COMRADES determines in vivo RNA structures and interactions

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Characterization of cis -Acting RNA Elements of Zika Virus by Using a Self-Splicing Ribozyme-Dependent Infectious Clone

(2017) Zhong-Yu Liu et al.   JOURNAL OF VIROLOGY

Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression

(2016) Belinda Phipson et al.   Annals of Applied Statistics

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

(2016) Zhipeng Lu et al.   CELL

The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures

(2016) Nathan Pirakitikulr et al.   MOLECULAR CELL

In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation

(2016) Jong Ghut Ashley Aw et al.   MOLECULAR CELL

Global Mapping of Human RNA-RNA Interactions

(2016) Eesha Sharma et al.   MOLECULAR CELL

rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome

(2016) Chun Kit Kwok et al.   NATURE METHODS

Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease

(2016) B. M. Akiyama et al.   SCIENCE

Viral RNA switch mediates the dynamic control of flavivirus replicase recruitment by genome cyclization

(2016) Zhong-Yu Liu et al.   eLife

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

(2015) Yoichiro Sugimoto et al.   NATURE

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

High-throughput determination of RNA structure by proximity ligation

(2015) Vijay Ramani et al.   NATURE BIOTECHNOLOGY

Virus Meets Host MicroRNA: the Destroyer, the Booster, the Hijacker

(2014) Y. E. Guo et al.   MOLECULAR AND CELLULAR BIOLOGY

De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly

(2014) Aaron T.L. Lun et al.   NUCLEIC ACIDS RESEARCH

Structural basis for microRNA targeting

(2014) N. T. Schirle et al.   SCIENCE

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

Novel cis-Acting Element within the Capsid-Coding Region Enhances Flavivirus Viral-RNA Replication by Regulating Genome Cyclization

(2013) Z.-Y. Liu et al.   JOURNAL OF VIROLOGY

Hyb: A bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data

(2013) Anthony J. Travis et al.   METHODS

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

R- chie : a web server and R package for visualizing RNA secondary structures

(2012) Daniel Lai et al.   NUCLEIC ACIDS RESEARCH

Identification ofCis-Acting Elements in the 3′-Untranslated Region of the Dengue Virus Type 2 RNA That Modulate Translation and Replication

(2011) Mark Manzano et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

Whole-exome sequencing for finding de novo mutations in sporadic mental retardation

(2011) Peter N Robinson   GENOME BIOLOGY

Interplay of RNA Elements in the Dengue Virus 5' and 3' Ends Required for Viral RNA Replication

(2010) P. Friebe et al.   JOURNAL OF VIROLOGY

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Architecture and secondary structure of an entire HIV-1 RNA genome

(2009) Joseph M. Watts et al.   NATURE