Published in Nat Rev Genet on August 01, 2008
Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci U S A (2013) 5.03
The evolutionary origin of orphan genes. Nat Rev Genet (2011) 2.98
Origins, evolution, and phenotypic impact of new genes. Genome Res (2010) 2.98
Biochemistry and evolution of anaerobic energy metabolism in eukaryotes. Microbiol Mol Biol Rev (2012) 2.65
Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet (2011) 2.54
TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics (2009) 2.36
A higher level classification of all living organisms. PLoS One (2015) 2.27
The endosymbiotic origin, diversification and fate of plastids. Philos Trans R Soc Lond B Biol Sci (2010) 2.22
Autonomous plasmid-like replication of a conjugative transposon. Mol Microbiol (2009) 2.11
Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. Genome Res (2011) 2.03
Draft genome sequencing of giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species? PLoS Pathog (2009) 1.97
Horizontal gene transfer between bacteria and animals. Trends Genet (2011) 1.96
Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends Ecol Evol (2010) 1.95
Mobile genetic elements of Staphylococcus aureus. Cell Mol Life Sci (2010) 1.95
A role for host-parasite interactions in the horizontal transfer of transposons across phyla. Nature (2010) 1.83
Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes. Proc Natl Acad Sci U S A (2011) 1.71
The RelA/SpoT homolog (RSH) superfamily: distribution and functional evolution of ppGpp synthetases and hydrolases across the tree of life. PLoS One (2011) 1.70
Horizontal gene transfer in evolution: facts and challenges. Proc Biol Sci (2009) 1.65
Streptophyte algae and the origin of embryophytes. Ann Bot (2009) 1.63
Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling. Genome Biol (2013) 1.62
A congruent phylogenomic signal places eukaryotes within the Archaea. Proc Biol Sci (2012) 1.51
Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi. Plant Cell (2009) 1.50
Horizontal transfer of microRNAs: molecular mechanisms and clinical applications. Protein Cell (2012) 1.49
Big data and other challenges in the quest for orthologs. Bioinformatics (2014) 1.48
Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals. PLoS One (2012) 1.47
How the microbial world saved evolution from the scylla of molecular biology and the charybdis of the modern synthesis. Microbiol Mol Biol Rev (2009) 1.47
Trans-kingdom horizontal DNA transfer from bacteria to yeast is highly plastic due to natural polymorphisms in auxiliary nonessential recipient genes. PLoS One (2013) 1.44
Endosymbiotic origin and differential loss of eukaryotic genes. Nature (2015) 1.43
Endosymbiotic associations within protists. Philos Trans R Soc Lond B Biol Sci (2010) 1.43
Adaptive horizontal transfer of a bacterial gene to an invasive insect pest of coffee. Proc Natl Acad Sci U S A (2012) 1.37
Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite. Genome Biol (2011) 1.36
Biochemical diversification through foreign gene expression in bdelloid rotifers. PLoS Genet (2012) 1.35
Deep phylogeny, ancestral groups and the four ages of life. Philos Trans R Soc Lond B Biol Sci (2010) 1.34
Discovery of nuclear-encoded genes for the neurotoxin saxitoxin in dinoflagellates. PLoS One (2011) 1.34
Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses? BMC Genomics (2009) 1.32
Widespread impact of horizontal gene transfer on plant colonization of land. Nat Commun (2012) 1.31
Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes. Genome Biol (2015) 1.30
Antibacterial gene transfer across the tree of life. Elife (2014) 1.28
Transferred interbacterial antagonism genes augment eukaryotic innate immune function. Nature (2014) 1.28
Horizontal transfer of chloroplast genomes between plant species. Proc Natl Acad Sci U S A (2012) 1.27
Transcriptomic evidence that longevity of acquired plastids in the photosynthetic slugs Elysia timida and Plakobranchus ocellatus does not entail lateral transfer of algal nuclear genes. Mol Biol Evol (2010) 1.24
The evolution of novel fungal genes from non-retroviral RNA viruses. BMC Biol (2009) 1.24
SPRIT: Identifying horizontal gene transfer in rooted phylogenetic trees. BMC Evol Biol (2010) 1.23
Horizontal gene transfer in the acquisition of novel traits by metazoans. Proc Biol Sci (2014) 1.23
Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires. Genome Biol (2011) 1.22
Pervasive horizontal transfer of rolling-circle transposons among animals. Genome Biol Evol (2010) 1.21
Characterization of a nitric oxide synthase from the plant kingdom: NO generation from the green alga Ostreococcus tauri is light irradiance and growth phase dependent. Plant Cell (2010) 1.19
Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. G3 (Bethesda) (2013) 1.18
Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes. Proc Natl Acad Sci U S A (2015) 1.17
Biosynthesis and molecular genetics of polyketides in marine dinoflagellates. Mar Drugs (2010) 1.17
Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes. Genome Biol (2013) 1.17
Evolution of saxitoxin synthesis in cyanobacteria and dinoflagellates. Mol Biol Evol (2012) 1.16
Horizontal transposon transfer in eukarya: detection, bias, and perspectives. Genome Biol Evol (2012) 1.15
Horizontal gene transfer in eukaryotes: the weak-link model. Bioessays (2013) 1.15
Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion. Proc Natl Acad Sci U S A (2010) 1.15
Getting a better picture of microbial evolution en route to a network of genomes. Philos Trans R Soc Lond B Biol Sci (2009) 1.15
Horizontal transfer of expressed genes in a parasitic flowering plant. BMC Genomics (2012) 1.14
Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes. BMC Biol (2010) 1.14
Reevaluating the green contribution to diatom genomes. Genome Biol Evol (2012) 1.12
Phylogenomics of primates and their ancestral populations. Genome Res (2009) 1.12
Mobile DNA and evolution in the 21st century. Mob DNA (2010) 1.12
The population and evolutionary dynamics of homologous gene recombination in bacterial populations. PLoS Genet (2009) 1.12
Taming of the shrewd: novel eukaryotic genes from RNA viruses. BMC Biol (2010) 1.11
Neo-Darwinism, the modern synthesis and selfish genes: are they of use in physiology? J Physiol (2010) 1.11
Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage. Genome Biol (2012) 1.10
The fundamental units, processes and patterns of evolution, and the tree of life conundrum. Biol Direct (2009) 1.09
DNA RECOMBINATION. Base triplet stepping by the Rad51/RecA family of recombinases. Science (2015) 1.08
Gain and loss of multiple functionally related, horizontally transferred genes in the reduced genomes of two microsporidian parasites. Proc Natl Acad Sci U S A (2012) 1.08
Comparative genomics of parasitic silkworm microsporidia reveal an association between genome expansion and host adaptation. BMC Genomics (2013) 1.07
Inheritance of DNA transferred from American trypanosomes to human hosts. PLoS One (2010) 1.07
Ancient horizontal gene transfer from bacteria enhances biosynthetic capabilities of fungi. PLoS One (2009) 1.06
Recurrent horizontal transfer of bacterial toxin genes to eukaryotes. Mol Biol Evol (2012) 1.05
Integrating horizontal gene transfer and common descent to depict evolution and contrast it with "common design". J Eukaryot Microbiol (2009) 1.05
Red and green algal origin of diatom membrane transporters: insights into environmental adaptation and cell evolution. PLoS One (2011) 1.05
Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer. BMC Evol Biol (2011) 1.05
Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples. PLoS Comput Biol (2013) 1.04
Insertion of horizontally transferred genes within conserved syntenic regions of yeast genomes. PLoS One (2009) 1.04
Origins and evolution of the formin multigene family that is involved in the formation of actin filaments. Mol Biol Evol (2008) 1.03
Transfer of a chromosomal Maverick to endogenous bracovirus in a parasitoid wasp. Genetica (2011) 1.03
Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. Proc Natl Acad Sci U S A (2010) 1.03
Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes. Mol Biol Evol (2014) 1.02
Evidence for an early prokaryotic endosymbiosis. Nature (2009) 1.02
A horizontal gene transfer supported the evolution of an early metazoan biomineralization strategy. BMC Evol Biol (2011) 1.01
Evolution of and horizontal gene transfer in the Endornavirus genus. PLoS One (2013) 1.01
Preview. The incredible expanding ancestor of eukaryotes. Cell (2010) 1.00
The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes. Genome Biol (2009) 1.00
Cell-to-cell movement of plastids in plants. Proc Natl Acad Sci U S A (2012) 1.00
Phylogenomics with paralogs. Proc Natl Acad Sci U S A (2015) 1.00
Amplification of a Zygosaccharomyces bailii DNA segment in wine yeast genomes by extrachromosomal circular DNA formation. PLoS One (2011) 0.99
Rampant horizontal transfer of SPIN transposons in squamate reptiles. Mol Biol Evol (2011) 0.99
Recurrent rearrangement during adaptive evolution in an interspecific yeast hybrid suggests a model for rapid introgression. PLoS Genet (2013) 0.98
Computational identification and analysis of orphan assembly-line polyketide synthases. J Antibiot (Tokyo) (2013) 0.97
Population genomics supports baculoviruses as vectors of horizontal transfer of insect transposons. Nat Commun (2014) 0.97
A domain-centric analysis of oomycete plant pathogen genomes reveals unique protein organization. Plant Physiol (2010) 0.97
Transposable elements: powerful contributors to angiosperm evolution and diversity. Genome Biol Evol (2013) 0.96
Evidence for acquisition of virulence effectors in pathogenic chytrids. BMC Evol Biol (2011) 0.96
The mixed lineage nature of nitrogen transport and assimilation in marine eukaryotic phytoplankton: a case study of micromonas. Mol Biol Evol (2010) 0.96
How reticulated are species? Bioessays (2015) 0.96
Longicorn beetle that vectors pinewood nematode carries many Wolbachia genes on an autosome. Proc Biol Sci (2009) 0.96
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature (2008) 5.54
Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogenetics. Trends Plant Sci (2004) 3.53
Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol Phylogenet Evol (2003) 3.24
Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature (2003) 2.75
Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants. Proc Natl Acad Sci U S A (2004) 2.70
Horizontal gene transfer in plants. J Exp Bot (2006) 2.27
Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proc Natl Acad Sci U S A (2002) 2.24
Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Mol Biol Evol (2010) 2.22
The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Mol Biol Evol (2006) 2.15
Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. Proc Natl Acad Sci U S A (2004) 1.88
Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants. BMC Evol Biol (2007) 1.80
Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates. PLoS Biol (2012) 1.76
Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots? BMC Evol Biol (2004) 1.71
Plant genetics: gene transfer from parasitic to host plants. Nature (2004) 1.70
An exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters. BMC Biol (2006) 1.58
The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats. PLoS One (2011) 1.49
Localized hypermutation and associated gene losses in legume chloroplast genomes. Genome Res (2010) 1.48
Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella. Science (2013) 1.48
Homologous recombination and retention of a single form of most genes shape the highly chimeric mitochondrial genome of a cybrid plant. New Phytol (2014) 1.45
Genes for two mitochondrial ribosomal proteins in flowering plants are derived from their chloroplast or cytosolic counterparts. Plant Cell (2002) 1.44
Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber. Plant Cell (2011) 1.32
Patterns of partial RNA editing in mitochondrial genes of Beta vulgaris. Mol Genet Genomics (2006) 1.30
Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae. BMC Evol Biol (2005) 1.29
Frequent, phylogenetically local horizontal transfer of the cox1 group I Intron in flowering plant mitochondria. Mol Biol Evol (2008) 1.25
Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion. Proc Natl Acad Sci U S A (2010) 1.15
Extensive loss of RNA editing sites in rapidly evolving Silene mitochondrial genomes: selection vs. retroprocessing as the driving force. Genetics (2010) 1.15
Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes. BMC Biol (2010) 1.14
Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia. BMC Evol Biol (2010) 1.09
Fine-scale mergers of chloroplast and mitochondrial genes create functional, transcompartmentally chimeric mitochondrial genes. Proc Natl Acad Sci U S A (2009) 1.08
The "fossilized" mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate. BMC Biol (2013) 1.07
Gene transfer from mitochondrion to nucleus: novel mechanisms for gene activation from Cox2. Plant J (2002) 1.01
Recent acceleration of plastid sequence and structural evolution coincides with extreme mitochondrial divergence in the angiosperm genus Silene. Genome Biol Evol (2012) 0.99
Many independent origins of trans splicing of a plant mitochondrial group II intron. J Mol Evol (2004) 0.97
Evidence from small-subunit ribosomal RNA sequences for a fungal origin of Microsporidia. Mol Phylogenet Evol (2005) 0.96
The Amborella genome: an evolutionary reference for plant biology. Genome Biol (2008) 0.95
Phylogenetic analysis reveals five independent transfers of the chloroplast gene rbcL to the mitochondrial genome in angiosperms. Curr Genet (2003) 0.94
Multiple recent horizontal transfers of the cox1 intron in Solanaceae and extended co-conversion of flanking exons. BMC Evol Biol (2011) 0.94
Pervasive survival of expressed mitochondrial rps14 pseudogenes in grasses and their relatives for 80 million years following three functional transfers to the nucleus. BMC Evol Biol (2006) 0.90
Molecular phylogenies of Parabasalia inferred from four protein genes and comparison with rRNA trees. Mol Phylogenet Evol (2004) 0.86
HGT turbulence: Confounding phylogenetic influence of duplicative horizontal transfer and differential gene conversion. Mob Genet Elements (2011) 0.83
Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns. BMC Evol Biol (2007) 0.82
Comment on "The evolution of modern eukaryotic phytoplankton". Science (2004) 0.82
Unique role for translation initiation factor 3 in the light color regulation of photosynthetic gene expression. Proc Natl Acad Sci U S A (2013) 0.78