RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction

Modeling and automation of sequencing-based characterization of RNA structure

(2011) S. Aviran 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

A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA

(2011) W. Kladwang et al.   RNA

tRNA Stabilization by Modified Nucleotides

(2010) Yuri Motorin et al.   BIOCHEMISTRY

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

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

(2010) Jason G Underwood et al.   NATURE METHODS

Evaluation of the information content of RNA structure mapping data for secondary structure prediction

(2010) S. Quarrier et al.   RNA

Riboswitches: Structures and Mechanisms

(2010) A. D. Garst et al.   Cold Spring Harbor Perspectives in Biology

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

(2009) Joseph M. Watts et al.   NATURE

One RNA aptamer sequence, two structures: a collaborating pair that inhibits AMPA receptors

(2009) Zhen Huang et al.   NUCLEIC ACIDS RESEARCH

Improved RNA secondary structure prediction by maximizing expected pair accuracy

(2009) Z. J. Lu et al.   RNA

Generation of synthetic RNA-based thermosensors

(2008) Torsten Waldminghaus et al.   BIOLOGICAL CHEMISTRY

High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis

(2008) Somdeb Mitra et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways. 2008 update

(2008) A. Czerwoniec 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

ShapeFinder: A software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis

(2008) S. M. Vasa et al.   RNA

The Eukaryotic Genome as an RNA Machine

(2008) P. P. Amaral et al.   SCIENCE