ncRNA orthologies in the vertebrate lineage.

PubWeight™: 0.75‹?›

🔗 View Article (PMID 26980512)

Published in Database (Oxford) on March 15, 2016

Authors

Miguel Pignatelli1, Albert J Vilella2, Matthieu Muffato2, Leo Gordon2, Simon White3, Paul Flicek4, Javier Herrero5

Author Affiliations

1: European Molecular Biology Laboratory, European Bioinformatics Institute mp@ebi.ac.uk.
2: European Molecular Biology Laboratory, European Bioinformatics Institute.
3: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
4: European Molecular Biology Laboratory, European Bioinformatics Institute Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK mp@ebi.ac.uk.
5: European Molecular Biology Laboratory, European Bioinformatics Institute UCL Cancer Institute, University College London, London WC1E 6BT, UK.

Articles cited by this

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

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res (1997) 142.55

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

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (2006) 87.59

An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res (1981) 61.59

MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet (2004) 37.83

The transcriptional landscape of the mammalian genome. Science (2005) 37.63

Most mammalian mRNAs are conserved targets of microRNAs. Genome Res (2008) 37.16

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48

Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol (1994) 31.57

FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One (2010) 26.15

Distinguishing homologous from analogous proteins. Syst Zool (1970) 25.10

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

Causes and consequences of microRNA dysregulation in cancer. Nat Rev Genet (2009) 16.58

RNA sequence analysis using covariance models. Nucleic Acids Res (1994) 14.60

miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res (2013) 13.41

Dysregulation of cardiogenesis, cardiac conduction, and cell cycle in mice lacking miRNA-1-2. Cell (2007) 12.72

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res (2008) 12.72

Non-coding RNAs in human disease. Nat Rev Genet (2011) 11.40

TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics (2006) 10.24

QuickTree: building huge Neighbour-Joining trees of protein sequences. Bioinformatics (2002) 9.36

Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2011) 8.62

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res (2012) 8.54

The evolution of gene regulation by transcription factors and microRNAs. Nat Rev Genet (2007) 7.92

The muscle-specific microRNA miR-1 regulates cardiac arrhythmogenic potential by targeting GJA1 and KCNJ2. Nat Med (2007) 7.59

PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res (2003) 7.21

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science (2008) 6.35

Processing of intronic microRNAs. EMBO J (2007) 6.32

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

The expanding snoRNA world. Biochimie (2002) 6.10

phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics (2009) 6.02

Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nat Med (2008) 5.62

MicroRNAs--the micro steering wheel of tumour metastases. Nat Rev Cancer (2009) 5.47

Loss of microRNA cluster miR-29a/b-1 in sporadic Alzheimer's disease correlates with increased BACE1/beta-secretase expression. Proc Natl Acad Sci U S A (2008) 5.24

Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat Rev Mol Cell Biol (2007) 4.91

The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science (2005) 4.54

Moving messages: the intracellular localization of mRNAs. Nat Rev Mol Cell Biol (2005) 4.48

The expression of microRNA miR-107 decreases early in Alzheimer's disease and may accelerate disease progression through regulation of beta-site amyloid precursor protein-cleaving enzyme 1. J Neurosci (2008) 4.28

ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. Cell (2011) 4.26

Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics (2013) 4.16

Computational genomics of noncoding RNA genes. Cell (2002) 3.90

The human phylome. Genome Biol (2007) 3.81

Pathogenic LRRK2 negatively regulates microRNA-mediated translational repression. Nature (2010) 3.41

Rfam 12.0: updates to the RNA families database. Nucleic Acids Res (2014) 3.13

miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. Nucleic Acids Res (2007) 3.05

CAFE: a computational tool for the study of gene family evolution. Bioinformatics (2006) 3.02

MicroRNAs: critical regulators of development, cellular physiology and malignancy. Cell Cycle (2005) 2.99

Structured RNAs in the ENCODE selected regions of the human genome. Genome Res (2007) 2.69

A beginner's guide to eukaryotic genome annotation. Nat Rev Genet (2012) 2.67

C. elegans piRNAs mediate the genome-wide surveillance of germline transcripts. Cell (2012) 2.65

eHive: an artificial intelligence workflow system for genomic analysis. BMC Bioinformatics (2010) 2.52

The genomic binding sites of a noncoding RNA. Proc Natl Acad Sci U S A (2011) 2.34

The evolution of supertrees. Trends Ecol Evol (2004) 2.21

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. BMC Bioinformatics (2010) 1.99

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics (2010) 1.98

Annotating noncoding RNA genes. Annu Rev Genomics Hum Genet (2007) 1.74

RNAcentral: A vision for an international database of RNA sequences. RNA (2011) 1.73

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. Nucleic Acids Res (2013) 1.69

Waste not, want not--transcript excess in multicellular eukaryotes. Trends Genet (2005) 1.66

Birth and expression evolution of mammalian microRNA genes. Genome Res (2012) 1.64

Accelerated rate of gene gain and loss in primates. Genetics (2007) 1.62

miROrtho: computational survey of microRNA genes. Nucleic Acids Res (2008) 1.60

RAxML-Light: a tool for computing terabyte phylogenies. Bioinformatics (2012) 1.56

Mammalian small nucleolar RNAs are mobile genetic elements. PLoS Genet (2006) 1.55

RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences. Mol Phylogenet Evol (2003) 1.38

The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees. Bioinformatics (2007) 1.35

The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes. Insect Mol Biol (2010) 1.31

TreeFam v9: a new website, more species and orthology-on-the-fly. Nucleic Acids Res (2013) 1.29

Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution. Mol Biol Evol (2002) 1.27

Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information. Brief Bioinform (2011) 1.20

Retroposed SNOfall--a mammalian-wide comparison of platypus snoRNAs. Genome Res (2008) 1.11

BadiRate: estimating family turnover rates by likelihood-based methods. Bioinformatics (2011) 1.11

Evolutionarily stable association of intronic snoRNAs and microRNAs with their host genes. Genome Biol Evol (2009) 1.01

Human microRNAs originated from two periods at accelerated rates in mammalian evolution. Mol Biol Evol (2012) 0.98

Ensembl comparative genomics resources. Database (Oxford) (2016) 0.94

Genome-wide analysis of chicken snoRNAs provides unique implications for the evolution of vertebrate snoRNAs. BMC Genomics (2009) 0.93

The use of covariance models to annotate RNAs in whole genomes. Brief Funct Genomic Proteomic (2009) 0.91

Genome-scale NCRNA homology search using a Hamming distance-based filtration strategy. BMC Bioinformatics (2012) 0.80

piRNAs and siRNAs collaborate in Caenorhabditis elegans genome defense. Genome Biol (2012) 0.77