Published in PLoS One on September 18, 2014
Long non-coding RNA regulation of reproduction and development. Mol Reprod Dev (2015) 0.82
A novel long non-coding RNA in the rheumatoid arthritis risk locus TRAF1-C5 influences C5 mRNA levels. Genes Immun (2015) 0.80
FARNA: knowledgebase of inferred functions of non-coding RNA transcripts. Nucleic Acids Res (2016) 0.78
Genetics of RA susceptibility, what comes next? RMD Open (2015) 0.78
Mapping Human Pluripotent-to-Cardiomyocyte Differentiation: Methylomes, Transcriptomes, and Exon DNA Methylation "Memories". EBioMedicine (2016) 0.76
Long Noncoding RNAs as Biomarkers in Cancer. Dis Markers (2017) 0.75
Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools. Genes (Basel) (2016) 0.75
BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori. BMC Bioinformatics (2016) 0.75
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
MicroRNAs: target recognition and regulatory functions. Cell (2009) 92.17
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol (2013) 32.42
miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res (2010) 25.85
The UCSC Table Browser data retrieval tool. Nucleic Acids Res (2004) 25.12
Long non-coding RNAs: insights into functions. Nat Rev Genet (2009) 19.61
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (2007) 18.59
Evolution and functions of long noncoding RNAs. Cell (2009) 17.54
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev (2011) 16.77
Ensembl 2012. Nucleic Acids Res (2011) 14.55
Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci U S A (2002) 12.33
A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature (2006) 9.88
CpG islands and the regulation of transcription. Genes Dev (2011) 9.50
A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell (2011) 9.24
Characterization of the piRNA complex from rat testes. Science (2006) 7.86
Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A (2008) 7.19
JBrowse: a next-generation genome browser. Genome Res (2009) 6.77
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res (2007) 5.88
lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements. Nature (2011) 5.42
The eukaryotic genome as an RNA machine. Science (2008) 5.29
The NCBI BioSystems database. Nucleic Acids Res (2009) 4.80
PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics (2011) 4.50
lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res (2010) 4.49
Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev (2007) 4.34
Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Methods Enzymol (2006) 4.30
No-nonsense functions for long noncoding RNAs. Cell (2011) 4.23
A gene expression bar code for microarray data. Nat Methods (2007) 4.20
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res (2011) 3.81
Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comput Biol (2008) 3.66
Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. Bioessays (2003) 3.59
RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat Rev Mol Cell Biol (2013) 3.47
CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res (2013) 2.88
NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res (2011) 2.82
Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc Natl Acad Sci U S A (2013) 2.75
LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res (2012) 2.73
Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res (2011) 2.55
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet (2006) 2.48
Understanding the transcriptome through RNA structure. Nat Rev Genet (2011) 2.46
The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. Nucleic Acids Res (2011) 2.42
LNCipedia: a database for annotated human lncRNA transcript sequences and structures. Nucleic Acids Res (2012) 2.40
NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res (2013) 2.37
Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol (2012) 2.22
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res (2007) 2.07
A major epigenetic programming mechanism guided by piRNAs. Dev Cell (2013) 1.89
DNA methylation directly silences genes with non-CpG island promoters and establishes a nucleosome occupied promoter. Hum Mol Genet (2011) 1.83
deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res (2009) 1.78
Systematic transcriptome wide analysis of lncRNA-miRNA interactions. PLoS One (2013) 1.68
Non-coding RNAs in imprinted gene clusters. Biol Cell (2008) 1.67
Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin abusers. J Neurochem (2010) 1.67
The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity. Nat Struct Mol Biol (2014) 1.55
Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs. Development (2013) 1.54
Analysis of long non-coding RNA expression profiles in gastric cancer. World J Gastroenterol (2013) 1.50
Collection of mRNA-like non-coding RNAs. Nucleic Acids Res (1999) 1.22
The role of small non-coding RNAs in genome stability and chromatin organization. J Cell Sci (2010) 1.19
Polyadenylation-dependent control of long noncoding RNA expression by the poly(A)-binding protein nuclear 1. PLoS Genet (2012) 1.15
When one is better than two: RNA with dual functions. Biochimie (2010) 1.09
Setting up the JBrowse genome browser. Curr Protoc Bioinformatics (2010) 1.07
lncRNome: a comprehensive knowledgebase of human long noncoding RNAs. Database (Oxford) (2013) 1.02
Steroid Receptor RNA Activator bi-faceted genetic system: Heads or Tails? Biochimie (2011) 1.00
ncRNAimprint: a comprehensive database of mammalian imprinted noncoding RNAs. RNA (2010) 0.99
Expression profiling reveals developmentally regulated lncRNA repertoire in the mouse male germline. Biol Reprod (2013) 0.94
Mutation in a primate-conserved retrotransposon reveals a noncoding RNA as a mediator of infantile encephalopathy. Proc Natl Acad Sci U S A (2012) 0.91
Critical evaluation of the FANTOM3 non-coding RNA transcripts. Genomics (2009) 0.89
Identification of potentially new bifunctional RNA based on genome-wide data-mining of alternative splicing events. Biochimie (2011) 0.88
Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs. Biol Direct (2012) 0.86
Tackling structures of long noncoding RNAs. Int J Mol Sci (2013) 0.82
A novel nuclear miRNA mediated modulation of a non-coding antisense RNA and its cognate sense coding mRNA. EMBO J (2011) 0.79
Computational Framework for Prediction of Peptide Sequences That May Mediate Multiple Protein Interactions in Cancer-Associated Hub Proteins. PLoS One (2016) 0.77
Stromal cell-mediated mitochondrial redox adaptation regulates drug resistance in childhood acute lymphoblastic leukemia. Oncotarget (2015) 0.77
MicroRNA 26a (miR-26a)/KLF4 and CREB-C/EBPβ regulate innate immune signaling, the polarization of macrophages and the trafficking of Mycobacterium tuberculosis to lysosomes during infection. PLoS Pathog (2017) 0.75
Dissecting the variation in transcriptional circuits between naïve and primed pluripotent states. FEBS Lett (2017) 0.75