Published in Nucleic Acids Res on April 26, 2017
Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res (2003) 77.89
Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA. Nature (1988) 19.07
A segment of the 5' nontranslated region of encephalomyocarditis virus RNA directs internal entry of ribosomes during in vitro translation. J Virol (1988) 13.93
The mechanism of eukaryotic translation initiation and principles of its regulation. Nat Rev Mol Cell Biol (2010) 11.19
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci U S A (2004) 10.35
Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers (1999) 7.80
A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initiation of hepatitis C and classical swine fever virus RNAs. Genes Dev (1998) 7.72
RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). J Am Chem Soc (2005) 6.46
Architecture and secondary structure of an entire HIV-1 RNA genome. Nature (2009) 6.12
Accurate SHAPE-directed RNA structure determination. Proc Natl Acad Sci U S A (2008) 5.44
A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J Am Chem Soc (2007) 4.81
Initiation of protein synthesis from the A site of the ribosome. Cell (2000) 4.56
Functional dissection of eukaryotic initiation factor 4F: the 4A subunit and the central domain of the 4G subunit are sufficient to mediate internal entry of 43S preinitiation complexes. Mol Cell Biol (1996) 4.42
High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol (2008) 4.40
Functional sites in the 5' region of human immunodeficiency virus type 1 RNA form defined structural domains. J Mol Biol (1993) 4.08
RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA (2005) 3.80
Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions. Nat Protoc (2007) 3.31
On the recognition of helical RNA by cobra venom V1 nuclease. J Biol Chem (1986) 2.66
Mutational analysis of the 5' non-coding region of human immunodeficiency virus type 1: effects of secondary structure on translation. EMBO J (1988) 2.65
p24 antigen capture assay for quantification of human immunodeficiency virus using readily available inexpensive reagents. Methods (1997) 2.65
Structure and function of the human immunodeficiency virus leader RNA. Prog Nucleic Acid Res Mol Biol (1996) 2.59
Physical association of eukaryotic initiation factor 4G (eIF4G) with eIF4A strongly enhances binding of eIF4G to the internal ribosomal entry site of encephalomyocarditis virus and is required for internal initiation of translation. Mol Cell Biol (2000) 2.58
Human immunodeficiency virus envelope V1 and V2 regions influence replication efficiency in macrophages by affecting virus spread. Virology (1995) 2.55
Cap-independent translation is required for starvation-induced differentiation in yeast. Science (2007) 2.05
Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit. Nature (2013) 1.95
Cell-cycle-dependent translational control. Curr Opin Genet Dev (2001) 1.91
La autoantigen alleviates translational repression by the 5' leader sequence of the human immunodeficiency virus type 1 mRNA. J Virol (1994) 1.87
The human immunodeficiency virus type 1 gag gene encodes an internal ribosome entry site. J Virol (2001) 1.87
tRNA-mRNA mimicry drives translation initiation from a viral IRES. Nat Struct Mol Biol (2007) 1.84
Improved RNA secondary structure prediction by maximizing expected pair accuracy. RNA (2009) 1.78
RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nat Methods (2014) 1.72
The leader of human immunodeficiency virus type 1 genomic RNA harbors an internal ribosome entry segment that is active during the G2/M phase of the cell cycle. J Virol (2003) 1.71
Initiation of translation by cricket paralysis virus IRES requires its translocation in the ribosome. Cell (2014) 1.62
Quantitative analysis of protein-RNA interactions by gel mobility shift. Methods Mol Biol (2008) 1.60
The human immunodeficiency virus type 1 5' packaging signal structure affects translation but does not function as an internal ribosome entry site structure. J Virol (1996) 1.57
Conversion of 48S translation preinitiation complexes into 80S initiation complexes as revealed by toeprinting. FEBS Lett (2003) 1.56
Direct functional interaction of initiation factor eIF4G with type 1 internal ribosomal entry sites. Proc Natl Acad Sci U S A (2009) 1.54
Activity of the hepatitis A virus IRES requires association between the cap-binding translation initiation factor (eIF4E) and eIF4G. J Virol (2001) 1.50
Identification of cryptic MHC I-restricted epitopes encoded by HIV-1 alternative reading frames. J Exp Med (2004) 1.48
Polypurine (A)-rich sequences promote cross-kingdom conservation of internal ribosome entry. Proc Natl Acad Sci U S A (2002) 1.45
Eukaryotic initiation factors 4G and 4A mediate conformational changes downstream of the initiation codon of the encephalomyocarditis virus internal ribosomal entry site. Mol Cell Biol (2003) 1.40
The unusual nucleotide content of the HIV RNA genome results in a biased amino acid composition of HIV proteins. Nucleic Acids Res (1994) 1.36
HIV-2 genomic RNA contains a novel type of IRES located downstream of its initiation codon. Nat Struct Mol Biol (2005) 1.35
DEAD-box protein DDX3 associates with eIF4F to promote translation of selected mRNAs. EMBO J (2012) 1.31
Translational control of retroviruses. Nat Rev Microbiol (2007) 1.29
RNA secondary structure analysis using the Vienna RNA package. Curr Protoc Bioinformatics (2009) 1.26
Primer extension analysis of eukaryotic ribosome-mRNA complexes. Nucleic Acids Res (1998) 1.26
RNA helicase A modulates translation of HIV-1 and infectivity of progeny virions. Nucleic Acids Res (2009) 1.22
Regulated HIV-2 RNA dimerization by means of alternative RNA conformations. Nucleic Acids Res (2002) 1.20
Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity. J Am Chem Soc (2012) 1.18
Back to basics: the untreated rabbit reticulocyte lysate as a competitive system to recapitulate cap/poly(A) synergy and the selective advantage of IRES-driven translation. Nucleic Acids Res (2007) 1.16
A cross-kingdom internal ribosome entry site reveals a simplified mode of internal ribosome entry. Mol Cell Biol (2005) 1.13
The mechanism of translation initiation on Type 1 picornavirus IRESs. EMBO J (2013) 1.12
R-CHIE: a web server and R package for visualizing RNA secondary structures. Nucleic Acids Res (2012) 1.12
Structure of the mammalian 80S initiation complex with initiation factor 5B on HCV-IRES RNA. Nat Struct Mol Biol (2014) 1.08
A new type of IRES within gag coding region recruits three initiation complexes on HIV-2 genomic RNA. Nucleic Acids Res (2009) 1.07
Lentiviral RNAs can use different mechanisms for translation initiation. Biochem Soc Trans (2008) 1.03
A conserved structure within the HIV gag open reading frame that controls translation initiation directly recruits the 40S subunit and eIF3. Nucleic Acids Res (2010) 1.02
Thriving under stress: selective translation of HIV-1 structural protein mRNA during Vpr-mediated impairment of eIF4E translation activity. PLoS Pathog (2012) 1.02
Detailed analysis of the requirements of hepatitis A virus internal ribosome entry segment for the eukaryotic initiation factor complex eIF4F. J Virol (2001) 1.01
The activity of the HIV-1 IRES is stimulated by oxidative stress and controlled by a negative regulatory element. Nucleic Acids Res (2010) 1.00
Poly(A) leader of eukaryotic mRNA bypasses the dependence of translation on initiation factors. Proc Natl Acad Sci U S A (2008) 1.00
Taura syndrome virus IRES initiates translation by binding its tRNA-mRNA-like structural element in the ribosomal decoding center. Proc Natl Acad Sci U S A (2014) 0.99
Activity of the human immunodeficiency virus type 1 cell cycle-dependent internal ribosomal entry site is modulated by IRES trans-acting factors. Nucleic Acids Res (2011) 0.99
Retrovirus translation initiation: Issues and hypotheses derived from study of HIV-1. Curr HIV Res (2006) 0.95
RNA secondary structure of the feline immunodeficiency virus 5'UTR and Gag coding region. Nucleic Acids Res (2008) 0.90
An internal ribosome entry site promotes translation of a novel SIV Pr55(Gag) isoform. Virology (2006) 0.90
Cryo-EM structure of Hepatitis C virus IRES bound to the human ribosome at 3.9-Å resolution. Nat Commun (2015) 0.89
Trinucleotide repeat system for sequence specificity analysis of RNA structure probing reagents. Anal Biochem (2010) 0.89
The DEAD-box helicase DDX3 substitutes for the cap-binding protein eIF4E to promote compartmentalized translation initiation of the HIV-1 genomic RNA. Nucleic Acids Res (2013) 0.89
The 5'-untranslated region of the mouse mammary tumor virus mRNA exhibits cap-independent translation initiation. Nucleic Acids Res (2009) 0.88
The different pathways of HIV genomic RNA translation. Biochem Soc Trans (2010) 0.87
CTL escape mediated by proteasomal destruction of an HIV-1 cryptic epitope. PLoS Pathog (2011) 0.87
SHAPE directed RNA folding. Bioinformatics (2015) 0.87
Dual mechanisms of translation initiation of the full-length HIV-1 mRNA contribute to gag synthesis. PLoS One (2013) 0.87
Translation initiation is driven by different mechanisms on the HIV-1 and HIV-2 genomic RNAs. Virus Res (2012) 0.86
Cell type specificity and structural determinants of IRES activity from the 5' leaders of different HIV-1 transcripts. Nucleic Acids Res (2013) 0.84
Attachment of ribosomal complexes and retrograde scanning during initiation on the Halastavi árva virus IRES. Nucleic Acids Res (2016) 0.82
HIV-1 replication and the cellular eukaryotic translation apparatus. Viruses (2015) 0.81
In vitro studies reveal that different modes of initiation on HIV-1 mRNA have different levels of requirement for eukaryotic initiation factor 4F. FEBS J (2012) 0.81
40S recruitment in the absence of eIF4G/4A by EMCV IRES refines the model for translation initiation on the archetype of Type II IRESs. Nucleic Acids Res (2014) 0.79
LOOP IIId of the HCV IRES is essential for the structural rearrangement of the 40S-HCV IRES complex. Nucleic Acids Res (2015) 0.79
The 5' untranslated region of the human T-cell lymphotropic virus type 1 mRNA enables cap-independent translation initiation. J Virol (2014) 0.77
HIV-1 transcripts use IRES-initiation under conditions where Cap-dependent translation is restricted by poliovirus 2A protease. PLoS One (2014) 0.77
Polypyrimidine tract-binding protein binds to the 5' untranslated region of the mouse mammary tumor virus mRNA and stimulates cap-independent translation initiation. FEBS J (2016) 0.76
Translational Control of the HIV Unspliced Genomic RNA. Viruses (2015) 0.76
Does HIV-1 mRNA 5'-untranslated region bear an internal ribosome entry site? Biochimie (2015) 0.76
HIV-1 sequences isolated from patients promote expression of shorter isoforms of the Gag polyprotein. Arch Virol (2016) 0.76
Secondary Structure Prediction of Single Sequences Using RNAstructure. Methods Mol Biol (2016) 0.75
Functional analysis of Kaposi's sarcoma-associated herpesvirus vFLIP expression reveals a new mode of IRES-mediated translation. RNA (2014) 0.75
Structural domains within the HIV-1 mRNA and the ribosomal protein S25 influence cap-independent translation initiation. FEBS J (2016) 0.75
LOOP IIId of the HCV IRES is essential for the structural rearrangement of the 40S-HCV IRES complex. Nucleic Acids Res (2015) 0.79
Two ribosome recruitment sites direct multiple translation events within HIV1 Gag open reading frame. Nucleic Acids Res (2017) 0.75