Published in Sci Rep on November 16, 2016
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics (2014) 44.23
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol (2014) 27.48
The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet (2010) 15.87
DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet (2008) 15.45
MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res (2006) 15.32
Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet (2012) 15.21
miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res (2013) 13.41
Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet (2009) 12.08
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics (2011) 9.79
CpG islands and the regulation of transcription. Genes Dev (2011) 9.50
DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res (1980) 9.34
FIMO: scanning for occurrences of a given motif. Bioinformatics (2011) 8.89
Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science (2010) 8.46
Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics (2011) 8.05
Phylogenomics resolves the timing and pattern of insect evolution. Science (2014) 6.66
Detecting differential usage of exons from RNA-seq data. Genome Res (2012) 6.34
Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res (2004) 6.31
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature (2011) 5.50
Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nat Genet (2003) 5.38
Nutritional control of reproductive status in honeybees via DNA methylation. Science (2008) 5.13
Small dsRNAs induce transcriptional activation in human cells. Proc Natl Acad Sci U S A (2006) 4.90
Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics (2004) 4.37
An operational definition of epigenetics. Genes Dev (2009) 4.26
Death of an order: a comprehensive molecular phylogenetic study confirms that termites are eusocial cockroaches. Biol Lett (2007) 3.66
The honey bee epigenomes: differential methylation of brain DNA in queens and workers. PLoS Biol (2010) 3.42
The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells. RNA (2005) 3.14
Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature (2011) 2.70
Genome-wide and caste-specific DNA methylomes of the ants Camponotus floridanus and Harpegnathos saltator. Curr Biol (2012) 2.50
Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res (2012) 2.45
Reversible switching between epigenetic states in honeybee behavioral subcastes. Nat Neurosci (2012) 2.44
Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data. BMC Bioinformatics (2010) 2.24
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. Nucleic Acids Res (2010) 2.02
Polyphenism in insects. Curr Biol (2011) 1.77
Protection of germline gene expression by the C. elegans Argonaute CSR-1. Dev Cell (2013) 1.55
DNA methylation in insects: on the brink of the epigenomic era. Insect Mol Biol (2011) 1.51
Ecdysone control of developmental transitions: lessons from Drosophila research. Annu Rev Entomol (2012) 1.47
Intragenic DNA methylation: implications of this epigenetic mechanism for cancer research. Br J Cancer (2011) 1.44
The locust genome provides insight into swarm formation and long-distance flight. Nat Commun (2014) 1.42
Transcriptional inhibiton of Hoxd4 expression by miRNA-10a in human breast cancer cells. BMC Mol Biol (2009) 1.42
Life history and development--a framework for understanding developmental plasticity in lower termites. Biol Rev Camb Philos Soc (2008) 1.38
Molecular traces of alternative social organization in a termite genome. Nat Commun (2014) 1.33
Cuticular hydrocarbons of dampwood termites,Zootermopsis: Intra- and intercolony variation and potential as taxonomic characters. J Chem Ecol (1988) 1.26
MethylSig: a whole genome DNA methylation analysis pipeline. Bioinformatics (2014) 1.22
Functional conservation of DNA methylation in the pea aphid and the honeybee. Genome Biol Evol (2010) 1.21
CpG islands: features and distribution in the genomes of vertebrates. Gene (1991) 1.19
Regulation of polyphenic caste differentiation in the termite Reticulitermes flavipes by interaction of intrinsic and extrinsic factors. J Exp Biol (2007) 1.16
Function and evolution of DNA methylation in Nasonia vitripennis. PLoS Genet (2013) 1.14
Competition between DNA methylation and transcription factors determines binding of NRF1. Nature (2015) 1.14
DNA methylation and transcriptional noise. Epigenetics Chromatin (2013) 1.09
Exaggerated trait growth in insects. Annu Rev Entomol (2014) 1.01
HP1 is involved in regulating the global impact of DNA methylation on alternative splicing. Cell Rep (2015) 0.99
Patterning and regulatory associations of DNA methylation are mirrored by histone modifications in insects. Genome Biol Evol (2013) 0.96
Intronic non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees. BMC Genomics (2013) 0.94
Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies. Proc Natl Acad Sci U S A (2015) 0.92
The landscape of antisense gene expression in human cancers. Genome Res (2015) 0.91
Evidence of a conserved functional role for DNA methylation in termites. Insect Mol Biol (2012) 0.88
The function of intragenic DNA methylation: insights from insect epigenomes. Integr Comp Biol (2013) 0.88
Molting dynamics and juvenile hormone titer profiles in the nymphal stages of a lower termite, Cryptotermes secundus (Kalotermitidae)--signatures of developmental plasticity. J Insect Physiol (2012) 0.87
Differentially methylated obligatory epialleles modulate context-dependent LAM gene expression in the honeybee Apis mellifera. Epigenetics (2015) 0.84
Epigenetic inheritance and genome regulation: is DNA methylation linked to ploidy in haplodiploid insects? Proc Biol Sci (2014) 0.84
Robust DNA Methylation in the Clonal Raider Ant Brain. Curr Biol (2016) 0.82
Molecular traces of alternative social organization in a termite genome. Nat Commun (2014) 1.33
Social evolution. Genomic signatures of evolutionary transitions from solitary to group living. Science (2015) 1.15