Mapping RNA–RNA interactome and RNA structure in vivo by MARIO

hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1

(2015) Yoichiro Sugimoto et al.   NATURE

RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites

(2014) Jesse M. Engreitz et al.   CELL

Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA

(2014) Schraga Schwartz et al.   CELL

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

(2014) Alexandre Fort et al.   NATURE GENETICS

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

iCLIP: Protein–RNA interactions at nucleotide resolution

(2013) Ina Huppertz et al.   METHODS

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

System-wide identification of RNA-binding proteins by interactome capture

(2013) Alfredo Castello et al.   Nature Protocols

Argonaute proteins: functional insights and emerging roles

(2013) Gunter Meister   NATURE REVIEWS GENETICS

The RNA-binding protein repertoire of embryonic stem cells

(2013) S Chul Kwon et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNAstructure: web servers for RNA secondary structure prediction and analysis

(2013) Stanislav Bellaousov et al.   NUCLEIC ACIDS RESEARCH

Turbo FISH: A Method for Rapid Single Molecule RNA FISH

(2013) Sydney M. Shaffer et al.   PLoS One

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

miR-TRAP: A Benchtop Chemical Biology Strategy to Identify microRNA Targets

(2012) Huricha Baigude et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation

(2012) P. Yu et al.   GENOME RESEARCH

ChIA-PET analysis of transcriptional chromatin interactions

(2012) Jingyao Zhang et al.   METHODS

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

Transcriptome-wide miR-155 Binding Map Reveals Widespread Noncanonical MicroRNA Targeting

(2012) Gabriel B. Loeb et al.   MOLECULAR CELL

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

Control of somatic tissue differentiation by the long non-coding RNA TINCR

(2012) Markus Kretz et al.   NATURE

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

(2012) Yoichiro Sugimoto et al.   GENOME BIOLOGY

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq

(2011) Hana Yi et al.   NUCLEIC ACIDS RESEARCH

MicroRNA Genes Derived from Repetitive Elements and Expanded by Segmental Duplication Events in Mammalian Genomes

(2011) Zhidong Yuan et al.   PLoS One

Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast

(2011) G. Kudla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Capture of MicroRNA–Bound mRNAs Identifies the Tumor Suppressor miR-34a as a Regulator of Growth Factor Signaling

(2011) Ashish Lal et al.   PLoS Genetics

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Box H/ACA Small Ribonucleoproteins

(2010) Tamás Kiss et al.   MOLECULAR CELL

Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

(2010) Jing Zhao et al.   MOLECULAR CELL

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs

(2010) Markus Brameier et al.   NUCLEIC ACIDS RESEARCH

Optimization of enzymatic reaction conditions for generating representative pools of cDNA from small RNA

(2010) D. B. Munafo et al.   RNA

Electrochemically Controlled Deconjugation and Delivery of Single Quantum Dots into the Nucleus of Living Cells

(2010) Kyungsuk Yum et al.   Small

Repression of transposable-elements – a microRNA anti-cancer defense mechanism?

(2010) Reut Shalgi et al.   TRENDS IN GENETICS

iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

(2010) Zhen Wang et al.   PLOS BIOLOGY

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs

(2009) S. Granneman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Human snoRNA with MicroRNA-Like Functions

(2008) Christine Ender et al.   MOLECULAR CELL

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Quantum dots versus organic dyes as fluorescent labels

(2008) Ute Resch-Genger et al.   NATURE METHODS