Published in Genome Biol on July 17, 2009
Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Res (2011) 4.55
The miR-15/107 group of microRNA genes: evolutionary biology, cellular functions, and roles in human diseases. J Mol Biol (2010) 2.20
miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data. Genome Biol (2010) 2.18
MicroRNA-99a inhibits hepatocellular carcinoma growth and correlates with prognosis of patients with hepatocellular carcinoma. J Biol Chem (2011) 1.88
Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish. BMC Genomics (2010) 1.60
Characterization of the small RNA transcriptomes of androgen dependent and independent prostate cancer cell line by deep sequencing. PLoS One (2010) 1.21
Identification and differential expression of microRNAs during metamorphosis of the Japanese flounder (Paralichthys olivaceus). PLoS One (2011) 1.16
Identification and characterization of microRNAs in Clonorchis sinensis of human health significance. BMC Genomics (2010) 1.16
Discovery and characterization of medaka miRNA genes by next generation sequencing platform. BMC Genomics (2010) 1.07
Identification of novel and differentially expressed MicroRNAs of dairy goat mammary gland tissues using solexa sequencing and bioinformatics. PLoS One (2012) 1.06
YM500: a small RNA sequencing (smRNA-seq) database for microRNA research. Nucleic Acids Res (2012) 1.04
Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs: underestimated effects of contamination in NGS. RNA (2014) 1.00
Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel. BMC Genomics (2012) 0.97
Transcriptome analysis of microRNAs in developing cerebral cortex of rat. BMC Genomics (2012) 0.96
MicroRNA expression profiling of the fifth-instar posterior silk gland of Bombyx mori. BMC Genomics (2014) 0.96
Novel and conserved micrornas in Dalian purple urchin (Strongylocentrotus nudus) identified by next generation sequencing. Int J Biol Sci (2011) 0.96
Identification of a novel marine fish virus, Singapore grouper iridovirus-encoded microRNAs expressed in grouper cells by Solexa sequencing. PLoS One (2011) 0.95
miRNomes of haematopoietic stem cells and dendritic cells identify miR-30b as a regulator of Notch1. Nat Commun (2013) 0.95
UMARS: Un-MAppable Reads Solution. BMC Bioinformatics (2011) 0.93
Discovery of cashmere goat (Capra hircus) microRNAs in skin and hair follicles by Solexa sequencing. BMC Genomics (2013) 0.93
Identification and characterization of microRNAs in pearl oyster Pinctada martensii by Solexa deep sequencing. Mar Biotechnol (NY) (2013) 0.90
The integrative analysis of microRNA and mRNA expression in mouse uterus under delayed implantation and activation. PLoS One (2010) 0.90
Distinctive microRNA profiles in the salivary glands of Haemaphysalis longicornis related to tick blood-feeding. Exp Appl Acarol (2012) 0.89
Bioinformatic identification of cassava miRNAs differentially expressed in response to infection by Xanthomonas axonopodis pv. manihotis. BMC Plant Biol (2012) 0.88
Characterization and comparative analysis of small RNAs in three small RNA libraries of the brown planthopper (Nilaparvata lugens). PLoS One (2012) 0.87
High-throughput sequencing identification of novel and conserved miRNAs in the Brassica oleracea leaves. BMC Genomics (2013) 0.87
Identification of common carp (Cyprinus carpio) microRNAs and microRNA-related SNPs. BMC Genomics (2012) 0.87
YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research. Nucleic Acids Res (2014) 0.87
Expression profile of circulating microRNAs as a promising fingerprint for cervical cancer diagnosis and monitoring. Mol Clin Oncol (2015) 0.86
Expression of small RNA in Aphis gossypii and its potential role in the resistance interaction with melon. PLoS One (2012) 0.85
Systematic characterization of small RNAome during zebrafish early developmental stages. BMC Genomics (2014) 0.84
Discovery of potential piRNAs from next generation sequences of the sexually mature porcine testes. PLoS One (2012) 0.84
Characterisation and comparison of lactating mouse and bovine mammary gland miRNomes. PLoS One (2014) 0.84
Characterization of microRNAs from Orientobilharzia turkestanicum, a neglected blood fluke of human and animal health significance. PLoS One (2012) 0.84
A study of neural-related microRNAs in the developing amphioxus. Evodevo (2011) 0.84
Identification and characterization of argonaute protein, Ago2 and its associated small RNAs in Schistosoma japonicum. PLoS Negl Trop Dis (2012) 0.84
MiR-21 is involved in radiation-induced bystander effects. RNA Biol (2014) 0.83
Identification and profiling of microRNAs in goat endometrium during embryo implantation. PLoS One (2015) 0.83
Identification and characterization of novel serum microRNA candidates from deep sequencing in cervical cancer patients. Sci Rep (2014) 0.83
MicroRNA-mediated gene regulation plays a minor role in the transcriptomic plasticity of cold-acclimated zebrafish brain tissue. BMC Genomics (2011) 0.82
A novel class of somatic small RNAs similar to germ cell pachytene PIWI-interacting small RNAs. J Biol Chem (2014) 0.81
Computer-assisted annotation of murine Sertoli cell small RNA transcriptome. Biol Reprod (2013) 0.81
Identification of MicroRNA for Intermuscular Bone Development in Blunt Snout Bream (Megalobrama amblycephala). Int J Mol Sci (2015) 0.81
Deep sequencing and expression of microRNAs from early honeybee (Apis mellifera) embryos reveals a role in regulating early embryonic patterning. BMC Evol Biol (2012) 0.81
Identification and characterization of microRNAs by high through-put sequencing in mesenchymal stem cells and bone tissue from mice of age-related osteoporosis. PLoS One (2013) 0.80
Identification and characterization of microRNAs in the zoonotic fluke Fasciolopsis buski. Parasitol Res (2016) 0.80
Expression of microRNAs in Horse Plasma and Their Characteristic Nucleotide Composition. PLoS One (2016) 0.78
Expression profiling analysis of the microRNA response of Cynoglossus semilaevis to Vibrio anguillarum and other stimuli. Mar Biotechnol (NY) (2015) 0.78
Plant MicroRNA Prediction by Supervised Machine Learning Using C5.0 Decision Trees. J Nucleic Acids (2012) 0.78
Identification of conserved and novel microRNAs in the Pacific oyster Crassostrea gigas by deep sequencing. PLoS One (2014) 0.78
Identification, expression, and molecular evolution of microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp). RNA (2014) 0.78
Expression profiling of preadipocyte microRNAs by deep sequencing on chicken lines divergently selected for abdominal fatness. PLoS One (2015) 0.78
Combined analysis of mRNA and miRNA identifies dehydration and salinity responsive key molecular players in citrus roots. Sci Rep (2017) 0.78
Identification of Known and Novel microRNAs and Their Targets in Peach (Prunus persica) Fruit by High-Throughput Sequencing. PLoS One (2016) 0.77
Identification and Function Prediction of Novel MicroRNAs in Laoshan Dairy Goats. Asian-Australas J Anim Sci (2013) 0.76
Global Identification of MicroRNAs and Their Targets in Barley under Salinity Stress. PLoS One (2015) 0.76
Identification and Characterization of Novel Maize Mirnas Involved in Different Genetic Background. Int J Biol Sci (2015) 0.76
Identification and characterization of microRNAs in small brown planthopper (Laodephax striatellus) by next-generation sequencing. PLoS One (2014) 0.76
Identification of miRNomes reveals ssc-miR-30d-R_1 as a potential therapeutic target for PRRS viral infection. Sci Rep (2016) 0.76
Lipopolysaccharide-Induced Differential Expression of miRNAs in Male and Female Rhipicephalus haemaphysaloides Ticks. PLoS One (2015) 0.75
Virus versus host plant microRNAs: who determines the outcome of the interaction? PLoS One (2014) 0.75
Identification of microRNA expression profiles in the gill, intestine and hepatic caecum of Branchiostoma belcheri. Protein Cell (2017) 0.75
RNA sequencing analysis to capture the transcriptome landscape during skin ulceration syndrome progression in sea cucumber Apostichopus japonicus. BMC Genomics (2016) 0.75
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SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13
Identification of tissue-specific microRNAs from mouse. Curr Biol (2002) 34.55
The microRNA Registry. Nucleic Acids Res (2004) 29.45
Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res (2005) 29.17
Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res (2008) 20.59
A uniform system for microRNA annotation. RNA (2003) 20.28
Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet (2005) 15.96
Phylogenetic shadowing and computational identification of human microRNA genes. Cell (2005) 13.24
The amphioxus genome and the evolution of the chordate karyotype. Nature (2008) 8.03
Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature (2006) 7.96
Clustering and conservation patterns of human microRNAs. Nucleic Acids Res (2005) 4.79
Approaches to microRNA discovery. Nat Genet (2006) 4.32
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res (2007) 3.69
MicroRNA expression profiling of single whole embryonic stem cells. Nucleic Acids Res (2006) 3.36
MicroRNAs and immunity: novel players in the regulation of normal immune function and inflammation. Semin Cancer Biol (2008) 3.32
MicroRNAs and the advent of vertebrate morphological complexity. Proc Natl Acad Sci U S A (2008) 3.00
The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev (2005) 2.94
The expansion of the metazoan microRNA repertoire. BMC Genomics (2006) 2.80
The evolution of adaptive immune systems. Cell (2006) 2.77
Distinctive microRNA profiles relating to patient survival in esophageal squamous cell carcinoma. Cancer Res (2008) 2.75
MicroRNAs of the mammalian eye display distinct and overlapping tissue specificity. Mol Vis (2006) 2.68
The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint. J Exp Zool B Mol Dev Evol (2006) 2.63
MicroRNA identification based on sequence and structure alignment. Bioinformatics (2005) 2.52
De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures. Bioinformatics (2007) 2.27
The evolution of animal microRNA function. Curr Opin Genet Dev (2007) 2.22
Origin and early evolution of the vertebrates: new insights from advances in molecular biology, anatomy, and palaeontology. Bioessays (2001) 1.54
Quantitative differential expression analysis reveals miR-7 as major islet microRNA. Biochem Biophys Res Commun (2007) 1.54
Amphioxus and tunicates as evolutionary model systems. Trends Ecol Evol (2006) 1.28
The chordate amphioxus: an emerging model organism for developmental biology. Cell Mol Life Sci (2004) 1.26
Sensory systems in amphioxus: a window on the ancestral chordate condition. Brain Behav Evol (2004) 1.20
Evolution of the heart from bacteria to man. Ann N Y Acad Sci (2005) 1.03
The basal chordate amphioxus as a simple model for elucidating developmental mechanisms in vertebrates. Birth Defects Res C Embryo Today (2008) 0.91
Computational prediction of amphioxus microRNA genes and their targets. Gene (2008) 0.90
Characterization of microRNAs in cephalochordates reveals a correlation between microRNA repertoire homology and morphological similarity in chordate evolution. Evol Dev (2009) 0.89
Immunohistochemical localization of polypeptide hormones in endocrine cells of the digestive tract of Branchiostoma lanceolatum. Cell Tissue Res (1981) 0.86
SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics (2009) 39.47
Enterotypes of the human gut microbiome. Nature (2011) 24.36
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience (2012) 20.89
Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res (2008) 20.59
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
International network of cancer genome projects. Nature (2010) 20.35
Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy (2012) 20.08
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
SNP detection for massively parallel whole-genome resequencing. Genome Res (2009) 15.96
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
Transcriptional co-activator PGC-1 alpha drives the formation of slow-twitch muscle fibres. Nature (2002) 14.37
WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (2006) 13.06
Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature (2012) 11.68
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
Capturing and profiling adult hair follicle stem cells. Nat Biotechnol (2004) 10.35
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res (2006) 8.83
Defects in adaptive energy metabolism with CNS-linked hyperactivity in PGC-1alpha null mice. Cell (2004) 8.58
The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23
The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19
Stem cells in the hair follicle bulge contribute to wound repair but not to homeostasis of the epidermis. Nat Med (2005) 8.01
An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science (2012) 7.94
Genome sequence and analysis of the tuber crop potato. Nature (2011) 7.77
The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
A double-negative feedback loop between ZEB1-SIP1 and the microRNA-200 family regulates epithelial-mesenchymal transition. Cancer Res (2008) 7.45
Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med (2011) 7.11
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
TreeFam: 2008 Update. Nucleic Acids Res (2007) 6.63
A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science (2004) 6.62
Aberrant excitatory neuronal activity and compensatory remodeling of inhibitory hippocampal circuits in mouse models of Alzheimer's disease. Neuron (2007) 6.60
Essential role for Nix in autophagic maturation of erythroid cells. Nature (2008) 6.49
Serum microRNA signatures identified in a genome-wide serum microRNA expression profiling predict survival of non-small-cell lung cancer. J Clin Oncol (2010) 5.92
Secreted monocytic miR-150 enhances targeted endothelial cell migration. Mol Cell (2010) 5.77
Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat Genet (2011) 5.73
Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet (2011) 5.70
Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell (2012) 5.62
Analyses of pig genomes provide insight into porcine demography and evolution. Nature (2012) 5.58
Building the sequence map of the human pan-genome. Nat Biotechnol (2009) 5.53
Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet (2010) 5.44
The oyster genome reveals stress adaptation and complexity of shell formation. Nature (2012) 5.30
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24
Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet (2010) 5.20
Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell (2012) 5.16
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80
BAD and glucokinase reside in a mitochondrial complex that integrates glycolysis and apoptosis. Nature (2003) 4.80
Adipose tissue mass can be regulated through the vasculature. Proc Natl Acad Sci U S A (2002) 4.77
Hippo pathway inhibits Wnt signaling to restrain cardiomyocyte proliferation and heart size. Science (2011) 4.76
Respiratory effects of exposure to diesel traffic in persons with asthma. N Engl J Med (2007) 4.58
Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Res (2011) 4.55
Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study. BMJ (2011) 4.50
betaAR signaling required for diet-induced thermogenesis and obesity resistance. Science (2002) 4.47
Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A (2012) 4.26
The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol (2010) 4.25
Pleiotropic defects in lymphocyte activation caused by caspase-8 mutations lead to human immunodeficiency. Nature (2002) 4.21
Glucose sensing by POMC neurons regulates glucose homeostasis and is impaired in obesity. Nature (2007) 4.20
Accuracy improvement for identifying translation initiation sites in microbial genomes. Bioinformatics (2004) 4.16
Regression of castrate-recurrent prostate cancer by a small-molecule inhibitor of the amino-terminus domain of the androgen receptor. Cancer Cell (2010) 4.16
KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics (2006) 4.15
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11
Dynamic T cell migration program provides resident memory within intestinal epithelium. J Exp Med (2010) 4.09
Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet (2012) 4.07
Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet (2010) 4.06
Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell (2012) 4.03
In vitro studies with recombinant Plasmodium falciparum apical membrane antigen 1 (AMA1): production and activity of an AMA1 vaccine and generation of a multiallelic response. Infect Immun (2002) 4.02
Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers. Nature (2010) 3.95
T-cadherin is a receptor for hexameric and high-molecular-weight forms of Acrp30/adiponectin. Proc Natl Acad Sci U S A (2004) 3.90
Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation. Nat Genet (2013) 3.87
Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol (2012) 3.83