Published in Mol Biol Evol on January 19, 2005
Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Res (2006) 3.30
Origins and evolution of eukaryotic RNA interference. Trends Ecol Evol (2008) 2.15
U12DB: a database of orthologous U12-type spliceosomal introns. Nucleic Acids Res (2006) 2.09
Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res (2007) 2.06
The origin and early evolution of eukaryotes in the light of phylogenomics. Genome Biol (2010) 1.92
Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res (2007) 1.86
Topological network alignment uncovers biological function and phylogeny. J R Soc Interface (2010) 1.73
Origin and evolution of spliceosomal introns. Biol Direct (2012) 1.65
Extensive, recent intron gains in Daphnia populations. Science (2009) 1.64
The origins of phagocytosis and eukaryogenesis. Biol Direct (2009) 1.49
Evolution of genome architecture. Int J Biochem Cell Biol (2008) 1.48
Mitochondria, the Cell Cycle, and the Origin of Sex via a Syncytial Eukaryote Common Ancestor. Genome Biol Evol (2016) 1.43
A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes. PLoS Comput Biol (2011) 1.40
The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nat Rev Microbiol (2010) 1.40
The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner. Biol Direct (2008) 1.40
Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biol (2008) 1.36
Comparative genomic evidence for a complete nuclear pore complex in the last eukaryotic common ancestor. PLoS One (2010) 1.33
Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing. BMC Evol Biol (2007) 1.30
Comparative analysis of RNA families reveals distinct repertoires for each domain of life. PLoS Comput Biol (2012) 1.29
Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion. Genome Res (2005) 1.28
Optimal network alignment with graphlet degree vectors. Cancer Inform (2010) 1.28
Very little intron loss/gain in Plasmodium: intron loss/gain mutation rates and intron number. Genome Res (2006) 1.26
Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns. BMC Genomics (2006) 1.26
Evolution of spliceosomal snRNA genes in metazoan animals. J Mol Evol (2008) 1.25
Evolutionarily conserved genes preferentially accumulate introns. Genome Res (2007) 1.25
Evolutionary convergence on highly-conserved 3' intron structures in intron-poor eukaryotes and insights into the ancestral eukaryotic genome. PLoS Genet (2008) 1.22
The evolution of the cytoskeleton. J Cell Biol (2011) 1.22
Endosymbiotic theories for eukaryote origin. Philos Trans R Soc Lond B Biol Sci (2015) 1.19
An ancient spliceosomal intron in the ribosomal protein L7a gene (Rpl7a) of Giardia lamblia. BMC Evol Biol (2005) 1.14
The spliceosomal proteome: at the heart of the largest cellular ribonucleoprotein machine. Proteomics (2010) 1.13
The peculiarities of large intron splicing in animals. PLoS One (2009) 1.13
Eukaryotic origins: How and when was the mitochondrion acquired? Cold Spring Harb Perspect Biol (2014) 1.11
Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components. Nucleic Acids Res (2008) 1.09
Intron-dominated genomes of early ancestors of eukaryotes. J Hered (2009) 1.07
Archaeal and eukaryotic homologs of Hfq: A structural and evolutionary perspective on Sm function. RNA Biol (2013) 1.07
Intron mis-splicing: no alternative? Genome Biol (2008) 1.04
Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis. Nucleic Acids Res (2007) 1.03
Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes. Mol Biol Evol (2014) 1.02
A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution. BMC Genomics (2007) 1.01
RNase MRP and the RNA processing cascade in the eukaryotic ancestor. BMC Evol Biol (2007) 1.01
Preview. The incredible expanding ancestor of eukaryotes. Cell (2010) 1.00
Comparative analysis of information contents relevant to recognition of introns in many species. BMC Genomics (2011) 1.00
Secondary structure is required for 3' splice site recognition in yeast. Nucleic Acids Res (2011) 0.98
Evolution of GHF5 endoglucanase gene structure in plant-parasitic nematodes: no evidence for an early domain shuffling event. BMC Evol Biol (2008) 0.97
Malin: maximum likelihood analysis of intron evolution in eukaryotes. Bioinformatics (2008) 0.94
High throughput genome-wide survey of small RNAs from the parasitic protists Giardia intestinalis and Trichomonas vaginalis. Genome Biol Evol (2009) 0.94
Intrinsic disorder in the human spliceosomal proteome. PLoS Comput Biol (2012) 0.93
Accumulation of GC donor splice signals in mammals. Biol Direct (2008) 0.93
An overview of the introns-first theory. J Mol Evol (2009) 0.92
Multiple gains of spliceosomal introns in a superfamily of vertebrate protease inhibitor genes. BMC Evol Biol (2009) 0.90
Archaeal ancestors of eukaryotes: not so elusive any more. BMC Biol (2015) 0.90
Origin of spliceosomal introns and alternative splicing. Cold Spring Harb Perspect Biol (2014) 0.90
U12 intron positions are more strongly conserved between animals and plants than U2 intron positions. Biol Direct (2008) 0.89
The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments. PLoS Genet (2014) 0.89
Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome. Biol Direct (2011) 0.88
Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier? Philos Trans R Soc Lond B Biol Sci (2015) 0.87
Proteomic analysis of the U1 snRNP of Schizosaccharomyces pombe reveals three essential organism-specific proteins. Nucleic Acids Res (2007) 0.87
Signature of a primitive genetic code in ancient protein lineages. J Mol Evol (2007) 0.87
Comparative genomics of proteins involved in RNA nucleocytoplasmic export. BMC Evol Biol (2011) 0.87
Computational identification of four spliceosomal snRNAs from the deep-branching eukaryote Giardia intestinalis. PLoS One (2008) 0.87
Evolutionary diversification of the Sm family of RNA-associated proteins. Mol Biol Evol (2008) 0.87
A complex cell division machinery was present in the last common ancestor of eukaryotes. PLoS One (2009) 0.84
The relative ages of eukaryotes and akaryotes. J Mol Evol (2014) 0.84
Resurrection of an Urbilaterian U1A/U2B″/SNF protein. J Mol Biol (2013) 0.84
Intron gains and losses in the evolution of Fusarium and Cryptococcus fungi. Genome Biol Evol (2012) 0.83
Sm/Lsm genes provide a glimpse into the early evolution of the spliceosome. PLoS Comput Biol (2009) 0.83
A single ancient origin for prototypical serine/arginine-rich splicing factors. Plant Physiol (2011) 0.83
Primordial spliceosomal introns were probably U2-type. Trends Genet (2008) 0.83
Exon definition as a potential negative force against intron losses in evolution. Biol Direct (2008) 0.82
Splicing diversity revealed by reduced spliceosomes in C. merolae and other organisms. RNA Biol (2015) 0.82
The eukaryotic ancestor had a complex ubiquitin signaling system of archaeal origin. Mol Biol Evol (2014) 0.82
Phylogenetic distribution of intron positions in alpha-amylase genes of bilateria suggests numerous gains and losses. PLoS One (2011) 0.82
Characterization of newly gained introns in Daphnia populations. Genome Biol Evol (2014) 0.81
The complex intron landscape and massive intron invasion in a picoeukaryote provides insights into intron evolution. Genome Biol Evol (2013) 0.81
Evolution of spliceosomal introns following endosymbiotic gene transfer. BMC Evol Biol (2010) 0.81
Characterization of RNase MRP RNA and novel snoRNAs from Giardia intestinalis and Trichomonas vaginalis. BMC Genomics (2011) 0.80
Selective forces for the origin of spliceosomes. J Mol Evol (2012) 0.79
Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding RNA processing motif in Giardia lamblia. Nucleic Acids Res (2012) 0.79
A maximum likelihood method for reconstruction of the evolution of eukaryotic gene structure. Methods Mol Biol (2009) 0.79
Using profiles based on nucleotide hydrophobicity to define essential regions for splicing. Int J Biol Sci (2008) 0.79
Origination of the split structure of spliceosomal genes from random genetic sequences. PLoS One (2008) 0.78
Splicing-related features of introns serve to propel evolution. PLoS One (2013) 0.78
Organization of Plasmodium falciparum spliceosomal core complex and role of arginine methylation in its assembly. Malar J (2013) 0.78
Climbing the vertebrate branch of U1A/U2B″ protein evolution. RNA (2014) 0.78
Primal eukaryogenesis: on the communal nature of precellular States, ancestral to modern life. Life (Basel) (2012) 0.78
Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae. Protein Cell (2011) 0.78
Splice Sites Seldom Slide: Intron Evolution in Oomycetes. Genome Biol Evol (2016) 0.77
Beyond BLASTing: tertiary and quaternary structure analysis helps identify major vault proteins. Genome Biol Evol (2013) 0.77
Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution. Microbiol Spectr (2015) 0.77
Characterizing ncRNAs in Human Pathogenic Protists Using High-Throughput Sequencing Technology. Front Genet (2011) 0.77
Selection for reduced translation costs at the intronic 5' end in fungi. DNA Res (2016) 0.77
The multiple evolutionary origins of the eukaryotic N-glycosylation pathway. Biol Direct (2016) 0.77
The emergence of predators in early life: there was no Garden of Eden. PLoS One (2009) 0.76
The falsifiability of the models for the origin of eukaryotes. Curr Genet (2011) 0.76
Origin and evolution of the eukaryotic SSU processome revealed by a comprehensive genomic analysis and implications for the origin of the nucleolus. Genome Biol Evol (2013) 0.76
In silico resurrection of the major vault protein suggests it is ancestral in modern eukaryotes. Genome Biol Evol (2013) 0.75
Evolutionary Dynamics of GLD-1-mRNA complexes in Caenorhabditis nematodes. Genome Biol Evol (2014) 0.75
A novel spliceosome-mediated trans-splicing can change our view on genome complexity of the divergent eukaryote Giardia intestinalis. Biophys Rev (2011) 0.75
Correlated Evolution of Nucleotide Positions within Splice Sites in Mammals. PLoS One (2015) 0.75
Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci U S A (2002) 5.48
The modern molecular clock. Nat Rev Genet (2003) 3.97
Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol (2004) 3.58
Evaluating hypotheses for the origin of eukaryotes. Bioessays (2007) 3.28
Origin of land plants using the multispecies coalescent model. Trends Plant Sci (2013) 2.50
Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution. Mol Biol Evol (2006) 2.48
A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol (2004) 2.32
The biology of intron gain and loss. Trends Genet (2005) 2.07
The root of the mammalian tree inferred from whole mitochondrial genomes. Mol Phylogenet Evol (2003) 1.89
Patterns of intron loss and gain in plants: intron loss-dominated evolution and genome-wide comparison of O. sativa and A. thaliana. Mol Biol Evol (2006) 1.53
Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes. Mol Biol Evol (2006) 1.49
Spectronet: a package for computing spectra and median networks. Appl Bioinformatics (2002) 1.38
Evolutionary biology: relativity for molecular clocks. Nature (2005) 1.38
Comment on "Hexapod origins: monophyletic or paraphyletic?". Science (2003) 1.35
Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. Mol Biol Evol (2002) 1.30
Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing. BMC Evol Biol (2007) 1.30
Tinamous and moa flock together: mitochondrial genome sequence analysis reveals independent losses of flight among ratites. Syst Biol (2009) 1.30
Combined mitochondrial and nuclear DNA sequences resolve the interrelations of the major Australasian marsupial radiations. Syst Biol (2006) 1.29
Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Reconstructing the origins and dispersal of the Polynesian bottle gourd (Lagenaria siceraria). Mol Biol Evol (2006) 1.28
Coevolution of genomic intron number and splice sites. Trends Genet (2007) 1.26
Four new avian mitochondrial genomes help get to basic evolutionary questions in the late cretaceous. Mol Biol Evol (2004) 1.24
Mitochondrial genomes and avian phylogeny: complex characters and resolvability without explosive radiations. Mol Biol Evol (2006) 1.22
A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction. Bioinformatics (2003) 1.20
Origin of introns by 'intronization' of exonic sequences. Trends Genet (2008) 1.20
Resolving the root of the avian mitogenomic tree by breaking up long branches. Mol Phylogenet Evol (2006) 1.16
Toward resolving deep neoaves phylogeny: data, signal enhancement, and priors. Mol Biol Evol (2008) 1.15
Distinct patterns of evolution between respiratory syncytial virus subgroups A and B from New Zealand isolates collected over thirty-seven years. J Med Virol (2006) 1.10
Genomic analysis of hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation. Viruses (2011) 1.09
Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires. Gene (2002) 1.09
Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis. Mol Biol Evol (2007) 1.08
Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution. Genome Res (2006) 1.05
Systematic error in seed plant phylogenomics. Genome Biol Evol (2011) 1.03
Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis. Nucleic Acids Res (2007) 1.03
Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Investigating the intron recognition mechanism in eukaryotes. Mol Biol Evol (2005) 1.03
Widespread intron loss suggests retrotransposon activity in ancient apicomplexans. Mol Biol Evol (2007) 1.02
Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features. Gene (2003) 1.01
Bird evolution: testing the Metaves clade with six new mitochondrial genomes. BMC Evol Biol (2008) 1.01
RNase MRP and the RNA processing cascade in the eukaryotic ancestor. BMC Evol Biol (2007) 1.01
Measuring fit of sequence data to phylogenetic model: gain of power using marginal tests. J Mol Evol (2009) 1.01
Streptophyte algae and the origin of land plants revisited using heterogeneous models with three new algal chloroplast genomes. Mol Biol Evol (2013) 1.01
Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata. Mol Biol Evol (2007) 1.00
The RNA infrastructure: dark matter of the eukaryotic cell? Trends Genet (2009) 1.00
Eukaryote evolution: engulfed by speculation. Nature (2007) 0.99
The place of Amborella within the radiation of angiosperms. Trends Plant Sci (2005) 0.98
On the incidence of intron loss and gain in paralogous gene families. Mol Biol Evol (2007) 0.98
Prokaryote and eukaryote evolvability. Biosystems (2003) 0.98
A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain. Mol Biol Evol (2007) 0.97
The problem of rooting rapid radiations. Mol Biol Evol (2007) 0.97
Smoke without fire: most reported cases of intron gain in nematodes instead reflect intron losses. Mol Biol Evol (2006) 0.96
Using ancestral sequences to uncover potential gene homologues. Appl Bioinformatics (2003) 0.94
Treeness triangles: visualizing the loss of phylogenetic signal. Mol Biol Evol (2007) 0.94
High throughput genome-wide survey of small RNAs from the parasitic protists Giardia intestinalis and Trichomonas vaginalis. Genome Biol Evol (2009) 0.94
Beyond phylogeny: pelecaniform and ciconiiform birds, and long-term niche stability. Mol Phylogenet Evol (2013) 0.92
The modern RNP world of eukaryotes. J Hered (2009) 0.92
Very little intron gain in Entamoeba histolytica genes laterally transferred from prokaryotes. Mol Biol Evol (2006) 0.91
Index-free de novo assembly and deconvolution of mixed mitochondrial genomes. Genome Biol Evol (2010) 0.90
Evolutionary conservation of UTR intron boundaries in Cryptococcus. Mol Biol Evol (2007) 0.90
A bias in ML estimates of branch lengths in the presence of multiple signals. Mol Biol Evol (2007) 0.89
Intron length distributions and gene prediction. Nucleic Acids Res (2007) 0.89
Missing data and influential sites: choice of sites for phylogenetic analysis can be as important as taxon sampling and model choice. Genome Biol Evol (2013) 0.88
Computational identification of four spliceosomal snRNAs from the deep-branching eukaryote Giardia intestinalis. PLoS One (2008) 0.87
Origins of life: Common ancestry put to the test. Nature (2010) 0.85
Hepatitis E virus infection, Papua New Guinea, Fiji, and Kiribati, 2003-2005. Emerg Infect Dis (2014) 0.85
Phylogenetic position of avian nocturnal and diurnal raptors. Genome Biol Evol (2014) 0.83
Infection frequency of hepatitis C virus and IL28B haplotypes in Papua New Guinea, Fiji, and Kiribati. PLoS One (2013) 0.83
Gaps: an elusive source of phylogenetic information. Syst Biol (2012) 0.82
Generation of novel long-acting globular adiponectin molecules. J Mol Biol (2010) 0.81
LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites. BMC Evol Biol (2008) 0.81
Estimating changes in mutational mechanisms of evolution. J Mol Evol (2003) 0.80
Characterization of RNase MRP RNA and novel snoRNAs from Giardia intestinalis and Trichomonas vaginalis. BMC Genomics (2011) 0.80
Optimal alphabets for an RNA world. Proc Biol Sci (2003) 0.80
Correcting the apparent mutation rate acceleration at shorter time scales under a Jukes-Cantor model. Mol Biol Evol (2012) 0.79
Cooperation and selfishness both occur during molecular evolution. Biol Direct (2014) 0.79
Beyond reasonable doubt: evolution from DNA sequences. PLoS One (2013) 0.78
Phylogenetic tree reconstruction accuracy and model fit when proportions of variable sites change across the tree. Syst Biol (2010) 0.78
Two aspects along the continuum of pigeon evolution: A South-Pacific radiation and the relationship of pigeons within Neoaves. Mol Phylogenet Evol (2010) 0.78
Evolutionary biology: our relative genetics. Nature (2004) 0.77
Beyond BLASTing: tertiary and quaternary structure analysis helps identify major vault proteins. Genome Biol Evol (2013) 0.77
Response to Dagan and Martin. Bioessays (2007) 0.77
The emergence of predators in early life: there was no Garden of Eden. PLoS One (2009) 0.76
The Q2 mitochondrial haplogroup in Oceania. PLoS One (2012) 0.75
Does the Ribosome Challenge our Understanding of the RNA World? J Mol Evol (2016) 0.75
In silico resurrection of the major vault protein suggests it is ancestral in modern eukaryotes. Genome Biol Evol (2013) 0.75
Evolutionary biology: mass survivals. Nature (2007) 0.75
How old are RNA networks? Adv Exp Med Biol (2011) 0.75