Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue

Spatiotemporal mapping of RNA editing in the developing mouse brain using in situ sequencing reveals regional and cell-type-specific regulation

(2020) Elin Lundin et al.   BMC BIOLOGY

Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration

(2020) Michaela Asp et al.   BIOESSAYS

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

(2020) Elisabetta Mereu et al.   NATURE BIOTECHNOLOGY

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

(2020) Jiarui Ding et al.   NATURE BIOTECHNOLOGY

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

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

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma

(2019) Berit Carow et al.   Nature Communications

Spatiotemporal structure of cell fate decisions in murine neural crest

(2019) Ruslan Soldatov et al.   SCIENCE

Starfish enterprise: finding RNA patterns in single cells

(2019) Jeffrey M. Perkel   NATURE

Conserved cell types with divergent features in human versus mouse cortex

(2019) Rebecca D. Hodge et al.   NATURE

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

Generation of in situ sequencing based OncoMaps to spatially resolve gene expression profiles of diagnostic and prognostic markers in breast cancer

(2019) Jessica Svedlund et al.   EBioMedicine

Probabilistic cell typing enables fine mapping of closely related cell types in situ

(2019) Xiaoyan Qian et al.   NATURE METHODS

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart

(2019) Michaela Asp et al.   CELL

Placing RNA in context and space - methods for spatially resolved transcriptomics

(2018) Carina Strell et al.   FEBS Journal

Network Visualization and Analysis of Spatially Aware Gene Expression Data with InsituNet

(2018) John Salamon et al.   Cell Systems

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

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

(2018) Jeffrey R. Moffitt et al.   SCIENCE

Neuronal cell-type classification: challenges, opportunities and the path forward

(2017) Hongkui Zeng et al.   NATURE REVIEWS NEUROSCIENCE

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

(2017) Ed Lein et al.   SCIENCE

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Fourth Generation of Next-Generation Sequencing Technologies: Promise and Consequences

(2016) Rongqin Ke et al.   HUMAN MUTATION

Disentangling neural cell diversity using single-cell transcriptomics

(2016) Jean-Francois Poulin et al.   NATURE NEUROSCIENCE

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

(2016) P. L. Stahl et al.   SCIENCE

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

(2015) A. Zeisel et al.   SCIENCE

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

An anatomically comprehensive atlas of the adult human brain transcriptome

(2012) Michael J. Hawrylycz et al.   NATURE

In situ detection and genotyping of individual mRNA molecules

(2010) Chatarina Larsson et al.   NATURE METHODS

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE