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

Ribosome RNA Assembly Intermediates Visualized in Living Cells

(2014) Jennifer L. McGinnis et al.   BIOCHEMISTRY

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

RNA secondary structure modeling at consistent high accuracy using differential SHAPE

(2014) G. M. Rice et al.   RNA

Mod-seq: high-throughput sequencing for chemical probing of RNA structure

(2014) J. Talkish et al.   RNA

The Cellular Environment Stabilizes Adenine Riboswitch RNA Structure

(2013) Jillian Tyrrell et al.   BIOCHEMISTRY

Directed polymerase evolution

(2013) Tingjian Chen et al.   FEBS LETTERS

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

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

(2013) C. E. Hajdin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Guanosine-Centric Mechanism for RNA Chaperone Function

(2013) J. K. Grohman et al.   SCIENCE

Comparison of SIV and HIV-1 Genomic RNA Structures Reveals Impact of Sequence Evolution on Conserved and Non-Conserved Structural Motifs

(2013) Elizabeth Pollom et al.   PLoS Pathogens

Fingerprinting Noncanonical and Tertiary RNA Structures by Differential SHAPE Reactivity

(2012) Kady-Ann Steen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Functional complexity and regulation through RNA dynamics

(2012) Elizabeth A. Dethoff et al.   NATURE

RNA SHAPE analysis in living cells

(2012) Robert C Spitale et al.   Nature Chemical Biology

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The role of the 3' untranslated region in post-transcriptional regulation of protein expression in mammalian cells.

(2012) Eva Matoulkova et al.   RNA Biology

Exploring RNA Structural Codes with SHAPE Chemistry

(2011) Kevin M. Weeks et al.   ACCOUNTS OF CHEMICAL RESEARCH

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

RNA structure probing dash seq

(2011) K. M. Weeks   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

(2011) C. B. Jabara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

(2011) J. B. Lucks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Advances in RNA structure analysis by chemical probing

(2010) Kevin M Weeks   CURRENT OPINION IN STRUCTURAL BIOLOGY

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Toward global RNA structure analysis

(2010) David M Mauger et al.   NATURE BIOTECHNOLOGY

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

(2010) Jason G Underwood et al.   NATURE METHODS

Definition of a high-affinity Gag recognition structure mediating packaging of a retroviral RNA genome

(2010) C. Gherghe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Centrality of RNA

(2009) Phillip A. Sharp   CELL

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

(2009) Joseph M. Watts et al.   NATURE

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

High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States

(2008) Kevin A Wilkinson et al.   PLOS BIOLOGY