Plate II.1
Single-cell and spatial atlases
Effects of High-Dose Oral Insulin on Immune Responses in Children at H…Topological Constructions in the o–Graph CalculusAssociation of bronchial steroid inducible methylation quantitative tr…Evaluation of Deep Learning Strategies for Nucleus Segmentation in Flu…The Sox17‐mCherry fusion mouse line allows visualization of endoderm a…Steady‐state robustness of qualitative gene regulation networksOptimization Algorithms for Sparse Representations and ApplicationsA Hybridization of Simulated Annealing and Local PCA for Automatic Com…Extended Sparse Nonnegative Matrix FactorizationFunctional MRI Analysis by a Novel Spatiotemporal ICA AlgorithmA Fast and Efficient Method for Compressing fMRI Data SetsBispectrum-Based Statistical Tests for VADHybridizing Sparse Component Analysis with Genetic Algorithms for Blin…Uniqueness of Non-Gaussian Subspace AnalysisEstimating Non-Gaussian Subspaces by Characteristic FunctionsSparse Nonnegative Matrix Factorization Applied to Microarray Data SetsRegion of Interest Based Independent Component AnalysisAn improved geometric overcomplete blind source separation algorithmA Generalized Eigendecomposition Approach using Matrix Pencils to remo…Generalizing Geometric ICA to Nonlinear SettingsAn Adaptive Approach to Blind Source Separation Using a Self-Organzing…Pattern Repulsion RevisitedOvercomplete ICA with a Geometric AlgorithmOptimization Techniques for Date Representions with Biomedical Applica…Sparse Component Analysis: a New Tool for Data MiningRobust Stability Analysis and Design Under Consideration of Multiple F…An Ensemble Approach for Inferring Semi-quantitative Regulatory Dynami…Modularity Maximization and Tree Clustering: Novel Ways to Determine E…Systems Biology Meets MetabolismSystematic Complexity Reduction of Signaling Models and Application to…Posttranscriptional Regulatory Networks: From Expression Profiling to…PhenomiR: MicroRNAs in Human Diseases and Biological ProcessesArtificial Neural Networks and Machine Learning – ICANN 2019: Theoreti…Artificial Neural Networks and Machine Learning – ICANN 2019: Workshop…Learning Tn5 Sequence Bias from ATAC-seq on Naked ChromatinNoise Transfer for Unsupervised Domain Adaptation of Retinal OCT ImagesB-Cos Aligned Transformers Learn Human-Interpretable FeaturesTarDis: Achieving Robust and Structured Disentanglement of Multiple Co…Centroid Clustering of Cellular Lineage TreesUncertainty Analysis for Non-identifiable Dynamical Systems: Profile L…Bayesian Model Selection Methods and Their Application to Biological O…An Affine Equivariant Robust Second-Order BSS MethodApproximate Bayesian Computation for Stochastic Single-Cell Time-Lapse…Mitosis Detection in Intestinal Crypt Images with Hough Forest and Con…MicroRNA as an Integral Part of Cell Communication: Regularized Target…Information Theoretic Concepts to Unravel Cell–Cell CommunicationLNA++: Linear Noise Approximation with First and Second Order Sensitiv…3D Spatial Analysis of fMRI Data on a Word Perception TaskDenoising Using Local ICA and a Generalized Eigendecomposition with Ti…Blind Source Separation of Linear Mixtures with Singular MatricesPostnonlinear Overcomplete Blind Source Separation Using Sparse SourcesSecond-Order Blind Source Separation Based on Multi-dimensional Autoco…New Geometric ICA Approach for Blind Source SeparationEffective Emission Tomography Image Reconstruction Algorithms for SPEC…Colored Subspace AnalysisPivot Selection Strategies in Jacobi Joint Block-DiagonalizationA Toolbox for Model-Free Analysis of fMRI DataIdentifiability Conditions and Subspace Clustering in Sparse BSSIndependent Subspace Analysis Is Unique, Given IrreducibilityBlind Matrix Decomposition Techniques to Identify Marker Genes from Mi…Blind Matrix Decomposition Via Genetic Optimization of Sparseness and…Exploiting Blind Matrix Decomposition Techniques to Identify Diagnosti…Statistical Analysis of Sample-Size Effects in ICAHierarchical Extraction of Independent Subspaces of Unknown DimensionsSoft Dimension Reduction for ICA by Joint Diagonalization on the Stief…Estimating Hidden Influences in Metabolic and Gene Regulatory NetworksBlind Decomposition of Spectral Imaging Microscopy: A Study on Artific…The 2010 Signal Separation Evaluation Campaign (SiSEC2010): Audio Sour…The 2010 Signal Separation Evaluation Campaign (SiSEC2010): Biomedical…Information-Theoretic Model Selection for Independent ComponentsSecond Order Subspace Analysis and Simple DecompositionsSecond-Order Source Separation Based on Prior Knowledge Realized in a…Robust Second-Order Source Separation Identifies Experimental Response…ICA over Finite FieldsJoint Diagonalization of Several Scatter Matrices for ICATo Infinity and Beyond: On ICA over Hilbert SpacesBayesian Inference of Latent Causes in Gene Regulatory DynamicsBayesian Fuzzy Clustering of Colored GraphsModerne Informations- und Kommunikationstechnologie in der Rehabilitat…Feature ranking of type 1 diabetes susceptibility genes improves predi…Lactation is associated with altered metabolomic signatures in women w…Peptide serum markers in islet autoantibody-positive childrenTwo membrane anchors of Wolinella succinogenes hydrogenase and their f…Method of conditional moments (MCM) for the Chemical Master EquationLifetime study in mice after acute low-dose ionizing radiation: a mult…OME-Zarr: a cloud-optimized bioimaging file format with international…A strategy to find gene combinations that identify children who progre…A bilinear algorithm for sparse representationsAn adaptive scheduling scheme for calculating Bayes factors with therm…Metabolite profiling reveals new insights into the regulation of serum…Gender-specific pathway differences in the human serum metabolomeMetabolomics reveals effects of maternal smoking on endogenous metabol…Characterization of missing values in untargeted MS-based metabolomics…Künstliche Intelligenz und maschinelles Lernen in der DiabetesforschungTheoretical Analysis of Time-to-Peak Responses in Biological Reaction…Effective Parameters Determining the Information Flow in Hierarchical…Blind Source Separation Techniques for the Decomposition of Multiply L…Blind Source Separation Techniques For The Decomposition Of Multiply L…Stability and Multiattractor Dynamics of a Toggle Switch Based on a Tw…Spatial proteo-transcriptomic profiling reveals the molecular landscap…SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Air…SARS-CoV-2 infection triggers profibrotic macrophage responses and lun…Spatial proteomics in three-dimensional intact specimensDistinct molecular profiles of skull bone marrow in health and neurolo…Time-resolved single-cell transcriptomics defines immune trajectories…The future of rapid and automated single-cell data analysis using refe…Large-scale proteomics across neurological disorders uncovers biomarke…RegVelo: Gene-regulatory-informed dynamics of single cellsStem-Cell-like Properties and Epithelial Plasticity Arise as Stable Tr…Increasing Neural Stem Cell Division Asymmetry and Quiescence Are Pred…Systemic alterations in neutrophils and their precursors in early-stag…Combinatorial Histone Acetylation Patterns Are Generated by Motif-Spec…Analysis of Cell Lineage Trees by Exact Bayesian Inference Identifies…Parallelization and High-Performance Computing Enables Automated Stati…Efficient Parameter Estimation Enables the Prediction of Drug Response…AutoGeneS: Automatic gene selection using multi-objective optimization…Machine learning for perturbational single-cell omicsWhat do you most hope spatial molecular profiling will help us underst…What is the main bottleneck in deriving biological understanding from…A combinatorial transcription factor screening platform for immune cel…From modality-specific to compositional foundation models for cell bio…TarDis: Achieving robust and structured disentanglement of multiple co…Longitudinal Effects of 1-Year Smoking Cessation on Human Bronchial Ep…Single cells make big data: New challenges and opportunities in transc…Graph representation learning for single-cell biologyComputational approaches for systems metabolomicsEditorial overview: Systems biology-the intersection of experiments an…Epithelial Planar Bipolarity Emerges from Notch-Mediated Asymmetric In…Blind source separation based on self-organizing neural networkICA, kernel methods and nonnegativity: New paradigms for dynamical com…Polygenic Burden Analysis of Longitudinal Clusters of Psychopathologic…Integrating Polygenic Allele Burden Information And Phenomic Data To C…POLYGENIC BURDEN ANALYSIS OF LONGITUDINAL CLUSTERS OF QUALITY OF LIFE…The Role Of Micrornas In The Course Of Severe Mental DisordersWHAT SHAPES THE CHILD'S EPIGENOME: GENOTYPE, PRENATAL ENVIRONMENT OR B…POLYGENIC BURDEN ANALYSIS OF LONGITUDINAL CLUSTERS OF PSYCHOPATHOLOGIC…GENOTYPE, PRENATAL ENVIRONMENT OR BOTH–WHAT SHAPES THE NEWBORN'S EPIGE…F96POLYGENIC RISK SCORE ANALYSIS OF TRAJECTORIES OF COGNITIVE PERFORMA…SA125POLYGENIC BURDEN ANALYSIS OF LONGITUDINAL CLUSTERS OF PSYCHOPATHO…S.11.01 Brain organoids as models of the developing human brain: decip…Extrinsically regulated Gadd45γ balances hematopoietic stem cell self-…The cytokine-induced microrna193b modulates ckit expression and STAT5…Myeloid lineage choice is not controlled by the PU.1 - Gata1 switchDecoding the transcriptional program for blood development from whole…Cytokine-regulated GADD45G induces differentiation and lineage selecti…Quantitative comparison of competing PDE models for Pomlp dynamics in…Mobile decision support for transplantation patient dataMetabolism gene signatures and surgical site infections in abdominal s…The Heckscher–Ohlin model and the network structure of international t…Progressive disruption of hematopoietic architecture from clonal hemat…Human pluripotent stem cell fate trajectories toward lung and hepatocy…A novel molecular disease classifier for eczema and psoriasisA computational model to predict severity of atopic eczema from 30 ser…Label Free Identification of Peripheral Blood Eosinophils Using High-T…Toll-like receptor 7/8 agonists stimulate plasmacytoid dendritic cells…The neglected twin: Nummular eczema is a variant of atopic dermatitis…Polyploidisation pleiotropically buffers ageing in hepatocytes340 Interface dermatitis shows a distinctive molecular signature indep…360 Interface Dermatitis is characterized by a type I immune response…489 TLR7/8 agonists stimulate plasmacytoid dendritic cells to initiate…Type I Immune Response Induces Keratinocyte Necroptosis and Is Associa…CD23 Levels on B Cells Determine Long-Term Therapeutic Response in Pat…Gene Expression–Based Molecular Test as Diagnostic Aid for the Differe…Uniqueness of linear factorizations into independent subspacesBiologically meaningful update rules increase the critical connectivit…High-dimensional Bayesian parameter estimation: Case study for a model…Proteomics of spatially identified tissues in whole organsThe global gene expression profile of the secondary transition during…Systematic single-cell analysis provides new insights into heterogenei…Establishment of a high-resolution 3D modeling system for studying pan…CD81 marks immature and dedifferentiated pancreatic β-cellsVertical sleeve gastrectomy triggers fast β-cell recovery upon overt d…Toward modeling metabolic state from single-cell transcriptomicsA transcriptional cross species map of pancreatic islet cellsA geometric algorithm for overcomplete linear ICAOn model identifiability in analytic postnonlinear ICASeparation of water artifacts in 2D NOESY protein spectra using congru…Denoising using local projective subspace methodsA robust model for spatiotemporal dependenciesHybridizing sparse component analysis with genetic algorithms for micr…Ketamine exerts its sustained antidepressant effects via cell-type-spe…A sparse deep learning approach for automatic segmentation of human va…Wound-healing growth factor, basic FGF, induces Erk1/2-dependent mecha…Metabolomic profiles in individuals with negative affectivity and soci…Uniqueness of complex and multidimensional independent component analy…On the use of sparse signal decomposition in the analysis of multi-cha…Joint low-rank approximation for extracting non-Gaussian subspacesICA over finite fields—Separability and algorithmsThe signal separation evaluation campaign (2007–2010): Achievements an…Model selection using limiting distributions of second-order blind sou…Combined Single-Cell Functional and Gene Expression Analysis Resolves…Transcriptional Mechanisms of Proneural Factors and REST in Regulating…Cytokine-Regulated GADD45G Induces Differentiation and Lineage Selecti…Inductive and Selective Effects of GSK3 and MEK Inhibition on Nanog He…Single-cell characterization of neovascularization using hiPSC-derived…Reconstruction of graphs based on random walksMature neutrophils and a NF-κB-to-IFN transition determine the unifyin…Modulation of TCR stimulation and pifithrin-α improve the genomic safe…Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated s…Comparison of maximum entropy and minimal mutual information in a nonl…Large-scale modeling of cancer signaling: Mechanistic modeling meets B…Identification of predictive response and resistance factors to target…Toward a ToxAtlas of Carbon-Based Nanomaterials: Single-Cell RNA Seque…Rapid Inhibitor Discovery by Exploiting Synthetic LethalityBayesian Independent Component Analysis Recovers Pathway Signatures fr…Network-Based Approach for Analyzing Intra- and Interfluid Metabolite…Identification and Quantification of 1-Hydroxybutene-2-yl Mercapturic…A map of β-cell differentiation pathways supports cell therapies for d…Whither systems medicine?A strategy for combining minor genetic susceptibility genes to improve…miR-23a-3p Causes Cellular Senescence by Targeting Hyaluronan Synthase…Clinical impact of GATA2 mutations in acute myeloid leukemia patients…Interleukin-4 and interferon-γ orchestrate an epithelial polarization…Early myeloid lineage choice is not initiated by random PU.1 to GATA1…Computational analysis of cell-to-cell heterogeneity in single-cell RN…Decoding the regulatory network of early blood development from single…Software tools for single-cell tracking and quantification of cellular…Characterization of transcriptional networks in blood stem and progeni…Network plasticity of pluripotency transcription factors in embryonic…Label-free cell cycle analysis for high-throughput imaging flow cytome…A BaSiC tool for background and shading correction of optical microsco…Genome-wide association analyses identify 18 new loci associated with…An atlas of genetic influences on human blood metabolitesEpigenetic germline inheritance of diet-induced obesity and insulin re…Diffusion pseudotime robustly reconstructs lineage branchingProspective identification of hematopoietic lineage choice by deep lea…Live imaging of astrocyte responses to acute injury reveals selective…Fast clonal expansion and limited neural stem cell self-renewal in the…Single-cell characterization of the adult male hippocampus suggests a…Exon-variant interplay and multi-modal evidence identify endocrine dys…Tolerance of repeated toxic injuries of murine livers is associated wi…Evaluation of OCT biomarker changes in treatment-naive neovascular AMD…Reconstructing cell cycle and disease progression using deep learningNetwork inference from glycoproteomics data reveals new reactions in t…Lineage marker synchrony in hematopoietic genealogies refutes the PU.1…Single-cell RNA-seq denoising using a deep count autoencoderIRE1α-XBP1s pathway promotes prostate cancer by activating c-MYC signa…An atlas of the aging lung mapped by single cell transcriptomics and d…Integrated analysis of environmental and genetic influences on cord bl…Post-surgical adhesions are triggered by calcium-dependent membrane br…Alveolar regeneration through a Krt8+ transitional stem cell state tha…Deep learning the collisional cross sections of the peptide universe f…Asc-1 regulates white versus beige adipocyte fate in a subcutaneous st…Cellular connectomes as arbiters of local circuit models in the cerebr…Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-re…EpiScanpy: integrated single-cell epigenomic analysisscPower accelerates and optimizes the design of multi-sample single ce…scCODA is a Bayesian model for compositional single-cell data analysisIntegration of single-cell transcriptomes and chromatin landscapes rev…Ly6D+Siglec-H+ precursors contribute to conventional dendritic cells v…Synaptotagmin-13 orchestrates pancreatic endocrine cell egression and…Primary cilia and SHH signaling impairments in human and mouse models…Spatial transcriptomics landscape of lesions from non-communicable inf…Reconstructing disease dynamics for mechanistic insights and clinical…A reversible state of hypometabolism in a human cellular model of spor…Explainable machine learning for profiling the immunological synapse a…Shared inflammatory glial cell signature after stab wound injury, reve…Multi-modal generative modeling for joint analysis of single-cell T ce…scTab: Scaling cross-tissue single-cell annotation modelsPredicting cell morphological responses to perturbations using generat…Graph neural networks learn emergent tissue properties from spatial mo…A multimodal cross-species comparison of pancreas developmentSpatial single-cell atlas reveals regional variations in healthy and d…TNF alpha unmasks enteric malate aspartate shuttle dysfunction bridgin…Non-destructive transcriptomics via vesicular exportConvexGating infers gating strategies from clusters in single cell cyt…Multi-experiment nonlinear mixed effect modeling of single-cell transl…Heterogeneity-driven phenotypic plasticity and treatment response in b…Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineag…Epithelial cell plasticity drives endoderm formation during gastrulationBiologically informed deep learning to query gene programs in single-c…Biases in machine-learning models of human single-cell dataSystematic analysis of drug combinations against Gram-positive bacteriaDeep learning: new computational modelling techniques for genomicsBest practices for single-cell analysis across modalitiesTowards 3D-oid models that integrate molecular, morphological and spat…scSLAM-seq reveals core features of transcription dynamics in single c…The proteome landscape of the kingdoms of lifeLifeTime and improving European healthcare through cell-based intercep…Inhibition of LTβR signalling activates WNT-induced regeneration in lungSwarm Learning for decentralized and confidential clinical machine lea…A liver immune rheostat regulates CD8 T cell immunity in chronic HBV i…An integrated transcriptomic cell atlas of human neural organoidsMapping cells through time and space with moscotTowards multimodal foundation models in molecular cell biologyA foundation model to predict and capture human cognitionCreating bottom-up RNA transfer vehicles from synthetic protein assemb…Inferring population dynamics from single-cell RNA-sequencing time ser…Generalizing RNA velocity to transient cell states through dynamical m…Mapping single-cell data to reference atlases by transfer learningSpatial components of molecular tissue biologyA Python library for probabilistic analysis of single-cell omics dataModeling intercellular communication in tissues using spatial graphs o…Epicardioid single-cell genomics uncovers principles of human epicardi…The scverse project provides a computational ecosystem for single-cell…Defining and benchmarking open problems in single-cell analysisIdentifying 3D signal overlaps in spatial transcriptomics data with ov…Origin and function of activated fibroblast states during zebrafish he…Quantitative characterization of cell niches in spatially resolved omi…Causal machine learning for single-cell genomicsAn integrated transcriptomic cell atlas of human endoderm-derived orga…Single-cell atlas of the transcriptome and chromatin accessibility in…Plasticity of human microglia and brain perivascular macrophages in ag…ArchMap is a web-based platform for reference-based analysis of single…A cellular census of human lungs identifies novel cell states in healt…An integrated cell atlas of the lung in health and diseaseAn open-source framework for end-to-end analysis of electronic health…An open-source framework for electronic health record and patient fate…Type 2 diabetes prevention across the life courseA test metric for assessing single-cell RNA-seq batch correctionscGen predicts single-cell perturbation responsesBenchmarking atlas-level data integration in single-cell genomicsCellRank for directed single-cell fate mappingSquidpy: a scalable framework for spatial omics analysisLearning consistent subcellular landmarks to quantify changes in multi…Deciphering subcellular organization with multiplexed imaging and deep…Deep generative modeling of transcriptional dynamics for RNA velocity…Population-level integration of single-cell datasets enables multi-sca…Modeling fragment counts improves single-cell ATAC-seq analysisSpatialData: an open and universal data framework for spatial omicsCellRank 2: unified fate mapping in multiview single-cell dataTransformers in single-cell omics: a review and new perspectivesSmall data methods in omics: the power of oneVitessce: integrative visualization of multimodal and spatially resolv…Probe set selection for targeted spatial transcriptomicsConsiderations for building and using integrated single-cell atlasesMultiplexing cortical brain organoids for the longitudinal dissection…Optimizing Xenium In Situ data utility by quality assessment and best-…Feature selection methods affect the performance of scRNA-seq data int…Nicheformer: a foundation model for single-cell and spatial omicsscooby: modeling multimodal genomic profiles from DNA sequence at sing…Pertpy: an end-to-end framework for perturbation analysisSpatioTemporal Omics Consortium: a global effort for biological discov…TDP-43 condensates and lipid droplets regulate the reactivity of micro…Opportunities and challenges of single-cell and spatially resolved gen…CellRank: consistent and data view agnostic fate mapping for single-ce…Maternal whole blood cell miRNA-340 is elevated in gestational diabete…Common patterns of gene regulation associated with Cesarean section an…Pheno-seq – linking visual features and gene expression in 3D cell cul…Generative models of cell dynamics: from Neural ODEs to flow matchingTargeted pharmacological therapy restores β-cell function for diabetes…Diet-induced alteration of intestinal stem cell function underlies obe…Delineating mouse β-cell identity during lifetime and in diabetes with…GIPR agonism and antagonism decrease body weight and food intake via d…Self-supervised retinal thickness prediction enables deep learning fro…Reporting electricity consumption is essential for sustainable AIDelineating the effective use of self-supervised learning in single-ce…Transformers and genome language modelsSingle-cell profiling to explore pancreatic cancer heterogeneity, plas…MISATO: machine learning dataset of protein–ligand complexes for struc…Integrated manufacturing platform for cortical organoids reveals early…Pulmonary microRNA profiles identify involvement of Creb1 and Sec14l3…Metabolomics screening identifies reduced L-carnitine to be associated…Identifying latent dynamic components in biological systemsInferring catalysis in biological systemsImpact of Brain Fatty Acid Signaling on Peripheral Insulin Action in M…Deep Learning-Based Retinal Layer Segmentation in Optical Coherence To…Essstörungen im Internet: Eine experimentelle Studie zu den Auswirkung…Phase-specific differential gene expression of peripheral blood mononu…Spatial ICA of fMRI data in time windowsBlind source recovery: algorithm comparison and fusionParameterizing cell-to-cell regulatory heterogeneities via stochastic…GATA2/3-TFAP2A/C transcription factor network couples human pluripoten…Aldh1b1 expression defines progenitor cells in the adult pancreas and…Posterior subcapsular cataracts are a late effect after acute exposure…SimiRa: A tool to identify coregulation between microRNAs and RNA-bind…In vivo identification of apoptotic and extracellular vesicle‐bound li…Dynamic regimes of random fuzzy logic networkscgCorrect: a method to correct for confounding cell–cell variation due…Bayesian Blind Source Separation for Data with Network StructureUnbiased Prediction and Feature Selection in High-Dimensional Survival…Huge Splicing Frequency in Human Y Chromosomal UTY GeneMulti-omics regulatory network inference in the presence of missing dataContinuous multi-omics pathway enrichment analysis resolves hidden fun…Copy number aberrations from Affymetrix SNP 6.0 genotyping data—how ac…Automatic identification of relevant genes from low-dimensional embedd…Conditional out-of-distribution generation for unpaired data using tra…longmixr: a tool for robust clustering of high-dimensional cross-secti…GraphCompass: spatial metrics for differential analyses of cell organi…Spatial transcriptomics deconvolution methods generalize well to spati…QuiCAT: a scalable and flexible framework for mapping synthetic sequen…Knowledge-based gene expression classification via matrix factorizationA novel approach for resolving differences in single-cell gene express…Probabilistic PCA of censored data: accounting for uncertainties in th…RAMONA: a Web application for gene set analysis on multilevel omics dataReconstructing gene regulatory dynamics from high-dimensional single-c…Diffusion maps for high-dimensional single-cell analysis of differenti…Data2Dynamics: a modeling environment tailored to parameter estimation…destiny: diffusion maps for large-scale single-cell data in RMEMO: multi-experiment mixture model analysis of censored dataParameter estimation for dynamical systems with discrete events and lo…fastER: a user-friendly tool for ultrafast and robust cell segmentatio…A scalable moment-closure approximation for large-scale biochemical re…Model-based branching point detection in single-cell data by K-branche…netReg: network-regularized linear models for biological association s…Bayesian parameter estimation for biochemical reaction networks using…394 Gene expression based molecular test proves clinical validity as d…Interpretable surface-based detection of focal cortical dysplasias: a…Multimodal discovery of a pathogenic B-cell-dependent T-cell state in…Mouse IDGenes: a reference database for genetic interactions in the de…MetaMap: an atlas of metatranscriptomic reads in human disease-related…Novel genetic associations with serum level metabolites identified by…Complex Principal Component and Correlation Structure of 16 Yeast Geno…Predicting single-cell gene expression profiles of imaging flow cytome…OmniPath: integrated knowledgebase for multi-omics analysisUniversalEPI: robust prediction of cell type-specific and differential…MIPS: curated databases and comprehensive secondary data resources in…A modular framework for gene set analysis integrating multilevel omics…TALEN/CRISPR-mediated engineering of a promoterless anti-viral RNAi ha…Impulse model-based differential expression analysis of time course se…Single-cell reference mapping to construct and extend cell-type hierar…Charting the single-cell and spatial landscape of IDH-wild-type gliobl…The dynamic range of the human metabolome revealed by challengesDeep Learning-based Propensity Scores for Confounding Control in Compa…Mechanistic description of spatial processes using integrative modelli…Joining forces of Bayesian and frequentist methodology: a study for in…Opposing effects of allogrooming on disease transmission in ant societ…Cell-type specific impact of glucocorticoid receptor activation on the…Alterations of multiple alveolar macrophage states in chronic obstruct…Query to reference single-cell integration with transfer learningWnt/PCP-primed intestinal stem cells directly differentiate into enter…Identification and characterization of distinct murine brown adipocyte…Learning interpretable latent autoencoder representations with annotat…Squidpy: a scalable framework for spatial single cell analysisSingle cell trajectory analysis of human pluripotent stem cells differ…Low numbers of cytokine transcripts drive inflammatory skin diseases b…Out-of-distribution prediction with disentangled representations for s…Multi-omics and 3D-imaging reveal bone heterogeneity and unique calvar…Repeated toxic injuries of murine liver are tolerated through microste…Integration and querying of multimodal single-cell data with PoE-VAEMultimodal single cell data integration challenge: results and lessons…Gene expression based molecular test proves clinical validity as diagn…MultiCPA: Multimodal Compositional Perturbation AutoencoderCIARA: a cluster-independent algorithm for the identification of marke…Variant-risk-exon interplay impacts circadian rhythm and dopamine sign…Modeling Single-Cell Dynamics Using Unbalanced Parameterized Monge MapsPytometry: Flow and mass cytometry analytics in PythonHigh-throughput profiling of drug interactions in Gram-positive bacteriaHBV rewires liver cancer signaling by altering PP2A complexesscARE: Attribution Regularization for Single Cell Representation Learn…Unified fate mapping in multiview single-cell datahadge: a comprehensive pipeline for donor deconvolution in single cellIdentification of cell types, states and programs by learning gene set…Scaling cross-tissue single-cell annotation modelsflowVI: Flow Cytometry Variational InferenceExploratory electronic health record analysis with ehrapyOptimal distance metrics for single-cell RNA-seq populationsCell circuits underlying nanomaterial specific respiratory toxicologyQuantitative characterization of cell niches in spatial atlasesMapping the human hematopoietic stem and progenitor cell hierarchy thr…Weakly supervised learning uncovers phenotypic signatures in single-ce…Scalable and universal prediction of cellular phenotypes enables in si…Endothelial regulatory circuits control cranial neural crest migration…Disentangling cellular heterogeneity into interpretable biological fac…inVAE: Conditionally invariant representation learning for generating…ProCyon: A multimodal foundation model for protein phenotypesTGIF2 is a major regulator of neural stem cell fate and neurogenic pri…CellFlow enables generative single-cell phenotype modeling with flow m…Automated evaluation of single-cell reference atlas mappings enables t…Biologically Informed Variational Inference Enables Interpretable Cell…Beyond Visual Inspection: Principled Benchmarking of Single-Cell Traje…Integration of cell-type resolved spatial proteomics and transcriptomi…Im-seq: Multimodal droplet barcoding enables high-throughput linking o…scPortrait integrates single-cell images into multimodal modelingscConcept: Contrastive pretraining for technology-agnostic single-cell…FADVI: disentangled representation learning for robust integration of…Language may be all omics needs: Harmonizing multimodal data for omics…FASTGenomics: An analytical ecosystem for single-cell RNA sequencing d…MetaMap, an interactive webtool for the exploration of metatranscripto…Generative modeling and latent space arithmetics predict single-cell p…A cellular census of healthy lung and asthmatic airway wall identifies…Deep learning does not outperform classical machine learning for cell-…Longitudinal single cell transcriptomics reveals Krt8+ alveolar epithe…Vertex centralities in input-output networks reveal the structure of m…Blind source separation and sparse component analysis of overcomplete…Adaptive signal analysis of immunological dataA new ica method based on a lattice of the observation spaceSOMICA and geometric ICAA Fast Predictive Lossless Coder for fMRI Data SetsHow to extract marker genes from microarray data setsLocal features in biomedical image clusters extracted with independent…SOMICA - an application of self-organizing maps to geometric independe…Clustering of dependent components: a new paradigm for fMRI signal det…Kernel-PCA denoising of artifact-free protein NMR spectraDenoising using local ICA and kernel-PCAPostnonlinear blind source separation via linearization identification3D spatial analysis of fMRI data: a comparison of ICA and GLM analysis…An algorithm for automatic assignment of artifact-related independent…Stability Analysis of an Unsupervised Competitive Neural NetworkSparse Nonnegative Matrix Factorization with Genetic Algorithms for Mi…Anatomic-landmark detection using graphical context modellingBlind signal separation into groups of dependent signals using joint b…On the use of joint diagonalization in blind signal processingNew Riemannian metrics for speeding-up the convergence of over- and un…Blind Sensor Characteristics Estimation in a Multi-Sensor Network Appl…Removing water artefacts from 2D protein NMR spectra using GEVD with c…Neural network signal analysis in immunologyMathematics in independent component analysisMedian-based clustering for underdetermined blind signal processingMoney Circulation, Trackable Items, and the Emergence of Universal Hum…Visualizing edge-edge relations in graphsOn the use of simulated annealing to automatically assign decorrelated…Colored Subspace Analysis: Dimension Reduction Based on a Signal's Aut…Sparse Component Analysis and Blind Source Separation of Underdetermin…Uniqueness of Non-Gaussianity-Based Dimension ReductionIntegrative genetic and metabolite profiling analysis suggests altered…Identification of a plasma miRNA biomarker signature for allergic asth…A strategy for high‐dimensional multivariable analysis classifies chil…Determinants of expression of SARS‐CoV‐2 entry‐related genes in upper…A novel molecular disease classifier for psoriasis and eczemaThe quinone‐reactive Ni/Fe‐hydrogenase of Wolinella succinogenesMulti‐scale modeling of GMP differentiation based on single‐cell genea…Is the humoral immunity dispensable for the pathogenesis of psoriasis?IL‐17C amplifies epithelial inflammation in human psoriasis and atopic…Separation of Uncorrelated Stationary time series using Autocovariance…Asthma in farm children is more determined by genetic polymorphisms an…Prediction of type 1 diabetes using a genetic risk model in the Diabet…Tree-dependent and topographic independent component analysis for fMRI…Gene regulatory networks simplified by nonlinear balanced truncationGaussian graphical modeling reveals specific lipid correlations in gli…Single-cell molecular profiling of all three components of the HPA axi…Synthetic enforcement of STING signaling in cancer cells appropriates…Early life adversity shapes social subordination and cell type–specifi…Chronic exposure to glucocorticoids amplifies inhibitory neuron cell f…Single-cell multiome and spatial profiling reveals pancreas cell type–…Transcriptional repression by TGIF2 coordinates neurogenic priming and…Live imaging of adult neural stem cell behavior in the intact and inju…Cell type atlas and lineage tree of a whole complex animal by single-c…Pathogenic variants damage cell composition and single cell transcript…Active learning framework leveraging transcriptomics identifies modula…Mapping early human blood cell differentiation using single-cell prote…Intraindividual genome expression analysis reveals a specific molecula…Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal mul…A subset of metastatic pancreatic ductal adenocarcinomas depends quant…Dynamic landscape of pancreatic carcinogenesis reveals early molecular…Altered relaxation times in MRI indicate bronchopulmonary dysplasiaTruth-Content and Phase Transitions of Random Boolean Networks with Ge…Robust Sparse Component Analysis Based on a Generalized Hough TransformCorrecting Classifiers for Sample Selection Bias in Two-Phase Case-Con…Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and…HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellul…Abstract 1945: Identification of a miRNA/mRNA network driving non-smal…Abstract P1-06-02: A force-sensitive organoid assay to quantify regene…Epigenetically Regulated Chromosome 14q32 miRNA Cluster Induces Metast…Linear Geometric ICA: Fundamentals and AlgorithmsA New Concept for Separability Problems in Blind Source SeparationChronic Wnt Signaling Contributes to Lung Epithelial Senescence and Ag…Early Identification of Bronchopulmonary Dysplasia Using Novel Biomark…The Human Lung Cell Atlas: A High-Resolution Reference Map of the Huma…Current Smoking Alters Gene Expression and DNA Methylation in the Nasa…Data-Driven Modelling of Biological Multi-Scale ProcessesCell-Type-Specific Impact of Glucocorticoid Receptor Activation on the…Data Driven Computational Modeling of Hematopoiesis in Myelodysplastic…2D cross-omics integrated enrichment analysis reveals insights into CO…Sfrp1 inhibits lung fibroblast invasion during transition to injury-in…The discovAIR project: a roadmap towards the Human Lung Cell AtlasLSC Abstract – Systemic and local metabolomics profiling reveals novel…LSC Abstract – Systemic and local metabolomics profiling reveals novel…LSC Abstract – Early biomarkers indicating the development of neonatal…Aged alveolar epithelium contributes to inflammaging and reduced stem…Chronic WNT/ß-catenin signaling impairs mitochondrial function in lung…Ex vivo modeling of human lung fibrogenesis and drug mode of action sc…Single cell transcriptomic dissection of virus induced immunopathology…Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal mul…A spatially resolved extracellular matrix proteome atlas of the distal…Mode of actions of nanomaterial-induced respiratory toxicityComparison of genome-wide gene expression profiling by RNA Sequencing…Odefy - From discrete to continuous modelsStructuring heterogeneous biological information using fuzzy clusterin…Knowledge-based matrix factorization temporally resolves the cellular…On the hypothesis-free testing of metabolite ratios in genome-wide and…An automatic method for robust and fast cell detection in bright field…Modeling of 2D diffusion processes based on microscopy data: parameter…iVUN: interactive Visualization of Uncertain biochemical reaction Netw…MCA: Multiresolution Correlation Analysis, a graphical tool for subpop…Analyzing M-CSF dependent monocyte/macrophage differentiation: Express…Intronic microRNAs support their host genes by mediating synergistic a…An evolutionary and structural characterization of mammalian protein c…Dependent component analysisErythropoietin enhances hippocampal long-term potentiation and memoryEffects of smoking and smoking cessation on human serum metabolite pro…Transforming Boolean models to continuous models: methodology and appl…MicroRNAs coordinately regulate protein complexesGaussian graphical modeling reconstructs pathway reactions from high-t…Bayesian model selection validates a biokinetic model for zirconium pr…Sharpening of expression domains induced by transcription and microRNA…Zebrafish reward mutants reveal novel transcripts mediating the behavi…PhenomiR: a knowledgebase for microRNA expression in diseases and biol…pulver: an R package for parallel ultra-rapid p-value computation for…Integrating single-cell RNA-seq datasets with substantial batch effectsProtocol of a population-based prospective COVID-19 cohort study Munic…Multi-omic signature of body weight change: results from a population-…Inference of spatiotemporal effects on cellular state transitions from…Tailored parameter optimization methods for ordinary differential equa…Comprehensive benchmarking of Markov chain Monte Carlo methods for dyn…Early transcriptional responses of bronchial epithelial cells to whole…Next-generation sequencing reveals novel differentially regulated mRNA…SCANPY: large-scale single-cell gene expression data analysisPAGA: graph abstraction reconciles clustering with trajectory inferenc…BART-Seq: cost-effective massively parallelized targeted sequencing fo…MPRAnalyze: statistical framework for massively parallel reporter assaysEleven grand challenges in single-cell data scienceSfaira accelerates data and model reuse in single cell genomicsOver 1000 tools reveal trends in the single-cell RNA-seq analysis land…hadge: a comprehensive pipeline for donor deconvolution in single-cell…Panpipes: a pipeline for multiomic single-cell and spatial transcripto…Mapping lineage-traced cells across time points with moslinNetwork reconstruction for trans acting genetic loci using multi-omics…Machine learning integrative approaches to advance computational immun…A Vine-copula Based Adaptive MCMC Sampler for Efficient Inference of D…RejoindermiR-335 promotes mesendodermal lineage segregation and shapes a transc…Quantification of regenerative potential in primary human mammary epit…Concepts and limitations for learning developmental trajectories from…Comprehensive single cell mRNA profiling reveals a detailed roadmap fo…CIARA: a cluster-independent algorithm for identifying markers of rare…miTALOS: Analyzing the tissue-specific regulation of signaling pathway…Effect of Atmospheric Aging on Soot Particle Toxicity in Lung Cell Mod…The a d coefficient as a descriptive measure of the within‐group agree…Social Transfer of Pathogenic Fungus Promotes Active Immunisation in A…A field guide to cultivating computational biologyHypergraphs and Cellular NetworksSpatial Analysis of Expression Patterns Predicts Genetic Interactions…Patterns of Subnet Usage Reveal Distinct Scales of Regulation in the T…ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulati…Inference for Stochastic Chemical Kinetics Using Moment Equations and…Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Ne…Model-based analysis of response and resistance factors of cetuximab t…DeepWAS: Multivariate genotype-phenotype associations by directly inte…Discovery of Sexual Dimorphisms in Metabolic and Genetic BiomarkersMining the Unknown: A Systems Approach to Metabolite Identification Co…The Human Blood Metabolome-Transcriptome InterfaceTissue-Specific Target Analysis of Disease-Associated MicroRNAs in Hum…The Structure of Borders in a Small WorldHierarchical Differentiation of Myeloid Progenitors Is Encoded in the…The Nature and Perception of Fluctuations in Human Musical RhythmsBody Fat Free Mass Is Associated with the Serum Metabolite Profile in…Lessons Learned from Quantitative Dynamical Modeling in Systems BiologyAllergic Contact Dermatitis in Psoriasis Patients: Typical, Delayed, a…A Critical Period for Postnatal Adaptive Plasticity in a Model of Moto…Integrative Analysis of MicroRNA and mRNA Data Reveals an Orchestrated…CERENA: ChEmical REaction Network Analyzer—A Toolbox for the Simulatio…Pitchfork and Gprasp2 Target Smoothened to the Primary Cilium for Hedg…miTALOS v2: Analyzing Tissue Specific microRNA FunctionDynamic modelling of an ACADS genotype in fatty acid oxidation – Appli…A Unilateral Negative Feedback Loop Between miR-200 microRNAs and Sox2…MicroRNA Loss Enhances Learning and Memory in MiceHypothalamic miR-103 Protects from Hyperphagic Obesity in MiceMetabolic regulation of pluripotency and germ cell fate through α‐keto…Atrx promotes heterochromatin formation at retrotransposonsIntegrative analysis of cell state changes in lung fibrosis with perip…Parkinson's disease motor symptoms rescue by CRISPRa‐reprogramming ast…Current best practices in single‐cell RNA‐seq analysis: a tutorialPredicting antigen specificity of single T cells based on TCR CDR3 reg…Integrated intra‐ and intercellular signaling knowledge for multicellu…RNA velocity—current challenges and future perspectivesUltra‐high sensitivity mass spectrometry quantifies single‐cell proteo…Probing cell identity hierarchies by fate titration and collision duri…Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth…Predicting cellular responses to complex perturbations in high‐through…Single‐cell biology: what does the future hold?Proteome-wide analysis reveals an age-associated cellular phenotype of…Calcium-regulatory proteins as modulators of chemotherapy in human neu…MicroRNA-138 promotes acquired alkylator resistance in glioblastoma by…anndata: Access and store annotated data matricesEpisode-Specific Differential Gene Expression of Peripheral Blood Mono…AI Scientists for Building Virtual-Cell ModelsCommunity effort to unravel the complex human neuronal landscape exemp…Protocol for Predicting Cell Fate Responses to in Silico Perturbation…Heterogeneous Development of β-Cell Populations in Diabetes-Resistant…From Binary to Multivalued to Continuous Models: The lac Operon as a C…Mathematical concepts and their challenges in predicting severity of a…The role of humoral immunity in the pathogenesis of psoriasisIdentification and characterization of distinct brown adipocyte subtyp…Cloning and Sequencing of the Genes Encoding the Periplasmic-Cytochrom…Unified Guidance for Geometry-Conditioned Molecular Generationggplot.multistats: Multiple Summary Statistics for Binned Stats/Geomet…IRdisplay: 'Jupyter' Display MachineryIRkernel: Native R Kernel for the 'Jupyter Notebook'knn.covertree: An Accurate kNN Implementation with Multiple Distance M…repr: Serializable RepresentationsInferring Interaction Networks From Multi-Omics DataMeeting the Challenges of High-Dimensional Single-Cell Data Analysis i…Alveolar macrophages in early stage COPD show functional deviations wi…Editorial: Integrative Computational Systems Biology Approaches in Imm…Model Based Targeting of IL-6-Induced Inflammatory Responses in Cultur…Concept of the Munich/Augsburg Consortium Precision in Mental Health f…Group Testing for SARS-CoV-2 Allows for Up to 10-Fold Efficiency Incre…MicroRNA-Target Network Inference and Local Network Enrichment Analysi…Faculty Opinions recommendation of Deep generative modeling for single…AURKA, DLGAP5, TPX2, KIF11 and CKAP5: Five specific mitosis-associated…Specific temperature-induced perturbations of secondary mRNA structure…The human transcriptome is enriched for miRNA-binding sites located in…Single cell transcriptomic analysis of epithelial and mesenchymal tumo…theislab/atlas-feature-selection-benchmark: 2025-03-15: PublicationUniversalEPI: a generalized attention-based deep ensemble model to acc…Spatial profiling of human pancreas during type 1 diabetes progressionStress in the ventral hippocampus under single-cell resolutionSingle cell decomposition of multicellular aging programs associated w…Advancing spatial biology analysis across programming languagesDisentangling Transcription Factor Programs for Direct Reprogramming w…Source Data Li et al Science Advances 2026NetworkVI: Biologically Guided Variational Inference for Interpretable…ArchMapCP-BG-1M: A CONTROLLED MULTI-VIEW BENCH- MARK FOR DENSITY AND BACKGROU…[DEPRECATED] Theislab sfaira Model RepositorySTATISTICAL METHODS FOR THE ANALYSIS OF HIGH-THROUGHPUT METABOLOMICS D…Benchmarking atlas-level data integration in single-cell genomics - in…NicheFlow - Data, Checkpoints, and ResultsData for "Feature selection methods affect the performance of scRNA-se…Pseudodynamics+: Reconstructing Population Dynamics from Time-Resolved…Exploration of RNA outside segmented cells in spatial transcriptomics…DISCO-seq: 3D single-cell transcriptomics of intact biological systemsA single-cell cytokine dictionary of human peripheral bloodBrain Region-Specific Oligodendrocyte States Highlight Mitochondrial G…IDTrack: Time- and Namespace-Aware Identifier Harmonization for Reprod…Beyond alignment: synergistic integration is required for multimodal c…Longitudinal modality prediction learns gene regulatory patterns: insi…Perturbation-guided mapping of colorectal cancer cell states to causal…An integrated single cell and spatial omics atlas of human prenatal de…Pan-cancer virtual spatial transcriptomics from routine histology with…InterScale reveals multi-scale cellular interaction programs in spatia…Cellpin enables reference-based imputation and denoising of spatial tr…Benchmarking gene expression reconstruction from single-cell latent re…Multimodal temporal mapping of macrophage transcriptome remodeling dur…Learning the shared structure of human health across diseases, modalit…Rectangle: robust and scalable multiscale deconvolution informed by si…An interpretable omnigenic neural network architecture for the human g…Multi-scale modeling of human tissues from spatial transcriptomics wit…Building optimized single-cell reference atlases with scAtlasTbLearning Discrete Cell and Niche Codes from Spatial Transcriptomics Us…Chemokine Landscapes of the Tumor MicroenvironmentG2T: Tissue Reconstruction from Gene Expression via Embedding-Distance…Designing antimicrobials with programmable mechanism and safetyAlphaPeptTools: scverse-native analysis of mass spectrometry-based pro…Time-resolved predictability of end-of-therapy outcome and relapse aft…A Community-Driven Single-Cell PBMC Reference Integrating Landmark Dat…Generative inverse design steers human hematopoietic cell fate in vitroThe Human Gut Cell Atlas v1.0: A Unified, Community-Built Reference of…The Human Cell AtlasThe single-cell eQTLGen consortiumT cells modulate the microglial response to brain ischemia
- Mapping cells through time and space with moscot2025
- anndata: Access and store annotated data matrices2024
- Best practices for single-cell analysis across modalities2023
- Benchmarking atlas-level data integration in single-cell genomics2021
- Mapping single-cell data to reference atlases by transfer learning2021
- Generalizing RNA velocity to transient cell states through dynamical modeling2020
- SCANPY: large-scale single-cell gene expression data analysis2018
Pl. II.1 Placeholder summary about building reference maps of cells and tissues. On the map of publications (Plate II) the 7 works of this theme are drawn large and ringed in the colour of their island, every other work a small ink dot; the key beside it lists them.
7 of 742 works marked · data synced 6 Nov 2026
Placeholder narrative. This paragraph stands in for the description of how the lab builds reference atlases of cells and tissues, and why such maps matter. The theme’s leads write the real text before launch.
Placeholder second paragraph about current directions. People, publications and tools on this page are not written here: they are derived from the theme’s topics.
People4
Publications7
Mapping cells through time and space with moscot
anndata: Access and store annotated data matrices
Best practices for single-cell analysis across modalities
Benchmarking atlas-level data integration in single-cell genomics
Mapping single-cell data to reference atlases by transfer learning
Generalizing RNA velocity to transient cell states through dynamical modeling
SCANPY: large-scale single-cell gene expression data analysis
Software14
scVelo
RNA velocity generalized through dynamical modeling.
515v0.3.49 mo agoPython
scib
Benchmarking analysis of data integration tools.
436v1.2.16 mo agoPython
scArches
Reference mapping for single-cell genomics.
414v0.5.13 y agoJupyter Notebook
Scanpy
Single-cell analysis in Python. Scales to >100M cells.
2.6K1.12.58 d agoPython
Single-cell best practices
https://www.sc-best-practices.org
1.3K0.2.08 d agoJupyter Notebook
anndata
Annotated data.
7830.13.449 d agoPython
moscot
Multi-omic single-cell optimal transport tools.
219v0.5.22 mo agoPython
zellkonverter
Conversion between scRNA-seq objects
209v1.22.06 mo agoR
scCODA
A Bayesian model for compositional single-cell data analysis
205v0.1.94 y agoJupyter Notebook
chemCPA
Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.
162Jupyter Notebook
anndata2ri
Convert between AnnData and SingleCellExperiment
154v2.0.14 mo agoPython
DRVI
Unsupervised Deep Disentangled Representation of Single-Cell Omics
83v0.2.823 d agoPython
scib-reproducibility
Additional code and analysis from the single-cell integration benchmarking project
76Jupyter Notebook
trVAE
Conditional out-of-distribution prediction
63v1.1.26 y agoPython