting Cell Fate Responses to in Silico Perturbation using RegVelo, from Code to Agentic Platform Analysis
202558 publications
Pertpy: an end-to-end framework for perturbation analysis
A single-cell cytokine dictionary of human peripheral blood
DISCO-seq: 3D single-cell transcriptomics of intact biological systems
Exploration of RNA outside segmented cells in spatial transcriptomics reveals extrasomatic RNA organization
Pseudodynamics+: Reconstructing Population Dynamics from Time-Resolved Single Cell Landscapes with Physics Informed Neural Networks
Active learning framework leveraging transcriptomics identifies modulators of disease phenotypes
OmniPath: integrated knowledgebase for multi-omics analysis
QuiCAT: a scalable and flexible framework for mapping synthetic sequences
Language may be all omics needs: Harmonizing multimodal data for omics understanding with CellHermes
Spatial single-cell atlas reveals regional variations in healthy and diseased human lung
FADVI: disentangled representation learning for robust integration of single-cell and spatial omics data
Toward a ToxAtlas of Carbon-Based Nanomaterials: Single-Cell RNA Sequencing Reveals Initiating Cell Circuits in Pulmonary Inflammation
Nicheformer: a foundation model for single-cell and spatial omics
Integrating single-cell RNA-seq datasets with substantial batch effects
NicheFlow - Data, Checkpoints, and Results
A multimodal cross-species comparison of pancreas development
scooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution
Mapping early human blood cell differentiation using single-cell proteomics and transcriptomics
Disentangling Transcription Factor Programs for Direct Reprogramming with Generative Modeling
scConcept: Contrastive pretraining for technology-agnostic single-cell representations beyond reconstruction
Advancing spatial biology analysis across programming languages
Graph neural networks learn emergent tissue properties from spatial molecular profiles
scPortrait integrates single-cell images into multimodal modeling
Single-cell multiome and spatial profiling reveals pancreas cell type–specific gene regulatory programs of type 1 diabetes progression
Im-seq: Multimodal droplet barcoding enables high-throughput linking of single-cell imaging and gene expression
Integration of cell-type resolved spatial proteomics and transcriptomics reveals novel mechanisms in early ovarian cancer
Spatial proteo-transcriptomic profiling reveals the molecular landscape of borderline ovarian tumors and their invasive progression
Single cell decomposition of multicellular aging programs associated with impaired lung regeneration
A foundation model to predict and capture human cognition
Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data
Defining and benchmarking open problems in single-cell analysis
Beyond Visual Inspection: Principled Benchmarking of Single-Cell Trajectory Representations with scTRAM
Biologically Informed Variational Inference Enables Interpretable Cell Phenotyping and Discovery
Automated evaluation of single-cell reference atlas mappings enables the identification of disease-associated cell states
Charting the single-cell and spatial landscape of IDH-wild-type glioblastoma with GBmap
An integrated transcriptomic cell atlas of human endoderm-derived organoids
GIPR agonism and antagonism decrease body weight and food intake via different mechanisms in male mice
Exon-variant interplay and multi-modal evidence identify endocrine dysregulation in severe psychiatric disorders impacting excitatory neurons
CellFlow enables generative single-cell phenotype modeling with flow matching
Towards multimodal foundation models in molecular cell biology
Stress in the ventral hippocampus under single-cell resolution
Causal machine learning for single-cell genomics
UniversalEPI: a generalized attention-based deep ensemble model to accurately predict enhancer-promoter interactions across diverse cell types and conditions
Quantitative characterization of cell niches in spatially resolved omics data
theislab/atlas-feature-selection-benchmark: 2025-03-15: Publication
Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows
Feature selection methods affect the performance of scRNA-seq data integration and querying
Transformers and genome language models
Biases in machine-learning models of human single-cell data
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
Spatial profiling of human pancreas during type 1 diabetes progression
What is the main bottleneck in deriving biological understanding from spatial transcriptomic profiling?
Unified Guidance for Geometry-Conditioned Molecular Generation
Mapping cells through time and space with moscot
Predicting cell morphological responses to perturbations using generative modeling
TarDis: Achieving Robust and Structured Disentanglement of Multiple Covariates
Data for "Feature selection methods affect the performance of scRNA-seq data integration and querying"
202444 publications
Delineating the effective use of self-supervised learning in single-cell genomics
ProCyon: A multimodal foundation model for protein phenotypes
Considerations for building and using integrated single-cell atlases
inVAE: Conditionally invariant representation learning for generating multivariate single-cell reference maps
Heterogeneity-driven phenotypic plasticity and treatment response in branched-organoid models of pancreatic ductal adenocarcinoma
Multiplexing cortical brain organoids for the longitudinal dissection of developmental traits at single-cell resolution
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
Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery
An integrated transcriptomic cell atlas of human neural organoids
Probe set selection for targeted spatial transcriptomics
Disentangling cellular heterogeneity into interpretable biological factors through structured latent representations
Mapping lineage-traced cells across time points with moslin
An open-source framework for electronic health record and patient fate exploration
Endothelial regulatory circuits control cranial neural crest migration and plasticity
anndata: Access and store annotated data matrices
Mode of actions of nanomaterial-induced respiratory toxicity
An open-source framework for end-to-end analysis of electronic health record data
Small data methods in omics: the power of one
Scalable and universal prediction of cellular phenotypes enables in silico experiments
scTab: Scaling cross-tissue single-cell annotation models
Polyploidisation pleiotropically buffers ageing in hepatocytes
Transformers in single-cell omics: a review and new perspectives
Weakly supervised learning uncovers phenotypic signatures in single-cell data
Evaluation of OCT biomarker changes in treatment-naive neovascular AMD using a deep semantic segmentation algorithm
A liver immune rheostat regulates CD8 T cell immunity in chronic HBV infection
Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis
Mapping the human hematopoietic stem and progenitor cell hierarchy through integrated single-cell proteomics and transcriptomics
Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data
GraphCompass: spatial metrics for differential analyses of cell organization across conditions
CellRank 2: unified fate mapping in multiview single-cell data
Machine learning integrative approaches to advance computational immunology
MISATO: machine learning dataset of protein–ligand complexes for structure-based drug discovery
The future of rapid and automated single-cell data analysis using reference mapping
hadge: a comprehensive pipeline for donor deconvolution in single-cell studies
Shared inflammatory glial cell signature after stab wound injury, revealed by spatial, temporal, and cell-type-specific profiling of the murine cerebral cortex
SpatialData: an open and universal data framework for spatial omics
longmixr: a tool for robust clustering of high-dimensional cross-sectional and longitudinal variables of mixed data types
Quantitative characterization of cell niches in spatial atlases
Community effort to unravel the complex human neuronal landscape exemplified for the striatum
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
Single cell transcriptomic analysis of epithelial and mesenchymal tumour cells
202350 publications
Optimal distance metrics for single-cell RNA-seq populations
Deep Learning-Based Retinal Layer Segmentation in Optical Coherence Tomography Scans of Patients with Inherited Retinal Diseases
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
Modeling fragment counts improves single-cell ATAC-seq analysis
Early life adversity shapes social subordination and cell type–specific transcriptomic patterning in the ventral hippocampus
Explainable machine learning for profiling the immunological synapse and functional characterization of therapeutic antibodies
A reversible state of hypometabolism in a human cellular model of sporadic Parkinson’s disease
flowVI: Flow Cytometry Variational Inference
Reporting electricity consumption is essential for sustainable AI
Human pluripotent stem cell fate trajectories toward lung and hepatocyte progenitors
Reconstructing disease dynamics for mechanistic insights and clinical benefit
Scaling cross-tissue single-cell annotation models
Population-level integration of single-cell datasets enables multi-scale analysis across samples
Single-cell characterization of neovascularization using hiPSC-derived endothelial cells in a 3D microenvironment
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
Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas
Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multi-lineage cell circuit dynamics in human lung fibrogenesis
A spatially resolved extracellular matrix proteome atlas of the distal human lung
Multi-omics regulatory network inference in the presence of missing data
Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel
Distinct molecular profiles of skull bone marrow in health and neurological disorders
Progressive disruption of hematopoietic architecture from clonal hematopoiesis to MDS
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
hadge: a comprehensive pipeline for donor deconvolution in single cell
Unified fate mapping in multiview single-cell data
Tolerance of repeated toxic injuries of murine livers is associated with steatosis and inflammation
OME-Zarr: a cloud-optimized bioimaging file format with international community support
scARE: Attribution Regularization for Single Cell Representation Learning
Single-cell reference mapping to construct and extend cell-type hierarchies
Longitudinal Effects of 1-Year Smoking Cessation on Human Bronchial Epithelial Transcriptome
Single‐cell biology: what does the future hold?
CIARA: a cluster-independent algorithm for identifying markers of rare cell types from single-cell sequencing data
Systemic alterations in neutrophils and their precursors in early-stage chronic obstructive pulmonary disease
What do you most hope spatial molecular profiling will help us understand? Part 1
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
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps
Deciphering subcellular organization with multiplexed imaging and deep learning
Predicting cellular responses to complex perturbations in high‐throughput screens
The scverse project provides a computational ecosystem for single-cell omics data analysis
Epicardioid single-cell genomics uncovers principles of human epicardium biology in heart development and disease
Best practices for single-cell analysis across modalities
Single-cell profiling to explore pancreatic cancer heterogeneity, plasticity and response to therapy
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
Biologically informed deep learning to query gene programs in single-cell atlases
B-Cos Aligned Transformers Learn Human-Interpretable Features
Earlier years1992 to 2022 · 525 publications
202246 publications
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
A transcriptional cross species map of pancreatic islet cells
TDP-43 condensates and lipid droplets regulate the reactivity of microglia and regeneration after traumatic brain injury
Network reconstruction for trans acting genetic loci using multi-omics data and prior information
Modeling intercellular communication in tissues using spatial graphs of cells
Pytometry: Flow and mass cytometry analytics in Python
Modeling Single-Cell Dynamics Using Unbalanced Parameterized Monge Maps
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
Probing cell identity hierarchies by fate titration and collision during direct reprogramming
Primary cilia and SHH signaling impairments in human and mouse models of Parkinson’s disease
Variant-risk-exon interplay impacts circadian rhythm and dopamine signaling pathway in severe psychiatric disorders
Interpretable surface-based detection of focal cortical dysplasias: a Multi-centre Epilepsy Lesion Detection study
Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies
Synaptotagmin-13 orchestrates pancreatic endocrine cell egression and islet morphogenesis
CIARA: a cluster-independent algorithm for the identification of markers of rare cell types from single-cell RNA seq data
Association of bronchial steroid inducible methylation quantitative trait loci with asthma and chronic obstructive pulmonary disease treatment response
Proteomics of spatially identified tissues in whole organs
Alveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation
Origin and function of activated fibroblast states during zebrafish heart regeneration
MultiCPA: Multimodal Compositional Perturbation Autoencoder
Ketamine exerts its sustained antidepressant effects via cell-type-specific regulation of Kcnq2
Heterogeneous Development of β-Cell Populations in Diabetes-Resistant and -Susceptible Mice
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
Cell-Type-Specific Impact of Glucocorticoid Receptor Activation on the Developing Brain: A Cerebral Organoid Study
Multimodal single cell data integration challenge: results and lessons learned
Parkinson's disease motor symptoms rescue by CRISPRa‐reprogramming astrocytes into GABAergic neurons
Integration and querying of multimodal single-cell data with PoE-VAE
Concept of the Munich/Augsburg Consortium Precision in Mental Health for the German Center of Mental Health
Toward modeling metabolic state from single-cell transcriptomics
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation
Spatial components of molecular tissue biology
A Python library for probabilistic analysis of single-cell omics data
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)
Squidpy: a scalable framework for spatial omics analysis
The discovAIR project: a roadmap towards the Human Lung Cell Atlas
Integration of single-cell transcriptomes and chromatin landscapes reveals regulatory programs driving pharyngeal organ development
CellRank for directed single-cell fate mapping
Repeated toxic injuries of murine liver are tolerated through microsteatosis and mild inflammation
Noise Transfer for Unsupervised Domain Adaptation of Retinal OCT Images
Benchmarking atlas-level data integration in single-cell genomics - integration task datasets
202141 publications
Multi-omics and 3D-imaging reveal bone heterogeneity and unique calvaria cells in neuroinflammation
Benchmarking atlas-level data integration in single-cell genomics
SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis
Graph representation learning for single-cell biology
Vertical sleeve gastrectomy triggers fast β-cell recovery upon overt diabetes
scCODA is a Bayesian model for compositional single-cell data analysis
scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies
Determinants of expression of SARS‐CoV‐2 entry‐related genes in upper and lower airways
Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape
A field guide to cultivating computational biology
Künstliche Intelligenz und maschinelles Lernen in der Diabetesforschung
Current Smoking Alters Gene Expression and DNA Methylation in the Nasal Epithelium of Patients with Asthma
Diet-induced alteration of intestinal stem cell function underlies obesity and prediabetes in mice
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
Out-of-distribution prediction with disentangled representations for single-cell RNA sequencing data
EpiScanpy: integrated single-cell epigenomic analysis
Mapping single-cell data to reference atlases by transfer learning
Sfaira accelerates data and model reuse in single cell genomics
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
Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through ‘reverse phenotyping’
AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution
CD81 marks immature and dedifferentiated pancreatic β-cells
Epithelial cell plasticity drives endoderm formation during gastrulation
Low numbers of cytokine transcripts drive inflammatory skin diseases by initiating amplification cascades in localized epidermal clusters
Machine learning for perturbational single-cell omics
Swarm Learning for decentralized and confidential clinical machine learning
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?
Asc-1 regulates white versus beige adipocyte fate in a subcutaneous stromal cell population
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
Posterior subcapsular cataracts are a late effect after acute exposure to 0.5 Gy ionizing radiation in mice
Single cell trajectory analysis of human pluripotent stem cells differentiating towards lung and hepatocyte progenitors
Squidpy: a scalable framework for spatial single cell analysis
Deep learning the collisional cross sections of the peptide universe from a million experimental values
Deep Learning-based Propensity Scores for Confounding Control in Comparative Effectiveness Research
Single-cell molecular profiling of all three components of the HPA axis reveals adrenal ABCB1 as a regulator of stress adaptation
Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates
202033 publications
Learning interpretable latent autoencoder representations with annotations of feature sets
[DEPRECATED] Theislab sfaira Model Repository
A sparse deep learning approach for automatic segmentation of human vasculature in multispectral optoacoustic tomography
Conditional out-of-distribution generation for unpaired data using transfer VAE
Identification and characterization of distinct brown adipocyte subtypes in C57BL/6J mice
Self-supervised retinal thickness prediction enables deep learning from unlabelled data to boost classification of diabetic retinopathy
Inhibition of LTβR signalling activates WNT-induced regeneration in lung
Predicting single-cell gene expression profiles of imaging flow cytometry data with machine learning
Asthma in farm children is more determined by genetic polymorphisms and in non‐farm children by environmental factors
LifeTime and improving European healthcare through cell-based interceptive medicine
Protocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19)
Identification and characterization of distinct murine brown adipocyte lineages
Wnt/PCP-primed intestinal stem cells directly differentiate into enteroendocrine or Paneth cells
Generalizing RNA velocity to transient cell states through dynamical modeling
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
Query to reference single-cell integration with transfer learning
Post-surgical adhesions are triggered by calcium-dependent membrane bridges between mesothelial surfaces
The proteome landscape of the kingdoms of life
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
Chronic Wnt Signaling Contributes to Lung Epithelial Senescence and Aging
Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data
The single-cell eQTLGen consortium
Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines
Epithelial Planar Bipolarity Emerges from Notch-Mediated Asymmetric Inhibition of Emx2
Targeted pharmacological therapy restores β-cell function for diabetes remission
Eleven grand challenges in single-cell data science
DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning
IL‐17C amplifies epithelial inflammation in human psoriasis and atopic eczema
Cell-type specific impact of glucocorticoid receptor activation on the developing brain
Learning Tn5 Sequence Bias from ATAC-seq on Naked Chromatin
201940 publications
S.11.01 Brain organoids as models of the developing human brain: deciphering the molecular signature of prenatal stress
Establishment of a high-resolution 3D modeling system for studying pancreatic epithelial cell biology in vitro
Aldh1b1 expression defines progenitor cells in the adult pancreas and is required for Kras-induced pancreatic cancer
MPRAnalyze: statistical framework for massively parallel reporter assays
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
scGen predicts single-cell perturbation responses
Longitudinal single cell transcriptomics reveals Krt8+ alveolar epithelial progenitors in lung regeneration
Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images
scSLAM-seq reveals core features of transcription dynamics in single cells
Faculty Opinions recommendation of Deep generative modeling for single-cell transcriptomics.
Meeting the Challenges of High-Dimensional Single-Cell Data Analysis in Immunology
The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease
A cellular census of human lungs identifies novel cell states in health and in asthma
Concepts and limitations for learning developmental trajectories from single cell genomics
Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis
Inferring Interaction Networks From Multi-Omics Data
Integrated analysis of environmental and genetic influences on cord blood DNA methylation in new-borns
Current best practices in single‐cell RNA‐seq analysis: a tutorial
Deep learning does not outperform classical machine learning for cell-type annotation
Dynamic modelling of an ACADS genotype in fatty acid oxidation – Application of cellular models for the analysis of common genetic variants
A map of β-cell differentiation pathways supports cell therapies for diabetes
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
Deep learning: new computational modelling techniques for genomics
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
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
Single-cell RNA-seq denoising using a deep count autoencoder
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
Artificial Neural Networks and Machine Learning – ICANN 2019: Theoretical Neural Computation
Artificial Neural Networks and Machine Learning – ICANN 2019: Workshop and Special Sessions
WHAT SHAPES THE CHILD'S EPIGENOME: GENOTYPE, PRENATAL ENVIRONMENT OR BOTH?
POLYGENIC BURDEN ANALYSIS OF LONGITUDINAL CLUSTERS OF PSYCHOPATHOLOGICAL FEATURES IN A CROSS-DIAGNOSTIC GROUP OF INDIVIDUALS WITH SEVERE MENTAL ILLNESS
GENOTYPE, PRENATAL ENVIRONMENT OR BOTH–WHAT SHAPES THE NEWBORN'S EPIGENOME?
F96POLYGENIC RISK SCORE ANALYSIS OF TRAJECTORIES OF COGNITIVE PERFORMANCE IN PSYCHIATRIC PATIENTS
SA125POLYGENIC BURDEN ANALYSIS OF LONGITUDINAL CLUSTERS OF PSYCHOPATHOLOGICAL FEATURES IN A CROSS-DIAGNOSTIC GROUP OF INDIVIDUALS WITH SEVERE MENTAL ILLNESS
201831 publications
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
Generative modeling and latent space arithmetics predict single-cell perturbation response across cell types, studies and species
Data Driven Computational Modeling of Hematopoiesis in Myelodysplastic Syndromes Unveils Differences in Hematopoietic Stem Cell Kinetics Compared to Age-Matched Healthy Controls
Impact of Brain Fatty Acid Signaling on Peripheral Insulin Action in Mice
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
Metabolic regulation of pluripotency and germ cell fate through α‐ketoglutarate
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
Lineage marker synchrony in hematopoietic genealogies refutes the PU.1/GATA1 toggle switch paradigm
Is the humoral immunity dispensable for the pathogenesis of psoriasis?
Inductive and Selective Effects of GSK3 and MEK Inhibition on Nanog Heterogeneity in Embryonic Stem Cells
Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering
MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data
The role of humoral immunity in the pathogenesis of psoriasis
Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics
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
FASTGenomics: An analytical ecosystem for single-cell RNA sequencing data
Epigenetically Regulated Chromosome 14q32 miRNA Cluster Induces Metastasis and Predicts Poor Prognosis in Lung Adenocarcinoma Patients
Whither systems medicine?
SCANPY: large-scale single-cell gene expression data analysis
Maternal whole blood cell miRNA-340 is elevated in gestational diabetes and inversely regulated by glucose and insulin
Lifetime study in mice after acute low-dose ionizing radiation: a multifactorial study with special focus on cataract risk
LNA++: Linear Noise Approximation with First and Second Order Sensitivities
201734 publications
The Human Cell Atlas
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
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
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
pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms
Reconstructing cell cycle and disease progression using deep learning
Systematic single-cell analysis provides new insights into heterogeneity and plasticity of the pancreas
2D cross-omics integrated enrichment analysis reveals insights into COPD pathogenesis
MicroRNA as an Integral Part of Cell Communication: Regularized Target Prediction and Network Prediction
Information Theoretic Concepts to Unravel Cell–Cell Communication
Single cells make big data: New challenges and opportunities in transcriptomics
A scalable moment-closure approximation for large-scale biochemical reaction networks
Prediction of type 1 diabetes using a genetic risk model in the Diabetes Autoimmunity Study in the Young
Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems
Identification of a plasma miRNA biomarker signature for allergic asthma: A translational approach
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
Pulmonary microRNA profiles identify involvement of Creb1 and Sec14l3 in bronchial epithelial changes in allergic asthma
fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy
Prospective identification of hematopoietic lineage choice by deep learning
Calcium-regulatory proteins as modulators of chemotherapy in human neuroblastoma
Parallelization and High-Performance Computing Enables Automated Statistical Inference of Multi-scale Models
Label Free Identification of Peripheral Blood Eosinophils Using High-Throughput Imaging Flow Cytometry
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
AURKA, DLGAP5, TPX2, KIF11 and CKAP5: Five specific mitosis-associated genes correlate with poor prognosis for non-small cell lung cancer patients
Polygenic Burden Analysis of Longitudinal Clusters of Psychopathological Features In A Cross-Diagnostic Group of Individuals with Severe Mental Illness
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POLYGENIC BURDEN ANALYSIS OF LONGITUDINAL CLUSTERS OF QUALITY OF LIFE AND FUNCTIONING IN PATIENTS WITH SEVERE MENTAL ILLNESS
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Correcting Classifiers for Sample Selection Bias in Two-Phase Case-Control Studies
201641 publications
Parameter estimation for dynamical systems with discrete events and logical operations
Large-scale modeling of cancer signaling: Mechanistic modeling meets Big Data
Identification of predictive response and resistance factors to targeted therapy in gastric cancer using a systems medicine approach
Inferring catalysis in biological systems
Peptide serum markers in islet autoantibody-positive children
Analysis of Cell Lineage Trees by Exact Bayesian Inference Identifies Negative Autoregulation of Nanog in Mouse Embryonic Stem Cells
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
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
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
Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios
Software tools for single-cell tracking and quantification of cellular and molecular properties
Computational approaches for systems metabolomics
Editorial overview: Systems biology-the intersection of experiments and computation, underpinning biotechnology
A novel molecular disease classifier for eczema and psoriasis
MEMO: multi-experiment mixture model analysis of censored data
Unbiased Prediction and Feature Selection in High-Dimensional Survival Regression
miTALOS v2: Analyzing Tissue Specific microRNA Function
Epigenetic germline inheritance of diet-induced obesity and insulin resistance
Metabolomics reveals effects of maternal smoking on endogenous metabolites from lipid metabolism in cord blood of newborns
Pitchfork and Gprasp2 Target Smoothened to the Primary Cilium for Hedgehog Pathway Activation
Abstract P1-06-02: A force-sensitive organoid assay to quantify regenerative potential of single primary human mammary cells
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
CERENA: ChEmical REaction Network Analyzer—A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics
Metabolomics screening identifies reduced L-carnitine to be associated with progressive emphysema
Label-free cell cycle analysis for high-throughput imaging flow cytometry
Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions
Mitosis Detection in Intestinal Crypt Images with Hough Forest and Conditional Random Fields
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.
201537 publications
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
Network plasticity of pluripotency transcription factors in embryonic stem cells
Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy
Separation of Uncorrelated Stationary time series using Autocovariance Matrices
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
Model selection using limiting distributions of second-order blind source separation algorithms
Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems
Transcriptional Mechanisms of Proneural Factors and REST in Regulating Neuronal Reprogramming of Astrocytes
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
Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations
Opposing effects of allogrooming on disease transmission in ant societies
Diffusion maps for high-dimensional single-cell analysis of differentiation data
Atrx promotes heterochromatin formation at retrotransposons
Live imaging of adult neural stem cell behavior in the intact and injured zebrafish brain
Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer
Effects of High-Dose Oral Insulin on Immune Responses in Children at High Risk for Type 1 Diabetes
A Critical Period for Postnatal Adaptive Plasticity in a Model of Motor Axon Miswiring
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
Fast clonal expansion and limited neural stem cell self-renewal in the adult subependymal zone
Decoding the regulatory network of early blood development from single-cell gene expression measurements
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
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
A subset of metastatic pancreatic ductal adenocarcinomas depends quantitatively on oncogenic Kras/Mek/Erk-induced hyperactive mTOR signalling
Quantification of regenerative potential in primary human mammary epithelial cells
Stem-Cell-like Properties and Epithelial Plasticity Arise as Stable Traits after Transient Twist1 Activation
An Affine Equivariant Robust Second-Order BSS Method
Approximate Bayesian Computation for Stochastic Single-Cell Time-Lapse Data Using Multivariate Test Statistics
201422 publications
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
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
Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain
Hypothalamic miR-103 Protects from Hyperphagic Obesity in Mice
Decoding the transcriptional program for blood development from whole tissue single-cell gene expression measurements
Cytokine-regulated GADD45G induces differentiation and lineage selection in hematopoietic stem cells
Allergic Contact Dermatitis in Psoriasis Patients: Typical, Delayed, and Non-Interacting
MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data
Intraindividual genome expression analysis reveals a specific molecular signature of psoriasis and eczema
ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics
Cytokine-Regulated GADD45G Induces Differentiation and Lineage Selection in Hematopoietic Stem Cells
Novel genetic associations with serum level metabolites identified by phenotype set enrichment analyses
An atlas of genetic influences on human blood metabolites
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
Posttranscriptional Regulatory Networks: From Expression Profiling to Integrative Analysis of mRNA and MicroRNA Data
Centroid Clustering of Cellular Lineage Trees
Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More
201327 publications
High-dimensional Bayesian parameter estimation: Case study for a model of JAK2/STAT5 signaling
Dependent component analysis
A strategy to find gene combinations that identify children who progress rapidly to type 1 diabetes after islet autoantibody seroconversion
iVUN: interactive Visualization of Uncertain biochemical reaction Networks
An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy
Wound-healing growth factor, basic FGF, induces Erk1/2-dependent mechanical hyperalgesia
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
Extrinsically regulated Gadd45γ balances hematopoietic stem cell self-renewal and differentiation
The cytokine-induced microrna193b modulates ckit expression and STAT5 signaling
Myeloid lineage choice is not controlled by the PU.1 - Gata1 switch
Metabolomic profiles in individuals with negative affectivity and social inhibition: A population-based study of Type D personality
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
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
Live imaging of astrocyte responses to acute injury reveals selective juxtavascular proliferation
Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis
Effects of smoking and smoking cessation on human serum metabolite profile: results from the KORA cohort study
A Vine-copula Based Adaptive MCMC Sampler for Efficient Inference of Dynamical Systems
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Integrative genetic and metabolite profiling analysis suggests altered phosphatidylcholine metabolism in asthma
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
201225 publications
Genome-wide association analyses identify 18 new loci associated with serum urate concentrations
Uniqueness of linear factorizations into independent subspaces
Mining the Unknown: A Systems Approach to Metabolite Identification Combining Genetic and Metabolic Information
Specific temperature-induced perturbations of secondary mRNA structures are associated with the cold-adapted temperature-sensitive phenotype of influenza A virus
A Unilateral Negative Feedback Loop Between miR-200 microRNAs and Sox2/E2F3 Controls Neural Progenitor Cell-Cycle Exit and Differentiation
A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst
A strategy for combining minor genetic susceptibility genes to improve prediction of disease in type 1 diabetes
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
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
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
The dynamic range of the human metabolome revealed by challenges
Essstörungen im Internet: Eine experimentelle Studie zu den Auswirkungen von Pro-Essstörungs- und Selbsthilfewebsites
Stability and Multiattractor Dynamics of a Toggle Switch Based on a Two-Stage Model of Stochastic Gene Expression
Systems Biology Meets Metabolism
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
201120 publications
The Sox17‐mCherry fusion mouse line allows visualization of endoderm and vascular endothelial development
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
The Nature and Perception of Fluctuations in Human Musical Rhythms
Modularity Maximization and Tree Clustering: Novel Ways to Determine Effective Geographic Borders
Uniqueness of Non-Gaussianity-Based Dimension Reduction
MicroRNAs coordinately regulate protein complexes
Discovery of Sexual Dimorphisms in Metabolic and Genetic Biomarkers
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
Moderne Informations- und Kommunikationstechnologie in der Rehabilitation
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
201024 publications
Effective Parameters Determining the Information Flow in Hierarchical Biological Systems
Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation
MIPS: curated databases and comprehensive secondary data resources in 2010
The Structure of Borders in a Small World
MicroRNA Loss Enhances Learning and Memory in Mice
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
Tissue-Specific Target Analysis of Disease-Associated MicroRNAs in Human Signaling Pathways
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
PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes
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
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
200912 publications
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
Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine
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
200811 publications
An evolutionary and structural characterization of mammalian protein complex organization
Optimization Techniques for Date Representions with Biomedical Applications
Money Circulation, Trackable Items, and the Emergence of Universal Human Mobility Patterns
Erythropoietin enhances hippocampal long-term potentiation and memory
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
A robust model for spatiotemporal dependencies
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
Effective Emission Tomography Image Reconstruction Algorithms for SPECT Data
200715 publications
Phase-specific differential gene expression of peripheral blood mononuclear cells in rapid cycling syndrome
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
A Toolbox for Model-Free Analysis of fMRI Data
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
200616 publications
Robust Sparse Component Analysis Based on a Generalized Hough Transform
A Fast Predictive Lossless Coder for fMRI Data Sets
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
Stability Analysis of an Unsupervised Competitive Neural Network
On the use of joint diagonalization in blind signal processing
New Riemannian metrics for speeding-up the convergence of over- and underdetermined ICA
200510 publications
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
A Fast and Efficient Method for Compressing fMRI Data Sets
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
200419 publications
A New Concept for Separability Problems in Blind Source Separation
Mobile decision support for transplantation patient data
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
3D Spatial Analysis of fMRI Data on a Word Perception Task
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
200314 publications
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
Neural network signal analysis in immunology
Mathematics in independent component analysis
20023 publications
Topological Constructions in the o–Graph Calculus
Comparison of maximum entropy and minimal mutual information in a nonlinear setting
Overcomplete ICA with a Geometric Algorithm