Published in Bioinformatics on September 21, 2010
Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa. Mol Biol Evol (2011) 1.39
Dynamic nucleotide-binding site and leucine-rich repeat-encoding genes in the grass family. Plant Physiol (2012) 1.16
Deep-sequencing protocols influence the results obtained in small-RNA sequencing. PLoS One (2012) 1.03
Small RNA deep sequencing identifies microRNAs and other small noncoding RNAs from human herpesvirus 6B. J Virol (2011) 0.92
Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies. Biomed Res Int (2015) 0.80
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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
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Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res (2002) 76.95
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Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature (2008) 10.71
ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics (2009) 8.69
Rb-mediated heterochromatin formation and silencing of E2F target genes during cellular senescence. Cell (2003) 11.40
Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature (2012) 9.75
Two classes of short interfering RNA in RNA silencing. EMBO J (2002) 8.54
A cellular microRNA mediates antiviral defense in human cells. Science (2005) 8.48
Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics (2004) 8.29
Antiviral immunity directed by small RNAs. Cell (2007) 8.09
A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science (2006) 7.74
Widespread translational inhibition by plant miRNAs and siRNAs. Science (2008) 7.51
Criteria for annotation of plant MicroRNAs. Plant Cell (2008) 7.49
Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science (2006) 6.33
A critical function for transforming growth factor-beta, interleukin 23 and proinflammatory cytokines in driving and modulating human T(H)-17 responses. Nat Immunol (2008) 6.09
Multivesicular bodies associate with components of miRNA effector complexes and modulate miRNA activity. Nat Cell Biol (2009) 6.03
Mouse polycomb proteins bind differentially to methylated histone H3 and RNA and are enriched in facultative heterochromatin. Mol Cell Biol (2006) 5.99
Epigenetic dynamics of imprinted X inactivation during early mouse development. Science (2003) 5.80
Revisiting the principles of microRNA target recognition and mode of action. Nat Rev Mol Cell Biol (2009) 4.38
The diversity of RNA silencing pathways in plants. Trends Genet (2006) 4.32
A role for RNAi in the selective correction of DNA methylation defects. Science (2009) 4.30
Transitivity-dependent and -independent cell-to-cell movement of RNA silencing. EMBO J (2003) 4.01
DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal. Nat Genet (2005) 4.00
In vivo investigation of the transcription, processing, endonucleolytic activity, and functional relevance of the spatial distribution of a plant miRNA. Genes Dev (2004) 3.77
Retracted Probing the microRNA and small interfering RNA pathways with virus-encoded suppressors of RNA silencing. Plant Cell (2004) 3.71
LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation. Cell (2010) 3.70
Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation. Nat Cell Biol (2006) 3.66
Differentially methylated forms of histone H3 show unique association patterns with inactive human X chromosomes. Nat Genet (2001) 3.63
A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced. Genes Dev (2006) 3.41
Imprinted X-inactivation in extra-embryonic endoderm cell lines from mouse blastocysts. Development (2005) 2.91
Retracted RNAi-dependent and independent control of LINE1 accumulation and mobility in mouse embryonic stem cells. PLoS Genet (2013) 2.91
Antiviral RNA interference in mammalian cells. Science (2013) 2.89
Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays. Genome Biol (2009) 2.88
Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics (2011) 2.86
Retracted An endogenous, systemic RNAi pathway in plants. EMBO J (2010) 2.82
Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics (2010) 2.79
Retracted Small RNA duplexes function as mobile silencing signals between plant cells. Science (2010) 2.76
Eutherian mammals use diverse strategies to initiate X-chromosome inactivation during development. Nature (2011) 2.75
Roles of plant small RNAs in biotic stress responses. Annu Rev Plant Biol (2009) 2.65
SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data. Bioinformatics (2010) 2.63
The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. Genes Dev (2011) 2.53
Regulation of X-chromosome inactivation by the X-inactivation centre. Nat Rev Genet (2011) 2.50
Intra- and intercellular RNA interference in Arabidopsis thaliana requires components of the microRNA and heterochromatic silencing pathways. Nat Genet (2007) 2.48
Monomethylation of histone H4-lysine 20 is involved in chromosome structure and stability and is essential for mouse development. Mol Cell Biol (2009) 2.47
Evidence for de novo imprinted X-chromosome inactivation independent of meiotic inactivation in mice. Nature (2005) 2.46
Classification of microarray data using gene networks. BMC Bioinformatics (2007) 2.44
Differential histone H3 Lys-9 and Lys-27 methylation profiles on the X chromosome. Mol Cell Biol (2004) 2.43
Biochemical evidence for translational repression by Arabidopsis microRNAs. Plant Cell (2009) 2.27
Role of histone methyltransferase G9a in CpG methylation of the Prader-Willi syndrome imprinting center. J Biol Chem (2003) 2.25
miR-181a and miR-630 regulate cisplatin-induced cancer cell death. Cancer Res (2010) 2.24
Suppression of the microRNA pathway by bacterial effector proteins. Science (2008) 2.17
Beta-catenin status in paediatric medulloblastomas: correlation of immunohistochemical expression with mutational status, genetic profiles, and clinical characteristics. J Pathol (2009) 2.15
Concern Misregulation of AUXIN RESPONSE FACTOR 8 underlies the developmental abnormalities caused by three distinct viral silencing suppressors in Arabidopsis. PLoS Pathog (2011) 2.12
X inactivation and the complexities of silencing a sex chromosome. Curr Opin Cell Biol (2009) 2.09
Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments. Genome Res (2013) 2.05
Retracted RNA silencing of host transcripts by cauliflower mosaic virus requires coordinated action of the four Arabidopsis Dicer-like proteins. Proc Natl Acad Sci U S A (2006) 2.04
RNA silencing and the mobile silencing signal. Plant Cell (2002) 2.03
Nuclear import of CaMV P6 is required for infection and suppression of the RNA silencing factor DRB4. EMBO J (2008) 2.02
High-resolution analysis of epigenetic changes associated with X inactivation. Genome Res (2009) 2.02
Highly dynamic and sex-specific expression of microRNAs during early ES cell differentiation. PLoS Genet (2009) 1.96
Frequent PTEN genomic alterations and activated phosphatidylinositol 3-kinase pathway in basal-like breast cancer cells. Breast Cancer Res (2008) 1.94
Tsix transcription across the Xist gene alters chromatin conformation without affecting Xist transcription: implications for X-chromosome inactivation. Genes Dev (2005) 1.92
Selective autophagy degrades DICER and AGO2 and regulates miRNA activity. Nat Cell Biol (2012) 1.91
Mouse cytomegalovirus microRNAs dominate the cellular small RNA profile during lytic infection and show features of posttranscriptional regulation. J Virol (2007) 1.90
Induction, suppression and requirement of RNA silencing pathways in virulent Agrobacterium tumefaciens infections. Nat Genet (2006) 1.88
VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles. Bioinformatics (2006) 1.87
The long and the short of noncoding RNAs. Curr Opin Cell Biol (2009) 1.87
The pluripotent genome in three dimensions is shaped around pluripotency factors. Nature (2013) 1.82
Deterministic and stochastic allele specific gene expression in single mouse blastomeres. PLoS One (2011) 1.82
Argonaute quenching and global changes in Dicer homeostasis caused by a pathogen-encoded GW repeat protein. Genes Dev (2010) 1.80
Spatial normalization of array-CGH data. BMC Bioinformatics (2006) 1.79
RNA silencing suppression by plant pathogens: defence, counter-defence and counter-counter-defence. Nat Rev Microbiol (2013) 1.74
MicroRNA regulation of Cbx7 mediates a switch of Polycomb orthologs during ESC differentiation. Cell Stem Cell (2012) 1.72
Germline BAP1 mutations predispose to renal cell carcinomas. Am J Hum Genet (2013) 1.69
BAC array CGH distinguishes mutually exclusive alterations that define clinicogenetic subtypes of gliomas. Int J Cancer (2008) 1.66
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics (2007) 1.65
The oncogenic EWS-FLI1 protein binds in vivo GGAA microsatellite sequences with potential transcriptional activation function. PLoS One (2009) 1.63
Differential effects of viral silencing suppressors on siRNA and miRNA loading support the existence of two distinct cellular pools of ARGONAUTE1. EMBO J (2012) 1.62
A comprehensive modular map of molecular interactions in RB/E2F pathway. Mol Syst Biol (2008) 1.61
The diversity, biogenesis, and activities of endogenous silencing small RNAs in Arabidopsis. Annu Rev Plant Biol (2014) 1.60
Retracted Extreme resistance as a host counter-counter defense against viral suppression of RNA silencing. PLoS Pathog (2013) 1.57
Antisense RNA in imprinting: spreading silence through Air. Trends Genet (2002) 1.57
Dynamic changes in paternal X-chromosome activity during imprinted X-chromosome inactivation in mice. Proc Natl Acad Sci U S A (2009) 1.56
Mathematical modelling of cell-fate decision in response to death receptor engagement. PLoS Comput Biol (2010) 1.49
Smchd1-dependent and -independent pathways determine developmental dynamics of CpG island methylation on the inactive X chromosome. Dev Cell (2012) 1.47
Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods? Bioessays (2013) 1.45
Prognostic impact of vitamin B6 metabolism in lung cancer. Cell Rep (2012) 1.45
The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila. Proc Natl Acad Sci U S A (2009) 1.44
Establishment and characterization of a panel of human uveal melanoma xenografts derived from primary and/or metastatic tumors. Clin Cancer Res (2010) 1.42
Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense. Proc Natl Acad Sci U S A (2013) 1.40
Reconstructing de novo silencing of an active plant retrotransposon. Nat Genet (2013) 1.40
The complex interplay between plant viruses and host RNA-silencing pathways. Curr Opin Plant Biol (2005) 1.39
Genome-wide redistribution of meiotic double-strand breaks in Saccharomyces cerevisiae. Mol Cell Biol (2006) 1.38