Published in PLoS Comput Biol on September 28, 2007
A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell (2012) 2.72
Implication of sperm RNAs in transgenerational inheritance of the effects of early trauma in mice. Nat Neurosci (2014) 2.58
A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. BMC Genomics (2009) 2.27
A survey of small RNAs in human sperm. Hum Reprod (2011) 1.62
Production of artificial piRNAs in flies and mice. RNA (2011) 1.37
Repertoire of porcine microRNAs in adult ovary and testis by deep sequencing. Int J Biol Sci (2011) 1.22
A k-mer scheme to predict piRNAs and characterize locust piRNAs. Bioinformatics (2011) 1.22
Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution. Proc Natl Acad Sci U S A (2009) 1.14
MicroRNAs and HIV-1: complex interactions. J Biol Chem (2012) 1.13
Transcriptome profiling of testis during sexual maturation stages in Eriocheir sinensis using Illumina sequencing. PLoS One (2012) 1.04
piR_015520 belongs to Piwi-associated RNAs regulates expression of the human melatonin receptor 1A gene. PLoS One (2011) 0.98
The mosquito Aedes aegypti has a large genome size and high transposable element load but contains a low proportion of transposon-specific piRNAs. BMC Genomics (2011) 0.97
Prediction of piRNAs using transposon interaction and a support vector machine. BMC Bioinformatics (2014) 0.91
The capacity of target silencing by Drosophila PIWI and piRNAs. RNA (2014) 0.91
Deciphering a methylome: what can we read into patterns of DNA methylation? J Exp Biol (2011) 0.88
Conserved generation of short products at piRNA loci. BMC Genomics (2011) 0.87
Functions of PIWI proteins in spermatogenesis. Clin Exp Reprod Med (2011) 0.84
Evolution of animal Piwi-interacting RNAs and prokaryotic CRISPRs. Brief Funct Genomics (2012) 0.82
Cloning of the quail PIWI gene and characterization of PIWI binding to small RNAs. PLoS One (2012) 0.80
Accurate Prediction of Transposon-Derived piRNAs by Integrating Various Sequential and Physicochemical Features. PLoS One (2016) 0.80
Differential expression of non-coding RNAs and continuous evolution of the X chromosome in testicular transcriptome of two mouse species. PLoS One (2011) 0.79
The characterisation of piRNA-related 19mers in the mouse. BMC Genomics (2011) 0.78
Endogenous siRNAs and piRNAs derived from transposable elements and genes in the malaria vector mosquito Anopheles gambiae. BMC Genomics (2015) 0.77
A genetic algorithm-based weighted ensemble method for predicting transposon-derived piRNAs. BMC Bioinformatics (2016) 0.77
Towards a piRNA prediction using multiple kernel fusion and support vector machine. Bioinformatics (2014) 0.76
Identification and characterization of piRNA-like small RNAs in the gonad of sea urchin (Strongylocentrotus nudus). Mar Biotechnol (NY) (2011) 0.76
Piwi Proteins and piRNAs step onto the systems biology stage. Adv Exp Med Biol (2014) 0.76
Developmental piRNA profiles of the invasive vector mosquito Aedes albopictus. Parasit Vectors (2016) 0.76
Characterization of piRNAs across postnatal development in mouse brain. Sci Rep (2016) 0.75
qiRNApredictor: A Novel Computational Program for the Prediction of qiRNAs in Neurospora crassa. PLoS One (2016) 0.75
Computational Detection of piRNA in Human Using Support Vector Machine. Avicenna J Med Biotechnol (2016) 0.75
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell (2007) 18.35
A distinct small RNA pathway silences selfish genetic elements in the germline. Science (2006) 11.63
The small RNA profile during Drosophila melanogaster development. Dev Cell (2003) 11.46
A slicer-mediated mechanism for repeat-associated siRNA 5' end formation in Drosophila. Science (2007) 10.73
A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature (2006) 9.88
A novel class of small RNAs bind to MILI protein in mouse testes. Nature (2006) 8.80
Characterization of the piRNA complex from rat testes. Science (2006) 7.86
Developmentally regulated piRNA clusters implicate MILI in transposon control. Science (2007) 7.68
MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev Cell (2007) 7.66
The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev (2002) 7.61
Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome. Genes Dev (2006) 6.60
A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish. Cell (2007) 6.31
A novel class of small RNAs in mouse spermatogenic cells. Genes Dev (2006) 5.85
miwi, a murine homolog of piwi, encodes a cytoplasmic protein essential for spermatogenesis. Dev Cell (2002) 5.85
Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in tetrahymena. Cell (2002) 5.78
Mili, a mammalian member of piwi family gene, is essential for spermatogenesis. Development (2004) 5.47
The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC. Curr Biol (2007) 5.35
Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev (2006) 4.97
Pimet, the Drosophila homolog of HEN1, mediates 2'-O-methylation of Piwi- interacting RNAs at their 3' ends. Genes Dev (2007) 4.68
Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi. Nature (2003) 4.09
Identification of eight members of the Argonaute family in the human genome. Genomics (2003) 3.55
The role of PIWI and the miRNA machinery in Drosophila germline determination. Curr Biol (2006) 3.06
Mighty Piwis defend the germline against genome intruders. Cell (2007) 3.06
The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev (2005) 2.94
Mouse Piwi-interacting RNAs are 2'-O-methylated at their 3' termini. Nat Struct Mol Biol (2007) 2.89
A novel repeat-associated small interfering RNA-mediated silencing pathway downregulates complementary sense gypsy transcripts in somatic cells of the Drosophila ovary. J Virol (2006) 2.87
The chromatoid body of male germ cells: similarity with processing bodies and presence of Dicer and microRNA pathway components. Proc Natl Acad Sci U S A (2006) 2.75
The 3' termini of mouse Piwi-interacting RNAs are 2'-O-methylated. Nat Struct Mol Biol (2007) 2.71
Gene silencing mechanisms mediated by Aubergine piRNA complexes in Drosophila male gonad. RNA (2007) 2.55
piRNAs in the germ line. Science (2007) 2.39
The coming of age for Piwi proteins. Mol Cell (2007) 2.20
Small RNAs just got bigger: Piwi-interacting RNAs (piRNAs) in mammalian testes. Genes Dev (2006) 2.17
Two classes of endogenous small RNAs in Tetrahymena thermophila. Genes Dev (2005) 2.08
piRNAs--the ancient hunters of genome invaders. Genes Dev (2007) 1.84
The mouse homolog of HEN1 is a potential methylase for Piwi-interacting RNAs. RNA (2007) 1.77
The chromatoid body in spermatogenesis. Int J Androl (2005) 1.23
RNA silencing: genomic defence with a slice of pi. Nature (2007) 1.12
Human MicroRNA targets. PLoS Biol (2004) 34.51
A mammalian microRNA expression atlas based on small RNA library sequencing. Cell (2007) 34.03
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov (2012) 26.98
Integrative genomic profiling of human prostate cancer. Cancer Cell (2010) 23.61
MicroRNA targets in Drosophila. Genome Biol (2003) 23.59
Global mapping of the yeast genetic interaction network. Science (2004) 21.34
International network of cancer genome projects. Nature (2010) 20.35
Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal (2013) 19.54
The microRNA.org resource: targets and expression. Nucleic Acids Res (2007) 16.26
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
Characterizing gene sets with FuncAssociate. Bioinformatics (2003) 14.10
Identification of microRNAs of the herpesvirus family. Nat Methods (2005) 12.98
Identification of virus-encoded microRNAs. Science (2004) 12.56
The somatic genomic landscape of glioblastoma. Cell (2013) 11.73
The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet (2013) 11.29
Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res (2011) 10.99
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res (2010) 9.18
A novel class of small RNAs bind to MILI protein in mouse testes. Nature (2006) 8.80
The Systems Biology Graphical Notation. Nat Biotechnol (2009) 8.53
Mutual exclusivity analysis identifies oncogenic network modules. Genome Res (2011) 7.22
Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol (2010) 7.15
Cellular cofactors affecting hepatitis C virus infection and replication. Proc Natl Acad Sci U S A (2007) 6.79
(V600E)BRAF is associated with disabled feedback inhibition of RAF-MEK signaling and elevated transcriptional output of the pathway. Proc Natl Acad Sci U S A (2009) 6.78
Genome sequencing identifies a basis for everolimus sensitivity. Science (2012) 6.71
Emerging landscape of oncogenic signatures across human cancers. Nat Genet (2013) 6.48
miR-122, a mammalian liver-specific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1. RNA Biol (2004) 6.44
Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy. Nat Genet (2010) 6.10
Pathguide: a pathway resource list. Nucleic Acids Res (2006) 6.05
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71
Cooperativity of TMPRSS2-ERG with PI3-kinase pathway activation in prostate oncogenesis. Nat Genet (2009) 5.31
MicroRNA profiling of the murine hematopoietic system. Genome Biol (2005) 4.94
Protein 3D structure computed from evolutionary sequence variation. PLoS One (2011) 4.71
Genetic dissection of the miR-17~92 cluster of microRNAs in Myc-induced B-cell lymphomas. Genes Dev (2009) 4.43
Evaluating cell lines as tumour models by comparison of genomic profiles. Nat Commun (2013) 4.35
Functional copy-number alterations in cancer. PLoS One (2008) 4.27
Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A (2011) 4.08
Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development. Cell (2005) 3.95
Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol (2009) 3.66
Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia. Blood (2007) 3.64
Automated network analysis identifies core pathways in glioblastoma. PLoS One (2010) 3.64
A series of PDB related databases for everyday needs. Nucleic Acids Res (2010) 3.60
Determinants of protein function revealed by combinatorial entropy optimization. Genome Biol (2007) 3.46
The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma. Nat Genet (2011) 3.41
Target mRNA abundance dilutes microRNA and siRNA activity. Mol Syst Biol (2010) 3.37
Characterization of small RNAs in Aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB. Neuron (2009) 3.27
cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics (2006) 3.24
A specificity map for the PDZ domain family. PLoS Biol (2008) 3.16
Three-dimensional structures of membrane proteins from genomic sequencing. Cell (2012) 3.02
CancerGenes: a gene selection resource for cancer genome projects. Nucleic Acids Res (2006) 3.00
Pathway information for systems biology. FEBS Lett (2005) 2.97
The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev (2005) 2.94
Introducing meta-services for biomedical information extraction. Genome Biol (2008) 2.78
A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell (2012) 2.72
Evaluation of annotation strategies using an entire genome sequence. Bioinformatics (2003) 2.66
NetPath: a public resource of curated signal transduction pathways. Genome Biol (2010) 2.62
The amino-acid mutational spectrum of human genetic disease. Genome Biol (2003) 2.55
Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies. Nat Genet (2009) 2.51
Protein structure prediction from sequence variation. Nat Biotechnol (2012) 2.50
DGCR8-dependent microRNA biogenesis is essential for skin development. Proc Natl Acad Sci U S A (2008) 2.49
RNA targets of wild-type and mutant FET family proteins. Nat Struct Mol Biol (2011) 2.46
Gene expression profiling of liposarcoma identifies distinct biological types/subtypes and potential therapeutic targets in well-differentiated and dedifferentiated liposarcoma. Cancer Res (2007) 2.44
Models from experiments: combinatorial drug perturbations of cancer cells. Mol Syst Biol (2008) 2.33
Adverse outcomes in clear cell renal cell carcinoma with mutations of 3p21 epigenetic regulators BAP1 and SETD2: a report by MSKCC and the KIRC TCGA research network. Clin Cancer Res (2013) 2.26
miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics (2012) 2.13
The tyrosine phosphatase PTPRD is a tumor suppressor that is frequently inactivated and mutated in glioblastoma and other human cancers. Proc Natl Acad Sci U S A (2009) 2.09
Prevalence and co-occurrence of actionable genomic alterations in high-grade bladder cancer. J Clin Oncol (2013) 1.92
Frequent alterations and epigenetic silencing of differentiation pathway genes in structurally rearranged liposarcomas. Cancer Discov (2011) 1.85
The mutational landscape of adenoid cystic carcinoma. Nat Genet (2013) 1.83
An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma. Cancer Cell (2016) 1.79
ChiBE: interactive visualization and manipulation of BioPAX pathway models. Bioinformatics (2009) 1.76
Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma. PLoS One (2012) 1.76
Signatures of RNA binding proteins globally coupled to effective microRNA target sites. Genome Res (2010) 1.75
Identification of PHLPP1 as a tumor suppressor reveals the role of feedback activation in PTEN-mutant prostate cancer progression. Cancer Cell (2011) 1.74
Distinct patterns of dysregulated expression of enzymes involved in androgen synthesis and metabolism in metastatic prostate cancer tumors. Cancer Res (2012) 1.71
Genetic and immunological comparison of anti-botulinum type A antibodies from immune and non-immune human phage libraries. Vaccine (2002) 1.69