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

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

Transcriptional and Posttranscriptional Regulation of HIV-1 Gene Expression

(2013) J. Karn et al.   Cold Spring Harbor Perspectives in Medicine

SHAPE-directed Discovery of Potent shRNA Inhibitors of HIV-1

(2012) Justin T Low et al.   MOLECULAR THERAPY

Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing

(2012) Karen E. Ocwieja et al.   NUCLEIC ACIDS RESEARCH

The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus

(2012) Antoinette C van der Kuyl et al.   Retrovirology

Structural Determinants and Mechanism of HIV-1 Genome Packaging

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

The in vitro loose dimer structure and rearrangements of the HIV-2 leader RNA

(2011) Katarzyna J. Purzycka et al.   NUCLEIC ACIDS RESEARCH

NMR Detection of Structures in the HIV-1 5'-Leader RNA That Regulate Genome Packaging

(2011) K. Lu et al.   SCIENCE

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Structural basis for cooperative RNA binding and export complex assembly by HIV Rev

(2010) Matthew D Daugherty et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Regulation of vif mRNA Splicing by Human Immunodeficiency Virus Type 1 Requires 5' Splice Site D2 and an Exonic Splicing Enhancer To Counteract Cellular Restriction Factor APOBEC3G

(2009) D. Mandal et al.   JOURNAL OF VIROLOGY

Secondary Structure of the Mature Ex Virio Moloney Murine Leukemia Virus Genomic RNA Dimerization Domain

(2009) C. Gherghe et al.   JOURNAL OF VIROLOGY

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

(2009) Joseph M. Watts et al.   NATURE

Fidelity of plus-strand priming requires the nucleic acid chaperone activity of HIV-1 nucleocapsid protein

(2009) Klara Post et al.   NUCLEIC ACIDS RESEARCH

Destabilization of the TAR hairpin leads to extension of the polyA hairpin and inhibition of HIV-1 polyadenylation

(2009) Martine M Vrolijk et al.   Retrovirology

SHAPE Analysis of Long-Range Interactions Reveals Extensive and Thermodynamically Preferred Misfolding in a Fragile Group I Intron RNA†

(2008) Caia D. S. Duncan et al.   BIOCHEMISTRY

Recombination analysis and structure prediction show correlation between breakpoint clusters and RNA hairpins in the pol gene of human immunodeficiency virus type 1 unique recombinant forms

(2008) A. Galli et al.   JOURNAL OF GENERAL VIROLOGY

Negative and Positive mRNA Splicing Elements Act Competitively To Regulate Human Immunodeficiency Virus Type 1 Vif Gene Expression

(2008) C. M. Exline et al.   JOURNAL OF VIROLOGY

Compensatory Evolution in RNA Secondary Structures Increases Substitution Rate Variation among Sites

(2008) J. L. Knies et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Lack of secondary structure characterizes the 5' ends of mammalian mitochondrial mRNAs

(2008) C. N. Jones et al.   RNA

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