Published in Nucleic Acids Res on June 08, 2013
Identification of differentially expressed microRNAs in Culex pipiens and their potential roles in pyrethroid resistance. Insect Biochem Mol Biol (2014) 0.89
Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs. PLoS One (2015) 0.81
MiRduplexSVM: A High-Performing MiRNA-Duplex Prediction and Evaluation Methodology. PLoS One (2015) 0.81
Secondary structural entropy in RNA switch (Riboswitch) identification. BMC Bioinformatics (2015) 0.79
MatPred: Computational Identification of Mature MicroRNAs within Novel Pre-MicroRNAs. Biomed Res Int (2015) 0.77
Improved Pre-miRNA Classification by Reducing the Effect of Class Imbalance. Biomed Res Int (2015) 0.77
An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress. BMC Genomics (2015) 0.77
miRLocator: Machine Learning-Based Prediction of Mature MicroRNAs within Plant Pre-miRNA Sequences. PLoS One (2015) 0.76
Identification and Characterization of Microsatellite Loci in Maqui (Aristotelia chilensis [Molina] Stunz) Using Next-Generation Sequencing (NGS). PLoS One (2016) 0.75
miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining. Sci Rep (2016) 0.75
Improving classification of mature microRNA by solving class imbalance problem. Sci Rep (2016) 0.75
The functions of animal microRNAs. Nature (2004) 64.85
Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature (2005) 48.95
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res (2006) 39.25
miRBase: tools for microRNA genomics. Nucleic Acids Res (2007) 38.61
Identification of tissue-specific microRNAs from mouse. Curr Biol (2002) 34.55
Asymmetry in the assembly of the RNAi enzyme complex. Cell (2003) 22.18
bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell (2003) 22.14
MicroRNA genes are transcribed by RNA polymerase II. EMBO J (2004) 20.65
The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat Genet (2005) 17.07
Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta (1975) 17.03
A pancreatic islet-specific microRNA regulates insulin secretion. Nature (2004) 15.02
Identification of microRNAs of the herpesvirus family. Nat Methods (2005) 12.98
Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell (2004) 12.97
Role of microRNAs in plant and animal development. Science (2003) 12.45
Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol (2008) 10.17
A signature pattern of stress-responsive microRNAs that can evoke cardiac hypertrophy and heart failure. Proc Natl Acad Sci U S A (2006) 10.09
Human embryonic stem cells express a unique set of microRNAs. Dev Biol (2004) 8.87
A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nat Genet (2006) 8.37
RNA and disease. Cell (2009) 7.98
The promises and pitfalls of RNA-interference-based therapeutics. Nature (2009) 7.53
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res (2011) 5.83
Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet (2007) 5.33
A miRNA involved in phosphate-starvation response in Arabidopsis. Curr Biol (2005) 4.62
Approaches to microRNA discovery. Nat Genet (2006) 4.32
Critical roles for Dicer in the female germline. Genes Dev (2007) 4.23
Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell (2006) 4.06
A hierarchy of regulatory genes controls a larva-to-adult developmental switch in C. elegans. Cell (1989) 4.03
Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci U S A (2004) 3.97
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
Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol (2008) 3.43
MicroRNAs: regulators of gene expression and cell differentiation. Blood (2006) 3.08
Evolution and functional diversification of MIRNA genes. Plant Cell (2011) 3.07
Evidence that miRNAs are different from other RNAs. Cell Mol Life Sci (2006) 3.05
MicroRNA control of muscle development and disease. Curr Opin Cell Biol (2009) 3.04
Widespread regulatory activity of vertebrate microRNA* species. RNA (2010) 2.97
miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res (2009) 2.90
Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics (2005) 2.76
Identification and characterization of human cytomegalovirus-encoded microRNAs. J Virol (2005) 2.73
Energizing miRNA research: a review of the role of miRNAs in lipid metabolism, with a prediction that miR-103/107 regulates human metabolic pathways. Mol Genet Metab (2007) 2.52
MicroRNA identification based on sequence and structure alignment. Bioinformatics (2005) 2.52
Dicer recognizes the 5' end of RNA for efficient and accurate processing. Nature (2011) 2.49
Human microRNA prediction through a probabilistic co-learning model of sequence and structure. Nucleic Acids Res (2005) 2.48
miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res (2011) 2.25
MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. Plant Cell (2010) 2.22
MicroRNAs in biological processes and carcinogenesis. Carcinogenesis (2006) 2.14
Current tools for the identification of miRNA genes and their targets. Nucleic Acids Res (2009) 2.12
microPred: effective classification of pre-miRNAs for human miRNA gene prediction. Bioinformatics (2009) 2.11
Molecular biology. Glimpses of a tiny RNA world. Science (2001) 2.04
Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design. J Biol Chem (2004) 2.01
Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma. Nucleic Acids Res (2010) 1.77
MiRenSVM: towards better prediction of microRNA precursors using an ensemble SVM classifier with multi-loop features. BMC Bioinformatics (2010) 1.63
MicroRNAs: expression, avoidance and subversion by vertebrate viruses. Nat Rev Microbiol (2006) 1.54
MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. Bioinformatics (2010) 1.53
MicroRNAs and endocrine biology. J Endocrinol (2005) 1.47
Computational approaches for microRNA studies: a review. Mamm Genome (2009) 1.39
miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res (2012) 1.37
High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis. Genome Res (2011) 1.27
MaturePred: efficient identification of microRNAs within novel plant pre-miRNAs. PLoS One (2011) 1.25
ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs. Nucleic Acids Res (2006) 1.23
MatureBayes: a probabilistic algorithm for identifying the mature miRNA within novel precursors. PLoS One (2010) 1.21
HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models. BMC Bioinformatics (2009) 1.16
Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants. PLoS Comput Biol (2007) 1.16
Prediction of novel microRNA genes in cancer-associated genomic regions--a combined computational and experimental approach. Nucleic Acids Res (2009) 1.05
MiRmat: mature microRNA sequence prediction. PLoS One (2012) 0.88
Small RNAs and large DNA viruses. N Engl J Med (2007) 0.79
An epigenetic silencing influence. Nat Rev Genet (2010) 0.78
SplamiR--prediction of spliced miRNAs in plants. Bioinformatics (2011) 0.78
Identification and characterization of multi-species conserved sequences. Genome Res (2003) 10.18
Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nat Genet (2009) 4.72
Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Mol Cell (2007) 4.58
Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biol (2005) 4.48
Reconstructing contiguous regions of an ancestral genome. Genome Res (2006) 3.68
PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics (2004) 3.63
Genome-wide orchestration of cardiac functions by the orphan nuclear receptors ERRalpha and gamma. Cell Metab (2007) 3.00
Phylo: a citizen science approach for improving multiple sequence alignment. PLoS One (2012) 2.64
A probabilistic approach for SNP discovery in high-throughput human resequencing data. Genome Res (2009) 2.55
Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics (2004) 2.50
PReMod: a database of genome-wide mammalian cis-regulatory module predictions. Nucleic Acids Res (2006) 2.27
Evolutionarily conserved sequence elements that positively regulate IFN-gamma expression in T cells. Proc Natl Acad Sci U S A (2004) 2.21
The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts. Genome Biol (2014) 2.01
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling. BMC Bioinformatics (2011) 1.78
The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet (2013) 1.69
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet (2013) 1.68
Chromatin conformation signatures of cellular differentiation. Genome Biol (2009) 1.68
BH3-ligand regulates access of MCL-1 to its E3 ligase. FEBS Lett (2005) 1.49
A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. PLoS Genet (2013) 1.37
The three-dimensional architecture of Hox cluster silencing. Nucleic Acids Res (2010) 1.36
Exact and heuristic algorithms for the Indel Maximum Likelihood Problem. J Comput Biol (2007) 1.35
High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes. Methods (2009) 1.24
The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase II. Mol Cell Proteomics (2010) 1.23
On the inference of parsimonious indel evolutionary scenarios. J Bioinform Comput Biol (2006) 1.14
Seeder: discriminative seeding DNA motif discovery. Bioinformatics (2008) 1.10
Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment. Genome Biol (2013) 1.06
A flexible ancestral genome reconstruction method based on gapped adjacencies. BMC Bioinformatics (2012) 1.03
Modeling contaminants in AP-MS/MS experiments. J Proteome Res (2010) 1.03
Ancestors 1.0: a web server for ancestral sequence reconstruction. Bioinformatics (2009) 1.01
Computational analysis of whole-genome differential allelic expression data in human. PLoS Comput Biol (2010) 0.99
Detecting non-coding selective pressure in coding regions. BMC Evol Biol (2007) 0.98
Long-range regulation is a major driving force in maintaining genome integrity. BMC Evol Biol (2009) 0.94
FootPrinter3: phylogenetic footprinting in partially alignable sequences. Nucleic Acids Res (2006) 0.92
Combining computational prediction of cis-regulatory elements with a new enhancer assay to efficiently label neuronal structures in the medaka fish. PLoS One (2011) 0.90
Hox in motion: tracking HoxA cluster conformation during differentiation. Nucleic Acids Res (2013) 0.90
Computing chromosome conformation. Methods Mol Biol (2010) 0.90
Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees. BMC Bioinformatics (2007) 0.89
Predicting direct protein interactions from affinity purification mass spectrometry data. Algorithms Mol Biol (2010) 0.86
Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania. BMC Bioinformatics (2008) 0.85
Detection of locally over-represented GO terms in protein-protein interaction networks. J Comput Biol (2010) 0.85
Genome-wide mouse mutagenesis reveals CD45-mediated T cell function as critical in protective immunity to HSV-1. PLoS Pathog (2013) 0.84
Nuclear import of RNA polymerase II is coupled with nucleocytoplasmic shuttling of the RNA polymerase II-associated protein 2. Nucleic Acids Res (2013) 0.84
Classifying leukemia types with chromatin conformation data. Genome Biol (2014) 0.83
An N-ethyl-N-nitrosourea (ENU)-induced dominant negative mutation in the JAK3 kinase protects against cerebral malaria. PLoS One (2012) 0.83
A whole genome study and identification of specific carcinogenic regions of the human papilloma viruses. J Comput Biol (2009) 0.82
Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI). Biochem Cell Biol (2008) 0.81
Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus. Genome Res (2011) 0.80
Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry. J Proteome Res (2012) 0.80
Genetic map refinement using a comparative genomic approach. J Comput Biol (2009) 0.79
Mapping association between long-range cis-regulatory regions and their target genes using synteny. J Comput Biol (2011) 0.77
Predicting site-specific human selective pressure using evolutionary signatures. Bioinformatics (2011) 0.77
SPARCS: a web server to analyze (un)structured regions in coding RNA sequences. Nucleic Acids Res (2013) 0.76
Positional mapping and candidate gene analysis of the mouse Ccs3 locus that regulates differential susceptibility to carcinogen-induced colorectal cancer. PLoS One (2013) 0.76
A probabilistic model for sequence alignment with context-sensitive indels. J Comput Biol (2011) 0.76
Gene maps linearization using genomic rearrangement distances. J Comput Biol (2007) 0.75
StructMiner: a tool for alignment and detection of conserved secondary structure. Genome Inform (2004) 0.75
A practical algorithm for estimation of the maximum likelihood ancestral reconstruction error. Pac Symp Biocomput (2010) 0.75
An approximation algorithm for the Noah's Ark problem with random feature loss. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.75