Cell2location maps fine-grained cell types in spatial transcriptomics

Comprehensive Integration of Single-Cell Data

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Solving Least Squares Problems

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Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

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Molecular Architecture of the Mouse Nervous System

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Scrublet: computational identification of cell doublets in single-cell transcriptomic data

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Probabilistic programming in Python using PyMC3

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Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

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Single-cell reconstruction of the early maternal–fetal interface in humans

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Shared and distinct transcriptomic cell types across neocortical areas

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Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

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A molecular cell atlas of the human lung from single-cell RNA sequencing

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Robust decomposition of cell type mixtures in spatial transcriptomics

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Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

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High-definition spatial transcriptomics for in situ tissue profiling

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Multiplex digital spatial profiling of proteins and RNA in fixed tissue

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A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

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A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

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Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

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Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

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BBKNN: fast batch alignment of single cell transcriptomes

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Identification of region-specific astrocyte subtypes at single cell resolution

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A Python library for probabilistic analysis of single-cell omics data

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Neural Circuit-Specialized Astrocytes: Transcriptomic, Proteomic, Morphological, and Functional Evidence

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Pyro: Deep Universal Probabilistic ProgrammingPreprint

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SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes

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Development and Functional Diversification of Cortical Interneurons

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Cells of the human intestinal tract mapped across space and time

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Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro

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Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq

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Functional diversity of astrocytes in neural circuit regulation

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Astroglial Kir4.1 in the lateral habenula drives neuronal bursts in depression

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Identification of diverse astrocyte populations and their malignant analogs

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Class-Switch Recombination Occurs Infrequently in Germinal Centers

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scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation

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Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map

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Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography

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Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons

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The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing

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Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling

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Genome-wide RNA Tomography in the Zebrafish Embryo

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Human germinal centres engage memory and naive B cells after influenza vaccination

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Distinct microbial and immune niches of the human colon

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Cellular and Molecular Probing of Intact Human Organs

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Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics

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A repeated molecular architecture across thalamic pathways

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A cell atlas of human thymic development defines T cell repertoire formationPreprint

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Shared and distinct transcriptomic cell types across neocortical areasPreprint

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Region-Specific Transcriptional Control of Astrocyte Function Oversees Local Circuit Activities

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The human intestinal B-cell response

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De novo gene signature identification from single‐cell RNA‐seq with hierarchical Poisson factorization

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AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution

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scvi-tools: a library for deep probabilistic analysis of single-cell omics dataPreprint

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T Helper Cell Differentiation and Their Function

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Single-cell roadmap of human gonadal developmentPreprint

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Automation of Multiplexed RNAscope Single-Molecule Fluorescent In Situ Hybridization and Immunohistochemistry for Spatial Tissue Mapping

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Methods and applications for single-cell and spatial multi-omics

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Best practices for single-cell analysis across modalities

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Spatial multi-omic map of human myocardial infarction

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Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST

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The expanding vistas of spatial transcriptomics

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Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution

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Spatially resolved multiomics of human cardiac niches

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Spatial profiling of chromatin accessibility in mouse and human tissues

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Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease

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DestVI identifies continuums of cell types in spatial transcriptomics data

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LIANA+ Provides an All-in-One Framework for Cell–Cell Communication Inference

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Impact of the Human Cell Atlas on medicine

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Slide-tags enables single-nucleus barcoding for multimodal spatial genomics

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A spatially resolved atlas of the human lung characterizes a gland-associated immune niche

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A human embryonic limb cell atlas resolved in space and time

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