Cell2location maps fine-grained cell types in spatial transcriptomics

Spatiotemporal analysis of human intestinal development at single-cell resolution

(2021) David Fawkner-Corbett et al.   CELL

Robust decomposition of cell type mixtures in spatial transcriptomics

(2021) Dylan M. Cable et al.   NATURE BIOTECHNOLOGY

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

(2021) Marc Elosua-Bayes et al.   NUCLEIC ACIDS RESEARCH

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

(2021) Hamish W. King et al.   Science Immunology

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

(2021) Zizhen Yao et al.   CELL

Cells of the human intestinal tract mapped across space and time

(2021) Rasa Elmentaite et al.   NATURE

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

(2021) Hananeh Aliee et al.   Cell Systems

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

(2021) Luz Garcia-Alonso et al.   NATURE GENETICS

Cellular and Molecular Probing of Intact Human Organs

(2020) Shan Zhao et al.   CELL

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

(2020) Reuben Moncada et al.   NATURE BIOTECHNOLOGY

Distinct microbial and immune niches of the human colon

(2020) Kylie R. James et al.   NATURE IMMUNOLOGY

Identification of region-specific astrocyte subtypes at single cell resolution

(2020) Mykhailo Y. Batiuk et al.   Nature Communications

Multiplex digital spatial profiling of proteins and RNA in fixed tissue

(2020) Christopher R. Merritt et al.   NATURE BIOTECHNOLOGY

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

(2020) Omer Ali Bayraktar et al.   NATURE NEUROSCIENCE

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

(2020) Anna Yu-Szu Huang et al.   NEURON

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

(2020) Jackson S. Turner et al.   NATURE

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

(2020) Alma Andersson et al.   Communications Biology

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

(2020) Kyle J. Travaglini et al.   NATURE

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

(2020) Robert R. Stickels et al.   NATURE BIOTECHNOLOGY

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

(2019) Samuel G. Rodriques et al.   SCIENCE

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

(2019) Hanna Mendes Levitin et al.   Molecular Systems Biology

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Class-Switch Recombination Occurs Infrequently in Germinal Centers

(2019) Jonathan A. Roco et al.   IMMUNITY

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

(2019) Dylan Kotliar et al.   eLife

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

A repeated molecular architecture across thalamic pathways

(2019) James W. Phillips et al.   NATURE NEUROSCIENCE

Layer-specific morphological and molecular differences in neocortical astrocytes and their dependence on neuronal layers

(2018) Darin Lanjakornsiripan et al.   Nature Communications

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

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

(2018) Yihui Cui et al.   NATURE

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

(2018) Roser Vento-Tormo et al.   NATURE

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

Development and Functional Diversification of Cortical Interneurons

(2018) Lynette Lim et al.   NEURON

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

(2017) Keren Bahar Halpern et al.   NATURE

Identification of diverse astrocyte populations and their malignant analogs

(2017) Chia-Ching John Lin et al.   NATURE NEUROSCIENCE

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

(2017) Hua Chai et al.   NEURON

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

(2017) Ed Lein et al.   SCIENCE

The human intestinal B-cell response

(2016) J Spencer et al.   Mucosal Immunology

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

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

(2016) Suguna Rani Krishnaswami et al.   Nature Protocols

Functional diversity of astrocytes in neural circuit regulation

(2016) Lucile Ben Haim et al.   NATURE REVIEWS NEUROSCIENCE

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

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

(2016) Susanne Nichterwitz et al.   Nature Communications

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

(2015) A. Zeisel et al.   SCIENCE

Genome-wide RNA Tomography in the Zebrafish Embryo

(2014) Jan Philipp Junker et al.   CELL

Gut-associated lymphoid tissue, T cell trafficking, and chronic intestinal inflammation

(2010) Iurii Koboziev et al.   Annals of the New York Academy of Sciences