Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes

Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA

(2015) Christopher A. Lavender et al.   PLoS Computational Biology

Structure and Dynamics of the HIV-1 Frameshift Element RNA

(2014) Justin T. Low et al.   BIOCHEMISTRY

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

(2014) Nathan A Siegfried et al.   NATURE METHODS

Quantifying Selection against Synonymous Mutations in HIV-1 env Evolution

(2013) F. Zanini et al.   JOURNAL OF VIROLOGY

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

On the role of four small hairpins in the HIV-1 RNA genome

(2013) Stefanie A. Knoepfel et al.   RNA Biology

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

Efficient SIVcpz replication in human lymphoid tissue requires viral matrix protein adaptation

(2012) Frederic Bibollet-Ruche et al.   JOURNAL OF CLINICAL INVESTIGATION

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Structural Determinants and Mechanism of HIV-1 Genome Packaging

(2011) Kun Lu et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2009) Joseph M. Watts et al.   NATURE

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

Following translation by single ribosomes one codon at a time

(2008) Jin-Der Wen et al.   NATURE

The A-rich RNA sequences of HIV-1 pol are important for the synthesis of viral cDNA

(2008) C. P. Keating 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

Evidence of a novel RNA secondary structurein the coding region of HIV-1 pol gene

(2008) Q. Wang et al.   RNA

A pause for thought along the co-translational folding pathway

(2008) Anton A. Komar   TRENDS IN BIOCHEMICAL SCIENCES