Published in Genome Biol on June 01, 2005
Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell (2005) 7.58
Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell (2006) 7.06
Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development (2006) 4.16
A pathogen-inducible endogenous siRNA in plant immunity. Proc Natl Acad Sci U S A (2006) 3.48
Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster. Nat Struct Mol Biol (2008) 3.40
Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms. EMBO Rep (2006) 2.96
Evidence for a major role of antisense RNAs in cyanobacterial gene regulation. Mol Syst Biol (2009) 2.02
Roles of RNA polymerase IV in gene silencing. Trends Plant Sci (2008) 2.00
Clusters of internally primed transcripts reveal novel long noncoding RNAs. PLoS Genet (2006) 1.95
Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc Natl Acad Sci U S A (2011) 1.85
Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Mol Biol (2008) 1.73
Characterization and expression profiles of miRNAs in rice seeds. Nucleic Acids Res (2008) 1.73
Distinct expression patterns of natural antisense transcripts in Arabidopsis. Plant Physiol (2007) 1.52
Prediction of trans-antisense transcripts in Arabidopsis thaliana. Genome Biol (2006) 1.50
RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts. Nucleic Acids Res (2011) 1.48
Proper regulation of a sperm-specific cis-nat-siRNA is essential for double fertilization in Arabidopsis. Genes Dev (2010) 1.44
Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation. Nat Struct Mol Biol (2012) 1.34
Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana. BMC Evol Biol (2011) 1.30
Transcriptome-wide analysis of uncapped mRNAs in Arabidopsis reveals regulation of mRNA degradation. Plant Cell (2008) 1.29
Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa. Genome Res (2008) 1.28
Sense-antisense pairs in mammals: functional and evolutionary considerations. Genome Biol (2007) 1.26
RNA interference is not involved in natural antisense mediated regulation of gene expression in mammals. Genome Biol (2006) 1.21
Characterization of the rice PHO1 gene family reveals a key role for OsPHO1;2 in phosphate homeostasis and the evolution of a distinct clade in dicotyledons. Plant Physiol (2010) 1.13
Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets. BMC Genomics (2007) 1.10
The Functions of RNA-Dependent RNA Polymerases in Arabidopsis. Arabidopsis Book (2011) 1.05
Gene discovery and transcript analyses in the corn smut pathogen Ustilago maydis: expressed sequence tag and genome sequence comparison. BMC Genomics (2007) 1.05
Gene trap lines define domains of gene regulation in Arabidopsis petals and stamens. Plant Cell (2005) 1.03
Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. Genome Res (2013) 0.99
A 125 kDa RNase E/G-like protein is present in plastids and is essential for chloroplast development and autotrophic growth in Arabidopsis. J Exp Bot (2008) 0.95
Characterization and identification of cis-regulatory elements in Arabidopsis based on single-nucleotide polymorphism information. Plant Physiol (2013) 0.94
Unexpected Diversity of Chloroplast Noncoding RNAs as Revealed by Deep Sequencing of the Arabidopsis Transcriptome. G3 (Bethesda) (2011) 0.90
EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics. BMC Genomics (2014) 0.89
Identification of sense and antisense transcripts regulated by drought in sugarcane. Plant Mol Biol (2012) 0.89
Double-stranded RNA binding proteins DRB2 and DRB4 have an antagonistic impact on polymerase IV-dependent siRNA levels in Arabidopsis. RNA (2011) 0.89
Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription. BMC Genomics (2008) 0.88
Functional genomics using RIKEN Arabidopsis thaliana full-length cDNAs. J Plant Res (2009) 0.88
RL-SAGE and microarray analysis of the rice transcriptome after Rhizoctonia solani infection. Mol Genet Genomics (2007) 0.88
Protein-coding cis-natural antisense transcripts have high and broad expression in Arabidopsis. Plant Physiol (2013) 0.87
Sense and antisense transcripts of convergent gene pairs in Arabidopsis thaliana can share a common polyadenylation region. PLoS One (2011) 0.83
New construct approaches for efficient gene silencing in plants. Plant Physiol (2006) 0.83
Magnaporthe grisea infection triggers RNA variation and antisense transcript expression in rice. Plant Physiol (2007) 0.83
Natural antisense transcripts and long non-coding RNA in Neurospora crassa. PLoS One (2014) 0.82
Molecular characterization of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene family from Citrus and the effect of fruit load on their expression. Front Plant Sci (2015) 0.80
A pair of partially overlapping Arabidopsis genes with antagonistic circadian expression. Int J Plant Genomics (2012) 0.78
Development of a rapid and inexpensive method to reveal natural antisense transcripts. Plant Methods (2012) 0.78
NERF encodes a RING E3 ligase important for drought resistance and enhances the expression of its antisense gene NFYA5 in Arabidopsis. Nucleic Acids Res (2014) 0.77
Natural antisense transcripts of Trifolium repens dehydrins. Plant Signal Behav (2013) 0.77
Sense and antisense OsDof12 transcripts in rice. BMC Mol Biol (2008) 0.76
Natural antisense transcripts in plants: a review and identification in soybean infected with Phakopsora pachyrhizi SuperSAGE library. ScientificWorldJournal (2013) 0.76
Small RNAs in Plant Responses to Abiotic Stresses: Regulatory Roles and Study Methods. Int J Mol Sci (2015) 0.75
Development of genodynamic metrics for exploring the biophysics of DNA polymorphisms. J Comput Biol Bioinform Res (2014) 0.75
Plant organ evolution revealed by phylotranscriptomics in Arabidopsis thaliana. Sci Rep (2017) 0.75
Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature (1998) 72.56
NCBI GEO: mining millions of expression profiles--database and tools. Nucleic Acids Res (2005) 17.61
BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res (2004) 15.43
Robust estimators for expression analysis. Bioinformatics (2002) 8.30
Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr Biol (2001) 7.06
An unwinding activity that covalently modifies its double-stranded RNA substrate. Cell (1988) 5.93
NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res (2004) 5.82
The fate of dsRNA in the nucleus: a p54(nrb)-containing complex mediates the nuclear retention of promiscuously A-to-I edited RNAs. Cell (2001) 4.72
In search of antisense. Trends Biochem Sci (2004) 3.93
Do natural antisense transcripts make sense in eukaryotes? Gene (1998) 3.66
Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res (2003) 3.40
Antisense transcripts in the human genome. Trends Genet (2002) 3.33
Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biol (2005) 2.80
Widespread distribution of antisense transcripts in the Plasmodium falciparum genome. Mol Biochem Parasitol (2004) 1.68
Transcriptional termination in the Balbiani ring 1 gene is closely coupled to 3'-end formation and excision of the 3'-terminal intron. Genes Dev (1998) 1.67
Expression of the thyroid hormone receptor gene, erbAalpha, in B lymphocytes: alternative mRNA processing is independent of differentiation but correlates with antisense RNA levels. Nucleic Acids Res (1997) 1.55
Antisense RNAs everywhere? Trends Genet (2002) 1.46
Overlapping antisense transcription in the human genome. Comp Funct Genomics (2002) 1.40
Phylogenetic conservation of the makorin-2 gene, encoding a multiple zinc-finger protein, antisense to the RAF1 proto-oncogene. Genomics (2001) 1.07
Expression of alternatively spliced FGF-2 antisense RNA transcripts in the central nervous system: regulation of FGF-2 mRNA translation. Mol Cell Endocrinol (2000) 1.03
Natural antisense (rTSalpha) RNA induces site-specific cleavage of thymidylate synthase mRNA. Biochim Biophys Acta (2002) 0.96
Enhanced homology searching through genome reading frame predetermination. Bioinformatics (2004) 0.84
The gene structure and expression of human ABHD1: overlapping polyadenylation signal sequence with Sec12. BMC Genomics (2003) 0.84
Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics (2004) 2.93
Mutation of TRPM6 causes familial hypomagnesemia with secondary hypocalcemia. Nat Genet (2002) 2.63
A primer on learning in Bayesian networks for computational biology. PLoS Comput Biol (2007) 2.60
Cerebrospinal fluid exchange in the optic nerve in normal-tension glaucoma. Br J Ophthalmol (2011) 2.23
metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella. Nucleic Acids Res (2005) 2.21
Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis. Nucleic Acids Res (2006) 2.19
Inference in Bayesian networks. Nat Biotechnol (2006) 2.03
Deposition, retention, and translocation of ultrafine particles from the central airways and lung periphery. Am J Respir Crit Care Med (2007) 1.83
Ligand binding: functional site location, similarity and docking. Curr Opin Struct Biol (2003) 1.78
The spectrum of WRN mutations in Werner syndrome patients. Hum Mutat (2006) 1.75
Insights into protein-protein interfaces using a Bayesian network prediction method. J Mol Biol (2006) 1.72
Association of the PDCD5 locus with lung cancer risk and prognosis in smokers. J Clin Oncol (2006) 1.71
Cerebrospinal fluid dynamics between the basal cisterns and the subarachnoid space of the optic nerve in patients with papilloedema. Br J Ophthalmol (2010) 1.69
Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication. Nucleic Acids Res (2006) 1.62
metaTIGER: a metabolic evolution resource. Nucleic Acids Res (2008) 1.60
TOPS: an enhanced database of protein structural topology. Nucleic Acids Res (2004) 1.55
Ethnic differences in past hysterectomy for benign conditions. Womens Health Issues (2005) 1.52
The Arabidopsis co-expression tool (ACT): a WWW-based tool and database for microarray-based gene expression analysis. Plant J (2006) 1.49
Two distinct auto-regulatory loops operate at the PU.1 locus in B cells and myeloid cells. Blood (2011) 1.41
Contrast-enhanced ultrasound imaging of atherosclerotic carotid plaque neovascularization: a new surrogate marker of atherosclerosis? Vasc Med (2007) 1.38
RUNX1 reshapes the epigenetic landscape at the onset of haematopoiesis. EMBO J (2012) 1.37
Deleterious SNP prediction: be mindful of your training data! Bioinformatics (2007) 1.29
Large-scale association study identifies ICAM gene region as breast and prostate cancer susceptibility locus. Cancer Res (2004) 1.29
Activation tagging identifies a gene from Petunia hybrida responsible for the production of active cytokinins in plants. Plant J (2002) 1.17
Simple sequence-based kernels do not predict protein-protein interactions. Bioinformatics (2010) 1.16
Sildenafil induces retinal vasodilatation in healthy subjects. Br J Ophthalmol (2002) 1.15
Annotating the Plasmodium genome and the enigma of the shikimate pathway. Trends Parasitol (2004) 1.13
Physiologic markers of chronic stress in premenopausal, middle-aged women. Psychosom Med (2002) 1.13
Rituximab blocks protective serologic response to influenza A (H1N1) 2009 vaccination in lymphoma patients during or within 6 months after treatment. Blood (2011) 1.11
Calculation of helix packing angles in protein structures. Bioinformatics (2003) 1.10
TMB-Hunt: a web server to screen sequence sets for transmembrane beta-barrel proteins. Nucleic Acids Res (2005) 1.10
Whole genome expression profiling based on paraffin embedded tissue can be used to classify diffuse large B-cell lymphoma and predict clinical outcome. Br J Haematol (2012) 1.09
An extended set of PRDM1/BLIMP1 target genes links binding motif type to dynamic repression. Nucleic Acids Res (2010) 1.07
A natural antisense transcript of the Petunia hybrida Sho gene suggests a role for an antisense mechanism in cytokinin regulation. Plant J (2007) 1.04
In vitro generation of long-lived human plasma cells. J Immunol (2012) 1.04
Meningothelial cells react to elevated pressure and oxidative stress. PLoS One (2011) 1.04
TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins. BMC Bioinformatics (2005) 1.03
TmaDB: a repository for tissue microarray data. BMC Bioinformatics (2005) 1.02
Investigation of the algT operon sequence in mucoid and non-mucoid Pseudomonas aeruginosa isolates from 115 Scandinavian patients with cystic fibrosis and in 88 in vitro non-mucoid revertants. Microbiology (2008) 1.02
Conservation, convergence, and divergence of light-responsive, circadian-regulated, and tissue-specific expression patterns during evolution of the Arabidopsis GATA gene family. Plant Physiol (2007) 1.02
Metabolic reconstruction and analysis for parasite genomes. Trends Parasitol (2007) 1.00
A CDC45 homolog in Arabidopsis is essential for meiosis, as shown by RNA interference-induced gene silencing. Plant Cell (2003) 1.00
The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes. Genome Biol (2009) 1.00
Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application. BMC Bioinformatics (2009) 1.00
A microarray platform-independent classification tool for cell of origin class allows comparative analysis of gene expression in diffuse large B-cell lymphoma. PLoS One (2013) 0.99
Beta edge strands in protein structure prediction and aggregation. Protein Sci (2003) 0.98
Stable transformation of petunia plastids. Transgenic Res (2004) 0.98
Evolutionary history of tissue kallikreins. PLoS One (2010) 0.96
A multi-centre prospective study of febrile neutropenia in Norway: microbiological findings and antimicrobial susceptibility. Scand J Infect Dis (2005) 0.96
Morphological and immunohistochemical changes after corneal cross-linking. Cornea (2013) 0.95
Predictors of quality of life at 1 month after implantation of a left ventricular assist device. Am J Crit Care (2002) 0.94
Immunohistochemical localization of angiotensin-converting enzyme, angiotensin II and AT1 receptor in human ocular tissues. Ophthalmic Res (2005) 0.92
Distribution of melatonin MT1 receptor immunoreactivity in human retina. J Histochem Cytochem (2002) 0.92
Anatomic site-specific patterns of gene copy number gains in skin, mucosal, and uveal melanomas detected by fluorescence in situ hybridization. Virchows Arch (2006) 0.91
Seizure 6-like (SEZ6L) gene and risk for lung cancer. Cancer Res (2007) 0.91
The MT2 melatonin receptor subtype is present in human retina and decreases in Alzheimer's disease. Curr Alzheimer Res (2007) 0.91
Predicting the effect of missense mutations on protein function: analysis with Bayesian networks. BMC Bioinformatics (2006) 0.90
A defect of CD16-positive monocytes can occur without disease. Immunobiology (2012) 0.90
Are common fragile sites merely structural domains or highly organized "functional" units susceptible to oncogenic stress? Cell Mol Life Sci (2014) 0.90
Diagnostic significance of measurements of specific IgG antibodies to Pseudomonas aeruginosa by three different serological methods. J Cyst Fibros (2008) 0.90
Anatomical and functional outcome in brilliant blue G assisted chromovitrectomy. Acta Ophthalmol (2009) 0.90
From gene expression to gene regulatory networks in Arabidopsis thaliana. BMC Syst Biol (2009) 0.89
MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format. Bioinformatics (2010) 0.89
Inactivation of MARCH5 prevents mitochondrial fragmentation and interferes with cell death in a neuronal cell model. PLoS One (2012) 0.89
L-PGDS (betatrace protein) inhibits astrocyte proliferation and mitochondrial ATP production in vitro. J Mol Neurosci (2009) 0.89
ARLTS1 variants and melanoma risk. Int J Cancer (2006) 0.88
Morphological changes of the retrobulbar optic nerve and its meningeal sheaths in glaucoma. Ophthalmologica (2006) 0.88
metaSHARK: a WWW platform for interactive exploration of metabolic networks. Nucleic Acids Res (2006) 0.88
Activated STAT 3 in choroidal neovascular membranes of patients with age-related macular degeneration. Ophthalmologica (2005) 0.86
Cooperative activity of DNA methyltransferases for maintenance of symmetrical and non-symmetrical cytosine methylation in Arabidopsis thaliana. Plant J (2008) 0.86
Autoantibody response to BPI predict disease severity and outcome in cystic fibrosis. J Cyst Fibros (2006) 0.86
Influence of race in heart failure and cardiac transplantation: mortality differences are eliminated by specialized, comprehensive care. J Card Fail (2003) 0.86
GO-At: in silico prediction of gene function in Arabidopsis thaliana by combining heterogeneous data. Plant J (2009) 0.85
Expression and amplification of therapeutic target genes in retinoblastoma. Graefes Arch Clin Exp Ophthalmol (2004) 0.85
Prediction of horizontal gene transfers in eukaryotes: approaches and challenges. Biochem Soc Trans (2009) 0.85
Techniques for the removal of marker genes from transgenic plants. Biochimie (2002) 0.84
Sequence analysis and high-throughput immunohistochemical profiling of KIT (CD 117) expression in uveal melanoma using tissue microarrays. Virchows Arch (2003) 0.84
Inactivity of nitric oxide synthase gene in the atherosclerotic human carotid artery. Basic Res Cardiol (2007) 0.84
Does immunohistochemistry allow easy detection of lymphatics in the optic nerve sheath? J Histochem Cytochem (2008) 0.83
Sense and antisense transcripts of convergent gene pairs in Arabidopsis thaliana can share a common polyadenylation region. PLoS One (2011) 0.83
Heat stress enhances the accumulation of polyadenylated mitochondrial transcripts in Arabidopsis thaliana. PLoS One (2008) 0.83
Bayesian refinement of protein functional site matching. BMC Bioinformatics (2007) 0.83
Numbers of neurons in the retinal ganglion cell layer of the rat do not change throughout life. Gerontology (2003) 0.83
Differential expression and extent of fungal/plant and fungal/bacterial chitinases of Aspergillus fumigatus. Arch Microbiol (2005) 0.83
Differences in prevalence and treatment of Pseudomonas aeruginosa in cystic fibrosis centres in Denmark, Norway and Sweden. J Cyst Fibros (2009) 0.83
Retinitis pigmentosa and ocular blood flow. EPMA J (2012) 0.83
Immunoreactivity of the septins SEPT4, SEPT5, and SEPT8 in the human eye. J Histochem Cytochem (2005) 0.82
Tissue-specific induction of ADAMTS2 in monocytes and macrophages by glucocorticoids. J Mol Med (Berl) (2007) 0.82
Analysis of hypermethylation in the RPS element suggests a signal function for short inverted repeats in de novo methylation. Plant Mol Biol (2002) 0.82
BRCA1/2 mutation screening and LOH analysis of lung adenocarcinoma tissue in a multiple-cancer patient with a strong family history of breast cancer. J Carcinog (2003) 0.82
Primary cell culture of meningothelial cells--a new model to study the arachnoid in glaucomatous optic neuropathy. Graefes Arch Clin Exp Ophthalmol (2010) 0.82
State-of-the-art bioinformatics protein structure prediction tools (Review). Int J Mol Med (2011) 0.82
Asymmetric mutation rates at enzyme-inhibitor interfaces: implications for the protein-protein docking problem. Protein Sci (2003) 0.82
Meningothelial cells participate in immunological processes in the cerebrospinal fluid. J Neuroimmunol (2012) 0.82
Chronic myelogenous leukemia with the e6a2 BCR-ABL and lacking imatinib response: presentation of two cases. Acta Haematol (2009) 0.81
PKCε signalling activates ERK1/2, and regulates aggrecan, ADAMTS5, and miR377 gene expression in human nucleus pulposus cells. PLoS One (2013) 0.81