Published in Mol Biol Evol on May 14, 2009
Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes. Genome Res (2010) 1.52
GC3 biology in corn, rice, sorghum and other grasses. BMC Genomics (2010) 1.24
The Anolis lizard genome: an amniote genome without isochores. Genome Biol Evol (2011) 1.08
Patterns and evolution of nucleotide landscapes in seed plants. Plant Cell (2012) 1.04
Chromosomal G + C content evolution in yeasts: systematic interspecies differences, and GC-poor troughs at centromeres. Genome Biol Evol (2010) 0.95
Cross-species analysis of genic GC3 content and DNA methylation patterns. Genome Biol Evol (2013) 0.94
GC3 of genes can be used as a proxy for isochore base composition: a reply to Elhaik et al. Mol Biol Evol (2010) 0.87
Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC(3) profiling in snake. BMC Genomics (2012) 0.87
The footprint of metabolism in the organization of mammalian genomes. BMC Genomics (2012) 0.86
The bimodal distribution of genic GC content is ancestral to monocot species. Genome Biol Evol (2014) 0.81
Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus. BMC Genomics (2015) 0.80
IsoPlotter(+): A Tool for Studying the Compositional Architecture of Genomes. ISRN Bioinform (2013) 0.80
Deciphering heterogeneity in pig genome assembly Sscrofa9 by isochore and isochore-like region analyses. PLoS One (2010) 0.79
Patterns of synonymous codon usage on human metapneumovirus and its influencing factors. J Biomed Biotechnol (2012) 0.79
Different types of secondary information in the genetic code. RNA (2014) 0.78
Biased gene conversion and GC-content evolution in the coding sequences of reptiles and vertebrates. Genome Biol Evol (2014) 0.78
A comparative study and a phylogenetic exploration of the compositional architectures of mammalian nuclear genomes. PLoS Comput Biol (2014) 0.77
Homology-independent metrics for comparative genomics. Comput Struct Biotechnol J (2015) 0.76
GC3-biased gene domains in mammalian genomes. Bioinformatics (2015) 0.75
Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer. Int J Mol Sci (2016) 0.75
The Anolis Lizard Genome: An Amniote Genome without Isochores? Genome Biol Evol (2016) 0.75
Selection pressure on human STR loci and its relevance in repeat expansion disease. Mol Genet Genomics (2016) 0.75
The bat genome: GC-biased small chromosomes associated with reduction in genome size. Chromosoma (2013) 0.75
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
The genome of the model beetle and pest Tribolium castaneum. Nature (2008) 6.50
The genome of the sea urchin Strongylocentrotus purpuratus. Science (2006) 6.41
Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science (2010) 5.56
Alu-containing exons are alternatively spliced. Genome Res (2002) 5.45
Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mol Biol Evol (2004) 3.62
GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res (2010) 2.95
Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle. Proc Natl Acad Sci U S A (2010) 2.76
Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control. OMICS (2004) 2.40
An alignment confidence score capturing robustness to guide tree uncertainty. Mol Biol Evol (2010) 2.39
GC composition of the human genome: in search of isochores. Mol Biol Evol (2005) 2.25
Public control could be a nightmare for researchers. Nature (2007) 2.24
The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. PLoS Genet (2011) 2.16
Heads or tails: a simple reliability check for multiple sequence alignments. Mol Biol Evol (2007) 2.04
Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proc Natl Acad Sci U S A (2011) 1.94
Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons. Mol Cell (2004) 1.93
Draft genome of the red harvester ant Pogonomyrmex barbatus. Proc Natl Acad Sci U S A (2011) 1.88
Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor. Mol Biol Evol (2008) 1.62
Ratios of radical to conservative amino acid replacement are affected by mutational and compositional factors and may not be indicative of positive Darwinian selection. Mol Biol Evol (2002) 1.60
Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events. Gene (2003) 1.60
Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proc Natl Acad Sci U S A (2012) 1.60
Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res (2011) 1.58
Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment. Genome Biol Evol (2009) 1.57
'Genome order index' should not be used for defining compositional constraints in nucleotide sequences. Comput Biol Chem (2007) 1.54
Chaperones divide yeast proteins into classes of expression level and evolutionary rate. Genome Biol Evol (2012) 1.49
Finding the missing honey bee genes: lessons learned from a genome upgrade. BMC Genomics (2014) 1.46
Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality. Genome Res (2013) 1.45
In search of the vertebrate phylotypic stage: a molecular examination of the developmental hourglass model and von Baer's third law. J Exp Zool B Mol Dev Evol (2005) 1.36
Playing chicken (Gallus gallus): methodological inconsistencies of molecular divergence date estimates due to secondary calibration points. Gene (2002) 1.34
A method for the simultaneous estimation of selection intensities in overlapping genes. PLoS One (2008) 1.28
The "inverse relationship between evolutionary rate and age of mammalian genes" is an artifact of increased genetic distance with rate of evolution and time of divergence. Mol Biol Evol (2005) 1.27
A comparative analysis of numt evolution in human and chimpanzee. Mol Biol Evol (2006) 1.24
Evolutionary dynamics of large numts in the human genome: rarity of independent insertions and abundance of post-insertion duplications. J Mol Evol (2003) 1.24
Genomes of Stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome Biol Evol (2013) 1.22
The "domino theory" of gene death: gradual and mass gene extinction events in three lineages of obligate symbiotic bacterial pathogens. Mol Biol Evol (2005) 1.21
Early bioenergetic evolution. Philos Trans R Soc Lond B Biol Sci (2013) 1.20
AluGene: a database of Alu elements incorporated within protein-coding genes. Nucleic Acids Res (2004) 1.19
An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin. Genome Biol Evol (2012) 1.14
Characterization of pairwise and multiple sequence alignment errors. Gene (2008) 1.11
Local reliability measures from sets of co-optimal multiple sequence alignments. Pac Symp Biocomput (2008) 1.11
A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families. Bioinformatics (2002) 1.11
A potentially novel overlapping gene in the genomes of Israeli acute paralysis virus and its relatives. Virol J (2009) 0.97
Neutral evolution of robustness in Drosophila microRNA precursors. Mol Biol Evol (2011) 0.95
Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm. Nucleic Acids Res (2010) 0.94
Inferring the pattern of spontaneous mutation from the pattern of substitution in unitary pseudogenes of Mycobacterium leprae and a comparison of mutation patterns among distantly related organisms. J Mol Evol (2005) 0.91
Same-strand overlapping genes in bacteria: compositional determinants of phase bias. Biol Direct (2008) 0.88
Comparative testing of DNA segmentation algorithms using benchmark simulations. Mol Biol Evol (2009) 0.85
Detection of functional overlapping genes: simulation and case studies. J Mol Evol (2010) 0.85
Detecting excess radical replacements in phylogenetic trees. Gene (2003) 0.85
Deep sequencing of Trichomonas vaginalis during the early infection of vaginal epithelial cells and amoeboid transition. Int J Parasitol (2013) 0.84
The evolutionary history of prosaposin: two successive tandem-duplication events gave rise to the four saposin domains in vertebrates. J Mol Evol (2002) 0.84
A computational tool for the genomic identification of regions of unusual compositional properties and its utilization in the detection of horizontally transferred sequences. Mol Biol Evol (2006) 0.84
Is there a twelfth protein-coding gene in the genome of influenza A? A selection-based approach to the detection of overlapping genes in closely related sequences. J Mol Evol (2011) 0.81
The comparative method rules! Codon volatility cannot detect positive Darwinian selection using a single genome sequence. Mol Biol Evol (2004) 0.80
pANT: a method for the pairwise assessment of nonfunctionalization times of processed pseudogenes. Mol Biol Evol (2003) 0.80
The multiple personalities of Watson and Crick strands. Biol Direct (2011) 0.79
Integration of two ancestral chaperone systems into one: the evolution of eukaryotic molecular chaperones in light of eukaryogenesis. Mol Biol Evol (2013) 0.78
Evolution of multicellularity in Metazoa: comparative analysis of the subcellular localization of proteins in Saccharomyces, Drosophila and Caenorhabditis. Cell Biol Int (2004) 0.78
Evolutionary conservation of bacterial operons: does transcriptional connectivity matter? Genetica (2005) 0.78
The parasite Trichomonas vaginalis expresses thousands of pseudogenes and long non-coding RNAs independently from functional neighbouring genes. BMC Genomics (2014) 0.78
'Genome order index' should not be used for defining compositional constraints in nucleotide sequences--a case study of the Z-curve. Biol Direct (2010) 0.77
Revisiting the operational RNA code for amino acids: Ensemble attributes and their implications. RNA (2009) 0.76
Solidarity with the oppressed flat-Earthers. Nature (2005) 0.75
Detecting negative selection on recurrent mutations using gene genealogy. BMC Genet (2013) 0.75