Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors

SHAPE Directed Discovery of New Functions in Large RNAs

(2021) Kevin M. Weeks   ACCOUNTS OF CHEMICAL RESEARCH

MET promotes the proliferation and differentiation of myoblasts

(2020) Yongyong Li et al.   EXPERIMENTAL CELL RESEARCH

Targeting the Oncogenic Long Non-coding RNA SLNCR1 by Blocking Its Sequence-Specific Binding to the Androgen Receptor

(2020) Karyn Schmidt et al.   Cell Reports

LncRNA ANRIL acts as a modular scaffold of WDR5 and HDAC3 complexes and promotes alteration of the vascular smooth muscle cell phenotype

(2020) Chengxin Zhang et al.   Cell Death & Disease

The lncRNA Growth Arrest Specific 5 Regulates Cell Survival via Distinct Structural Modules with Independent Functions

(2020) Filipp Frank et al.   Cell Reports

Analysis of RNA–protein networks with RNP-MaP defines functional hubs on RNA

(2020) Chase A. Weidmann et al.   NATURE BIOTECHNOLOGY

Structure of the bacterial ribosome at 2 Å resolution

(2020) Zoe L Watson et al.   eLife

Advances in RNA 3D Structure Modeling Using Experimental Data

(2020) Bing Li et al.   Frontiers in Genetics

Skeletal muscle-specific Prmt1 deletion causes muscle atrophy via deregulation of the PRMT6-FOXO3 axis

(2019) Seri Choi et al.   Autophagy

Guidelines for SHAPE Reagent Choice and Detection Strategy for RNA Structure Probing Studies

(2019) Steven Busan et al.   BIOCHEMISTRY

Physical and Functional Analysis of Viral RNA Genomes by SHAPE

(2019) Mark A. Boerneke et al.   Annual Review of Virology

Conserved Pseudoknots in lncRNA MEG3 Are Essential for Stimulation of the p53 Pathway

(2019) Tina Uroda et al.   MOLECULAR CELL

RNA base-pairing complexity in living cells visualized by correlated chemical probing

(2019) Anthony M. Mustoe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BART: a transcription factor prediction tool with query gene sets or epigenomic profiles

(2018) Zhenjia Wang et al.   BIOINFORMATICS

MUNC, an eRNA upstream from the MYOD gene, induces a subgroup of myogenic transcripts in trans, independently of MyoD

(2018) Magdalena A. Cichewicz et al.   MOLECULAR AND CELLULAR BIOLOGY

A Muscle-Specific Enhancer RNA Mediates Cohesin Recruitment and Regulates Transcription In trans

(2018) Pei-Fang Tsai et al.   MOLECULAR CELL

Viral RNA structure-based strategies to manipulate translation

(2018) Zane A. Jaafar et al.   NATURE REVIEWS MICROBIOLOGY

Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2

(2017) Steven Busan et al.   RNA

Multi-omics enrichment analysis using the GeneTrail2 web service

(2016) Daniel Stöckel et al.   BIOINFORMATICS

SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across theXistlncRNA in living cells

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

Detection of RNA–Protein Interactions in Living Cells with SHAPE

(2015) Matthew J. Smola et al.   BIOCHEMISTRY

Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis

(2015) Matthew J Smola et al.   Nature Protocols

RNA-PuzzlesRound II: assessment of RNA structure prediction programs applied to three large RNA structures

(2015) Zhichao Miao et al.   RNA

Runx1 Transcription Factor Is Required for Myoblasts Proliferation during Muscle Regeneration

(2015) Kfir Baruch Umansky et al.   PLoS Genetics

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

(2015) Rui Fang et al.   PLoS Genetics

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

MUNC, a Long Noncoding RNA That Facilitates the Function of MyoD in Skeletal Myogenesis

(2014) Adam C. Mueller et al.   MOLECULAR AND CELLULAR BIOLOGY

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment

(2013) Carla A. Klattenhoff et al.   CELL

eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci

(2013) Kambiz Mousavi et al.   MOLECULAR CELL

Systematic identification of transcriptional regulatory modules from protein–protein interaction networks

(2013) Diego Diez et al.   NUCLEIC ACIDS RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) T. Derrien et al.   GENOME RESEARCH

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

A NMR strategy to unambiguously distinguish nucleic acid hairpin and duplex conformations applied to a Xist RNA A-repeat

(2008) Malgorzata M. Duszczyk et al.   NUCLEIC ACIDS RESEARCH

Accurate SHAPE-directed RNA structure determination

(2008) K. E. Deigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Decorin enhances the proliferation and differentiation of myogenic cells through suppressing myostatin activity

(2007) Yasuhiro Kishioka et al.   JOURNAL OF CELLULAR PHYSIOLOGY