Published in PLoS Genet on October 13, 2011
Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. Nucleic Acids Res (2013) 1.44
Asymmetric Context-Dependent Mutation Patterns Revealed through Mutation-Accumulation Experiments. Mol Biol Evol (2015) 1.01
Error prevention and mitigation as forces in the evolution of genes and genomes. Nat Rev Genet (2011) 0.89
Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates. PLoS Genet (2015) 0.82
Open questions in the study of de novo genes: what, how and why. Nat Rev Genet (2016) 0.81
Effects of premature termination codon polymorphisms in the Drosophila pseudoobscura subclade. J Mol Evol (2012) 0.80
Transcriptional robustness complements nonsense-mediated decay in humans. PLoS Genet (2011) 0.77
A stepwise strategy for rapid and cost-effective RB1 screening in Indian retinoblastoma patients. J Hum Genet (2015) 0.77
Purifying Selection on Exonic Splice Enhancers in Intronless Genes. Mol Biol Evol (2016) 0.77
Directional next-generation RNA sequencing and examination of premature termination codon mutations in endoglin/hereditary haemorrhagic telangiectasia. Mol Syndromol (2013) 0.77
Genetic code evolution reveals the neutral emergence of mutational robustness, and information as an evolutionary constraint. Life (Basel) (2015) 0.76
Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum. Sci Rep (2016) 0.75
Molecular evolution: dealing with nonsense. Nat Rev Genet (2011) 0.75
Conserved nonsense-prone CpG sites in apoptosis-regulatory genes: conditional stop signs on the road to cell death. Evol Bioinform Online (2013) 0.75
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47
PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol (2007) 45.68
Ensembl 2008. Nucleic Acids Res (2007) 20.67
Predictive identification of exonic splicing enhancers in human genes. Science (2002) 16.86
A rule for termination-codon position within intron-containing genes: when nonsense affects RNA abundance. Trends Biochem Sci (1998) 9.06
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell (2008) 6.91
Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc Natl Acad Sci U S A (1999) 5.04
Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function. Genes Dev (2007) 4.97
RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucleic Acids Res (2004) 3.70
Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways. EMBO J (2003) 3.68
The human and mouse replication-dependent histone genes. Genomics (2002) 3.23
The multiple lives of NMD factors: balancing roles in gene and genome regulation. Nat Rev Genet (2008) 3.00
Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biol (2004) 2.77
Transient mutators: a semiquantitative analysis of the influence of translation and transcription errors on mutation rates. Genetics (1991) 2.58
Posttranscriptional gene regulation by spatial rearrangement of the 3' untranslated region. PLoS Biol (2008) 2.54
Rent1, a trans-effector of nonsense-mediated mRNA decay, is essential for mammalian embryonic viability. Hum Mol Genet (2001) 2.35
Splicing and the evolution of proteins in mammals. PLoS Biol (2007) 2.32
Robustness: mechanisms and consequences. Trends Genet (2009) 2.27
Translational control of intron splicing in eukaryotes. Nature (2008) 2.15
Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence. Genetics (2004) 2.15
Translationally optimal codons associate with structurally sensitive sites in proteins. Mol Biol Evol (2009) 1.96
Intron size, abundance, and distribution within untranslated regions of genes. Mol Biol Evol (2006) 1.72
Mammalian heat shock p70 and histone H4 transcripts, which derive from naturally intronless genes, are immune to nonsense-mediated decay. RNA (2001) 1.70
Utilization of splicing elements and polyadenylation signal elements in the coupling of polyadenylation and last-intron removal. Mol Cell Biol (1999) 1.48
Nonrandom patterns of codon usage and of nucleotide substitutions in human alpha- and beta-globin genes: an evolutionary strategy reducing the rate of mutations with drastic effects? Proc Natl Acad Sci U S A (1981) 1.45
GroEL dependency affects codon usage--support for a critical role of misfolding in gene evolution. Mol Syst Biol (2010) 1.43
Messenger RNA surveillance and the evolutionary proliferation of introns. Mol Biol Evol (2003) 1.36
Potential role of phenotypic mutations in the evolution of protein expression and stability. Proc Natl Acad Sci U S A (2009) 1.35
Use of an in vivo reporter assay to test for transcriptional and translational fidelity in yeast. J Biol Chem (2002) 1.30
The look-ahead effect of phenotypic mutations. Biol Direct (2008) 1.28
The human intronless melanocortin 4-receptor gene is NMD insensitive. Hum Mol Genet (2002) 1.19
Accuracy of wheat-germ RNA polymerase II. General enzymatic properties and effect of template conformational transition from right-handed B-DNA to left-handed Z-DNA. Eur J Biochem (1992) 1.17
The exon junction complex differentially marks spliced junctions. Nat Struct Mol Biol (2010) 1.12
Why are phenotypic mutation rates much higher than genotypic mutation rates? Genetics (2005) 1.07
Splicing-dependent NMD does not require the EJC in Schizosaccharomyces pombe. EMBO J (2010) 1.06
Position of the final intron in full-length transcripts: determined by NMD? Mol Biol Evol (2007) 0.98
Translationally optimal codons associate with aggregation-prone sites in proteins. Proteomics (2010) 0.96
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03
The zebrafish reference genome sequence and its relationship to the human genome. Nature (2013) 8.52
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature (2006) 5.06
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res (2005) 4.15
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics (2005) 3.62
Recombination drives the evolution of GC-content in the human genome. Mol Biol Evol (2004) 3.50
The impact of recombination on nucleotide substitutions in the human genome. PLoS Genet (2008) 3.16
Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence. Nat Genet (2009) 3.03
Genome-wide studies highlight indirect links between human replication origins and gene regulation. Proc Natl Acad Sci U S A (2008) 2.77
Gene loss and evolutionary rates following whole-genome duplication in teleost fishes. Mol Biol Evol (2006) 2.30
The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PLoS Genet (2010) 2.20
Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution. Trends Genet (2007) 2.18
Translational control of intron splicing in eukaryotes. Nature (2008) 2.15
Neutral effect of recombination on base composition in Drosophila. Genet Res (2003) 2.11
Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine. Genome Res (2002) 2.04
Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations. Nat Commun (2011) 2.03
Databases of homologous gene families for comparative genomics. BMC Bioinformatics (2009) 2.01
The endogenous retroviral locus ERVWE1 is a bona fide gene involved in hominoid placental physiology. Proc Natl Acad Sci U S A (2004) 1.98
Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science (2010) 1.86
The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Res (2013) 1.83
Genome-scale coestimation of species and gene trees. Genome Res (2012) 1.82
Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics (2010) 1.63
Evolutionary origin and maintenance of coexpressed gene clusters in mammals. Mol Biol Evol (2006) 1.62
Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster. Genetics (2004) 1.61
GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates. Trends Genet (2008) 1.54
Genomicus: five genome browsers for comparative genomics in eukaryota. Nucleic Acids Res (2012) 1.54
ROSO: optimizing oligonucleotide probes for microarrays. Bioinformatics (2004) 1.53
Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region. Hum Mol Genet (2010) 1.53
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Res (2008) 1.45
Male-driven biased gene conversion governs the evolution of base composition in human alu repeats. Mol Biol Evol (2005) 1.44
Transcription induces strand-specific mutations at the 5' end of human genes. Genome Res (2008) 1.41
Ultra-fast sequence clustering from similarity networks with SiLiX. BMC Bioinformatics (2011) 1.40
CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex. Nat Struct Mol Biol (2012) 1.40
HOPPSIGEN: a database of human and mouse processed pseudogenes. Nucleic Acids Res (2005) 1.38
The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences. PLoS Genet (2012) 1.38
Probing the SELEX process with next-generation sequencing. PLoS One (2011) 1.34
Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance. Hum Mol Genet (2004) 1.33
No evidence for tissue-specific adaptation of synonymous codon usage in humans. Mol Biol Evol (2005) 1.32
The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny. J Mol Evol (2004) 1.28
Single-cell based high-throughput sequencing of full-length immunoglobulin heavy and light chain genes. Eur J Immunol (2013) 1.28
Identification and characterization of human Mex-3 proteins, a novel family of evolutionarily conserved RNA-binding proteins differentially localized to processing bodies. Nucleic Acids Res (2007) 1.28
The majority of recent short DNA insertions in the human genome are tandem duplications. Mol Biol Evol (2007) 1.25
Detecting positive selection within genomes: the problem of biased gene conversion. Philos Trans R Soc Lond B Biol Sci (2010) 1.25
Human and non-human primate genomes share hotspots of positive selection. PLoS Genet (2010) 1.24
XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells. Nat Genet (2013) 1.20
Methylation and deamination of CpGs generate p53-binding sites on a genomic scale. Trends Genet (2008) 1.17
Evidence that functional transcription units cover at least half of the human genome. Trends Genet (2004) 1.15
Comparative genomic analysis reveals independent expansion of a lineage-specific gene family in vertebrates: the class II cytokine receptors and their ligands in mammals and fish. BMC Genomics (2003) 1.15
Homology-dependent methylation in primate repetitive DNA. Proc Natl Acad Sci U S A (2005) 1.13
Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia. BMC Genomics (2010) 1.12
Integrated databanks access and sequence/structure analysis services at the PBIL. Nucleic Acids Res (2003) 1.11
Evidence of selection on the domesticated ERVWE1 env retroviral element involved in placentation. Mol Biol Evol (2004) 1.09
Remarkable compartmentalization of transposable elements and pseudogenes in the heterochromatin of the Tetraodon nigroviridis genome. Proc Natl Acad Sci U S A (2002) 1.07
Expected relationship between the silent substitution rate and the GC content: implications for the evolution of isochores. J Mol Evol (2002) 1.06
Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA. Genome Biol (2006) 1.06
Polymorphix: a sequence polymorphism database. Nucleic Acids Res (2005) 1.03
Placenta-specific INSL4 expression is mediated by a human endogenous retrovirus element. Biol Reprod (2002) 1.03
Differential retention of metabolic genes following whole-genome duplication. Mol Biol Evol (2009) 1.02
The relationship between DNA replication and human genome organization. Mol Biol Evol (2009) 1.00
Evidence for widespread GC-biased gene conversion in eukaryotes. Genome Biol Evol (2012) 1.00
Detecting single DNA copy number variations in complex genomes using one nanogram of starting DNA and BAC-array CGH. Nucleic Acids Res (2004) 1.00
Solvable sequence evolution models and genomic correlations. Phys Rev Lett (2005) 0.99
Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization. Ecol Evol (2013) 0.99
Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries. BMC Bioinformatics (2004) 0.99
Twisted signatures of GC-biased gene conversion embedded in an evolutionary stable karyotype. Mol Biol Evol (2013) 0.97
Strong evidence for lineage and sequence specificity of substitution rates and patterns in Drosophila. Mol Biol Evol (2009) 0.96
GC-biased gene conversion in yeast is specifically associated with crossovers: molecular mechanisms and evolutionary significance. Mol Biol Evol (2013) 0.95
Unexpected observations after mapping LongSAGE tags to the human genome. BMC Bioinformatics (2007) 0.95
A calibrated diversity assay for nucleic acid libraries using DiStRO--a Diversity Standard of Random Oligonucleotides. Nucleic Acids Res (2009) 0.94
A novel method distinguishes between mutation rates and fixation biases in patterns of single-nucleotide substitution. J Mol Evol (2005) 0.93
DNA indels in coding regions reveal selective constraints on protein evolution in the human lineage. BMC Evol Biol (2007) 0.93
GC content evolution of the human and mouse genomes: insights from the study of processed pseudogenes in regions of different recombination rates. J Mol Evol (2006) 0.93
The GC content of primates and rodents genomes is not at equilibrium: a reply to Antezana. J Mol Evol (2006) 0.93
Patterns of selection against transposons inferred from the distribution of Tc1, Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans. Genetics (2003) 0.92
Meiotic recombination favors the spreading of deleterious mutations in human populations. Hum Mutat (2011) 0.91
The 3D organization of chromatin explains evolutionary fragile genomic regions. Cell Rep (2015) 0.89
ISG20L2, a novel vertebrate nucleolar exoribonuclease involved in ribosome biogenesis. Mol Cell Proteomics (2007) 0.89
Monoallelic expression and tissue specificity are associated with high crossover rates. Trends Genet (2009) 0.89
Inventing a sex-specific gene: a conserved role of DMRT1 in teleost fishes plus a recent duplication in the medaka Oryzias latipes resulted in DMY. J Mol Evol (2003) 0.88
Transcriptome-wide identification of RNA binding sites by CLIP-seq. Methods (2013) 0.88
Paleogenomics in vertebrates, or the recovery of lost genomes from the mist of time. Bioessays (2008) 0.88
Natural history of the ERVWE1 endogenous retroviral locus. Retrovirology (2005) 0.88
Nucleosome rotational setting is associated with transcriptional regulation in promoters of tissue-specific human genes. Genome Biol (2010) 0.87
Genetic alterations of HLA-class II in ovarian cancer. Int J Cancer (2008) 0.87
Silencing specific Paramecium tetraurelia genes by feeding double-stranded RNA. Cold Spring Harb Protoc (2010) 0.87
Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences. BMC Biol (2006) 0.87
Subcellular localization of 14-3-3 proteins in Toxoplasma gondii tachyzoites and evidence for a lipid raft-associated form. FEMS Microbiol Lett (2003) 0.87
HLA-class II haplotype associations with ovarian cancer. Int J Cancer (2006) 0.86
Meiotic recombination strongly influences GC-content evolution in short regions in the mouse genome. Mol Biol Evol (2013) 0.86
Paramecium tetraurelia: the renaissance of an early unicellular model. Cold Spring Harb Protoc (2010) 0.86
Comparative promoter region analysis powered by CORG. BMC Genomics (2005) 0.86
Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters. Gene (2005) 0.85
Long-range bidirectional strand asymmetries originate at CpG islands in the human genome. Genome Biol Evol (2009) 0.85
High-quality sequence clustering guided by network topology and multiple alignment likelihood. Bioinformatics (2012) 0.85
CorGen--measuring and generating long-range correlations for DNA sequence analysis. Nucleic Acids Res (2006) 0.84
Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7. BMC Genomics (2014) 0.84
How much does the amphioxus genome represent the ancestor of chordates? Brief Funct Genomics (2012) 0.84
The evolution of transcription-associated biases of mutations across vertebrates. BMC Evol Biol (2010) 0.84
Substitution patterns are under different influences in primates and rodents. Genome Biol Evol (2011) 0.83
Mass culture of Paramecium tetraurelia. Cold Spring Harb Protoc (2010) 0.81