Publications
Publications of 2026
The works of 2026 by the lab's members during their time here, from their ORCID records, Crossref and Europe PMC.
57 publications27 preprintsEarlier: 2025All publications
202657 publications
Topic: Metabolism and diabetes Topic: Brain and mental healthIntegrated manufacturing platform for cortical organoids reveals early phosphatase and prefoldin dysregulation in MAPT V337M neurons
Topic: Cell atlasesThe Human Gut Cell Atlas v1.0: A Unified, Community-Built Reference of Cellular Diversity Across the Gut
Topic: Cell fate and dynamicsGenerative inverse design steers human hematopoietic cell fate in vitro
Topic: Data integrationArchMap is a web-based platform for reference-based analysis of single-cell datasets
Topic: Cell atlasesA Community-Driven Single-Cell PBMC Reference Integrating Landmark Datasets Spanning Health and Disease
Topic: Single-cell genomicsConvexGating infers gating strategies from clusters in single cell cytometry data
Topic: Perturbation responsesAI Scientists for Building Virtual-Cell Models
Topic: Clinical and cohort dataTime-resolved predictability of end-of-therapy outcome and relapse after cure in Phase 3 tuberculosis trials
Topic: Open-source softwareAlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics
Topic: Immunity and inflammationMultimodal discovery of a pathogenic B-cell-dependent T-cell state in multiple sclerosis
Topic: Data integrationTowards 3D-oid models that integrate molecular, morphological and spatial cellular features
Topic: Deep learning and generative modelsCreating bottom-up RNA transfer vehicles from synthetic protein assemblies
Topic: Deep learning and generative modelsDesigning antimicrobials with programmable mechanism and safety
Topic: Deep learning and generative modelsG2T: Tissue Reconstruction from Gene Expression via Embedding-Distance Flow Matching
Topic: Deep learning and generative modelsLearning Discrete Cell and Niche Codes from Spatial Transcriptomics Using Dual Residual Vector Quantization
Topic: Open-source softwareArchMap
Topic: Immunity and inflammationChemokine Landscapes of the Tumor Microenvironment
Topic: Brain and mental healthPlasticity of human microglia and brain perivascular macrophages in aging and Alzheimer’s disease
Topic: Spatial omicsMulti-scale modeling of human tissues from spatial transcriptomics with TERRA
Topic: Cell atlasesBuilding optimized single-cell reference atlases with scAtlasTb
Topic: Metabolism and diabetesType 2 diabetes prevention across the life course
Topic: Deep learning and generative modelsAn interpretable omnigenic neural network architecture for the human genome
Topic: Spatial omicsSpatioTemporal Omics Consortium: a global effort for biological discovery across species, space and time
Topic: Clinical and cohort dataLearning the shared structure of human health across diseases, modalities, and time
Topic: Bulk omics and geneticsRectangle: robust and scalable multiscale deconvolution informed by single-cell RNA sequencing data
Topic: Data integrationNetworkVI: Biologically Guided Variational Inference for Interpretable Multimodal Single-Cell Integration and Discovery
Topic: Immunity and inflammationMultimodal temporal mapping of macrophage transcriptome remodeling during Salmonella infection
Topic: Gene regulationTranscriptional repression by TGIF2 coordinates neurogenic priming and neural stem cell maintenance
Topic: Benchmarks and best practicesBenchmarking gene expression reconstruction from single-cell latent representations
Topic: Deep learning and generative modelsCellpin enables reference-based imputation and denoising of spatial transcriptomes
Topic: Cell fate and dynamicsRegVelo: Gene-regulatory-informed dynamics of single cells
Topic: Deep learning and generative modelsUniversalEPI: robust prediction of cell type-specific and differential chromatin interactions from DNA sequence and chromatin accessibility
Source Data Li et al Science Advances 2026
Topic: Deep learning and generative modelsInterScale reveals multi-scale cellular interaction programs in spatial transcriptomics
Topic: Deep learning and generative modelsTarDis: Achieving robust and structured disentanglement of multiple covariates
Topic: Statistical inferenceContinuous multi-omics pathway enrichment analysis resolves hidden functional heterogeneity
Topic: Spatial omicsPan-cancer virtual spatial transcriptomics from routine histology with Phoenix
Topic: Cell fate and dynamicsNon-destructive transcriptomics via vesicular export
Topic: Brain and mental healthTNF alpha unmasks enteric malate aspartate shuttle dysfunction bridging Parkinson disease and intestinal inflammation
Topic: Cell atlasesAn integrated single cell and spatial omics atlas of human prenatal development
Topic: Bulk omics and geneticsLarge-scale proteomics across neurological disorders uncovers biomarker panel and targets in multiple sclerosis
Topic: Cell atlasesPerturbation-guided mapping of colorectal cancer cell states to causal mechanisms
Topic: Benchmarks and best practicesCP-BG-1M: A CONTROLLED MULTI-VIEW BENCH- MARK FOR DENSITY AND BACKGROUND SHORTCUTS IN MORPHOLOGY PROFILING
Topic: Cell fate and dynamicsGenerative models of cell dynamics: from Neural ODEs to flow matching
Topic: Benchmarks and best practicesLongitudinal modality prediction learns gene regulatory patterns: insights from a single-cell competition
Topic: Data integrationBeyond alignment: synergistic integration is required for multimodal cell foundation models
Topic: Spatial omicsIdentifying 3D signal overlaps in spatial transcriptomics data with ovrlpy
Topic: Open-source softwareIDTrack: Time- and Namespace-Aware Identifier Harmonization for Reproducible Workflows
Topic: Deep learning and generative modelsFrom modality-specific to compositional foundation models for cell biology
Topic: Cell fate and dynamicsCellRank: consistent and data view agnostic fate mapping for single-cell genomics
Topic: Cell atlasesSingle-cell atlas of the transcriptome and chromatin accessibility in the human retina
Topic: Brain and mental healthSingle-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
Topic: Brain and mental healthBrain Region-Specific Oligodendrocyte States Highlight Mitochondrial Gene Upregulation and Loss of Canonical Identity Signatures in Alzheimer’s Disease
Topic: Immunity and inflammationA combinatorial transcription factor screening platform for immune cell reprogramming
Topic: Immunity and inflammationMultimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers
Topic: Cell fate and dynamicsProtocol for Predicting Cell Fate Responses to in Silico Perturbation using RegVelo, from Code to Agentic Platform Analysis