Systematic characterization of small RNAome during zebrafish early developmental stages.

PubWeight™: 0.84‹?›

🔗 View Article (PMC 3932949)

Published in BMC Genomics on February 10, 2014

Authors

Yuangen Yao, Lili Ma, Qiong Jia, Wankun Deng, Zexian Liu, Yuanwei Zhang, Jian Ren, Yu Xue, Haibo Jia1, Qing Yang

Author Affiliations

1: Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China. haibo.jia@hust.edu.cn.

Articles cited by this

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12

MicroRNAs: genomics, biogenesis, mechanism, and function. Cell (2004) 198.59

Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A (1998) 192.97

Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell (2005) 96.87

MicroRNA expression profiles classify human cancers. Nature (2005) 69.12

WebLogo: a sequence logo generator. Genome Res (2004) 59.58

RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77

Stages of embryonic development of the zebrafish. Dev Dyn (1995) 42.72

miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res (2010) 25.85

Vienna RNA secondary structure server. Nucleic Acids Res (2003) 19.69

Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell (2007) 18.35

Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science (2006) 18.14

The UCSC Genome Browser database: update 2011. Nucleic Acids Res (2010) 16.24

MicroRNA expression in zebrafish embryonic development. Science (2005) 15.52

Small non-coding RNAs in animal development. Nat Rev Mol Cell Biol (2008) 12.35

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res (2008) 10.18

Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol (2008) 10.17

The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science (2007) 9.36

Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary. Cell (2009) 6.39

A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish. Cell (2007) 6.31

Rfam 11.0: 10 years of RNA families. Nucleic Acids Res (2012) 6.14

Small RNAs in transcriptional gene silencing and genome defence. Nature (2009) 5.98

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res (2011) 5.83

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

Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet (2011) 3.36

The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev (2005) 2.94

miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res (2009) 2.90

The maternal-zygotic transition: death and birth of RNAs. Science (2007) 2.57

piRNABank: a web resource on classified and clustered Piwi-interacting RNAs. Nucleic Acids Res (2007) 2.55

microPred: effective classification of pre-miRNAs for human miRNA gene prediction. Bioinformatics (2009) 2.11

Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol (2009) 1.82

MiRenSVM: towards better prediction of microRNA precursors using an ensemble SVM classifier with multi-loop features. BMC Bioinformatics (2010) 1.63

GPS-SNO: computational prediction of protein S-nitrosylation sites with a modified GPS algorithm. PLoS One (2010) 1.40

Small RNAs in early mammalian development: from gametes to gastrulation. Development (2011) 1.33

Large-scale genome analysis reveals unique features of microRNAs. Gene (2009) 1.28

Small RNA class transition from siRNA/piRNA to miRNA during pre-implantation mouse development. Nucleic Acids Res (2010) 1.27

Transcriptome-wide analysis of small RNA expression in early zebrafish development. RNA (2012) 1.13

CPSS: a computational platform for the analysis of small RNA deep sequencing data. Bioinformatics (2012) 1.10

miR-1 and miR-206 regulate angiogenesis by modulating VegfA expression in zebrafish. Development (2012) 1.10

MicroRNA-mediated posttranscriptional regulation is required for maintaining undifferentiated properties of blastoderm and primordial germ cells in chickens. Proc Natl Acad Sci U S A (2011) 1.05

Select microRNAs are essential for early development in the sea urchin. Dev Biol (2011) 0.95

Heterogeneous ensemble approach with discriminative features and modified-SMOTEbagging for pre-miRNA classification. Nucleic Acids Res (2012) 0.93

In vivo screening of zebrafish microRNA responses to bacterial infection and their possible roles in regulating immune response genes after lipopolysaccharide stimulation. Fish Physiol Biochem (2012) 0.92

Drastic expression change of transposon-derived piRNA-like RNAs and microRNAs in early stages of chicken embryos implies a role in gastrulation. RNA Biol (2012) 0.91

Prediction of novel pre-microRNAs with high accuracy through boosting and SVM. Bioinformatics (2011) 0.88

MicroRNA 22 regulates cell cycle length in cerebellar granular neuron precursors. Mol Cell Biol (2013) 0.81

A periaxonal net in the zebrafish central nervous system. Brain Res (2003) 0.78

Articles by these authors

Chronic inflammation in fat plays a crucial role in the development of obesity-related insulin resistance. J Clin Invest (2003) 32.01

Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics (2006) 5.59

GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. Mol Cell Proteomics (2008) 4.33

Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A (2003) 4.07

CSS-Palm 2.0: an updated software for palmitoylation sites prediction. Protein Eng Des Sel (2008) 2.86

Preperitoneal single-port transvesical enucleation of the prostate (STEP) for large-volume BPH: one-year follow-up of Qmax, IPSS, and QoL. Urology (2012) 2.78

DOG 1.0: illustrator of protein domain structures. Cell Res (2009) 2.77

China's facility-based birth strategy and neonatal mortality: a population-based epidemiological study. Lancet (2011) 2.64

Genome-wide association identifies a susceptibility locus for coronary artery disease in the Chinese Han population. Nat Genet (2011) 2.32

Fibroblast growth factor 21 regulates energy metabolism by activating the AMPK-SIRT1-PGC-1alpha pathway. Proc Natl Acad Sci U S A (2010) 2.27

Nuclear import of the MUC1-C oncoprotein is mediated by nucleoporin Nup62. J Biol Chem (2007) 2.23

GPS: a novel group-based phosphorylation predicting and scoring method. Biochem Biophys Res Commun (2004) 2.17

Iterative voting for inference of structural saliency and characterization of subcellular events. IEEE Trans Image Process (2007) 2.17

MUC1 oncoprotein activates the IkappaB kinase beta complex and constitutive NF-kappaB signalling. Nat Cell Biol (2007) 2.15

MUC1-C oncoprotein functions as a direct activator of the nuclear factor-kappaB p65 transcription factor. Cancer Res (2009) 2.04

Human MUC1 carcinoma antigen regulates intracellular oxidant levels and the apoptotic response to oxidative stress. J Biol Chem (2003) 1.98

DF3/MUC1 signaling in multiple myeloma cells is regulated by interleukin-7. Cancer Biol Ther (2003) 1.96

Identification of two new loci at IL23R and RAB32 that influence susceptibility to leprosy. Nat Genet (2011) 1.95

Transcriptional switch of dormant tumors to fast-growing angiogenic phenotype. Cancer Res (2009) 1.90

CD36 is important for chylomicron formation and secretion and may mediate cholesterol uptake in the proximal intestine. Gastroenterology (2006) 1.67

Wide dissemination of OXA-23-producing carbapenem-resistant Acinetobacter baumannii clonal complex 22 in multiple cities of China. J Antimicrob Chemother (2010) 1.56

Structural disorder in the complex of human pregnane X receptor and the macrolide antibiotic rifampicin. Mol Endocrinol (2005) 1.55

GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection. Protein Eng Des Sel (2010) 1.53

MMP-9 and IL-6 are potential biomarkers for disease activity in Takayasu's arteritis. Int J Cardiol (2012) 1.51

Comparison of single-surgeon series of transperitoneal laparoendoscopic single-site surgery and standard laparoscopic adrenalectomy. Urology (2012) 1.51

Structural basis of heroin and cocaine metabolism by a promiscuous human drug-processing enzyme. Nat Struct Biol (2003) 1.46

ITFP: an integrated platform of mammalian transcription factors. Bioinformatics (2008) 1.43

MUC1 oncoprotein blocks nuclear targeting of c-Abl in the apoptotic response to DNA damage. EMBO J (2006) 1.42

CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS). Bioinformatics (2006) 1.42

Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. Gigascience (2013) 1.42

Resveratrol differentially modulates inflammatory responses of microglia and astrocytes. J Neuroinflammation (2010) 1.41

Genomic analysis of the multidrug-resistant Acinetobacter baumannii strain MDR-ZJ06 widely spread in China. Antimicrob Agents Chemother (2011) 1.40

GPS-SNO: computational prediction of protein S-nitrosylation sites with a modified GPS algorithm. PLoS One (2010) 1.40

Retracted Gene-gene interaction network analysis of ovarian cancer using TCGA data. J Ovarian Res (2013) 1.40

MUC1 cytoplasmic domain coactivates Wnt target gene transcription and confers transformation. Cancer Biol Ther (2003) 1.39

Perioperative outcomes and cosmesis analysis of patients undergoing laparoendoscopic single-site adrenalectomy: a comparison of transumbilical, transperitoneal subcostal, and retroperitoneal subcostal approaches. Urology (2013) 1.39

Diagnosis of liver cancer using HPLC-based metabonomics avoiding false-positive result from hepatitis and hepatocirrhosis diseases. J Chromatogr B Analyt Technol Biomed Life Sci (2004) 1.35

Evidence of Arabidopsis salt acclimation induced by up-regulation of HY1 and the regulatory role of RbohD-derived reactive oxygen species synthesis. Plant J (2011) 1.35

Heregulin targets gamma-catenin to the nucleolus by a mechanism dependent on the DF3/MUC1 oncoprotein. Mol Cancer Res (2003) 1.34

Influence of mutations in hepatitis B virus surface protein on viral antigenicity and phenotype in occult HBV strains from blood donors. J Hepatol (2012) 1.29

Binocular coordination of saccades in children with strabismus before and after surgery. Invest Ophthalmol Vis Sci (2002) 1.29

Fasting and postprandial concentrations of GLP-1 in intestinal lymph and portal plasma: evidence for selective release of GLP-1 in the lymph system. Am J Physiol Regul Integr Comp Physiol (2007) 1.27

Dual specificity mitogen-activated protein (MAP) kinase phosphatase-4 plays a potential role in insulin resistance. J Biol Chem (2003) 1.27

Ordered nanowire array blue/near-UV light emitting diodes. Adv Mater (2010) 1.25

Prediction of Nepsilon-acetylation on internal lysines implemented in Bayesian Discriminant Method. Biochem Biophys Res Commun (2006) 1.24

Werner syndrome protein phosphorylation by abl tyrosine kinase regulates its activity and distribution. Mol Cell Biol (2003) 1.23

Epigenetic regulation, somatic homologous recombination, and abscisic acid signaling are influenced by DNA polymerase epsilon mutation in Arabidopsis. Plant Cell (2009) 1.23

Pre- and postsynaptic plasticity underlying augmented glutamatergic inputs to hypothalamic presympathetic neurons in spontaneously hypertensive rats. J Physiol (2008) 1.22

MR diffusion changes correlate with ultra-structurally defined axonal degeneration in murine optic nerve. Neuroimage (2007) 1.20

Dissemination of imipenem-resistant Acinetobacter baumannii strains carrying the ISAba1 blaOXA-23 genes in a Chinese hospital. J Med Microbiol (2007) 1.20

Carbon monoxide enhances salt tolerance by nitric oxide-mediated maintenance of ion homeostasis and up-regulation of antioxidant defence in wheat seedling roots. Plant Cell Environ (2008) 1.20

MRI identification of the rostral-caudal pattern of pathology within the corpus callosum in the cuprizone mouse model. J Magn Reson Imaging (2008) 1.20

Ethnoveterinary plant remedies used by Nu people in NW Yunnan of China. J Ethnobiol Ethnomed (2010) 1.19

GLP-1 reduces intestinal lymph flow, triglyceride absorption, and apolipoprotein production in rats. Am J Physiol Gastrointest Liver Physiol (2005) 1.18

Why does the gut choose apolipoprotein B48 but not B100 for chylomicron formation? Am J Physiol Gastrointest Liver Physiol (2007) 1.18

Clonal spread of imipenem-resistant Acinetobacter baumannii among different cities of China. J Clin Microbiol (2007) 1.17

c-Myb is required for neural progenitor cell proliferation and maintenance of the neural stem cell niche in adult brain. Stem Cells (2007) 1.16

A genome-wide analysis of sumoylation-related biological processes and functions in human nucleus. FEBS Lett (2005) 1.15

PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation. Mol Cell Proteomics (2009) 1.15

Systematic analysis of protein phosphorylation networks from phosphoproteomic data. Mol Cell Proteomics (2012) 1.15

Characteristics of embB mutations in multidrug-resistant Mycobacterium tuberculosis isolates in Henan, China. J Antimicrob Chemother (2011) 1.15

Design and implementation of the first nationwide, web-based Chinese Renal Data System (CNRDS). BMC Med Inform Decis Mak (2012) 1.14

Are health care providers still smoking? Data from the 2003 and 2006/2007 Tobacco Use Supplement-Current Population Surveys. Nicotine Tob Res (2010) 1.14

Widespread occurrence of aminoglycoside resistance due to ArmA methylase in imipenem-resistant Acinetobacter baumannii isolates in China. J Antimicrob Chemother (2007) 1.13

c-Jun N-terminal kinase enhances MST1-mediated pro-apoptotic signaling through phosphorylation at serine 82. J Biol Chem (2009) 1.12

Impacts on wetlands of large-scale land-use changes by agricultural development: the Small Sanjiang Plain, China. Ambio (2004) 1.11

Direct coupling of plasmonic and photonic nanowires for hybrid nanophotonic components and circuits. Nano Lett (2009) 1.11

Integrated genome sequence and linkage map of physic nut (Jatropha curcas L.), a biodiesel plant. Plant J (2015) 1.11

CPSS: a computational platform for the analysis of small RNA deep sequencing data. Bioinformatics (2012) 1.10

Chronic spontaneous activity generated in the somata of primary nociceptors is associated with pain-related behavior after spinal cord injury. J Neurosci (2010) 1.10

Typing and characterization of carbapenem-resistant Acinetobacter calcoaceticus-baumannii complex in a Chinese hospital. J Med Microbiol (2004) 1.10

MeMo: a web tool for prediction of protein methylation modifications. Nucleic Acids Res (2006) 1.09

Interaction of tumor necrosis factor-alpha- and thiazolidinedione-regulated pathways in obesity. Endocrinology (2004) 1.09

Effects of yo-yo diet, caloric restriction, and olestra on tissue distribution of hexachlorobenzene. Am J Physiol Gastrointest Liver Physiol (2004) 1.09

CPLA 1.0: an integrated database of protein lysine acetylation. Nucleic Acids Res (2010) 1.08

Sequence context- and temperature-dependent nucleotide excision repair of a benzo[a]pyrene diol epoxide-guanine DNA adduct catalyzed by thermophilic UvrABC proteins. Biochemistry (2007) 1.08

Stimulation of incretin secretion by dietary lipid: is it dose dependent? Am J Physiol Gastrointest Liver Physiol (2009) 1.08

Dynamic DNA methylation and histone modifications contribute to lentiviral transgene silencing in murine embryonic carcinoma cells. J Virol (2005) 1.08

Dual specificity MAPK phosphatase 3 activates PEPCK gene transcription and increases gluconeogenesis in rat hepatoma cells. J Biol Chem (2005) 1.08

Evidence for the location of the allosteric activation switch in the multisubunit phosphorylase kinase complex from mass spectrometric identification of chemically crosslinked peptides. J Mol Biol (2006) 1.07

Proliferating cell nuclear antigen (PCNA) regulates primordial follicle assembly by promoting apoptosis of oocytes in fetal and neonatal mouse ovaries. PLoS One (2011) 1.07

Enzymatic characterization of the pancreatic islet-specific glucose-6-phosphatase-related protein (IGRP). J Biol Chem (2004) 1.06

Clinical carbapenem-resistant Acinetobacter baylyi strain coharboring blaSIM-1 and blaOXA-23 from China. Antimicrob Agents Chemother (2011) 1.05

Epigenetic repression of phosphatidylethanolamine N-methyltransferase (PEMT) in BRCA1-mutated breast cancer. Oncotarget (2014) 1.05

A summary of computational resources for protein phosphorylation. Curr Protein Pept Sci (2010) 1.05

Laparoendoscopic single-site adrenalectomy versus conventional laparoscopic surgery: a systematic review and meta-analysis of observational studies. J Endourol (2013) 1.04

The regulation of the lymphatic secretion of glucagon-like peptide-1 (GLP-1) by intestinal absorption of fat and carbohydrate. Am J Physiol Gastrointest Liver Physiol (2007) 1.04

GPS-CCD: a novel computational program for the prediction of calpain cleavage sites. PLoS One (2011) 1.04

Interaction of human MUC1 and beta-catenin is regulated by Lck and ZAP-70 in activated Jurkat T cells. Biochem Biophys Res Commun (2004) 1.04

Young children's learning and transfer of biological information from picture books to real animals. Child Dev (2011) 1.04

Promoter hypomethylation, especially around the E26 transformation-specific motif, and increased expression of poly (ADP-ribose) polymerase 1 in BRCA-mutated serous ovarian cancer. BMC Cancer (2013) 1.04