Plate IV
Publications
ICA41Blind Source Separation40fMRI Data, Network58miRNA, Target, Cancer53Stem Cells, Lineage50Diabetes, Children, Risk47Single Cell RNA62Images, Deep Learning47Lung, Epithelial Cells39Brain50Representations, Single Cell67Spatial, Omics Data631992199720022007201220172022
| Series | Total works | By step from 1992 |
|---|---|---|
| ICA | 41 | 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 7, 4, 4, 7, 6, 0, 2, 3, 1, 4, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0 |
| Blind Source Separation | 40 | 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 7, 3, 6, 7, 2, 3, 4, 0, 1, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1 |
| fMRI Data, Network | 58 | 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 5, 2, 2, 1, 1, 3, 6, 3, 2, 9, 2, 3, 7, 5, 2, 3, 0, 1, 0, 0, 0, 0, 0 |
| miRNA, Target, Cancer | 53 | 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 3, 0, 3, 3, 6, 6, 6, 2, 2, 2, 2, 3, 3, 5, 2, 1 |
| Stem Cells, Lineage | 50 | 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 3, 3, 3, 5, 3, 2, 6, 3, 2, 5, 3, 4, 2, 2, 1 |
| Diabetes, Children, Risk | 47 | 1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 3, 4, 1, 1, 2, 5, 1, 3, 5, 4, 3, 4, 3, 0, 0, 3 |
| Single Cell RNA | 62 | 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 2, 0, 4, 7, 1, 2, 4, 7, 4, 7, 3, 5, 4, 5, 5 |
| Images, Deep Learning | 47 | 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 1, 1, 0, 0, 3, 5, 1, 4, 5, 5, 3, 7, 4, 1, 4 |
| Lung, Epithelial Cells | 39 | 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 4, 0, 0, 5, 6, 6, 6, 5, 3, 2, 0 |
| Brain | 50 | 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 1, 0, 0, 2, 1, 2, 0, 0, 1, 1, 2, 2, 11, 4, 3, 7, 8 |
| Representations, Single Cell | 67 | 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 3, 1, 2, 4, 5, 4, 3, 5, 9, 16, 12 |
| Spatial, Omics Data | 63 | 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 1, 1, 1, 3, 0, 2, 7, 6, 8, 17, 13 |
Pl. IV Every work by the lab's members during their time here, as the lab's history: one ridge per research area, years from left to right, its height the works of that year, the oldest area at the back and the newest in front. Areas are the larger islands of the map of publications (Plate II). Select a ridge to list its works.
617 of 742 works in the 12 largest of 16 areas, from ORCID, Crossref and Europe PMC · data synced 6 Nov 2026
202656 publications
Research area: Brain, Neurons, Reprogramming Research area: Cell Atlas, IntegrationThe Human Gut Cell Atlas v1.0: A Unified, Community-Built Reference of Cellular Diversity Across the Gut
Research area: Representations, Single CellGenerative inverse design steers human hematopoietic cell fate in vitro
Research area: Cell Atlas, IntegrationArchMap is a web-based platform for reference-based analysis of single-cell datasets
Research area: Cell Atlas, IntegrationA Community-Driven Single-Cell PBMC Reference Integrating Landmark Datasets Spanning Health and Disease
Research area: Images, Deep LearningConvexGating infers gating strategies from clusters in single cell cytometry data
Research area: Representations, Single CellAI Scientists for Building Virtual-Cell Models
Research area: Images, Deep LearningTime-resolved predictability of end-of-therapy outcome and relapse after cure in Phase 3 tuberculosis trials
Research area: Spatial, Omics DataAlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics
Research area: Brain, Neurons, ReprogrammingMultimodal discovery of a pathogenic B-cell-dependent T-cell state in multiple sclerosis
Research area: Spatial, Omics DataTowards 3D-oid models that integrate molecular, morphological and spatial cellular features
Research area: Representations, Single CellCreating bottom-up RNA transfer vehicles from synthetic protein assemblies
Research area: Diabetes, Children, RiskDesigning antimicrobials with programmable mechanism and safety
Research area: Spatial, Omics DataG2T: Tissue Reconstruction from Gene Expression via Embedding-Distance Flow Matching
Research area: Spatial, Omics DataLearning Discrete Cell and Niche Codes from Spatial Transcriptomics Using Dual Residual Vector Quantization
Research area: Cell Atlas, IntegrationArchMap
Research area: Spatial, Omics DataChemokine Landscapes of the Tumor Microenvironment
Research area: Brain, Neurons, ReprogrammingPlasticity of human microglia and brain perivascular macrophages in aging and Alzheimer’s disease
Research area: Spatial, Omics DataMulti-scale modeling of human tissues from spatial transcriptomics with TERRA
Research area: Cell Atlas, IntegrationBuilding optimized single-cell reference atlases with scAtlasTb
Research area: Diabetes, Children, RiskType 2 diabetes prevention across the life course
Research area: Images, Deep LearningAn interpretable omnigenic neural network architecture for the human genome
Research area: Representations, Single CellSpatioTemporal Omics Consortium: a global effort for biological discovery across species, space and time
Research area: Images, Deep LearningLearning the shared structure of human health across diseases, modalities, and time
Research area: Single Cell RNA, Gene ExpressionRectangle: robust and scalable multiscale deconvolution informed by single-cell RNA sequencing data
Research area: Representations, Single CellNetworkVI: Biologically Guided Variational Inference for Interpretable Multimodal Single-Cell Integration and Discovery
Research area: Brain, Neurons, ReprogrammingMultimodal temporal mapping of macrophage transcriptome remodeling during Salmonella infection
Research area: Stem Cells, LineageTranscriptional repression by TGIF2 coordinates neurogenic priming and neural stem cell maintenance
Research area: Representations, Single CellBenchmarking gene expression reconstruction from single-cell latent representations
Research area: Spatial, Omics DataCellpin enables reference-based imputation and denoising of spatial transcriptomes
Research area: Single Cell RNA, Gene ExpressionRegVelo: Gene-regulatory-informed dynamics of single cells
Research area: Representations, Single CellUniversalEPI: robust prediction of cell type-specific and differential chromatin interactions from DNA sequence and chromatin accessibility
Research area: Blind Source Separation, Sparse ComponentSource Data Li et al Science Advances 2026
Research area: Spatial, Omics DataInterScale reveals multi-scale cellular interaction programs in spatial transcriptomics
Research area: Representations, Single CellTarDis: Achieving robust and structured disentanglement of multiple covariates
Research area: Spatial, Omics DataContinuous multi-omics pathway enrichment analysis resolves hidden functional heterogeneity
Research area: Spatial, Omics DataPan-cancer virtual spatial transcriptomics from routine histology with Phoenix
Research area: Single Cell RNA, Gene ExpressionNon-destructive transcriptomics via vesicular export
Research area: Brain, Neurons, ReprogrammingTNF alpha unmasks enteric malate aspartate shuttle dysfunction bridging Parkinson disease and intestinal inflammation
Research area: Cell Atlas, IntegrationAn integrated single cell and spatial omics atlas of human prenatal development
Research area: Diabetes, Children, RiskLarge-scale proteomics across neurological disorders uncovers biomarker panel and targets in multiple sclerosis
Research area: Cell Atlas, IntegrationPerturbation-guided mapping of colorectal cancer cell states to causal mechanisms
Research area: Spatial, Omics DataCP-BG-1M: A CONTROLLED MULTI-VIEW BENCH- MARK FOR DENSITY AND BACKGROUND SHORTCUTS IN MORPHOLOGY PROFILING
Research area: Representations, Single CellGenerative models of cell dynamics: from Neural ODEs to flow matching
Research area: Representations, Single CellLongitudinal modality prediction learns gene regulatory patterns: insights from a single-cell competition
Research area: Representations, Single CellBeyond alignment: synergistic integration is required for multimodal cell foundation models
Research area: Spatial, Omics DataIdentifying 3D signal overlaps in spatial transcriptomics data with ovrlpy
Research area: Spatial, Omics DataIDTrack: Time- and Namespace-Aware Identifier Harmonization for Reproducible Workflows
Research area: Representations, Single CellFrom modality-specific to compositional foundation models for cell biology
Research area: Single Cell RNA, Gene ExpressionCellRank: consistent and data view agnostic fate mapping for single-cell genomics
Research area: Cell Atlas, IntegrationSingle-cell atlas of the transcriptome and chromatin accessibility in the human retina
Research area: Brain, Neurons, ReprogrammingSingle-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
Research area: Brain, Neurons, ReprogrammingBrain Region-Specific Oligodendrocyte States Highlight Mitochondrial Gene Upregulation and Loss of Canonical Identity Signatures in Alzheimer’s Disease
Research area: Brain, Neurons, ReprogrammingA combinatorial transcription factor screening platform for immune cell reprogramming
Research area: miRNA, Target, CancerMultimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers
Research area: Single Cell RNA, Gene ExpressionProtocol for Predicting Cell Fate Responses to in Silico Perturbation using RegVelo, from Code to Agentic Platform Analysis
202558 publications
Research area: Spatial, Omics DataPertpy: an end-to-end framework for perturbation analysis
Research area: Brain, Neurons, ReprogrammingA single-cell cytokine dictionary of human peripheral blood
Research area: Spatial, Omics DataDISCO-seq: 3D single-cell transcriptomics of intact biological systems
Research area: Spatial, Omics DataExploration of RNA outside segmented cells in spatial transcriptomics reveals extrasomatic RNA organization
Research area: Single Cell RNA, Gene ExpressionPseudodynamics+: Reconstructing Population Dynamics from Time-Resolved Single Cell Landscapes with Physics Informed Neural Networks
Research area: Images, Deep LearningActive learning framework leveraging transcriptomics identifies modulators of disease phenotypes
Research area: Spatial, Omics DataOmniPath: integrated knowledgebase for multi-omics analysis
Research area: Spatial, Omics DataQuiCAT: a scalable and flexible framework for mapping synthetic sequences
Research area: Representations, Single CellLanguage may be all omics needs: Harmonizing multimodal data for omics understanding with CellHermes
Research area: Cell Atlas, IntegrationSpatial single-cell atlas reveals regional variations in healthy and diseased human lung
Research area: Representations, Single CellFADVI: disentangled representation learning for robust integration of single-cell and spatial omics data
Research area: Lung, Epithelial CellsToward a ToxAtlas of Carbon-Based Nanomaterials: Single-Cell RNA Sequencing Reveals Initiating Cell Circuits in Pulmonary Inflammation
Research area: Spatial, Omics DataNicheformer: a foundation model for single-cell and spatial omics
Research area: Single Cell RNA, Gene ExpressionIntegrating single-cell RNA-seq datasets with substantial batch effects
Research area: Spatial, Omics DataNicheFlow - Data, Checkpoints, and Results
Research area: Stem Cells, LineageA multimodal cross-species comparison of pancreas development
Research area: Single Cell RNA, Gene Expressionscooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution
Research area: Single Cell RNA, Gene ExpressionMapping early human blood cell differentiation using single-cell proteomics and transcriptomics
Research area: Brain, Neurons, ReprogrammingDisentangling Transcription Factor Programs for Direct Reprogramming with Generative Modeling
Research area: Representations, Single CellscConcept: Contrastive pretraining for technology-agnostic single-cell representations beyond reconstruction
Research area: Spatial, Omics DataAdvancing spatial biology analysis across programming languages
Research area: Spatial, Omics DataGraph neural networks learn emergent tissue properties from spatial molecular profiles
Research area: Representations, Single CellscPortrait integrates single-cell images into multimodal modeling
Research area: Brain, Neurons, ReprogrammingSingle-cell multiome and spatial profiling reveals pancreas cell type–specific gene regulatory programs of type 1 diabetes progression
Research area: Single Cell RNA, Gene ExpressionIm-seq: Multimodal droplet barcoding enables high-throughput linking of single-cell imaging and gene expression
Research area: miRNA, Target, CancerIntegration of cell-type resolved spatial proteomics and transcriptomics reveals novel mechanisms in early ovarian cancer
Research area: miRNA, Target, CancerSpatial proteo-transcriptomic profiling reveals the molecular landscape of borderline ovarian tumors and their invasive progression
Research area: Lung, Epithelial CellsSingle cell decomposition of multicellular aging programs associated with impaired lung regeneration
Research area: Representations, Single CellA foundation model to predict and capture human cognition
Research area: Spatial, Omics DataSpatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data
Research area: Spatial, Omics DataDefining and benchmarking open problems in single-cell analysis
Research area: Representations, Single CellBeyond Visual Inspection: Principled Benchmarking of Single-Cell Trajectory Representations with scTRAM
Research area: Representations, Single CellBiologically Informed Variational Inference Enables Interpretable Cell Phenotyping and Discovery
Research area: Cell Atlas, IntegrationAutomated evaluation of single-cell reference atlas mappings enables the identification of disease-associated cell states
Research area: Spatial, Omics DataCharting the single-cell and spatial landscape of IDH-wild-type glioblastoma with GBmap
Research area: Cell Atlas, IntegrationAn integrated transcriptomic cell atlas of human endoderm-derived organoids
Research area: Brain, Neurons, ReprogrammingGIPR agonism and antagonism decrease body weight and food intake via different mechanisms in male mice
Research area: Brain, Neurons, ReprogrammingExon-variant interplay and multi-modal evidence identify endocrine dysregulation in severe psychiatric disorders impacting excitatory neurons
Research area: Representations, Single CellCellFlow enables generative single-cell phenotype modeling with flow matching
Research area: Representations, Single CellTowards multimodal foundation models in molecular cell biology
Research area: Brain, Neurons, ReprogrammingStress in the ventral hippocampus under single-cell resolution
Research area: Representations, Single CellCausal machine learning for single-cell genomics
Research area: Representations, Single CellUniversalEPI: a generalized attention-based deep ensemble model to accurately predict enhancer-promoter interactions across diverse cell types and conditions
Research area: Spatial, Omics DataQuantitative characterization of cell niches in spatially resolved omics data
Research area: Cell Atlas, Integrationtheislab/atlas-feature-selection-benchmark: 2025-03-15: Publication
Research area: Spatial, Omics DataOptimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows
Research area: Cell Atlas, IntegrationFeature selection methods affect the performance of scRNA-seq data integration and querying
Research area: Representations, Single CellTransformers and genome language models
Research area: Representations, Single CellBiases in machine-learning models of human single-cell data
Research area: Stem Cells, LineageTGIF2 is a major regulator of neural stem cell fate and neurogenic priming
Research area: Brain, Neurons, ReprogrammingChronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids
Research area: Spatial, Omics DataSpatial profiling of human pancreas during type 1 diabetes progression
Research area: Spatial, Omics DataWhat is the main bottleneck in deriving biological understanding from spatial transcriptomic profiling?
Research area: Representations, Single CellUnified Guidance for Geometry-Conditioned Molecular Generation
Research area: Spatial, Omics DataMapping cells through time and space with moscot
Research area: Representations, Single CellPredicting cell morphological responses to perturbations using generative modeling
Research area: Representations, Single CellTarDis: Achieving Robust and Structured Disentanglement of Multiple Covariates
Research area: Cell Atlas, IntegrationData for "Feature selection methods affect the performance of scRNA-seq data integration and querying"
202445 publications
Research area: Representations, Single CellDelineating the effective use of self-supervised learning in single-cell genomics
Research area: Representations, Single CellProCyon: A multimodal foundation model for protein phenotypes
Research area: Cell Atlas, IntegrationConsiderations for building and using integrated single-cell atlases
Research area: Representations, Single CellinVAE: Conditionally invariant representation learning for generating multivariate single-cell reference maps
Research area: miRNA, Target, CancerHeterogeneity-driven phenotypic plasticity and treatment response in branched-organoid models of pancreatic ductal adenocarcinoma
Research area: Single Cell RNA, Gene ExpressionMultiplexing cortical brain organoids for the longitudinal dissection of developmental traits at single-cell resolution
Research area: miRNA, Target, CancerHBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma
Research area: miRNA, Target, CancerModulation of TCR stimulation and pifithrin-α improve the genomic safety profile of CRISPR-engineered human T cells
Research area: Spatial, Omics DataOpportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery
Research area: Cell Atlas, IntegrationAn integrated transcriptomic cell atlas of human neural organoids
Research area: Spatial, Omics DataProbe set selection for targeted spatial transcriptomics
Research area: Representations, Single CellDisentangling cellular heterogeneity into interpretable biological factors through structured latent representations
Research area: Single Cell RNA, Gene ExpressionMapping lineage-traced cells across time points with moslin
Research area: Spatial, Omics DataVitessce: integrative visualization of multimodal and spatially resolved single-cell data
Research area: Images, Deep LearningAn open-source framework for electronic health record and patient fate exploration
Research area: Stem Cells, LineageEndothelial regulatory circuits control cranial neural crest migration and plasticity
Research area: Independent Component, Graphanndata: Access and store annotated data matrices
Research area: Lung, Epithelial CellsMode of actions of nanomaterial-induced respiratory toxicity
Research area: Images, Deep LearningAn open-source framework for end-to-end analysis of electronic health record data
Research area: Cell Atlas, IntegrationSmall data methods in omics: the power of one
Research area: Representations, Single CellScalable and universal prediction of cellular phenotypes enables in silico experiments
Research area: Representations, Single CellscTab: Scaling cross-tissue single-cell annotation models
Research area: Brain, Neurons, ReprogrammingPolyploidisation pleiotropically buffers ageing in hepatocytes
Research area: Representations, Single CellTransformers in single-cell omics: a review and new perspectives
Research area: Cell Atlas, IntegrationWeakly supervised learning uncovers phenotypic signatures in single-cell data
Research area: Images, Deep LearningEvaluation of OCT biomarker changes in treatment-naive neovascular AMD using a deep semantic segmentation algorithm
Research area: miRNA, Target, CancerA liver immune rheostat regulates CD8 T cell immunity in chronic HBV infection
Research area: Spatial, Omics DataPanpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis
Research area: Single Cell RNA, Gene ExpressionMapping the human hematopoietic stem and progenitor cell hierarchy through integrated single-cell proteomics and transcriptomics
Research area: Representations, Single CellMulti-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data
Research area: Spatial, Omics DataGraphCompass: spatial metrics for differential analyses of cell organization across conditions
Research area: Single Cell RNA, Gene ExpressionCellRank 2: unified fate mapping in multiview single-cell data
Research area: Representations, Single CellMachine learning integrative approaches to advance computational immunology
Research area: Images, Deep LearningMISATO: machine learning dataset of protein–ligand complexes for structure-based drug discovery
Research area: Cell Atlas, IntegrationThe future of rapid and automated single-cell data analysis using reference mapping
Research area: Spatial, Omics Datahadge: a comprehensive pipeline for donor deconvolution in single-cell studies
Research area: Brain, Neurons, ReprogrammingShared inflammatory glial cell signature after stab wound injury, revealed by spatial, temporal, and cell-type-specific profiling of the murine cerebral cortex
Research area: Spatial, Omics DataSpatialData: an open and universal data framework for spatial omics
Research area: Independent Component, Graphlongmixr: a tool for robust clustering of high-dimensional cross-sectional and longitudinal variables of mixed data types
Research area: Spatial, Omics DataQuantitative characterization of cell niches in spatial atlases
Research area: Brain, Neurons, ReprogrammingCommunity effort to unravel the complex human neuronal landscape exemplified for the striatum
Research area: Lung, Epithelial CellsCell circuits underlying nanomaterial specific respiratory toxicology
Research area: Lung, Epithelial CellsSfrp1 inhibits lung fibroblast invasion during transition to injury-induced myofibroblasts
Research area: Stem Cells, LineageTime-resolved single-cell transcriptomics defines immune trajectories in glioblastoma
Research area: miRNA, Target, CancerSingle cell transcriptomic analysis of epithelial and mesenchymal tumour cells
202351 publications
Research area: Single Cell RNA, Gene ExpressionOptimal distance metrics for single-cell RNA-seq populations
Research area: Images, Deep LearningDeep Learning-Based Retinal Layer Segmentation in Optical Coherence Tomography Scans of Patients with Inherited Retinal Diseases
Research area: Images, Deep LearningExploratory electronic health record analysis with ehrapy
Research area: Lung, Epithelial CellsEx vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis
Research area: Single Cell RNA, Gene ExpressionModeling fragment counts improves single-cell ATAC-seq analysis
Research area: Brain, Neurons, ReprogrammingEarly life adversity shapes social subordination and cell type–specific transcriptomic patterning in the ventral hippocampus
Research area: Images, Deep LearningExplainable machine learning for profiling the immunological synapse and functional characterization of therapeutic antibodies
Research area: Brain, Neurons, ReprogrammingA reversible state of hypometabolism in a human cellular model of sporadic Parkinson’s disease
Research area: Images, Deep LearningflowVI: Flow Cytometry Variational Inference
Research area: Images, Deep LearningReporting electricity consumption is essential for sustainable AI
Research area: Stem Cells, LineageHuman pluripotent stem cell fate trajectories toward lung and hepatocyte progenitors
Research area: Lung, Epithelial CellsReconstructing disease dynamics for mechanistic insights and clinical benefit
Research area: Representations, Single CellScaling cross-tissue single-cell annotation models
Research area: Cell Atlas, IntegrationPopulation-level integration of single-cell datasets enables multi-scale analysis across samples
Research area: Stem Cells, LineageSingle-cell characterization of neovascularization using hiPSC-derived endothelial cells in a 3D microenvironment
Research area: Diabetes, Children, RiskSystematic analysis of drug combinations against Gram-positive bacteria
Research area: Single Cell RNA, Gene ExpressionDeep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells
Research area: Cell Atlas, IntegrationIdentification of cell types, states and programs by learning gene set representations
Research area: Diabetes, Children, RiskDelineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas
Research area: Lung, Epithelial CellsEx vivo tissue perturbations coupled to single-cell RNA-seq reveal multi-lineage cell circuit dynamics in human lung fibrogenesis
Research area: Cell Atlas, IntegrationA spatially resolved extracellular matrix proteome atlas of the distal human lung
Research area: Spatial, Omics DataMulti-omics regulatory network inference in the presence of missing data
Research area: Diabetes, Children, RiskRobust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel
Research area: Brain, Neurons, ReprogrammingDistinct molecular profiles of skull bone marrow in health and neurological disorders
Research area: Stem Cells, LineageProgressive disruption of hematopoietic architecture from clonal hematopoiesis to MDS
Research area: Psoriasis, Atopic EczemaThe neglected twin: Nummular eczema is a variant of atopic dermatitis with codominant TH2/TH17 immune response
Research area: Psoriasis, Atopic EczemaGene 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
Research area: Spatial, Omics Datahadge: a comprehensive pipeline for donor deconvolution in single cell
Research area: Single Cell RNA, Gene ExpressionUnified fate mapping in multiview single-cell data
Research area: Brain, Neurons, ReprogrammingTolerance of repeated toxic injuries of murine livers is associated with steatosis and inflammation
Research area: Spatial, Omics DataOME-Zarr: a cloud-optimized bioimaging file format with international community support
Research area: Representations, Single CellscARE: Attribution Regularization for Single Cell Representation Learning
Research area: Cell Atlas, IntegrationSingle-cell reference mapping to construct and extend cell-type hierarchies
Research area: Lung, Epithelial CellsLongitudinal Effects of 1-Year Smoking Cessation on Human Bronchial Epithelial Transcriptome
Research area: Representations, Single CellSingle‐cell biology: what does the future hold?
Research area: Single Cell RNA, Gene ExpressionCIARA: a cluster-independent algorithm for identifying markers of rare cell types from single-cell sequencing data
Research area: Lung, Epithelial CellsSystemic alterations in neutrophils and their precursors in early-stage chronic obstructive pulmonary disease
Research area: Spatial, Omics DataWhat do you most hope spatial molecular profiling will help us understand? Part 1
Research area: Cell Atlas, IntegrationAn integrated cell atlas of the lung in health and disease
Research area: Psoriasis, Atopic Eczema394 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
Research area: Images, Deep LearningLearning consistent subcellular landmarks to quantify changes in multiplexed protein maps
Research area: Images, Deep LearningDeciphering subcellular organization with multiplexed imaging and deep learning
Research area: Representations, Single CellPredicting cellular responses to complex perturbations in high‐throughput screens
Research area: Spatial, Omics DataThe scverse project provides a computational ecosystem for single-cell omics data analysis
Research area: Stem Cells, LineageEpicardioid single-cell genomics uncovers principles of human epicardium biology in heart development and disease
Research area: Spatial, Omics DataBest practices for single-cell analysis across modalities
Research area: miRNA, Target, CancerSingle-cell profiling to explore pancreatic cancer heterogeneity, plasticity and response to therapy
Research area: miRNA, Target, CancerSynthetic enforcement of STING signaling in cancer cells appropriates the immune microenvironment for checkpoint inhibitor therapy
Research area: miRNA, Target, CancerHBV rewires liver cancer signaling by altering PP2A complexes
Research area: Cell Atlas, IntegrationBiologically informed deep learning to query gene programs in single-cell atlases
Research area: Representations, Single CellB-Cos Aligned Transformers Learn Human-Interpretable Features
Earlier years1992 to 2022 · 532 publications
202248 publications
Research area: Diabetes, Children, RiskHigh-throughput profiling of drug interactions in Gram-positive bacteria
Research area: Psoriasis, Atopic EczemaSpatial transcriptomics landscape of lesions from non-communicable inflammatory skin diseases
Research area: Brain, Neurons, ReprogrammingT cells modulate the microglial response to brain ischemia
Research area: Spatial, Omics DataSpatial proteomics in three-dimensional intact specimens
Research area: miRNA, Target, CancerA transcriptional cross species map of pancreatic islet cells
Research area: Brain, Neurons, ReprogrammingTDP-43 condensates and lipid droplets regulate the reactivity of microglia and regeneration after traumatic brain injury
Research area: Spatial, Omics DataNetwork reconstruction for trans acting genetic loci using multi-omics data and prior information
Research area: Spatial, Omics DataModeling intercellular communication in tissues using spatial graphs of cells
Research area: Images, Deep LearningPytometry: Flow and mass cytometry analytics in Python
Research area: Single Cell RNA, Gene ExpressionModeling Single-Cell Dynamics Using Unbalanced Parameterized Monge Maps
Research area: Lung, Epithelial CellsEx vivo modeling of human lung fibrogenesis and drug mode of action screens using single cell RNA-seq in precision-cut lung slices
Research area: Brain, Neurons, ReprogrammingSingle cell transcriptomic dissection of virus induced immunopathology in interferon gamma receptor null mice
Research area: Lung, Epithelial CellsEarly transcriptional responses of bronchial epithelial cells to whole cigarette smoke mirror those of in-vivo exposed human bronchial mucosa
Research area: Brain, Neurons, ReprogrammingProbing cell identity hierarchies by fate titration and collision during direct reprogramming
Research area: Brain, Neurons, ReprogrammingPrimary cilia and SHH signaling impairments in human and mouse models of Parkinson’s disease
Research area: Brain, Neurons, ReprogrammingVariant-risk-exon interplay impacts circadian rhythm and dopamine signaling pathway in severe psychiatric disorders
Research area: Images, Deep LearningInterpretable surface-based detection of focal cortical dysplasias: a Multi-centre Epilepsy Lesion Detection study
Research area: Brain, Neurons, ReprogrammingPathogenic variants damage cell composition and single cell transcription in cardiomyopathies
Research area: miRNA, Target, CancerSynaptotagmin-13 orchestrates pancreatic endocrine cell egression and islet morphogenesis
Research area: Single Cell RNA, Gene ExpressionCIARA: a cluster-independent algorithm for the identification of markers of rare cell types from single-cell RNA seq data
Research area: Lung, Epithelial CellsAssociation of bronchial steroid inducible methylation quantitative trait loci with asthma and chronic obstructive pulmonary disease treatment response
Research area: Spatial, Omics DataProteomics of spatially identified tissues in whole organs
Research area: Lung, Epithelial CellsAlveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation
Research area: Stem Cells, LineageOrigin and function of activated fibroblast states during zebrafish heart regeneration
Research area: Representations, Single CellMultiCPA: Multimodal Compositional Perturbation Autoencoder
Research area: Brain, Neurons, ReprogrammingKetamine exerts its sustained antidepressant effects via cell-type-specific regulation of Kcnq2
Research area: Diabetes, Children, RiskHeterogeneous Development of β-Cell Populations in Diabetes-Resistant and -Susceptible Mice
Research area: Stem Cells, LineageLy6D+Siglec-H+ precursors contribute to conventional dendritic cells via a Zbtb46+Ly6D+ intermediary stage
Research area: Lung, Epithelial CellsMature neutrophils and a NF-κB-to-IFN transition determine the unifying disease recovery dynamics in COVID-19
Research area: Psoriasis, Atopic EczemaGene 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
Research area: Brain, Neurons, ReprogrammingCell-Type-Specific Impact of Glucocorticoid Receptor Activation on the Developing Brain: A Cerebral Organoid Study
Research area: Representations, Single CellMultimodal single cell data integration challenge: results and lessons learned
Research area: Brain, Neurons, ReprogrammingParkinson's disease motor symptoms rescue by CRISPRa‐reprogramming astrocytes into GABAergic neurons
Research area: Cell Atlas, IntegrationIntegration and querying of multimodal single-cell data with PoE-VAE
Research area: Diabetes, Children, RiskConcept of the Munich/Augsburg Consortium Precision in Mental Health for the German Center of Mental Health
Research area: Representations, Single CellToward modeling metabolic state from single-cell transcriptomics
Research area: Diabetes, Children, RiskUltra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation
Research area: miRNA, Target, CancerRapid Inhibitor Discovery by Exploiting Synthetic Lethality
Research area: Spatial, Omics DataSpatial components of molecular tissue biology
Research area: Spatial, Omics DataA Python library for probabilistic analysis of single-cell omics data
Research area: Lung, Epithelial CellsEffect 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)
Research area: Spatial, Omics DataSquidpy: a scalable framework for spatial omics analysis
Research area: Cell Atlas, IntegrationThe discovAIR project: a roadmap towards the Human Lung Cell Atlas
Research area: Stem Cells, LineageIntegration of single-cell transcriptomes and chromatin landscapes reveals regulatory programs driving pharyngeal organ development
Research area: Single Cell RNA, Gene ExpressionCellRank for directed single-cell fate mapping
Research area: Brain, Neurons, ReprogrammingRepeated toxic injuries of murine liver are tolerated through microsteatosis and mild inflammation
Research area: Images, Deep LearningNoise Transfer for Unsupervised Domain Adaptation of Retinal OCT Images
Research area: Cell Atlas, IntegrationBenchmarking atlas-level data integration in single-cell genomics - integration task datasets
202141 publications
Research area: Brain, Neurons, ReprogrammingMulti-omics and 3D-imaging reveal bone heterogeneity and unique calvaria cells in neuroinflammation
Research area: Cell Atlas, IntegrationBenchmarking atlas-level data integration in single-cell genomics
Research area: Lung, Epithelial CellsSARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis
Research area: Representations, Single CellGraph representation learning for single-cell biology
Research area: Diabetes, Children, RiskVertical sleeve gastrectomy triggers fast β-cell recovery upon overt diabetes
Research area: Single Cell RNA, Gene ExpressionscCODA is a Bayesian model for compositional single-cell data analysis
Research area: Single Cell RNA, Gene ExpressionscPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies
Research area: Lung, Epithelial CellsDeterminants of expression of SARS‐CoV‐2 entry‐related genes in upper and lower airways
Research area: Single Cell RNA, Gene ExpressionOver 1000 tools reveal trends in the single-cell RNA-seq analysis landscape
Research area: Images, Deep LearningA field guide to cultivating computational biology
Research area: Images, Deep LearningKünstliche Intelligenz und maschinelles Lernen in der Diabetesforschung
Research area: Lung, Epithelial CellsCurrent Smoking Alters Gene Expression and DNA Methylation in the Nasal Epithelium of Patients with Asthma
Research area: Stem Cells, LineageDiet-induced alteration of intestinal stem cell function underlies obesity and prediabetes in mice
Research area: Stem Cells, LineageAged alveolar epithelium contributes to inflammaging and reduced stem cell function in the lung
Research area: Lung, Epithelial CellsChronic WNT/ß-catenin signaling impairs mitochondrial function in lung epithelial cells
Research area: Representations, Single CellOut-of-distribution prediction with disentangled representations for single-cell RNA sequencing data
Research area: Single Cell RNA, Gene ExpressionEpiScanpy: integrated single-cell epigenomic analysis
Research area: Cell Atlas, IntegrationMapping single-cell data to reference atlases by transfer learning
Research area: Representations, Single CellSfaira accelerates data and model reuse in single cell genomics
Research area: Images, Deep LearningGroup Testing for SARS-CoV-2 Allows for Up to 10-Fold Efficiency Increase Across Realistic Scenarios and Testing Strategies
Research area: Single Cell RNA, Gene ExpressionRNA velocity—current challenges and future perspectives
Research area: Lung, Epithelial CellsSingle-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through ‘reverse phenotyping’
Research area: Single Cell RNA, Gene ExpressionAutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution
Research area: miRNA, Target, CancerCD81 marks immature and dedifferentiated pancreatic β-cells
Research area: Stem Cells, LineageEpithelial cell plasticity drives endoderm formation during gastrulation
Research area: Psoriasis, Atopic EczemaLow numbers of cytokine transcripts drive inflammatory skin diseases by initiating amplification cascades in localized epidermal clusters
Research area: Representations, Single CellMachine learning for perturbational single-cell omics
Research area: Images, Deep LearningSwarm Learning for decentralized and confidential clinical machine learning
Research area: fMRI Data, NetworkCellular connectomes as arbiters of local circuit models in the cerebral cortex
Research area: Single Cell RNA, Gene ExpressionComparison 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?
Research area: miRNA, Target, CancerAsc-1 regulates white versus beige adipocyte fate in a subcutaneous stromal cell population
Research area: Lung, Epithelial CellsIntegrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers
Research area: Spatial, Omics DataIntegrated intra‐ and intercellular signaling knowledge for multicellular omics analysis
Research area: Psoriasis, Atopic EczemaCD23 Levels on B Cells Determine Long-Term Therapeutic Response in Patients with Atopic Eczema Treated with Selective IgE Immune Apheresis
Research area: Diabetes, Children, RiskPosterior subcapsular cataracts are a late effect after acute exposure to 0.5 Gy ionizing radiation in mice
Research area: Stem Cells, LineageSingle cell trajectory analysis of human pluripotent stem cells differentiating towards lung and hepatocyte progenitors
Research area: Spatial, Omics DataSquidpy: a scalable framework for spatial single cell analysis
Research area: Diabetes, Children, RiskDeep learning the collisional cross sections of the peptide universe from a million experimental values
Research area: Images, Deep LearningDeep Learning-based Propensity Scores for Confounding Control in Comparative Effectiveness Research
Research area: Brain, Neurons, ReprogrammingSingle-cell molecular profiling of all three components of the HPA axis reveals adrenal ABCB1 as a regulator of stress adaptation
Research area: Stem Cells, LineageNon-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates
202033 publications
Research area: Representations, Single CellLearning interpretable latent autoencoder representations with annotations of feature sets
Research area: Single Cell RNA, Gene Expression[DEPRECATED] Theislab sfaira Model Repository
Research area: Images, Deep LearningA sparse deep learning approach for automatic segmentation of human vasculature in multispectral optoacoustic tomography
Research area: Representations, Single CellConditional out-of-distribution generation for unpaired data using transfer VAE
Research area: miRNA, Target, CancerIdentification and characterization of distinct brown adipocyte subtypes in C57BL/6J mice
Research area: Images, Deep LearningSelf-supervised retinal thickness prediction enables deep learning from unlabelled data to boost classification of diabetic retinopathy
Research area: Lung, Epithelial CellsInhibition of LTβR signalling activates WNT-induced regeneration in lung
Research area: Images, Deep LearningPredicting single-cell gene expression profiles of imaging flow cytometry data with machine learning
Research area: Diabetes, Children, RiskAsthma in farm children is more determined by genetic polymorphisms and in non‐farm children by environmental factors
Research area: Lung, Epithelial CellsLifeTime and improving European healthcare through cell-based interceptive medicine
Research area: Images, Deep LearningProtocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19)
Research area: miRNA, Target, CancerIdentification and characterization of distinct murine brown adipocyte lineages
Research area: Stem Cells, LineageWnt/PCP-primed intestinal stem cells directly differentiate into enteroendocrine or Paneth cells
Research area: Single Cell RNA, Gene ExpressionGeneralizing RNA velocity to transient cell states through dynamical modeling
Research area: Representations, Single CellPredicting antigen specificity of single T cells based on TCR CDR3 regions
Research area: Lung, Epithelial CellsAlveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis
Research area: Images, Deep LearningIn vivo identification of apoptotic and extracellular vesicle‐bound live cells using image‐based deep learning
Research area: Cell Atlas, IntegrationQuery to reference single-cell integration with transfer learning
Research area: Brain, Neurons, ReprogrammingPost-surgical adhesions are triggered by calcium-dependent membrane bridges between mesothelial surfaces
Research area: Diabetes, Children, RiskThe proteome landscape of the kingdoms of life
Research area: Lung, Epithelial CellsAlterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease
Research area: Lung, Epithelial CellsSARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues
Research area: Lung, Epithelial CellsChronic Wnt Signaling Contributes to Lung Epithelial Senescence and Aging
Research area: Single Cell RNA, Gene ExpressionAutomatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data
Research area: Single Cell RNA, Gene ExpressionThe single-cell eQTLGen consortium
Research area: Diabetes, Children, RiskModel-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines
Research area: Stem Cells, LineageEpithelial Planar Bipolarity Emerges from Notch-Mediated Asymmetric Inhibition of Emx2
Research area: Diabetes, Children, RiskTargeted pharmacological therapy restores β-cell function for diabetes remission
Research area: Representations, Single CellEleven grand challenges in single-cell data science
Research area: Metabolite, Association, Metabolomics DataDeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning
Research area: Psoriasis, Atopic EczemaIL‐17C amplifies epithelial inflammation in human psoriasis and atopic eczema
Research area: Brain, Neurons, ReprogrammingCell-type specific impact of glucocorticoid receptor activation on the developing brain
Research area: Representations, Single CellLearning Tn5 Sequence Bias from ATAC-seq on Naked Chromatin
201942 publications
Research area: Brain, Neurons, ReprogrammingS.11.01 Brain organoids as models of the developing human brain: deciphering the molecular signature of prenatal stress
Research area: Stem Cells, LineageEstablishment of a high-resolution 3D modeling system for studying pancreatic epithelial cell biology in vitro
Research area: fMRI Data, Networkggplot.multistats: Multiple Summary Statistics for Binned Stats/Geometries
Research area: Independent Component, Graphknn.covertree: An Accurate kNN Implementation with Multiple Distance Measures
Research area: Stem Cells, LineageAldh1b1 expression defines progenitor cells in the adult pancreas and is required for Kras-induced pancreatic cancer
Research area: Representations, Single CellMPRAnalyze: statistical framework for massively parallel reporter assays
Research area: miRNA, Target, CancerPheno-seq – linking visual features and gene expression in 3D cell culture systems
Research area: Single Cell RNA, Gene ExpressionBART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis
Research area: Representations, Single CellscGen predicts single-cell perturbation responses
Research area: Lung, Epithelial CellsLongitudinal single cell transcriptomics reveals Krt8+ alveolar epithelial progenitors in lung regeneration
Research area: Images, Deep LearningEvaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images
Research area: Single Cell RNA, Gene ExpressionscSLAM-seq reveals core features of transcription dynamics in single cells
Research area: Representations, Single CellFaculty Opinions recommendation of Deep generative modeling for single-cell transcriptomics.
Research area: Representations, Single CellMeeting the Challenges of High-Dimensional Single-Cell Data Analysis in Immunology
Research area: Cell Atlas, IntegrationThe Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease
Research area: Lung, Epithelial CellsA cellular census of human lungs identifies novel cell states in health and in asthma
Research area: Single Cell RNA, Gene ExpressionConcepts and limitations for learning developmental trajectories from single cell genomics
Research area: Stem Cells, LineageComprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis
Research area: Spatial, Omics DataInferring Interaction Networks From Multi-Omics Data
Research area: Diabetes, Children, RiskIntegrated analysis of environmental and genetic influences on cord blood DNA methylation in new-borns
Research area: Single Cell RNA, Gene ExpressionCurrent best practices in single‐cell RNA‐seq analysis: a tutorial
Research area: Images, Deep LearningDeep learning does not outperform classical machine learning for cell-type annotation
Research area: Metabolite, Association, Metabolomics DataDynamic modelling of an ACADS genotype in fatty acid oxidation – Application of cellular models for the analysis of common genetic variants
Research area: Diabetes, Children, RiskA map of β-cell differentiation pathways supports cell therapies for diabetes
Research area: Lung, Epithelial CellsAltered relaxation times in MRI indicate bronchopulmonary dysplasia
Research area: Diabetes, Children, RiskCommon patterns of gene regulation associated with Cesarean section and the development of islet autoimmunity – indications of immune cell activation
Research area: Images, Deep LearningDeep learning: new computational modelling techniques for genomics
Research area: Single Cell RNA, Gene ExpressionInferring population dynamics from single-cell RNA-sequencing time series data
Research area: Diabetes, Children, RiskA strategy for high‐dimensional multivariable analysis classifies childhood asthma phenotypes from genetic, immunological, and environmental factors
Research area: Single Cell RNA, Gene ExpressionPAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells
Research area: Lung, Epithelial CellsAn atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics
Research area: miRNA, Target, CancerIRE1α-XBP1s pathway promotes prostate cancer by activating c-MYC signaling
Research area: Single Cell RNA, Gene ExpressionSingle-cell RNA-seq denoising using a deep count autoencoder
Research area: Lung, Epithelial CellsA cellular census of healthy lung and asthmatic airway wall identifies novel cell states in health and disease
Research area: Images, Deep LearningEditorial: Integrative Computational Systems Biology Approaches in Immunology and Medicine
Research area: fMRI Data, NetworkArtificial Neural Networks and Machine Learning – ICANN 2019: Theoretical Neural Computation
Research area: fMRI Data, NetworkArtificial Neural Networks and Machine Learning – ICANN 2019: Workshop and Special Sessions
Research area: Spatial, Omics DataWHAT SHAPES THE CHILD'S EPIGENOME: GENOTYPE, PRENATAL ENVIRONMENT OR BOTH?
Research area: Metabolite, Association, Metabolomics DataPOLYGENIC BURDEN ANALYSIS OF LONGITUDINAL CLUSTERS OF PSYCHOPATHOLOGICAL FEATURES IN A CROSS-DIAGNOSTIC GROUP OF INDIVIDUALS WITH SEVERE MENTAL ILLNESS
Research area: Spatial, Omics DataGENOTYPE, PRENATAL ENVIRONMENT OR BOTH–WHAT SHAPES THE NEWBORN'S EPIGENOME?
Research area: Diabetes, Children, RiskF96POLYGENIC RISK SCORE ANALYSIS OF TRAJECTORIES OF COGNITIVE PERFORMANCE IN PSYCHIATRIC PATIENTS
Research area: Metabolite, Association, Metabolomics DataSA125POLYGENIC BURDEN ANALYSIS OF LONGITUDINAL CLUSTERS OF PSYCHOPATHOLOGICAL FEATURES IN A CROSS-DIAGNOSTIC GROUP OF INDIVIDUALS WITH SEVERE MENTAL ILLNESS
201832 publications
Research area: Cell Atlas, IntegrationA test metric for assessing single-cell RNA-seq batch correction
Research area: Spatial, Omics DataMulti-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection
Research area: Stem Cells, LineageIncreasing Neural Stem Cell Division Asymmetry and Quiescence Are Predicted to Contribute to the Age-Related Decline in Neurogenesis
Research area: Diabetes, Children, RiskEfficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model
Research area: fMRI Data, NetworkMechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data
Research area: Representations, Single CellGenerative modeling and latent space arithmetics predict single-cell perturbation response across cell types, studies and species
Research area: Stem Cells, LineageData Driven Computational Modeling of Hematopoiesis in Myelodysplastic Syndromes Unveils Differences in Hematopoietic Stem Cell Kinetics Compared to Age-Matched Healthy Controls
Research area: ICA, Subspace, Joint DiagonalizationIRkernel: Native R Kernel for the 'Jupyter Notebook'
Research area: Brain, Neurons, ReprogrammingImpact of Brain Fatty Acid Signaling on Peripheral Insulin Action in Mice
Research area: Independent Component, GraphCopy number aberrations from Affymetrix SNP 6.0 genotyping data—how accurate are commonly used prediction approaches?
Research area: Single Cell RNA, Gene ExpressionMetaMap, an interactive webtool for the exploration of metatranscriptomic reads in human disease-related RNA-seq data
Research area: Stem Cells, LineageMetabolic regulation of pluripotency and germ cell fate through α‐ketoglutarate
Research area: Metabolite, Association, Metabolomics DataCharacterization of missing values in untargeted MS-based metabolomics data and evaluation of missing data handling strategies
Research area: Single Cell RNA, Gene ExpressionImpulse model-based differential expression analysis of time course sequencing data
Research area: Psoriasis, Atopic EczemaType I Immune Response Induces Keratinocyte Necroptosis and Is Associated with Interface Dermatitis
Research area: Stem Cells, LineageLineage marker synchrony in hematopoietic genealogies refutes the PU.1/GATA1 toggle switch paradigm
Research area: Psoriasis, Atopic EczemaIs the humoral immunity dispensable for the pathogenesis of psoriasis?
Research area: Stem Cells, LineageInductive and Selective Effects of GSK3 and MEK Inhibition on Nanog Heterogeneity in Embryonic Stem Cells
Research area: fMRI Data, NetworkBayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering
Research area: Single Cell RNA, Gene ExpressionMetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data
Research area: Psoriasis, Atopic EczemaThe role of humoral immunity in the pathogenesis of psoriasis
Research area: Stem Cells, LineageCell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics
Research area: Psoriasis, Atopic EczemaMathematical concepts and their challenges in predicting severity of atopic eczema patients
Research area: Psoriasis, Atopic EczemaToll-like receptor 7/8 agonists stimulate plasmacytoid dendritic cells to initiate TH17-deviated acute contact dermatitis in human subjects
Research area: Diabetes, Children, RiskEarly Identification of Bronchopulmonary Dysplasia Using Novel Biomarkers by Proteomic Screening
Research area: Representations, Single CellFASTGenomics: An analytical ecosystem for single-cell RNA sequencing data
Research area: miRNA, Target, CancerEpigenetically Regulated Chromosome 14q32 miRNA Cluster Induces Metastasis and Predicts Poor Prognosis in Lung Adenocarcinoma Patients
Research area: Images, Deep LearningWhither systems medicine?
Research area: Single Cell RNA, Gene ExpressionSCANPY: large-scale single-cell gene expression data analysis
Research area: miRNA, Target, CancerMaternal whole blood cell miRNA-340 is elevated in gestational diabetes and inversely regulated by glucose and insulin
Research area: Diabetes, Children, RiskLifetime study in mice after acute low-dose ionizing radiation: a multifactorial study with special focus on cataract risk
Research area: Metabolite, Association, Metabolomics DataLNA++: Linear Noise Approximation with First and Second Order Sensitivities
201734 publications
Research area: Cell Atlas, IntegrationThe Human Cell Atlas
Research area: Metabolite, Association, Metabolomics DataNetwork inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway
Research area: Stem Cells, LineageGATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency
Research area: Independent Component, GraphnetReg: network-regularized linear models for biological association studies
Research area: fMRI Data, NetworkModel Based Targeting of IL-6-Induced Inflammatory Responses in Cultured Primary Hepatocytes to Improve Application of the JAK Inhibitor Ruxolitinib
Research area: Psoriasis, Atopic Eczema360 Interface Dermatitis is characterized by a type I immune response and an epidermal reaction to IFN-γ and TNF-α
Research area: Psoriasis, Atopic Eczema489 TLR7/8 agonists stimulate plasmacytoid dendritic cells to initiate a Th17-deviated acute contact dermatitis in humans
Research area: Metabolite, Association, Metabolomics Datapulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms
Research area: Images, Deep LearningReconstructing cell cycle and disease progression using deep learning
Research area: miRNA, Target, CancerSystematic single-cell analysis provides new insights into heterogeneity and plasticity of the pancreas
Research area: Spatial, Omics Data2D cross-omics integrated enrichment analysis reveals insights into COPD pathogenesis
Research area: miRNA, Target, CancerMicroRNA as an Integral Part of Cell Communication: Regularized Target Prediction and Network Prediction
Research area: Independent Component, GraphInformation Theoretic Concepts to Unravel Cell–Cell Communication
Research area: Representations, Single CellSingle cells make big data: New challenges and opportunities in transcriptomics
Research area: fMRI Data, NetworkA scalable moment-closure approximation for large-scale biochemical reaction networks
Research area: Diabetes, Children, RiskPrediction of type 1 diabetes using a genetic risk model in the Diabetes Autoimmunity Study in the Young
Research area: fMRI Data, NetworkComprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems
Research area: miRNA, Target, CancerIdentification of a plasma miRNA biomarker signature for allergic asthma: A translational approach
Research area: Images, Deep LearningA BaSiC tool for background and shading correction of optical microscopy images
Research area: Single Cell RNA, Gene ExpressionModel-based branching point detection in single-cell data by K-branches clustering
Research area: Single Cell RNA, Gene ExpressioncgCorrect: a method to correct for confounding cell–cell variation due to cell growth in single-cell transcriptomics
Research area: miRNA, Target, CancerPulmonary microRNA profiles identify involvement of Creb1 and Sec14l3 in bronchial epithelial changes in allergic asthma
Research area: Images, Deep LearningfastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy
Research area: Stem Cells, LineageProspective identification of hematopoietic lineage choice by deep learning
Research area: miRNA, Target, CancerCalcium-regulatory proteins as modulators of chemotherapy in human neuroblastoma
Research area: fMRI Data, NetworkParallelization and High-Performance Computing Enables Automated Statistical Inference of Multi-scale Models
Research area: Images, Deep LearningLabel Free Identification of Peripheral Blood Eosinophils Using High-Throughput Imaging Flow Cytometry
Research area: fMRI Data, NetworkScalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
Research area: miRNA, Target, CancerAURKA, DLGAP5, TPX2, KIF11 and CKAP5: Five specific mitosis-associated genes correlate with poor prognosis for non-small cell lung cancer patients
Research area: Metabolite, Association, Metabolomics DataPolygenic Burden Analysis of Longitudinal Clusters of Psychopathological Features In A Cross-Diagnostic Group of Individuals with Severe Mental Illness
Research area: Metabolite, Association, Metabolomics DataIntegrating Polygenic Allele Burden Information And Phenomic Data To Characterize Complex Disease Trajectories In Severe Mental Illness
Research area: Metabolite, Association, Metabolomics DataPOLYGENIC BURDEN ANALYSIS OF LONGITUDINAL CLUSTERS OF QUALITY OF LIFE AND FUNCTIONING IN PATIENTS WITH SEVERE MENTAL ILLNESS
Research area: Metabolite, Association, Metabolomics DataThe Role Of Micrornas In The Course Of Severe Mental Disorders
Research area: Images, Deep LearningCorrecting Classifiers for Sample Selection Bias in Two-Phase Case-Control Studies
201643 publications
Research area: fMRI Data, NetworkParameter estimation for dynamical systems with discrete events and logical operations
Research area: Diabetes, Children, RiskLarge-scale modeling of cancer signaling: Mechanistic modeling meets Big Data
Research area: Diabetes, Children, RiskIdentification of predictive response and resistance factors to targeted therapy in gastric cancer using a systems medicine approach
Research area: fMRI Data, NetworkInferring catalysis in biological systems
Research area: Diabetes, Children, RiskPeptide serum markers in islet autoantibody-positive children
Research area: Stem Cells, LineageAnalysis of Cell Lineage Trees by Exact Bayesian Inference Identifies Negative Autoregulation of Nanog in Mouse Embryonic Stem Cells
Research area: Psoriasis, Atopic EczemaA computational model to predict severity of atopic eczema from 30 serum proteins
Research area: Psoriasis, Atopic EczemaA novel molecular disease classifier for psoriasis and eczema
Research area: miRNA, Target, CancerDynamic landscape of pancreatic carcinogenesis reveals early molecular networks of malignancy
Research area: miRNA, Target, CancerTALEN/CRISPR-mediated engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus
Research area: Psoriasis, Atopic Eczema340 Interface dermatitis shows a distinctive molecular signature independent from individual disease background
Research area: Independent Component, GraphLSC Abstract – Systemic and local metabolomics profiling reveals novel insights into the progression of emphysema
Research area: Independent Component, GraphLSC Abstract – Systemic and local metabolomics profiling reveals novel insights into the progression of emphysema
Research area: Lung, Epithelial CellsLSC Abstract – Early biomarkers indicating the development of neonatal chronic lung disease defined by clinical and imaging parameters
Research area: Independent Component, GraphDiffusion pseudotime robustly reconstructs lineage branching
Research area: fMRI Data, NetworkTailored parameter optimization methods for ordinary differential equation models with steady-state constraints
Research area: ICA, Subspace, Joint DiagonalizationIRdisplay: 'Jupyter' Display Machinery
Research area: fMRI Data, NetworkInference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion
Research area: Metabolite, Association, Metabolomics DataLactation is associated with altered metabolomic signatures in women with gestational diabetes
Research area: miRNA, Target, CancerAbstract 1945: Identification of a miRNA/mRNA network driving non-small cell lung cancer (NSCLC) dissemination
Research area: Diabetes, Children, RiskClinical impact of GATA2 mutations in acute myeloid leukemia patients harboring CEBPA mutations: a study of the AML study group
Research area: Lung, Epithelial CellsInterleukin-4 and interferon-γ orchestrate an epithelial polarization in the airways
Research area: Stem Cells, LineageEarly myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios
Research area: Representations, Single CellSoftware tools for single-cell tracking and quantification of cellular and molecular properties
Research area: Spatial, Omics DataComputational approaches for systems metabolomics
Research area: Images, Deep LearningEditorial overview: Systems biology-the intersection of experiments and computation, underpinning biotechnology
Research area: Representations, Single Cellrepr: Serializable Representations
Research area: Psoriasis, Atopic EczemaA novel molecular disease classifier for eczema and psoriasis
Research area: Single Cell RNA, Gene ExpressionMEMO: multi-experiment mixture model analysis of censored data
Research area: fMRI Data, NetworkUnbiased Prediction and Feature Selection in High-Dimensional Survival Regression
Research area: miRNA, Target, CancermiTALOS v2: Analyzing Tissue Specific microRNA Function
Research area: Diabetes, Children, RiskEpigenetic germline inheritance of diet-induced obesity and insulin resistance
Research area: Metabolite, Association, Metabolomics DataMetabolomics reveals effects of maternal smoking on endogenous metabolites from lipid metabolism in cord blood of newborns
Research area: miRNA, Target, CancerPitchfork and Gprasp2 Target Smoothened to the Primary Cilium for Hedgehog Pathway Activation
Research area: Lung, Epithelial CellsAbstract P1-06-02: A force-sensitive organoid assay to quantify regenerative potential of single primary human mammary cells
Research area: miRNA, Target, CancerMicroRNA-138 promotes acquired alkylator resistance in glioblastoma by targeting the Bcl-2-interacting mediator BIM
Research area: Stem Cells, LineageThe global gene expression profile of the secondary transition during pancreatic development
Research area: fMRI Data, NetworkCERENA: ChEmical REaction Network Analyzer—A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics
Research area: Lung, Epithelial CellsMetabolomics screening identifies reduced L-carnitine to be associated with progressive emphysema
Research area: Images, Deep LearningLabel-free cell cycle analysis for high-throughput imaging flow cytometry
Research area: Representations, Single CellCombinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions
Research area: Images, Deep LearningMitosis Detection in Intestinal Crypt Images with Hough Forest and Conditional Random Fields
Research area: fMRI Data, NetworkQuantitative 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
Research area: miRNA, Target, CancerMicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma
Research area: Single Cell RNA, Gene Expressiondestiny: diffusion maps for large-scale single-cell data in R
Research area: fMRI Data, NetworkBayesian Model Selection Methods and Their Application to Biological ODE Systems
Research area: fMRI Data, NetworkIdentifying latent dynamic components in biological systems
Research area: Stem Cells, LineageNetwork plasticity of pluripotency transcription factors in embryonic stem cells
Research area: Single Cell RNA, Gene ExpressionInference of spatiotemporal effects on cellular state transitions from time-lapse microscopy
Research area: Blind Source Separation, Sparse ComponentSeparation of Uncorrelated Stationary time series using Autocovariance Matrices
Research area: miRNA, Target, CancerSimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins
Research area: miRNA, Target, CancerIntegrative Analysis of MicroRNA and mRNA Data Reveals an Orchestrated Function of MicroRNAs in Skeletal Myocyte Differentiation in Response to TNF-α or IGF1
Research area: Metabolite, Association, Metabolomics DataGender-specific pathway differences in the human serum metabolome
Research area: Blind Source Separation, Sparse ComponentModel selection using limiting distributions of second-order blind source separation algorithms
Research area: fMRI Data, NetworkData2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems
Research area: Brain, Neurons, ReprogrammingTranscriptional Mechanisms of Proneural Factors and REST in Regulating Neuronal Reprogramming of Astrocytes
Research area: Metabolite, Association, Metabolomics DataThe Human Blood Metabolome-Transcriptome Interface
Research area: Single Cell RNA, Gene ExpressionReconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data
Research area: Spatial, Omics DataData-Driven Modelling of Biological Multi-Scale Processes
Research area: Stem Cells, LineageCombined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations
Research area: Diabetes, Children, RiskOpposing effects of allogrooming on disease transmission in ant societies
Research area: Single Cell RNA, Gene ExpressionDiffusion maps for high-dimensional single-cell analysis of differentiation data
Research area: Representations, Single CellAtrx promotes heterochromatin formation at retrotransposons
Research area: Stem Cells, LineageLive imaging of adult neural stem cell behavior in the intact and injured zebrafish brain
Research area: miRNA, Target, CancerNext-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer
Research area: Diabetes, Children, RiskEffects of High-Dose Oral Insulin on Immune Responses in Children at High Risk for Type 1 Diabetes
Research area: Brain, Neurons, ReprogrammingA Critical Period for Postnatal Adaptive Plasticity in a Model of Motor Axon Miswiring
Research area: Metabolite, Association, Metabolomics DataAnatomic-landmark detection using graphical context modelling
Research area: Metabolite, Association, Metabolomics DataMulti-omic signature of body weight change: results from a population-based cohort study
Research area: Cell Atlas, IntegrationAn adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson’s rule
Research area: Stem Cells, LineageFast clonal expansion and limited neural stem cell self-renewal in the adult subependymal zone
Research area: Single Cell RNA, Gene ExpressionDecoding the regulatory network of early blood development from single-cell gene expression measurements
Research area: Lung, Epithelial CellsMetabolism gene signatures and surgical site infections in abdominal surgery
Research area: miRNA, Target, CancermiR-23a-3p Causes Cellular Senescence by Targeting Hyaluronan Synthase 2: Possible Implication for Skin Aging
Research area: Single Cell RNA, Gene ExpressionComputational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
Research area: miRNA, Target, CancerA subset of metastatic pancreatic ductal adenocarcinomas depends quantitatively on oncogenic Kras/Mek/Erk-induced hyperactive mTOR signalling
Research area: Lung, Epithelial CellsQuantification of regenerative potential in primary human mammary epithelial cells
Research area: Stem Cells, LineageStem-Cell-like Properties and Epithelial Plasticity Arise as Stable Traits after Transient Twist1 Activation
Research area: Independent Component, GraphAn Affine Equivariant Robust Second-Order BSS Method
Research area: Single Cell RNA, Gene ExpressionApproximate Bayesian Computation for Stochastic Single-Cell Time-Lapse Data Using Multivariate Test Statistics
201422 publications
Research area: Metabolite, Association, Metabolomics DataNetwork-Based Approach for Analyzing Intra- and Interfluid Metabolite Associations in Human Blood, Urine, and Saliva
Research area: miRNA, Target, CancerProteome-wide analysis reveals an age-associated cellular phenotype of in situ aged human fibroblasts
Research area: Blind Source Separation, Sparse ComponentBayesian Blind Source Separation for Data with Network Structure
Research area: Spatial, Omics DataRAMONA: a Web application for gene set analysis on multilevel omics data
Research area: Diabetes, Children, RiskFeature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes
Research area: Brain, Neurons, ReprogrammingMouse IDGenes: a reference database for genetic interactions in the developing mouse brain
Research area: miRNA, Target, CancerHypothalamic miR-103 Protects from Hyperphagic Obesity in Mice
Research area: Single Cell RNA, Gene ExpressionDecoding the transcriptional program for blood development from whole tissue single-cell gene expression measurements
Research area: Stem Cells, LineageCytokine-regulated GADD45G induces differentiation and lineage selection in hematopoietic stem cells
Research area: Psoriasis, Atopic EczemaAllergic Contact Dermatitis in Psoriasis Patients: Typical, Delayed, and Non-Interacting
Research area: Single Cell RNA, Gene ExpressionMCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data
Research area: Psoriasis, Atopic EczemaIntraindividual genome expression analysis reveals a specific molecular signature of psoriasis and eczema
Research area: fMRI Data, NetworkODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics
Research area: Stem Cells, LineageCytokine-Regulated GADD45G Induces Differentiation and Lineage Selection in Hematopoietic Stem Cells
Research area: Metabolite, Association, Metabolomics DataNovel genetic associations with serum level metabolites identified by phenotype set enrichment analyses
Research area: Metabolite, Association, Metabolomics DataAn atlas of genetic influences on human blood metabolites
Research area: Single Cell RNA, Gene ExpressionProbabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data
Research area: Stem Cells, LineagemiR-335 promotes mesendodermal lineage segregation and shapes a transcription factor gradient in the endoderm
Research area: Single Cell RNA, Gene ExpressionParameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles
Research area: miRNA, Target, CancerPosttranscriptional Regulatory Networks: From Expression Profiling to Integrative Analysis of mRNA and MicroRNA Data
Research area: Independent Component, GraphCentroid Clustering of Cellular Lineage Trees
Research area: fMRI Data, NetworkUncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More
201327 publications
Research area: fMRI Data, NetworkHigh-dimensional Bayesian parameter estimation: Case study for a model of JAK2/STAT5 signaling
Research area: Independent Component, GraphDependent component analysis
Research area: Diabetes, Children, RiskA strategy to find gene combinations that identify children who progress rapidly to type 1 diabetes after islet autoantibody seroconversion
Research area: fMRI Data, NetworkiVUN: interactive Visualization of Uncertain biochemical reaction Networks
Research area: Images, Deep LearningAn automatic method for robust and fast cell detection in bright field images from high-throughput microscopy
Research area: miRNA, Target, CancerWound-healing growth factor, basic FGF, induces Erk1/2-dependent mechanical hyperalgesia
Research area: fMRI Data, NetworkLessons Learned from Quantitative Dynamical Modeling in Systems Biology
Research area: Spatial, Omics DataA modular framework for gene set analysis integrating multilevel omics data
Research area: fMRI Data, NetworkMethod of conditional moments (MCM) for the Chemical Master Equation
Research area: Stem Cells, LineageExtrinsically regulated Gadd45γ balances hematopoietic stem cell self-renewal and differentiation
Research area: miRNA, Target, CancerThe cytokine-induced microrna193b modulates ckit expression and STAT5 signaling
Research area: Stem Cells, LineageMyeloid lineage choice is not controlled by the PU.1 - Gata1 switch
Research area: Metabolite, Association, Metabolomics DataMetabolomic profiles in individuals with negative affectivity and social inhibition: A population-based study of Type D personality
Research area: fMRI Data, NetworkModeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis
Research area: Metabolite, Association, Metabolomics DataMetabolite profiling reveals new insights into the regulation of serum urate in humans
Research area: miRNA, Target, CancerThe human transcriptome is enriched for miRNA-binding sites located in cooperativity-permitting distance
Research area: Brain, Neurons, ReprogrammingSharpening of expression domains induced by transcription and microRNA regulationwithin a spatio-temporal model of mid-hindbrain boundary formation
Research area: Brain, Neurons, ReprogrammingLive imaging of astrocyte responses to acute injury reveals selective juxtavascular proliferation
Research area: Stem Cells, LineageCharacterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis
Research area: Metabolite, Association, Metabolomics DataEffects of smoking and smoking cessation on human serum metabolite profile: results from the KORA cohort study
Research area: fMRI Data, NetworkA Vine-copula Based Adaptive MCMC Sampler for Efficient Inference of Dynamical Systems
Research area: fMRI Data, NetworkRejoinder
Research area: Metabolite, Association, Metabolomics DataIntegrative genetic and metabolite profiling analysis suggests altered phosphatidylcholine metabolism in asthma
Research area: fMRI Data, NetworkJoining forces of Bayesian and frequentist methodology: a study for inference in the presence of non-identifiability
Research area: Independent Component, GraphVisualizing edge-edge relations in graphs
Research area: fMRI Data, NetworkTruth-Content and Phase Transitions of Random Boolean Networks with Generic Logics
Research area: Metabolite, Association, Metabolomics DataSTATISTICAL METHODS FOR THE ANALYSIS OF HIGH-THROUGHPUT METABOLOMICS DATA
201225 publications
Research area: Metabolite, Association, Metabolomics DataGenome-wide association analyses identify 18 new loci associated with serum urate concentrations
Research area: ICA, Subspace, Joint DiagonalizationUniqueness of linear factorizations into independent subspaces
Research area: Metabolite, Association, Metabolomics DataMining the Unknown: A Systems Approach to Metabolite Identification Combining Genetic and Metabolic Information
Research area: Diabetes, Children, RiskSpecific temperature-induced perturbations of secondary mRNA structures are associated with the cold-adapted temperature-sensitive phenotype of influenza A virus
Research area: Stem Cells, LineageA Unilateral Negative Feedback Loop Between miR-200 microRNAs and Sox2/E2F3 Controls Neural Progenitor Cell-Cycle Exit and Differentiation
Research area: Single Cell RNA, Gene ExpressionA novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst
Research area: Diabetes, Children, RiskA strategy for combining minor genetic susceptibility genes to improve prediction of disease in type 1 diabetes
Research area: fMRI Data, NetworkBayesian model selection validates a biokinetic model for zirconium processing in humans
Research area: ICA, Subspace, Joint DiagonalizationICA over finite fields—Separability and algorithms
Research area: Blind Source Separation, Sparse ComponentThe signal separation evaluation campaign (2007–2010): Achievements and remaining challenges
Research area: Metabolite, Association, Metabolomics DataIdentification 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
Research area: Metabolite, Association, Metabolomics DataBayesian Independent Component Analysis Recovers Pathway Signatures from Blood Metabolomics Data
Research area: Stem Cells, LineageMulti‐scale modeling of GMP differentiation based on single‐cell genealogies
Research area: Metabolite, Association, Metabolomics DataBody Fat Free Mass Is Associated with the Serum Metabolite Profile in a Population-Based Study
Research area: Metabolite, Association, Metabolomics DataOn the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies
Research area: Diabetes, Children, RiskSocial Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies
Research area: Metabolite, Association, Metabolomics DataThe dynamic range of the human metabolome revealed by challenges
Research area: Diabetes, Children, RiskEssstörungen im Internet: Eine experimentelle Studie zu den Auswirkungen von Pro-Essstörungs- und Selbsthilfewebsites
Research area: Stem Cells, LineageStability and Multiattractor Dynamics of a Toggle Switch Based on a Two-Stage Model of Stochastic Gene Expression
Research area: Images, Deep LearningSystems Biology Meets Metabolism
Research area: fMRI Data, NetworkSystematic Complexity Reduction of Signaling Models and Application to a CD95 Signaling Model for Apoptosis
Research area: ICA, Subspace, Joint DiagonalizationJoint Diagonalization of Several Scatter Matrices for ICA
Research area: ICA, Subspace, Joint DiagonalizationTo Infinity and Beyond: On ICA over Hilbert Spaces
Research area: Single Cell RNA, Gene ExpressionBayesian Inference of Latent Causes in Gene Regulatory Dynamics
Research area: Independent Component, GraphBayesian Fuzzy Clustering of Colored Graphs
201120 publications
Research area: Stem Cells, LineageThe Sox17‐mCherry fusion mouse line allows visualization of endoderm and vascular endothelial development
Research area: miRNA, Target, CancerPhenomiR: MicroRNAs in Human Diseases and Biological Processes
Research area: Stem Cells, LineageAn Ensemble Approach for Inferring Semi-quantitative Regulatory Dynamics for the Differentiation of Mouse Embryonic Stem Cells Using Prior Knowledge
Research area: Independent Component, GraphThe Nature and Perception of Fluctuations in Human Musical Rhythms
Research area: Independent Component, GraphModularity Maximization and Tree Clustering: Novel Ways to Determine Effective Geographic Borders
Research area: ICA, Subspace, Joint DiagonalizationUniqueness of Non-Gaussianity-Based Dimension Reduction
Research area: miRNA, Target, CancerMicroRNAs coordinately regulate protein complexes
Research area: Metabolite, Association, Metabolomics DataDiscovery of Sexual Dimorphisms in Metabolic and Genetic Biomarkers
Research area: Stem Cells, LineageHierarchical Differentiation of Myeloid Progenitors Is Encoded in the Transcription Factor Network
Research area: fMRI Data, NetworkSteady‐state robustness of qualitative gene regulation networks
Research area: Metabolite, Association, Metabolomics DataGaussian graphical modeling reveals specific lipid correlations in glioblastoma cells
Research area: Independent Component, GraphVertex centralities in input-output networks reveal the structure of modern economies
Research area: Images, Deep LearningModerne Informations- und Kommunikationstechnologie in der Rehabilitation
Research area: fMRI Data, NetworkThe Heckscher–Ohlin model and the network structure of international trade
Research area: Diabetes, Children, RiskComplex Principal Component and Correlation Structure of 16 Yeast Genomic Variables
Research area: miRNA, Target, CancermiTALOS: Analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs
Research area: Diabetes, Children, RiskHuge Splicing Frequency in Human Y Chromosomal UTY Gene
Research area: Diabetes, Children, RiskDynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets
Research area: Metabolite, Association, Metabolomics DataGaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data
Research area: fMRI Data, NetworkDynamic regimes of random fuzzy logic networks
201024 publications
Research area: fMRI Data, NetworkEffective Parameters Determining the Information Flow in Hierarchical Biological Systems
Research area: Independent Component, GraphKnowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation
Research area: Diabetes, Children, RiskMIPS: curated databases and comprehensive secondary data resources in 2010
Research area: Spatial, Omics DataThe Structure of Borders in a Small World
Research area: miRNA, Target, CancerMicroRNA Loss Enhances Learning and Memory in Mice
Research area: Independent Component, GraphStructuring heterogeneous biological information using fuzzy clustering of k-partite graphs
Research area: fMRI Data, NetworkBiologically meaningful update rules increase the critical connectivity of generalized Kauffman networks
Research area: Brain, Neurons, ReprogrammingPatterns of Subnet Usage Reveal Distinct Scales of Regulation in the Transcriptional Regulatory Network of Escherichia coli
Research area: ICA, Subspace, Joint DiagonalizationColored Subspace Analysis: Dimension Reduction Based on a Signal's Autocorrelation Structure
Research area: miRNA, Target, CancerTissue-Specific Target Analysis of Disease-Associated MicroRNAs in Human Signaling Pathways
Research area: fMRI Data, NetworkTheoretical Analysis of Time-to-Peak Responses in Biological Reaction Networks
Research area: fMRI Data, NetworkOdefy - From discrete to continuous models
Research area: Independent Component, GraphThe a d coefficient as a descriptive measure of the within‐group agreement of ratings
Research area: miRNA, Target, CancerPhenomiR: a knowledgebase for microRNA expression in diseases and biological processes
Research area: fMRI Data, NetworkRobust Stability Analysis and Design Under Consideration of Multiple Feedback Loops of the Tryptophan Regulatory Network of Escherichia coli
Research area: Blind Source Separation, Sparse ComponentThe 2010 Signal Separation Evaluation Campaign (SiSEC2010): Audio Source Separation
Research area: Blind Source Separation, Sparse ComponentThe 2010 Signal Separation Evaluation Campaign (SiSEC2010): Biomedical Source Separation
Research area: Independent Component, GraphInformation-Theoretic Model Selection for Independent Components
Research area: ICA, Subspace, Joint DiagonalizationSecond Order Subspace Analysis and Simple Decompositions
Research area: Blind Source Separation, Sparse ComponentSecond-Order Source Separation Based on Prior Knowledge Realized in a Graph Model
Research area: Blind Source Separation, Sparse ComponentRobust Second-Order Source Separation Identifies Experimental Responses in Biomedical Imaging
Research area: ICA, Subspace, Joint DiagonalizationICA over Finite Fields
Research area: miRNA, Target, CancerIntronic microRNAs support their host genes by mediating synergistic and antagonistic regulatory effects
Research area: fMRI Data, NetworkFrom Binary to Multivalued to Continuous Models: The lac Operon as a Case Study
200912 publications
Research area: Brain, Neurons, ReprogrammingSpatial Analysis of Expression Patterns Predicts Genetic Interactions at the Mid-Hindbrain Boundary
Research area: fMRI Data, NetworkTransforming Boolean models to continuous models: methodology and application to T-cell receptor signaling
Research area: Independent Component, GraphReconstruction of graphs based on random walks
Research area: Brain, Neurons, ReprogrammingZebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine
Research area: fMRI Data, NetworkICA, kernel methods and nonnegativity: New paradigms for dynamical component analysis of fMRI data
Research area: fMRI Data, NetworkHypergraphs and Cellular Networks
Research area: Blind Source Separation, Sparse ComponentBlind Source Separation Techniques for the Decomposition of Multiply Labeled Fluorescence Images
Research area: Blind Source Separation, Sparse ComponentBlind Source Separation Techniques For The Decomposition Of Multiply Labeled Fluorescence Images
Research area: ICA, Subspace, Joint DiagonalizationHierarchical Extraction of Independent Subspaces of Unknown Dimensions
Research area: ICA, Subspace, Joint DiagonalizationSoft Dimension Reduction for ICA by Joint Diagonalization on the Stiefel Manifold
Research area: Single Cell RNA, Gene ExpressionEstimating Hidden Influences in Metabolic and Gene Regulatory Networks
Research area: Blind Source Separation, Sparse ComponentBlind Decomposition of Spectral Imaging Microscopy: A Study on Artificial and Real Test Data
200811 publications
Research area: Diabetes, Children, RiskAn evolutionary and structural characterization of mammalian protein complex organization
Research area: fMRI Data, NetworkOptimization Techniques for Date Representions with Biomedical Applications
Research area: Cell Atlas, IntegrationMoney Circulation, Trackable Items, and the Emergence of Universal Human Mobility Patterns
Research area: Brain, Neurons, ReprogrammingErythropoietin enhances hippocampal long-term potentiation and memory
Research area: Blind Source Separation, Sparse ComponentKnowledge-based gene expression classification via matrix factorization
Research area: Brain, Neurons, ReprogrammingEpisode-Specific Differential Gene Expression of Peripheral Blood Mononuclear Cells in Rapid Cycling Supports Novel Treatment Approaches
Research area: Representations, Single CellA robust model for spatiotemporal dependencies
Research area: Blind Source Separation, Sparse ComponentHybridizing sparse component analysis with genetic algorithms for microarray analysis
Research area: Single Cell RNA, Gene ExpressionGene regulatory networks simplified by nonlinear balanced truncation
Research area: Independent Component, GraphAnalyzing M-CSF dependent monocyte/macrophage differentiation: Expression modes and meta-modes derived from an independent component analysis
Research area: Images, Deep LearningEffective Emission Tomography Image Reconstruction Algorithms for SPECT Data
200715 publications
Research area: Brain, Neurons, ReprogrammingPhase-specific differential gene expression of peripheral blood mononuclear cells in rapid cycling syndrome
Research area: ICA, Subspace, Joint DiagonalizationJoint low-rank approximation for extracting non-Gaussian subspaces
Research area: Blind Source Separation, Sparse ComponentHow to extract marker genes from microarray data sets
Research area: Blind Source Separation, Sparse ComponentSparse Nonnegative Matrix Factorization with Genetic Algorithms for Microarray Analysis
Research area: Blind Source Separation, Sparse ComponentA bilinear algorithm for sparse representations
Research area: Blind Source Separation, Sparse ComponentSparse Component Analysis: a New Tool for Data Mining
Research area: ICA, Subspace, Joint DiagonalizationColored Subspace Analysis
Research area: ICA, Subspace, Joint DiagonalizationPivot Selection Strategies in Jacobi Joint Block-Diagonalization
Research area: fMRI Data, NetworkA Toolbox for Model-Free Analysis of fMRI Data
Research area: ICA, Subspace, Joint DiagonalizationIdentifiability Conditions and Subspace Clustering in Sparse BSS
Research area: ICA, Subspace, Joint DiagonalizationIndependent Subspace Analysis Is Unique, Given Irreducibility
Research area: Blind Source Separation, Sparse ComponentBlind Matrix Decomposition Techniques to Identify Marker Genes from Microarrays
Research area: Blind Source Separation, Sparse ComponentBlind Matrix Decomposition Via Genetic Optimization of Sparseness and Nonnegativity Constraints
Research area: Blind Source Separation, Sparse ComponentExploiting Blind Matrix Decomposition Techniques to Identify Diagnostic Marker Genes
Research area: ICA, Subspace, Joint DiagonalizationStatistical Analysis of Sample-Size Effects in ICA
200616 publications
Research area: Blind Source Separation, Sparse ComponentRobust Sparse Component Analysis Based on a Generalized Hough Transform
Research area: fMRI Data, NetworkA Fast Predictive Lossless Coder for fMRI Data Sets
Research area: ICA, Subspace, Joint DiagonalizationDenoising using local projective subspace methods
Research area: Blind Source Separation, Sparse ComponentOn the use of simulated annealing to automatically assign decorrelated components in second-order blind source separation
Research area: Blind Source Separation, Sparse ComponentBlind source separation based on self-organizing neural network
Research area: Blind Source Separation, Sparse ComponentOn the use of sparse signal decomposition in the analysis of multi-channel surface electromyograms
Research area: ICA, Subspace, Joint DiagonalizationMedian-based clustering for underdetermined blind signal processing
Research area: ICA, Subspace, Joint DiagonalizationSeparation of water artifacts in 2D NOESY protein spectra using congruent matrix pencils
Research area: Blind Source Separation, Sparse ComponentOptimization Algorithms for Sparse Representations and Applications
Research area: ICA, Subspace, Joint DiagonalizationUniqueness of Non-Gaussian Subspace Analysis
Research area: ICA, Subspace, Joint DiagonalizationEstimating Non-Gaussian Subspaces by Characteristic Functions
Research area: Blind Source Separation, Sparse ComponentSparse Nonnegative Matrix Factorization Applied to Microarray Data Sets
Research area: Independent Component, GraphRegion of Interest Based Independent Component Analysis
Research area: fMRI Data, NetworkStability Analysis of an Unsupervised Competitive Neural Network
Research area: ICA, Subspace, Joint DiagonalizationOn the use of joint diagonalization in blind signal processing
Research area: ICA, Subspace, Joint DiagonalizationNew Riemannian metrics for speeding-up the convergence of over- and underdetermined ICA
200510 publications
Research area: Blind Source Separation, Sparse ComponentSparse Component Analysis and Blind Source Separation of Underdetermined Mixtures
Research area: ICA, Subspace, Joint DiagonalizationOn model identifiability in analytic postnonlinear ICA
Research area: ICA, Subspace, Joint DiagonalizationA Hybridization of Simulated Annealing and Local PCA for Automatic Component Assignment Within ICA
Research area: Blind Source Separation, Sparse ComponentExtended Sparse Nonnegative Matrix Factorization
Research area: ICA, Subspace, Joint DiagonalizationFunctional MRI Analysis by a Novel Spatiotemporal ICA Algorithm
Research area: fMRI Data, NetworkA Fast and Efficient Method for Compressing fMRI Data Sets
Research area: fMRI Data, NetworkBispectrum-Based Statistical Tests for VAD
Research area: Blind Source Separation, Sparse ComponentHybridizing Sparse Component Analysis with Genetic Algorithms for Blind Source Separation
Research area: Independent Component, GraphAn algorithm for automatic assignment of artifact-related independent components in biomedical signal analysis
Research area: ICA, Subspace, Joint DiagonalizationBlind signal separation into groups of dependent signals using joint block diagonalization
200419 publications
Research area: Blind Source Separation, Sparse ComponentA New Concept for Separability Problems in Blind Source Separation
Research area: Images, Deep LearningMobile decision support for transplantation patient data
Research area: Independent Component, GraphUniqueness of complex and multidimensional independent component analysis
Research area: Independent Component, GraphTree-dependent and topographic independent component analysis for fMRI analysis
Research area: ICA, Subspace, Joint DiagonalizationA geometric algorithm for overcomplete linear ICA
Research area: fMRI Data, Network3D Spatial Analysis of fMRI Data on a Word Perception Task
Research area: ICA, Subspace, Joint DiagonalizationDenoising Using Local ICA and a Generalized Eigendecomposition with Time-Delayed Signals
Research area: Blind Source Separation, Sparse ComponentBlind Source Separation of Linear Mixtures with Singular Matrices
Research area: Blind Source Separation, Sparse ComponentPostnonlinear Overcomplete Blind Source Separation Using Sparse Sources
Research area: Blind Source Separation, Sparse ComponentSecond-Order Blind Source Separation Based on Multi-dimensional Autocovariances
Research area: fMRI Data, NetworkSpatial ICA of fMRI data in time windows
Research area: Blind Source Separation, Sparse ComponentBlind source recovery: algorithm comparison and fusion
Research area: Blind Source Separation, Sparse ComponentBlind source separation and sparse component analysis of overcomplete mixtures
Research area: fMRI Data, NetworkClustering of dependent components: a new paradigm for fMRI signal detection
Research area: ICA, Subspace, Joint DiagonalizationKernel-PCA denoising of artifact-free protein NMR spectra
Research area: ICA, Subspace, Joint DiagonalizationDenoising using local ICA and kernel-PCA
Research area: Blind Source Separation, Sparse ComponentPostnonlinear blind source separation via linearization identification
Research area: fMRI Data, Network3D spatial analysis of fMRI data: a comparison of ICA and GLM analysis on a word perception task
Research area: fMRI Data, NetworkBlind Sensor Characteristics Estimation in a Multi-Sensor Network Applied to fMRI Analysis
200314 publications
Research area: ICA, Subspace, Joint DiagonalizationLinear Geometric ICA: Fundamentals and Algorithms
Research area: Blind Source Separation, Sparse ComponentAn improved geometric overcomplete blind source separation algorithm
Research area: ICA, Subspace, Joint DiagonalizationA Generalized Eigendecomposition Approach using Matrix Pencils to remove artefacts from 2D NMR Spectra
Research area: ICA, Subspace, Joint DiagonalizationGeneralizing Geometric ICA to Nonlinear Settings
Research area: Blind Source Separation, Sparse ComponentAn Adaptive Approach to Blind Source Separation Using a Self-Organzing Map and a Neural Gas
Research area: Blind Source Separation, Sparse ComponentNew Geometric ICA Approach for Blind Source Separation
Research area: ICA, Subspace, Joint DiagonalizationAdaptive signal analysis of immunological data
Research area: ICA, Subspace, Joint DiagonalizationA new ica method based on a lattice of the observation space
Research area: ICA, Subspace, Joint DiagonalizationSOMICA and geometric ICA
Research area: Independent Component, GraphLocal features in biomedical image clusters extracted with independent component analysis
Research area: Independent Component, GraphSOMICA - an application of self-organizing maps to geometric independent component analysis
Research area: ICA, Subspace, Joint DiagonalizationRemoving water artefacts from 2D protein NMR spectra using GEVD with congruent matrix pencils
Research area: fMRI Data, NetworkNeural network signal analysis in immunology
Research area: Independent Component, GraphMathematics in independent component analysis
20023 publications
Research area: Independent Component, GraphTopological Constructions in the o–Graph Calculus
Research area: Representations, Single CellComparison of maximum entropy and minimal mutual information in a nonlinear setting
Research area: ICA, Subspace, Joint DiagonalizationOvercomplete ICA with a Geometric Algorithm
20011 publication
20001 publication
19981 publication
19921 publication
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