Automated identification of the mouse brain’s spatial compartments from in situ sequencing data

TissUUmaps: Interactive visualization of large-scale spatial gene expression and tissue morphology data

(2020) Leslie Solorzano et al.   BIOINFORMATICS

Molecular atlas of the adult mouse brain

(2020) Cantin Ortiz et al.   Science Advances

LifeTime and improving European healthcare through cell-based interceptive medicine

(2020) Nikolaus Rajewsky et al.   NATURE

A community-based transcriptomics classification and nomenclature of neocortical cell types

(2020) Rafael Yuste et al.   NATURE NEUROSCIENCE

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

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

Anduril 2: upgraded large-scale data integration framework

(2019) Alejandra Cervera et al.   BIOINFORMATICS

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

(2019)   NATURE

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

(2019) Xiaoyan Qian et al.   NATURE METHODS

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

(2018) Carina Strell et al.   FEBS Journal

SpatialDE: identification of spatially variable genes

(2018) Valentine Svensson et al.   NATURE METHODS

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

(2018) Xiao Wang et al.   SCIENCE

Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics

(2018) Kenneth D. Harris et al.   PLOS BIOLOGY

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq

(2017) Jun Chen et al.   Nature Protocols

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

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

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

(2016) P. L. Stahl et al.   SCIENCE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

(2015) Kaia Achim et al.   NATURE BIOTECHNOLOGY

Genome-wide RNA Tomography in the Zebrafish Embryo

(2014) Jan Philipp Junker et al.   CELL

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Concise Representation of Mass Spectrometry Images by Probabilistic Latent Semantic Analysis

(2008) Michael Hanselmann et al.   ANALYTICAL CHEMISTRY

CellProfiler Analyst: data exploration and analysis software for complex image-based screens

(2008) Thouis R Jones et al.   BMC BIOINFORMATICS