Published in BMC Bioinformatics on October 31, 2006
Molecular Validation of PACE4 as a Target in Prostate Cancer. Transl Oncol (2011) 1.05
Development of an isoform-specific gene suppression system: the study of the human Pax-5B transcriptional element. Nucleic Acids Res (2008) 0.84
A novel ribozyme-based prophylaxis inhibits influenza A virus replication and protects from severe disease. PLoS One (2011) 0.78
A Conserved Target Site in HIV-1 Gag RNA is Accessible to Inhibition by Both an HDV Ribozyme and a Short Hairpin RNA. Mol Ther Nucleic Acids (2014) 0.78
Automated design of hammerhead ribozymes and validation by targeting the PABPN1 gene transcript. Nucleic Acids Res (2015) 0.76
Silencing of amyloid precursor protein expression using a new engineered delta ribozyme. Int J Alzheimers Dis (2012) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Identification of common molecular subsequences. J Mol Biol (1981) 130.53
Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol (2003) 16.63
Kinetic analysis of the RNAi enzyme complex. Nat Struct Mol Biol (2004) 7.26
3' UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat Methods (2006) 6.96
WU-Blast2 server at the European Bioinformatics Institute. Nucleic Acids Res (2003) 3.82
siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference. Nucleic Acids Res (2004) 2.30
Natural and engineered nucleic acids as tools to explore biology. Nature (2004) 2.26
The structure-function dilemma of the hammerhead ribozyme. Annu Rev Biophys Biomol Struct (2005) 1.96
Alternative splicing of Bcl-2-related genes: functional consequences and potential therapeutic applications. Cell Mol Life Sci (2004) 1.41
Ribozyme-based gene-inactivation systems require a fine comprehension of their substrate specificities; the case of delta ribozyme. Curr Med Chem (2003) 1.10
Target-dependent on/off switch increases ribozyme fidelity. Nucleic Acids Res (2005) 1.06
Functional characterization of the SOFA delta ribozyme. RNA (2005) 0.95
Gene discovery by ribozyme and siRNA libraries. Nat Rev Mol Cell Biol (2005) 0.93
RNA interference as a gene-specific approach for molecular medicine. Curr Med Chem (2005) 0.92
Gene targeting in the Gram-Positive bacterium Lactococcus lactis, using various delta ribozymes. Appl Environ Microbiol (2006) 0.89
Designing effective siRNAs with off-target control. Biochem Biophys Res Commun (2004) 0.89
Control of alternative splicing through siRNA-mediated transcriptional gene silencing. Nat Struct Mol Biol (2009) 3.47
Cancer-associated regulation of alternative splicing. Nat Struct Mol Biol (2009) 3.35
Identification of alternative splicing markers for breast cancer. Cancer Res (2008) 2.51
Multiple and specific mRNA processing targets for the major human hnRNP proteins. Mol Cell Biol (2008) 1.78
Developing three-dimensional models of putative-folding intermediates of the HDV ribozyme. Structure (2010) 1.49
5'-UTR G-quadruplex structures acting as translational repressors. Nucleic Acids Res (2010) 1.49
Reprogramming alternative pre-messenger RNA splicing through the use of protein-binding antisense oligonucleotides. J Biol Chem (2003) 1.48
Introns within ribosomal protein genes regulate the production and function of yeast ribosomes. Cell (2011) 1.25
Proteins associated with the exon junction complex also control the alternative splicing of apoptotic regulators. Mol Cell Biol (2011) 1.24
Ro-associated Y RNAs in metazoans: evolution and diversification. Mol Biol Evol (2007) 1.24
Evaluation of the RNA determinants for bacterial and yeast RNase III binding and cleavage. J Biol Chem (2003) 1.19
Alternative splicing of SYK regulates mitosis and cell survival. Nat Struct Mol Biol (2011) 1.17
High-throughput quantification of splicing isoforms. RNA (2009) 1.16
SubViral RNA: a database of the smallest known auto-replicable RNA species. Nucleic Acids Res (2003) 1.16
Delta ribozyme benefits from a good stability in vitro that becomes outstanding in vivo. RNA (2002) 1.13
Ribozyme-based gene-inactivation systems require a fine comprehension of their substrate specificities; the case of delta ribozyme. Curr Med Chem (2003) 1.10
Anticancer drugs affect the alternative splicing of Bcl-x and other human apoptotic genes. Mol Cancer Ther (2008) 1.08
Yeast RNase III triggers polyadenylation-independent transcription termination. Mol Cell (2009) 1.08
Exploring mRNA 3'-UTR G-quadruplexes: evidence of roles in both alternative polyadenylation and mRNA shortening. Nucleic Acids Res (2013) 1.07
Target-dependent on/off switch increases ribozyme fidelity. Nucleic Acids Res (2005) 1.06
Molecular Validation of PACE4 as a Target in Prostate Cancer. Transl Oncol (2011) 1.05
Fuzzy J-Means and VNS methods for clustering genes from microarray data. Bioinformatics (2004) 1.04
Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs. Nucleic Acids Res (2005) 1.03
RNase III-dependent regulation of yeast telomerase. J Biol Chem (2006) 1.03
Unbiased in vitro selection reveals the unique character of the self-cleaving antigenomic HDV RNA sequence. Nucleic Acids Res (2006) 1.02
Sequence dependence of substrate recognition and cleavage by yeast RNase III. J Mol Biol (2003) 1.02
Modern origin of numerous alternatively spliced human introns from tandem arrays. Proc Natl Acad Sci U S A (2007) 1.01
Formation of the P1.1 pseudoknot is critical for both the cleavage activity and substrate specificity of an antigenomic trans-acting hepatitis delta ribozyme. Nucleic Acids Res (2003) 1.00
Development and comparison of procedures for the selection of delta ribozyme cleavage sites within the hepatitis B virus. Nucleic Acids Res (2002) 0.98
Cross-linking experiments reveal the presence of novel structural features between a hepatitis delta virus ribozyme and its substrate. RNA (2004) 0.98
Kinetic and binding analysis of the catalytic involvement of ribose moieties of a trans-acting delta ribozyme. J Biol Chem (2002) 0.98
Modulating RNA structure and catalysis: lessons from small cleaving ribozymes. Cell Mol Life Sci (2009) 0.96
In vitro selection and characterization of RNA aptamers binding thyroxine hormone. Biochem J (2007) 0.95
Functional characterization of the SOFA delta ribozyme. RNA (2005) 0.95
RNase III-mediated silencing of a glucose-dependent repressor in yeast. Curr Biol (2005) 0.95
Development of ribozyme-based gene-inactivations; the example of the hepatitis delta virus ribozyme. Curr Gene Ther (2007) 0.94
New scoring system to identify RNA G-quadruplex folding. Nucleic Acids Res (2013) 0.94
Cell cycle-dependent nuclear localization of yeast RNase III is required for efficient cell division. Mol Biol Cell (2004) 0.94
In-depth sequencing of the siRNAs associated with peach latent mosaic viroid infection. BMC Mol Biol (2010) 0.93
Characterization of a viroid-derived RNA promoter for the DNA-dependent RNA polymerase from Escherichia coli. Biochemistry (2002) 0.93
Cancer-Associated Perturbations in Alternative Pre-messenger RNA Splicing. Cancer Treat Res (2013) 0.92
In-line probing of RNA G-quadruplexes. Methods (2013) 0.92
A physical interaction between Gar1p and Rnt1pi is required for the nuclear import of H/ACA small nucleolar RNA-associated proteins. Mol Cell Biol (2002) 0.91
Identification of proteins from prunus persica that interact with peach latent mosaic viroid. J Virol (2009) 0.90
The use of a combination of computer-assisted structure prediction and SHAPE probing to elucidate the secondary structures of five viroids. Mol Plant Pathol (2012) 0.90
Gene targeting in the Gram-Positive bacterium Lactococcus lactis, using various delta ribozymes. Appl Environ Microbiol (2006) 0.89
Monitoring of an RNA multistep folding pathway by isothermal titration calorimetry. Biophys J (2009) 0.89
Silencing of SPC2 expression using an engineered delta ribozyme in the mouse betaTC-3 endocrine cell line. J Biol Chem (2004) 0.89
A high-throughput method to measure the sensitivity of yeast cells to genotoxic agents in liquid cultures. Mutat Res (2006) 0.88
A novel structural rearrangement of hepatitis delta virus antigenomic ribozyme. Nucleic Acids Res (2007) 0.88
A G-tract element in apoptotic agents-induced alternative splicing. Nucleic Acids Res (2008) 0.88
Modulation of 5' splice site selection using tailed oligonucleotides carrying splicing signals. BMC Biotechnol (2006) 0.87
In vitro and in vivo cleavage of HIV-1 RNA by new SOFA-HDV ribozymes and their potential to inhibit viral replication. RNA Biol (2011) 0.86
The RNA strands of the plus and minus polarities of peach latent mosaic viroid fold into different structures. RNA (2010) 0.86
Influence of group embryo culture strategies on the blastocyst development and pregnancy outcome. J Assist Reprod Genet (2012) 0.86
Mapping studies of the Peach latent mosaic viroid reveal novel structural features. Mol Plant Pathol (2011) 0.86
Characterization of the reactivity determinants of a novel hairpin substrate of yeast RNase III. J Mol Biol (2006) 0.86
Tumor microenvironment-associated modifications of alternative splicing. RNA (2013) 0.85
Development of an isoform-specific gene suppression system: the study of the human Pax-5B transcriptional element. Nucleic Acids Res (2008) 0.84
Redirecting splicing with bifunctional oligonucleotides. Nucleic Acids Res (2013) 0.84
Examination of the folding pathway of the antigenomic hepatitis delta virus ribozyme reveals key interactions of the L3 loop. RNA (2006) 0.84
Potassium ions modulate a G-quadruplex-ribozyme's activity. RNA (2008) 0.84
Investigating a new generation of ribozymes in order to target HCV. PLoS One (2010) 0.84
Comment on "When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis". Bioessays (2008) 0.83
Identification of a peach latent mosaic viroid hairpin able to act as a Dicer-like substrate. J Virol (2005) 0.83
Characterization of the trans Watson-Crick GU base pair located in the catalytic core of the antigenomic HDV ribozyme. PLoS One (2012) 0.83
Kinetic and thermodynamic characterization of the RNA guanylyltransferase reaction. Biochemistry (2008) 0.82
RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures. Nucleic Acids Res (2007) 0.82
Binding site of Escherichia coli RNA polymerase to an RNA promoter. Biochem Biophys Res Commun (2004) 0.82
Structure of an AAGU tetraloop and its contribution to substrate selection by yeast RNase III. J Mol Biol (2006) 0.81
Elucidation of the structures of all members of the Avsunviroidae family. Mol Plant Pathol (2014) 0.80
Development of an efficient cis-trans-cis ribozyme cassette to inactivate plant genes. Plant Biotechnol J (2003) 0.80
Design and evaluation of clinically relevant SOFA-HDV ribozymes targeting HIV RNA. Methods Mol Biol (2014) 0.80
The peach latent mosaic viroid replication initiation site is located at a universal position that appears to be defined by a conserved sequence. Virology (2008) 0.80
Insights into the molecular determinants involved in cap recognition by the vaccinia virus D10 decapping enzyme. Nucleic Acids Res (2010) 0.79
A modern mode of activation for nucleic acid enzymes. PLoS One (2007) 0.79
Programming a highly structured ribozyme into complex allostery using RNA oligonucleotides. ACS Chem Biol (2012) 0.79
Target-induced SOFA-HDV ribozyme. Methods Mol Biol (2012) 0.79
Magnesium-binding studies reveal fundamental differences between closely related RNA triphosphatases. Nucleic Acids Res (2007) 0.79
Type 1 diabetes impairs vitamin B(6) metabolism at an early stage of women's adulthood. Appl Physiol Nutr Metab (2012) 0.78
Characterization of the vaccinia virus D10 decapping enzyme provides evidence for a two-metal-ion mechanism. Biochem J (2009) 0.78
A novel ribozyme-based prophylaxis inhibits influenza A virus replication and protects from severe disease. PLoS One (2011) 0.78
Free uptake of cell-penetrating peptides by fission yeast. FEBS Lett (2005) 0.78
Detection and characterization of transcription termination. Methods Mol Biol (2012) 0.77
Expression of melatoninergic receptors in human placental choriocarcinoma cell lines. Hum Reprod (2006) 0.77
Selection of the most potent specific on/off adaptor-hepatitis delta virus ribozymes for use in gene targeting. Nucleic Acid Ther (2011) 0.76
Short RNA duplexes guide sequence-dependent cleavage by human Dicer. RNA (2010) 0.76
Silencing of amyloid precursor protein expression using a new engineered delta ribozyme. Int J Alzheimers Dis (2012) 0.75
Unusual subcellular confinement of the fragile X mental retardation protein (FMRP) in circulating human platelets: complete polyribosome dissociation. Biochimie (2011) 0.75