CRISPR-assisted detection of RNA–protein interactions in living cells

Comprehensive identification of RNA–protein interactions in any organism using orthogonal organic phase separation (OOPS)

(2019) Rayner M. L. Queiroz et al.   NATURE BIOTECHNOLOGY

Xist RNA antagonizes the SWI/SNF chromatin remodeler BRG1 on the inactive X chromosome

(2019) Teddy Jégu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Purification of cross-linked RNA-protein complexes by phenol-toluol extraction

(2019) Erika C. Urdaneta et al.   Nature Communications

Methods to study RNA–protein interactions

(2019) Muthukumar Ramanathan et al.   NATURE METHODS

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Approaches for measuring the dynamics of RNA–protein interactions

(2019) Donny D. Licatalosi et al.   Wiley Interdisciplinary Reviews-RNA

Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors

(2018) Silvana Konermann et al.   CELL

Discovery of proteins associated with a predefined genomic locus via dCas9–APEX-mediated proximity labeling

(2018) Samuel A. Myers et al.   NATURE METHODS

RNA–protein interaction detection in living cells

(2018) Muthukumar Ramanathan et al.   NATURE METHODS

The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest

(2018) Jakob Trendel et al.   CELL

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

(2016) Zhipeng Lu et al.   CELL

New Xist -Interacting Proteins in X-Chromosome Inactivation

(2016) Hegias Mira-Bontenbal et al.   CURRENT BIOLOGY

Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses

(2016) Katannya Kapeli et al.   Nature Communications

ChIP bias as a function of cross-linking time

(2015) Laura Baranello et al.   CHROMOSOME RESEARCH

Extensive allele-specific translational regulation in hybrid mice

(2015) J. Hou et al.   Molecular Systems Biology

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

(2015) A. Minajigi et al.   SCIENCE

A cost-effective RNA sequencing protocol for large-scale gene expression studies

(2015) Zhonggang Hou et al.   Scientific Reports

Prognostic Value of Ezrin in Various Cancers: A Systematic Review and Updated Meta-analysis

(2015) Jianwei Li et al.   Scientific Reports

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

Quick Fluorescent In Situ Hybridization Protocol for Xist RNA Combined with Immunofluorescence of Histone Modification in X-chromosome Inactivation

(2014) Minghui Yue et al.   Jove-Journal of Visualized Experiments

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data

(2012) Jianxing Feng et al.   BIOINFORMATICS

Exosomes Mediate Stromal Mobilization of Autocrine Wnt-PCP Signaling in Breast Cancer Cell Migration

(2012) Valbona Luga et al.   CELL

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

Suppression of progenitor differentiation requires the long noncoding RNA ANCR

(2012) M. Kretz et al.   GENES & DEVELOPMENT

Epigenetic Regulation by Long Noncoding RNAs

(2012) J. T. Lee   SCIENCE

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

AlleleSeq: analysis of allele-specific expression and binding in a network framework

(2011) J. Rozowsky et al.   Molecular Systems Biology

X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription

(2011) Eda Yildirim et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Diverse factors are involved in maintaining X chromosome inactivation

(2011) K. M. Chan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Da Wei Huang et al.   Nature Protocols

3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA

(2008) Jeremy E. Wilusz et al.   CELL

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH