HT-smFISH: a cost-effective and flexible workflow for high-throughput single-molecule RNA imaging

FISH-quant v2: a scalable and modular tool for smFISH image analysis

(2022) Arthur Imbert et al.   RNA

Spatially resolved transcriptomics in neuroscience

(2021) Jennie L. Close et al.   NATURE METHODS

Spatially resolved single-cell genomics and transcriptomics by imaging

(2021) Xiaowei Zhuang   NATURE METHODS

Spatially resolved transcriptomics adds a new dimension to genomics

(2021) Ludvig Larsson et al.   NATURE METHODS

Method of the Year: spatially resolved transcriptomics

(2021) Vivien Marx   NATURE METHODS

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

(2021) Shahar Alon et al.   SCIENCE

Exon junction complex dependent mRNA localization is linked to centrosome organization during ciliogenesis

(2021) Oh Sung Kwon et al.   Nature Communications

A choreography of centrosomal mRNAs reveals a conserved localization mechanism involving active polysome transport

(2021) Adham Safieddine et al.   Nature Communications

Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses

(2021) Songlei Liu et al.   NUCLEIC ACIDS RESEARCH

deepBlink: threshold-independent detection and localization of diffraction-limited spots

(2021) Bastian Th Eichenberger et al.   NUCLEIC ACIDS RESEARCH

The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions

(2021) Xavier Pichon et al.   RNA

A Dual Protein-mRNA Localization Screen Reveals Compartmentalized Translation and Widespread Co-translational RNA Targeting

(2020) Racha Chouaib et al.   DEVELOPMENTAL CELL

Highly specific multiplexed RNA imaging in tissues with split-FISH

(2020) Jolene Jie Lin Goh et al.   NATURE METHODS

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

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

RNA is a critical element for the sizing and the composition of phase-separated RNA–protein condensates

(2019) Marina Garcia-Jove Navarro et al.   Nature Communications

Starfish enterprise: finding RNA patterns in single cells

(2019) Jeffrey M. Perkel   NATURE

ImJoy: an open-source computational platform for the deep learning era

(2019) Wei Ouyang et al.   NATURE METHODS

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

(2018) Sheel Shah et al.   CELL

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

Co-translational protein targeting facilitates centrosomal recruitment of PCNT during centrosome maturation in vertebrates

(2018) Guadalupe Sepulveda et al.   eLife

A Growing Toolbox to Image Gene Expression in Single Cells: Sensitive Approaches for Demanding Challenges

(2018) Xavier Pichon et al.   MOLECULAR CELL

ClampFISH detects individual nucleic acid molecules using click chemistry–based amplification

(2018) Sara H Rouhanifard et al.   NATURE BIOTECHNOLOGY

A computational framework to study sub-cellular RNA localization

(2018) Aubin Samacoits et al.   Nature Communications

Profiling the transcriptome with RNA SPOTs

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

Efficient in situ barcode sequencing using padlock probe-based BaristaSeq

(2017) Xiaoyin Chen et al.   NUCLEIC ACIDS RESEARCH

mRNA localization as a rheostat to regulate subcellular gene expression

(2017) Nevraj S. Kejiou et al.   Wiley Interdisciplinary Reviews-RNA

smiFISH and FISH-quant – a flexible single RNA detection approach with super-resolution capability

(2016) Nikolay Tsanov et al.   NUCLEIC ACIDS RESEARCH

Glutamate-induced RNA localization and translation in neurons

(2016) Young J. Yoon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Linking Long Noncoding RNA Localization and Function

(2016) Ling-Ling Chen   TRENDS IN BIOCHEMICAL SCIENCES

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

(2015) Je Hyuk Lee et al.   Nature Protocols

Glucose-Regulated Phosphorylation of the PUF Protein Puf3 Regulates the Translational Fate of Its Bound mRNAs and Association with RNA Granules

(2015) Chien-Der Lee 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

Mitochondrial ER Contacts Are Crucial for Mitophagy in Yeast

(2014) Stefan Böckler et al.   DEVELOPMENTAL CELL

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

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

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

Here, there, everywhere

(2014) Birgit Singer-Krüger et al.   RNA Biology

Fluorescence Imaging of Single-Copy DNA Sequences within the Human Genome Using PNA-Directed Padlock Probe Assembly

(2013) Anastasia I. Yaroslavsky et al.   CHEMISTRY & BIOLOGY

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Image-based transcriptomics in thousands of single human cells at single-molecule resolution

(2013) Nico Battich et al.   NATURE METHODS

FISH-quant: automatic counting of transcripts in 3D FISH images

(2013) Florian Mueller et al.   NATURE METHODS

RNA detection in situ with FISH-STICs

(2013) J. R. Sinnamon et al.   RNA

Structural messenger RNA contains cytokeratin polymerization and depolymerization signals

(2011) Malgorzata Kloc et al.   CELL AND TISSUE RESEARCH

Programmable in situ amplification for multiplexed imaging of mRNA expression

(2010) Harry M T Choi et al.   NATURE BIOTECHNOLOGY

Design of 240,000 orthogonal 25mer DNA barcode probes

(2009) Q. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA