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

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

(2019) Samuel G. Rodriques et al.   SCIENCE

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

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

Atlas of Subcellular RNA Localization Revealed by APEX-Seq

(2019) Furqan M. Fazal et al.   CELL

Multiplexed detection of RNA using MERFISH and branched DNA amplification

(2019) Chenglong Xia et al.   Scientific Reports

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

(2018) Xiao Wang et al.   SCIENCE

Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy

(2018) Guiping Wang et al.   Scientific Reports

Power in Numbers: Single-Cell RNA-Seq Strategies to Dissect Complex Tissues

(2018) Kenneth D. Birnbaum   Annual Review of Genetics

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

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

(2018) Jeffrey R. Moffitt et al.   SCIENCE

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

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

Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking

(2017) Pornchai Kaewsapsak et al.   eLife

Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression

(2016) Jesse M. Engreitz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

Intron retention in mRNA: No longer nonsense

(2015) Justin J.-L. Wong et al.   BIOESSAYS

Control of Transcript Variability in Single Mammalian Cells

(2015) Nico Battich et al.   CELL

Detained introns are a novel, widespread class of post-transcriptionally spliced introns

(2015) Paul L. Boutz et al.   GENES & DEVELOPMENT

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Expansion microscopy

(2015) F. Chen et al.   SCIENCE

Nuclear Retention of mRNA in Mammalian Tissues

(2015) Keren Bahar Halpern et al.   Cell Reports

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

(2015) Moran N Cabili et al.   GENOME BIOLOGY

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Spatially resolved transcriptomics and beyond

(2014) Nicola Crosetto et al.   NATURE REVIEWS GENETICS

In the right place at the right time: visualizing and understanding mRNA localization

(2014) Adina R. Buxbaum et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling

(2014) C. H. Jan et al.   SCIENCE

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

A Network of Cytosolic Factors Targets SRP-Independent Proteins to the Endoplasmic Reticulum

(2013) Tslil Ast et al.   CELL

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs

(2012) Beata Solnestam et al.   BMC GENOMICS

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Primary Role for Endoplasmic Reticulum-bound Ribosomes in Cellular Translation Identified by Ribosome Profiling

(2011) David W. Reid et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The JMJD2A demethylase regulates apoptosis and proliferation in colon cancer cells

(2011) Tae-Dong Kim et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Pre-mRNA Processing Reaches Back toTranscription and Ahead to Translation

(2009) Melissa J. Moore et al.   CELL

Fast unfolding of communities in large networks

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

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS