Publications
Publications of 2025
The works of 2025 by the lab's members during their time here, from their ORCID records, Crossref and Europe PMC.
58 publications16 preprintsLater: 2026Earlier: 2024All publications
202558 publications
Topic: Open-source software Topic: Immunity and inflammationA single-cell cytokine dictionary of human peripheral blood
Topic: Single-cell genomicsDISCO-seq: 3D single-cell transcriptomics of intact biological systems
Topic: Spatial omicsExploration of RNA outside segmented cells in spatial transcriptomics reveals extrasomatic RNA organization
Topic: Cell fate and dynamicsPseudodynamics+: Reconstructing Population Dynamics from Time-Resolved Single Cell Landscapes with Physics Informed Neural Networks
Topic: Deep learning and generative modelsActive learning framework leveraging transcriptomics identifies modulators of disease phenotypes
Topic: Open-source softwareOmniPath: integrated knowledgebase for multi-omics analysis
Topic: Open-source softwareQuiCAT: a scalable and flexible framework for mapping synthetic sequences
Topic: Deep learning and generative modelsLanguage may be all omics needs: Harmonizing multimodal data for omics understanding with CellHermes
Topic: Cell atlasesSpatial single-cell atlas reveals regional variations in healthy and diseased human lung
Topic: Data integrationFADVI: disentangled representation learning for robust integration of single-cell and spatial omics data
Topic: Immunity and inflammationToward a ToxAtlas of Carbon-Based Nanomaterials: Single-Cell RNA Sequencing Reveals Initiating Cell Circuits in Pulmonary Inflammation
Topic: Deep learning and generative modelsNicheformer: a foundation model for single-cell and spatial omics
Topic: Data integrationIntegrating single-cell RNA-seq datasets with substantial batch effects
Topic: Spatial omicsNicheFlow - Data, Checkpoints, and Results
Topic: Cell fate and dynamicsA multimodal cross-species comparison of pancreas development
Topic: Gene regulationscooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution
Topic: Single-cell genomicsMapping early human blood cell differentiation using single-cell proteomics and transcriptomics
Topic: Cell fate and dynamicsDisentangling Transcription Factor Programs for Direct Reprogramming with Generative Modeling
Topic: Deep learning and generative modelsscConcept: Contrastive pretraining for technology-agnostic single-cell representations beyond reconstruction
Topic: Spatial omicsAdvancing spatial biology analysis across programming languages
Topic: Deep learning and generative modelsGraph neural networks learn emergent tissue properties from spatial molecular profiles
Topic: ImagingscPortrait integrates single-cell images into multimodal modeling
Topic: Gene regulationSingle-cell multiome and spatial profiling reveals pancreas cell type–specific gene regulatory programs of type 1 diabetes progression
Topic: ImagingIm-seq: Multimodal droplet barcoding enables high-throughput linking of single-cell imaging and gene expression
Topic: Spatial omicsIntegration of cell-type resolved spatial proteomics and transcriptomics reveals novel mechanisms in early ovarian cancer
Topic: Spatial omicsSpatial proteo-transcriptomic profiling reveals the molecular landscape of borderline ovarian tumors and their invasive progression
Topic: Single-cell genomicsSingle cell decomposition of multicellular aging programs associated with impaired lung regeneration
Topic: Deep learning and generative modelsA foundation model to predict and capture human cognition
Topic: Benchmarks and best practicesSpatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data
Topic: Benchmarks and best practicesDefining and benchmarking open problems in single-cell analysis
Topic: Benchmarks and best practicesBeyond Visual Inspection: Principled Benchmarking of Single-Cell Trajectory Representations with scTRAM
Topic: Data integrationBiologically Informed Variational Inference Enables Interpretable Cell Phenotyping and Discovery
Topic: Cell atlasesAutomated evaluation of single-cell reference atlas mappings enables the identification of disease-associated cell states
Topic: Cell atlasesCharting the single-cell and spatial landscape of IDH-wild-type glioblastoma with GBmap
Topic: Cell atlasesAn integrated transcriptomic cell atlas of human endoderm-derived organoids
Topic: Metabolism and diabetesGIPR agonism and antagonism decrease body weight and food intake via different mechanisms in male mice
Topic: Brain and mental healthExon-variant interplay and multi-modal evidence identify endocrine dysregulation in severe psychiatric disorders impacting excitatory neurons
Topic: Perturbation responsesCellFlow enables generative single-cell phenotype modeling with flow matching
Topic: Deep learning and generative modelsTowards multimodal foundation models in molecular cell biology
Topic: Brain and mental healthStress in the ventral hippocampus under single-cell resolution
Topic: Single-cell genomicsCausal machine learning for single-cell genomics
Topic: Deep learning and generative modelsUniversalEPI: a generalized attention-based deep ensemble model to accurately predict enhancer-promoter interactions across diverse cell types and conditions
Topic: Deep learning and generative modelsQuantitative characterization of cell niches in spatially resolved omics data
Topic: Benchmarks and best practicestheislab/atlas-feature-selection-benchmark: 2025-03-15: Publication
Topic: Benchmarks and best practicesOptimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows
Topic: Benchmarks and best practicesFeature selection methods affect the performance of scRNA-seq data integration and querying
Topic: Deep learning and generative modelsTransformers and genome language models
Topic: Single-cell genomicsBiases in machine-learning models of human single-cell data
Topic: Cell fate and dynamicsTGIF2 is a major regulator of neural stem cell fate and neurogenic priming
Topic: Brain and mental healthChronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids
Topic: Metabolism and diabetesSpatial profiling of human pancreas during type 1 diabetes progression
Topic: Spatial omicsWhat is the main bottleneck in deriving biological understanding from spatial transcriptomic profiling?
Topic: Deep learning and generative modelsUnified Guidance for Geometry-Conditioned Molecular Generation
Topic: Single-cell genomicsMapping cells through time and space with moscot
Topic: ImagingPredicting cell morphological responses to perturbations using generative modeling
TarDis: Achieving Robust and Structured Disentanglement of Multiple Covariates
Topic: Benchmarks and best practicesData for "Feature selection methods affect the performance of scRNA-seq data integration and querying"