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

Identification of spatial expression trends in single-cell gene expression data

(2018) Daniel Edsgärd et al.   NATURE METHODS

SpatialDE: identification of spatially variable genes

(2018) Valentine Svensson et al.   NATURE METHODS

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

(2017) Keren Bahar Halpern et al.   NATURE

Data-analysis strategies for image-based cell profiling

(2017) Juan C Caicedo et al.   NATURE METHODS

TheDrosophilaembryo at single-cell transcriptome resolution

(2017) Nikos Karaiskos et al.   SCIENCE

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

Functional diversity of astrocytes in neural circuit regulation

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

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2016) Sheel Shah et al.   NEURON

Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse

(2016) Ye Zhang et al.   NEURON

High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing

(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

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity

(2016) Simon Joost et al.   Cell Systems

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

(2015) Aleksandra A. Kolodziejczyk et al.   Cell Stem Cell

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

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

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

(2015) A. Zeisel et al.   SCIENCE

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Microenvironmental regulation of tumor progression and metastasis

(2013) Daniela F Quail et al.   NATURE MEDICINE

Single-cell systems biology by super-resolution imaging and combinatorial labeling

(2012) Eric Lubeck et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system

(2012) Susan M. Sunkin et al.   NUCLEIC ACIDS RESEARCH

MRI Tissue Classification Using High-Resolution Bayesian Hidden Markov Normal Mixture Models

(2011) Dai Feng et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Single-cell dissection of transcriptional heterogeneity in human colon tumors

(2011) Piero Dalerba et al.   NATURE BIOTECHNOLOGY

COXPRESdb: a database to compare gene coexpression in seven model animals

(2010) T. Obayashi et al.   NUCLEIC ACIDS RESEARCH

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Rank-biased precision for measurement of retrieval effectiveness

(2008) Alistair Moffat et al.   ACM TRANSACTIONS ON INFORMATION SYSTEMS

Stem Cell Niche: Microenvironment and Beyond

(2008) Jiwang Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Glutamatergic Nonpyramidal Neurons From Neocortical Layer VI and Their Comparison With Pyramidal and Spiny Stellate Neurons

(2008) Sofija Andjelic et al.   JOURNAL OF NEUROPHYSIOLOGY

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Brain micro-ecologies: neural stem cell niches in the adult mammalian brain

(2007) P. A Riquelme et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES