Published in Bioinformatics on June 30, 2005
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res (2007) 3.69
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics (2005) 3.69
Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol (2007) 3.02
Current tools for the identification of miRNA genes and their targets. Nucleic Acids Res (2009) 2.12
Unique folding of precursor microRNAs: quantitative evidence and implications for de novo identification. RNA (2006) 1.85
Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol (2009) 1.82
Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol (2010) 1.81
Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.). BMC Plant Biol (2010) 1.80
MiRenSVM: towards better prediction of microRNA precursors using an ensemble SVM classifier with multi-loop features. BMC Bioinformatics (2010) 1.63
Anopheles gambiae miRNAs as actors of defence reaction against Plasmodium invasion. Nucleic Acids Res (2007) 1.51
MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans. BMC Bioinformatics (2007) 1.42
Cloning, characterization, and expression of microRNAs from the Asian malaria mosquito, Anopheles stephensi. BMC Genomics (2008) 1.41
Computational approaches for microRNA studies: a review. Mamm Genome (2009) 1.39
MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences. BMC Bioinformatics (2011) 1.38
Direct sequencing and expression analysis of a large number of miRNAs in Aedes aegypti and a multi-species survey of novel mosquito miRNAs. BMC Genomics (2009) 1.28
Identification of novel Drosophila melanogaster microRNAs. PLoS One (2007) 1.28
RNA stem-loops: to be or not to be cleaved by RNAse III. RNA (2007) 1.28
Ab initio identification of human microRNAs based on structure motifs. BMC Bioinformatics (2007) 1.27
Solexa sequencing of novel and differentially expressed microRNAs in testicular and ovarian tissues in Holstein cattle. Int J Biol Sci (2011) 1.26
miRRim: a novel system to find conserved miRNAs with high sensitivity and specificity. RNA (2007) 1.21
iMiRNA-SSF: Improving the Identification of MicroRNA Precursors by Combining Negative Sets with Different Distributions. Sci Rep (2016) 1.21
miRNAminer: a tool for homologous microRNA gene search. BMC Bioinformatics (2008) 1.21
Identification and differential expression of microRNAs during metamorphosis of the Japanese flounder (Paralichthys olivaceus). PLoS One (2011) 1.16
Identification and characteristics of microRNAs from Bombyx mori. BMC Genomics (2008) 1.14
Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM). BMC Bioinformatics (2010) 1.11
Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum. BMC Genomics (2010) 1.11
Computational methods in noncoding RNA research. J Math Biol (2007) 1.08
Discovery and characterization of medaka miRNA genes by next generation sequencing platform. BMC Genomics (2010) 1.07
Prediction of novel microRNA genes in cancer-associated genomic regions--a combined computational and experimental approach. Nucleic Acids Res (2009) 1.05
Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing. BMC Genomics (2014) 1.04
Computational analysis of noncoding RNAs. Wiley Interdiscip Rev RNA (2012) 1.01
A fast ab-initio method for predicting miRNA precursors in genomes. Nucleic Acids Res (2012) 1.00
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MicroRNAs -the next generation therapeutic targets in human diseases. Theranostics (2013) 0.97
Genome-wide comparative analysis of microRNAs in three non-human primates. BMC Res Notes (2010) 0.96
MicroRNA expression profiling of the fifth-instar posterior silk gland of Bombyx mori. BMC Genomics (2014) 0.96
miRNA genes of an invasive vector mosquito, Aedes albopictus. PLoS One (2013) 0.96
Identification and developmental profiling of conserved and novel microRNAs in Manduca sexta. Insect Biochem Mol Biol (2012) 0.96
Evolution of coding and non-coding genes in HOX clusters of a marsupial. BMC Genomics (2012) 0.95
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Computational Prediction of miRNA Genes from Small RNA Sequencing Data. Front Bioeng Biotechnol (2015) 0.94
Using a kernel density estimation based classifier to predict species-specific microRNA precursors. BMC Bioinformatics (2008) 0.94
Computational prediction of the localization of microRNAs within their pre-miRNA. Nucleic Acids Res (2013) 0.94
Review of current methodological approaches for characterizing microRNAs in plants. Int J Plant Genomics (2009) 0.93
Identification of microRNA precursors with support vector machine and string kernel. Genomics Proteomics Bioinformatics (2008) 0.93
Transcriptome-wide analysis of microRNA expression in the malaria mosquito Anopheles gambiae. BMC Genomics (2014) 0.92
Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila. BMC Bioinformatics (2007) 0.91
Improvement of whole-genome annotation of cereals through comparative analyses. Genome Res (2007) 0.90
Characterization of host microRNAs that respond to DNA virus infection in a crustacean. BMC Genomics (2012) 0.90
Identification of common carp (Cyprinus carpio) microRNAs and microRNA-related SNPs. BMC Genomics (2012) 0.87
Deep sequencing and microarray hybridization identify conserved and species-specific microRNAs during somatic embryogenesis in hybrid yellow poplar. PLoS One (2012) 0.86
Recipe for a busy bee: microRNAs in Honey Bee caste determination. PLoS One (2013) 0.85
A Comprehensive Prescription for Plant miRNA Identification. Front Plant Sci (2017) 0.83
Bioinformatics in China: a personal perspective. PLoS Comput Biol (2008) 0.83
Computational approaches in detecting non- coding RNA. Curr Genomics (2013) 0.82
Computational prediction of microRNAs encoded in viral and other genomes. J Biomed Biotechnol (2006) 0.81
Antiviral Stratagems Against HIV-1 Using RNA Interference (RNAi) Technology. Evol Bioinform Online (2013) 0.81
miRBoost: boosting support vector machines for microRNA precursor classification. RNA (2015) 0.80
MicroRNA screening identifies miR-134 as a regulator of poliovirus and enterovirus 71 infection. Sci Data (2017) 0.80
MicroRNA and brain tumors: a cause and a cure? DNA Cell Biol (2007) 0.80
Identification of new stress-induced microRNA and their targets in wheat using computational approach. Plant Signal Behav (2013) 0.80
The expression profile of Aedes albopictus miRNAs is altered by dengue virus serotype-2 infection. Cell Biosci (2015) 0.79
A complex genome-microRNA interplay in human mitochondria. Biomed Res Int (2015) 0.79
Emerging applications of read profiles towards the functional annotation of the genome. Front Genet (2015) 0.79
Identification of MicroRNAs in Meloidogyne incognita Using Deep Sequencing. PLoS One (2015) 0.79
MicroRNAs in the Host-Apicomplexan Parasites Interactions: A Review of Immunopathological Aspects. Front Cell Infect Microbiol (2016) 0.79
Combined Small RNA and Degradome Sequencing Reveals Novel MiRNAs and Their Targets in the High-Yield Mutant Wheat Strain Yunong 3114. PLoS One (2015) 0.78
Identification and Characterization of MicroRNAs in Macaca fascicularis by EST Analysis. Comp Funct Genomics (2012) 0.78
A framework for improving microRNA prediction in non-human genomes. Nucleic Acids Res (2015) 0.77
A novel representation of RNA secondary structure based on element-contact graphs. BMC Bioinformatics (2008) 0.77
Fine tuning of auxin signaling by miRNAs. Physiol Mol Biol Plants (2008) 0.77
MicroRNA discovery by similarity search to a database of RNA-seq profiles. Front Genet (2013) 0.77
miR-Explore: Predicting MicroRNA Precursors by Class Grouping and Secondary Structure Positional Alignment. Bioinform Biol Insights (2013) 0.76
Ensemble-based classification approach for micro-RNA mining applied on diverse metagenomic sequences. BMC Res Notes (2014) 0.76
Identification of miRNAs in sorghum by using bioinformatics approach. Plant Signal Behav (2012) 0.76
Role of bioinformatics in establishing microRNAs as modulators of abiotic stress responses: the new revolution. Front Physiol (2015) 0.76
miRLocator: Machine Learning-Based Prediction of Mature MicroRNAs within Plant Pre-miRNA Sequences. PLoS One (2015) 0.76
Contribution of bioinformatics prediction in microRNA-based cancer therapeutics. Adv Drug Deliv Rev (2014) 0.76
Virus versus host plant microRNAs: who determines the outcome of the interaction? PLoS One (2014) 0.75
Mi-DISCOVERER: A bioinformatics tool for the detection of mi-RNA in human genome. Bioinformation (2010) 0.75
ImiRP: a computational approach to microRNA target site mutation. BMC Bioinformatics (2016) 0.75
Integrated Strategy Improves the Prediction Accuracy of miRNA in Large Dataset. PLoS One (2016) 0.75
Composition and genomic organization of arthropod Hox clusters. Evodevo (2016) 0.75
Small RNAs in Plant Responses to Abiotic Stresses: Regulatory Roles and Study Methods. Int J Mol Sci (2015) 0.75
MicroRNAs in Taenia solium Neurocysticercosis: Insights as Promising Agents in Host-Parasite Interaction and Their Potential as Biomarkers. Front Microbiol (2017) 0.75
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics (2009) 14.83
The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
Astrocytic purinergic signaling coordinates synaptic networks. Science (2005) 6.55
Essential roles of PI(3)K-p110beta in cell growth, metabolism and tumorigenesis. Nature (2008) 6.04
Structural basis for double-stranded RNA processing by Dicer. Science (2006) 5.86
Development and characterization of gemcitabine-resistant pancreatic tumor cells. Ann Surg Oncol (2007) 4.12
New world bats harbor diverse influenza A viruses. PLoS Pathog (2013) 4.10
Meta-analysis of genome-wide association studies identifies common variants associated with blood pressure variation in east Asians. Nat Genet (2011) 4.04
Early repolarization pattern and risk for arrhythmia death: a meta-analysis. J Am Coll Cardiol (2013) 4.03
An emerging recombinant human enterovirus 71 responsible for the 2008 outbreak of hand foot and mouth disease in Fuyang city of China. Virol J (2010) 3.90
Antagonistic regulation of PIN phosphorylation by PP2A and PINOID directs auxin flux. Cell (2007) 3.84
Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data. Proc Natl Acad Sci U S A (2011) 3.80
RET fusions define a unique molecular and clinicopathologic subtype of non-small-cell lung cancer. J Clin Oncol (2012) 3.72
Extensive set of 16S rRNA-based probes for detection of bacteria in human feces. Appl Environ Microbiol (2002) 3.71
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics (2005) 3.69
Aggregated alpha-synuclein activates microglia: a process leading to disease progression in Parkinson's disease. FASEB J (2005) 3.60
DJ-1 and alpha-synuclein in human cerebrospinal fluid as biomarkers of Parkinson's disease. Brain (2010) 3.57
Mice genetically deficient in vasopressin V1a and V1b receptors are resistant to jet lag. Science (2013) 3.51
A prospective multicenter clinical study of extralevator abdominoperineal resection for locally advanced low rectal cancer. Dis Colon Rectum (2014) 3.30
GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics (2010) 3.20
R428, a selective small molecule inhibitor of Axl kinase, blocks tumor spread and prolongs survival in models of metastatic breast cancer. Cancer Res (2010) 2.87
Cerebrospinal fluid biomarkers for Parkinson disease diagnosis and progression. Ann Neurol (2011) 2.84
Gliosis and brain remodeling after treatment of stroke in rats with marrow stromal cells. Glia (2005) 2.68
Targeting SRC family kinases inhibits growth and lymph node metastases of prostate cancer in an orthotopic nude mouse model. Cancer Res (2008) 2.59
End-Stage Heart Failure With COVID-19: Strong Evidence of Myocardial Injury by 2019-nCoV. JACC Heart Fail (2020) 2.57
HIF-1alpha, STAT3, CBP/p300 and Ref-1/APE are components of a transcriptional complex that regulates Src-dependent hypoxia-induced expression of VEGF in pancreatic and prostate carcinomas. Oncogene (2005) 2.53
ABP1 mediates auxin inhibition of clathrin-dependent endocytosis in Arabidopsis. Cell (2010) 2.51
Predicting features of breast cancer with gene expression patterns. Breast Cancer Res Treat (2007) 2.49
Approaches for high internal quantum efficiency green InGaN light-emitting diodes with large overlap quantum wells. Opt Express (2011) 2.44
Subcellular homeostasis of phytohormone auxin is mediated by the ER-localized PIN5 transporter. Nature (2009) 2.40
In vitro derivation of functional insulin-producing cells from human embryonic stem cells. Cell Res (2007) 2.28
Targeted migration of mesenchymal stem cells modified with CXCR4 gene to infarcted myocardium improves cardiac performance. Mol Ther (2008) 2.25
Mass spectrometry based targeted protein quantification: methods and applications. J Proteome Res (2009) 2.20
Automatic detection and recognition of signs from natural scenes. IEEE Trans Image Process (2004) 2.19
Spectrum of oncogenic driver mutations in lung adenocarcinomas from East Asian never smokers. PLoS One (2011) 2.17
Lnk inhibits erythropoiesis and Epo-dependent JAK2 activation and downstream signaling pathways. Blood (2005) 2.17
Specific in vivo phosphorylation sites determine the assembly dynamics of vimentin intermediate filaments. J Cell Sci (2004) 2.17
Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq. Bioinformatics (2010) 2.17
Sperm, but not oocyte, DNA methylome is inherited by zebrafish early embryos. Cell (2013) 2.16
Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95. Nat Med (2010) 2.15
Hand, foot, and mouth disease in China: patterns of spread and transmissibility. Epidemiology (2011) 2.13
In vivo photodynamic therapy using upconversion nanoparticles as remote-controlled nanotransducers. Nat Med (2012) 2.13
A novel 3D mammalian cell perfusion-culture system in microfluidic channels. Lab Chip (2007) 2.03
NMDA receptors in dopaminergic neurons are crucial for habit learning. Neuron (2011) 2.02
Surgeon variation in patient quality of life after radical prostatectomy. J Urol (2012) 2.00
Detection of biomarkers with a multiplex quantitative proteomic platform in cerebrospinal fluid of patients with neurodegenerative disorders. J Alzheimers Dis (2006) 2.00
Normal and disease-related biological functions of Twist1 and underlying molecular mechanisms. Cell Res (2011) 1.99
Altered heart rate variability depend on the characteristics of coronary lesions in stable angina pectoris. Anatol J Cardiol (2014) 1.97
Reinvestigation of the role of humic acid in the oxidation of phenols by permanganate. Environ Sci Technol (2013) 1.96
Efficacy and safety of neoadjuvant intensity-modulated radiotherapy with concurrent capecitabine for locally advanced rectal cancer. Dis Colon Rectum (2015) 1.93
Composition and phase dependence of the intrinsic and extrinsic piezoelectric activity of domain engineered (1-x)Pb(Mg(13)Nb(23))O(3)-xPbTiO(3) crystals. J Appl Phys (2010) 1.92
High-resolution human core-promoter prediction with CoreBoost_HM. Genome Res (2008) 1.88
The Alzheimer's Association external quality control program for cerebrospinal fluid biomarkers. Alzheimers Dement (2011) 1.87
Endogenous oncogenic Nras mutation promotes aberrant GM-CSF signaling in granulocytic/monocytic precursors in a murine model of chronic myelomonocytic leukemia. Blood (2010) 1.86
Structural basis of ultraviolet-B perception by UVR8. Nature (2012) 1.86
The leptin-deficient (ob/ob) mouse: a new animal model of peripheral neuropathy of type 2 diabetes and obesity. Diabetes (2006) 1.84
Low but sustained coagulation activation ameliorates glucose-induced podocyte apoptosis: protective effect of factor V Leiden in diabetic nephropathy. Blood (2011) 1.83
RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II. Nature (2011) 1.79
Role of poly(ADP-ribose) polymerase activation in diabetic neuropathy. Diabetes (2004) 1.79
Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq. J Bioinform Comput Biol (2010) 1.78
Structure of the CRISPR interference complex CSM reveals key similarities with cascade. Mol Cell (2013) 1.74
Targeted disruption of hsf1 leads to lack of thermotolerance and defines tissue-specific regulation for stress-inducible Hsp molecular chaperones. J Cell Biochem (2002) 1.73
Framework for performance evaluation of face, text, and vehicle detection and tracking in video: data, metrics, and protocol. IEEE Trans Pattern Anal Mach Intell (2009) 1.72
CSF Aβ(42) and tau in Parkinson's disease with cognitive impairment. Mov Disord (2010) 1.71
Endogenous oncogenic Nras mutation initiates hematopoietic malignancies in a dose- and cell type-dependent manner. Blood (2011) 1.70
Matrix metalloproteinase 2 activation of transforming growth factor-beta1 (TGF-beta1) and TGF-beta1-type II receptor signaling within the aged arterial wall. Arterioscler Thromb Vasc Biol (2006) 1.69
Bariatric surgery reduces visceral adipose inflammation and improves endothelial function in type 2 diabetic mice. Arterioscler Thromb Vasc Biol (2011) 1.69
Rat aortic MCP-1 and its receptor CCR2 increase with age and alter vascular smooth muscle cell function. Arterioscler Thromb Vasc Biol (2004) 1.68
Enhance the optical absorptivity of nanocrystalline TiO2 film with high molar extinction coefficient ruthenium sensitizers for high performance dye-sensitized solar cells. J Am Chem Soc (2008) 1.68
Direct differentiation of atrial and ventricular myocytes from human embryonic stem cells by alternating retinoid signals. Cell Res (2010) 1.67
Conventional US, US elasticity imaging, and acoustic radiation force impulse imaging for prediction of malignancy in thyroid nodules. Radiology (2014) 1.67
Proinflammatory profile within the grossly normal aged human aortic wall. Hypertension (2007) 1.66
CXCR2-positive neutrophils are essential for cuprizone-induced demyelination: relevance to multiple sclerosis. Nat Neurosci (2010) 1.65
c-Jun N-terminal kinase 2 (JNK2) antagonizes the signaling of differentiation by JNK1 in human myeloid leukemia cells resistant to vitamin D. Leuk Res (2009) 1.64
Discovery of RG7388, a potent and selective p53-MDM2 inhibitor in clinical development. J Med Chem (2013) 1.63
Resveratrol improves endothelial function: role of TNF{alpha} and vascular oxidative stress. Arterioscler Thromb Vasc Biol (2009) 1.63
Hypertension alters GABA receptor-mediated inhibition of neurons in the nucleus of the solitary tract. Am J Physiol Regul Integr Comp Physiol (2003) 1.63
Toll-like receptor 3 agonist poly(I:C)-induced antiviral response in human corneal epithelial cells. Immunology (2006) 1.63
Isoprostanes and related products of lipid peroxidation in neurodegenerative diseases. Chem Phys Lipids (2004) 1.63
Toll-like receptor 2-mediated expression of beta-defensin-2 in human corneal epithelial cells. Microbes Infect (2005) 1.62
Cideb regulates diet-induced obesity, liver steatosis, and insulin sensitivity by controlling lipogenesis and fatty acid oxidation. Diabetes (2007) 1.62
Serum microRNA-29a is a promising novel marker for early detection of colorectal liver metastasis. Cancer Epidemiol (2011) 1.61
Electromechanical properties of tetragonal Pb(In(12)Nb(12))O(3)-Pb(Mg(13)Nb(23))O(3)-PbTiO(3) ferroelectric crystals. J Appl Phys (2010) 1.60
Cyclophilin A is overexpressed in human pancreatic cancer cells and stimulates cell proliferation through CD147. Cancer (2006) 1.59
Fine mapping and identification of a candidate gene SSH1 in disseminated superficial actinic porokeratosis. Hum Mutat (2004) 1.59
Comparative analysis of amino acid usage and protein length distribution between alternatively and non-alternatively spliced genes across six eukaryotic genomes. Mol Biol Evol (2003) 1.59
Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases. Genome Res (2012) 1.59
Neuregulin 1 regulates excitability of fast-spiking neurons through Kv1.1 and acts in epilepsy. Nat Neurosci (2011) 1.58
Evidence of recombination and genetic diversity in human rhinoviruses in children with acute respiratory infection. PLoS One (2009) 1.58
Risk of bone fractures associated with glucagon-like peptide-1 receptor agonists' treatment: a meta-analysis of randomized controlled trials. Endocrine (2014) 1.58
Use of an immunoaffinity-mass spectrometry-based approach for the quantification of protein biomarkers from serum samples of lung cancer patients. Mol Cell Proteomics (2008) 1.58
CpG island methylation pattern in different human tissues and its correlation with gene expression. Biochem Biophys Res Commun (2009) 1.58
Identification of New Delhi metallo-β-lactamase 1 in Acinetobacter lwoffii of food animal origin. PLoS One (2012) 1.58
The TWIST/Mi2/NuRD protein complex and its essential role in cancer metastasis. Cell Res (2010) 1.56
Intestinal farnesoid X receptor signaling promotes nonalcoholic fatty liver disease. J Clin Invest (2014) 1.55