Clustering spatial transcriptomics data

Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis

(2021) Madhav Mantri et al.   Nature Communications

Spatial omics and multiplexed imaging to explore cancer biology

(2021) Sabrina M. Lewis et al.   NATURE METHODS

CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues

(2020) Caleb R. Stoltzfus et al.   Cell Reports

Identifying signaling genes in spatial single cell expression data

(2020) Dongshunyi Li et al.   BIOINFORMATICS

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

The Human Lung Cell Atlas - A high-resolution reference map of the human lung in health and disease

(2019) Herbert B Schiller et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Understanding the kidney one cell at a time

(2019) Jihwan Park et al.   KIDNEY INTERNATIONAL

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

(2019) Chenglong Xia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis

(2019) Damien Arnol et al.   Cell Reports

Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-Cell RNA-Seq

(2018) Shristi Pandey et al.   CURRENT BIOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data

(2018) Qian Zhu et al.   NATURE BIOTECHNOLOGY

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

(2018) Jeffrey R. Moffitt et al.   SCIENCE

Profiling the transcriptome with RNA SPOTs

(2017) Chee-Huat Linus Eng et al.   NATURE METHODS

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

(2016) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

(2016) Jeffrey R. Moffitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

(2016) B. B. Lake et al.   SCIENCE

Identification of cell types from single-cell transcriptomes using a novel clustering method

(2015) Chen Xu et al.   BIOINFORMATICS

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Reframing sexual differentiation of the brain

(2011) Margaret M McCarthy et al.   NATURE NEUROSCIENCE

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT