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

Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation

(2017) Victoria Hung et al.   eLife

Programmable RNA Tracking in Live Cells with CRISPR/Cas9

(2016) David A. Nelles et al.   CELL

Proteomic Analysis of Unbounded Cellular Compartments: Synaptic Clefts

(2016) Ken H. Loh et al.   CELL

Diverse and pervasive subcellular distributions for both coding and long noncoding RNAs

(2016) Ronit Wilk et al.   GENES & DEVELOPMENT

A split horseradish peroxidase for the detection of intercellular protein–protein interactions and sensitive visualization of synapses

(2016) Jeffrey D Martell et al.   NATURE BIOTECHNOLOGY

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

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

Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing

(2016) C.-K. Chen et al.   SCIENCE

SNHG5 promotes colorectal cancer cell survival by counteracting STAU1-mediated mRNA destabilization

(2016) Nkerorema Djodji Damas et al.   Nature Communications

Proteomics of Primary Cilia by Proximity Labeling

(2015) David U. Mick et al.   DEVELOPMENTAL CELL

Efficient and quantitative high-throughput tRNA sequencing

(2015) Guanqun Zheng et al.   NATURE METHODS

Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display

(2015) David M Shechner et al.   NATURE METHODS

Localized translation near the mitochondrial outer membrane: An update

(2015) Chen Lesnik et al.   RNA Biology

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. 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

Influence of RNA extraction methods and library selection schemes on RNA-seq data

(2014) Marc Sultan et al.   BMC GENOMICS

Remote Control of Gene Function by Local Translation

(2014) Hosung Jung et al.   CELL

Proteomic Mapping of the Human Mitochondrial Intermembrane Space in Live Cells via Ratiometric APEX Tagging

(2014) Victoria Hung et al.   MOLECULAR CELL

Directed evolution of APEX2 for electron microscopy and proximity labeling

(2014) Stephanie S Lam et al.   NATURE METHODS

Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling

(2014) C. C. Williams et al.   SCIENCE

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

(2014) C. H. Jan et al.   SCIENCE

RNA and dynamic nuclear organization

(2014) J. Rinn et al.   SCIENCE

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Isolation of mRNAs Associated with Yeast Mitochondria to Study Mechanisms of Localized Translation

(2014) Chen Lesnik et al.   Jove-Journal of Visualized Experiments

The mitochondrial genome encodes abundant small noncoding RNAs

(2013) Seungil Ro et al.   CELL RESEARCH

Frac-seq reveals isoform-specific recruitment to polyribosomes

(2013) T. Sterne-Weiler et al.   GENOME RESEARCH

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

Proteomic Mapping of Mitochondria in Living Cells via Spatially Restricted Enzymatic Tagging

(2013) H.-W. Rhee et al.   SCIENCE

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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

(2012) T. Derrien et al.   GENOME RESEARCH

A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells

(2012) Kyle J. Roux et al.   JOURNAL OF CELL BIOLOGY

Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy

(2012) Jeffrey D Martell et al.   NATURE BIOTECHNOLOGY

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Single-molecule analysis of gene expression using two-color RNA labeling in live yeast

(2012) Sami Hocine et al.   NATURE METHODS

The Human Mitochondrial Transcriptome

(2011) Tim R. Mercer et al.   CELL

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

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

Hierarchical regulation of mRNA partitioning between the cytoplasm and the endoplasmic reticulum of mammalian cells

(2011) Qiang Chen et al.   MOLECULAR BIOLOGY OF THE CELL

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

RNA Mimics of Green Fluorescent Protein

(2011) J. S. Paige et al.   SCIENCE

Genome–nuclear lamina interactions and gene regulation

(2010) Jop Kind et al.   CURRENT OPINION IN CELL BIOLOGY

Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps

(2009) Sung Wook Chi et al.   NATURE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

A Mitochondrial Protein Compendium Elucidates Complex I Disease Biology

(2008) David J. Pagliarini et al.   CELL

Genome-wide screen reveals APC-associated RNAs enriched in cell protrusions

(2008) Stavroula Mili et al.   NATURE

Signal sequence- and translation-independent mRNA localization to the endoplasmic reticulum

(2008) B. Pyhtila et al.   RNA