Published in Biol Direct on August 23, 2011
Gene transfer agents: phage-like elements of genetic exchange. Nat Rev Microbiol (2012) 1.63
An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin. Genome Biol Evol (2012) 1.14
Gene similarity networks provide tools for understanding eukaryote origins and evolution. Proc Natl Acad Sci U S A (2013) 1.12
Interactions in the microbiome: communities of organisms and communities of genes. FEMS Microbiol Rev (2013) 1.05
Comparative genomics explains the evolutionary success of reef-forming corals. Elife (2016) 1.02
On the need for mechanistic models in computational genomics and metagenomics. Genome Biol Evol (2013) 0.99
Analysis of genome content evolution in pvc bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle. Genome Biol Evol (2012) 0.96
Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution. PLoS One (2012) 0.92
A pluralistic account of homology: adapting the models to the data. Mol Biol Evol (2013) 0.89
Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution. Trends Microbiol (2016) 0.89
EGN: a wizard for construction of gene and genome similarity networks. BMC Evol Biol (2013) 0.87
The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data. Philos Trans R Soc Lond B Biol Sci (2015) 0.85
Rethinking evolutionary individuality. Proc Natl Acad Sci U S A (2015) 0.81
"Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis. Genome Biol Evol (2016) 0.81
Viruses and mobile elements as drivers of evolutionary transitions. Philos Trans R Soc Lond B Biol Sci (2016) 0.80
Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes. Nat Commun (2016) 0.80
Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria. ISME J (2015) 0.77
Goods-thinking vs. tree-thinking: Finding a place for mobile genetic elements. Mob Genet Elements (2011) 0.77
Phenotypic Microdiversity and Phylogenetic Signal Analysis of Traits Related to Social Interaction in Bacillus spp. from Sediment Communities. Front Microbiol (2017) 0.75
The role of public goods in planetary evolution. Philos Trans A Math Phys Eng Sci (2017) 0.75
Bacterial evolution. Microbiol Rev (1987) 85.63
CRISPR provides acquired resistance against viruses in prokaryotes. Science (2007) 29.74
Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A (1977) 26.08
Genetic exchange in Salmonella. J Bacteriol (1952) 23.68
The Ribosomal Database Project. Nucleic Acids Res (1994) 20.01
The Main Outlines of Bacterial Classification. J Bacteriol (1941) 17.91
Toward automatic reconstruction of a highly resolved tree of life. Science (2006) 14.96
Phylogenetic classification and the universal tree. Science (1999) 14.28
Restriction endonucleases. CRC Crit Rev Biochem (1976) 13.22
Functional metagenomic profiling of nine biomes. Nature (2008) 11.00
The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol (1994) 10.00
Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet (2009) 8.51
Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci U S A (1999) 7.65
Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci U S A (1998) 7.40
Hybridization as an invasion of the genome. Trends Ecol Evol (2005) 6.34
Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics (1996) 5.88
Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet (2004) 5.49
The hydrogen hypothesis for the first eukaryote. Nature (1998) 5.26
Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol (2005) 5.21
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res (2008) 4.78
Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science (2007) 4.65
The energetics of genome complexity. Nature (2010) 4.58
Highways of gene sharing in prokaryotes. Proc Natl Acad Sci U S A (2005) 4.37
Genome-wide experimental determination of barriers to horizontal gene transfer. Science (2007) 4.37
Expression of animal virus genomes. Bacteriol Rev (1971) 4.33
Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res (2001) 4.22
Time for a change. Nature (2006) 3.92
Genomic evidence for two functionally distinct gene classes. Proc Natl Acad Sci U S A (1998) 3.72
Phylogenetics and the cohesion of bacterial genomes. Science (2003) 3.61
Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol (2010) 3.59
Pattern pluralism and the Tree of Life hypothesis. Proc Natl Acad Sci U S A (2007) 3.56
Horizontal gene transfer: a critical view. Proc Natl Acad Sci U S A (2003) 3.27
Comparison of 61 sequenced Escherichia coli genomes. Microb Ecol (2010) 2.96
Lateral genomics. Trends Cell Biol (1999) 2.85
Intercellular nanotubes mediate bacterial communication. Cell (2011) 2.84
Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol (2009) 2.66
Rapid evolutionary innovation during an Archaean genetic expansion. Nature (2010) 2.34
The convergence of carbohydrate active gene repertoires in human gut microbes. Proc Natl Acad Sci U S A (2008) 2.33
The net of life: reconstructing the microbial phylogenetic network. Genome Res (2005) 2.31
The tree of one percent. Genome Biol (2006) 2.23
Gene recombination in Escherichia coli. Nature (1946) 2.17
Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proc Biol Sci (2004) 2.05
Mosaic bacterial chromosomes: a challenge en route to a tree of genomes. Bioessays (1999) 2.04
Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc Natl Acad Sci U S A (2007) 1.96
Transposases are the most abundant, most ubiquitous genes in nature. Nucleic Acids Res (2010) 1.91
Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes. Proc Natl Acad Sci U S A (2010) 1.89
High frequency of horizontal gene transfer in the oceans. Science (2010) 1.84
Wolbachia genome integrated in an insect chromosome: evolution and fate of laterally transferred endosymbiont genes. Genome Res (2007) 1.83
The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol (2005) 1.79
Horizontal transfer of ATPase genes--the tree of life becomes a net of life. Biosystems (1993) 1.73
Network analyses structure genetic diversity in independent genetic worlds. Proc Natl Acad Sci U S A (2009) 1.73
Two empires or three? Proc Natl Acad Sci U S A (1998) 1.70
Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria. Appl Environ Microbiol (2000) 1.67
Enhanced translation of a chloroplast-expressed RbcS gene restores small subunit levels and photosynthesis in nuclear RbcS antisense plants. Proc Natl Acad Sci U S A (2004) 1.62
Evidence for a chimeric nature of nuclear genomes: eubacterial origin of eukaryotic glyceraldehyde-3-phosphate dehydrogenase genes. Proc Natl Acad Sci U S A (1993) 1.56
The tree and net components of prokaryote evolution. Genome Biol Evol (2010) 1.55
Mimivirus shows dramatic genome reduction after intraamoebal culture. Proc Natl Acad Sci U S A (2011) 1.54
Competence for natural transformation in Neisseria gonorrhoeae: components of DNA binding and uptake linked to type IV pilus expression. Mol Microbiol (2002) 1.52
Genetic analysis of a bacterial genetic exchange element: the gene transfer agent of Rhodobacter capsulatus. Proc Natl Acad Sci U S A (2000) 1.52
Enzymes of the shikimic acid pathway encoded in the genome of a basal metazoan, Nematostella vectensis, have microbial origins. Proc Natl Acad Sci U S A (2008) 1.51
Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales. Mol Biol Evol (2005) 1.50
Genetic barriers among bacteria. Trends Microbiol (1996) 1.50
Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation. Biol Direct (2006) 1.49
The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer. Mol Biol Evol (2010) 1.44
The prokaryotic tree of life: past, present... and future? Trends Ecol Evol (2008) 1.36
Lateral genetic transfer and the construction of genetic exchange communities. FEMS Microbiol Rev (2011) 1.31
Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction. Mol Biol Evol (2004) 1.21
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
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
Harvesting evolutionary signals in a forest of prokaryotic gene trees. Mol Biol Evol (2010) 0.98
Comparison of phylogenetic trees and search for a central trend in the "forest of life". J Comput Biol (2011) 0.98
How stands the Tree of Life a century and a half after The Origin? Biol Direct (2011) 0.95
The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods. BMC Evol Biol (2008) 0.93
Let them fall where they may: congruence analysis in massive phylogenetically messy data sets. Mol Biol Evol (2011) 0.91
Naturally occurring DNA transfer system associated with membrane vesicles in cellulolytic Ruminococcus spp. of ruminal origin. Appl Environ Microbiol (2005) 0.90
Trees and networks before and after Darwin. Biol Direct (2009) 0.90
Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli. Biol Direct (2011) 0.90
Genetics. Paradigm for life. Science (2007) 0.87
Revisiting the concept of lineage in prokaryotes: a phylogenetic perspective. Bioessays (2009) 0.85
The phylogenetic forest and the quest for the elusive tree of life. Cold Spring Harb Symp Quant Biol (2009) 0.85
Tree of life based on genome context networks. PLoS One (2008) 0.82
Philosophy and evolution: minding the gap between evolutionary patterns and tree-like patterns. Methods Mol Biol (2012) 0.79
The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science (2011) 5.15
Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol Biol Evol (2004) 3.65
Pattern pluralism and the Tree of Life hypothesis. Proc Natl Acad Sci U S A (2007) 3.56
The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils? Proc Natl Acad Sci U S A (2004) 3.33
Dinosaurs and the Cretaceous Terrestrial Revolution. Proc Biol Sci (2008) 3.06
Molecular timetrees reveal a Cambrian colonization of land and a new scenario for ecdysozoan evolution. Curr Biol (2013) 2.43
The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records. Philos Trans R Soc Lond B Biol Sci (2008) 2.25
A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata. Proc Biol Sci (2010) 2.20
Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proc Biol Sci (2004) 2.05
Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa. Mol Biol Evol (2009) 1.95
Eubacterial phylogeny based on translational apparatus proteins. Trends Genet (2002) 1.95
MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda. Proc Natl Acad Sci U S A (2011) 1.87
Network analyses structure genetic diversity in independent genetic worlds. Proc Natl Acad Sci U S A (2009) 1.73
Testing the molecular clock: molecular and paleontological estimates of divergence times in the Echinoidea (Echinodermata). Mol Biol Evol (2006) 1.61
Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations. MBio (2011) 1.47
Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. BMC Evol Biol (2005) 1.43
Measuring support and finding unsupported relationships in supertrees. Syst Biol (2005) 1.39
A role for TLR4 in Clostridium difficile infection and the recognition of surface layer proteins. PLoS Pathog (2011) 1.39
The prokaryotic tree of life: past, present... and future? Trends Ecol Evol (2008) 1.36
Ecdysozoan mitogenomics: evidence for a common origin of the legged invertebrates, the Panarthropoda. Genome Biol Evol (2010) 1.35
A selective barrier to horizontal gene transfer in the T4-type bacteriophages that has preserved a core genome with the viral replication and structural genes. Mol Biol Evol (2006) 1.29
The potential value of indels as phylogenetic markers: position of trichomonads as a case study. Mol Biol Evol (2002) 1.24
The shape of supertrees to come: tree shape related properties of fourteen supertree methods. Syst Biol (2005) 1.22
Metazoan opsin evolution reveals a simple route to animal vision. Proc Natl Acad Sci U S A (2012) 1.13
miRNAs: small genes with big potential in metazoan phylogenetics. Mol Biol Evol (2013) 1.13
Gene similarity networks provide tools for understanding eukaryote origins and evolution. Proc Natl Acad Sci U S A (2013) 1.12
Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments. Environ Microbiol (2008) 1.11
Evidence for heterogeneous selective pressures in the evolution of the env gene in different human immunodeficiency virus type 1 subtypes. J Virol (2005) 1.09
Androgenic dependence of exophytic tumor growth in a transgenic mouse model of bladder cancer: a role for thrombospondin-1. BMC Urol (2008) 1.08
Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study. Syst Biol (2012) 1.08
A supertree of temnospondyli: cladogenetic patterns in the most species-rich group of early tetrapods. Proc Biol Sci (2007) 1.08
Linking genomics and ecology to investigate the complex evolution of an invasive Drosophila pest. Genome Biol Evol (2013) 1.06
Heterogeneous models place the root of the placental mammal phylogeny. Mol Biol Evol (2013) 1.05
Molecular paleobiological insights into the origin of the Brachiopoda. Evol Dev (2011) 1.05
Deep genomic-scale analyses of the metazoa reject Coelomata: evidence from single- and multigene families analyzed under a supertree and supermatrix paradigm. Genome Biol Evol (2010) 1.04
Simultaneous miRNA and mRNA transcriptome profiling of human myoblasts reveals a novel set of myogenic differentiation-associated miRNAs and their target genes. BMC Genomics (2013) 1.04
Toward consilience in reptile phylogeny: miRNAs support an archosaur, not lepidosaur, affinity for turtles. Evol Dev (2014) 1.02
Evolution of the RNA polymerase B' subunit gene (rpoB') in Halobacteriales: a complementary molecular marker to the SSU rRNA gene. Mol Biol Evol (2004) 1.02
Properties of supertree methods in the consensus setting. Syst Biol (2007) 1.01
Evolution of rhodopsin ion pumps in haloarchaea. BMC Evol Biol (2007) 1.00
Harvesting evolutionary signals in a forest of prokaryotic gene trees. Mol Biol Evol (2010) 0.98
Relative time scales reveal multiple origins of parallel disjunct distributions of African caecilian amphibians. Biol Lett (2007) 0.98
Reconstruction of family-level phylogenetic relationships within Demospongiae (Porifera) using nuclear encoded housekeeping genes. PLoS One (2013) 0.98
Decreased bladder cancer growth in parous mice. Urology (2008) 0.94
Molecular phylogeny: reconstructing the forest. C R Biol (2008) 0.94
The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions. BMC Evol Biol (2008) 0.91
Let them fall where they may: congruence analysis in massive phylogenetically messy data sets. Mol Biol Evol (2011) 0.91
Interstitial cystitis antiproliferative factor (APF) as a cell-cycle modulator. BMC Urol (2004) 0.90
Evolutionary plasticity of methionine biosynthesis. Gene (2005) 0.90
Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli. Biol Direct (2011) 0.90
The role of BMI1 as a biomarker of cancer stem cells in head and neck cancer: a review. Oncology (2014) 0.90
A pluralistic account of homology: adapting the models to the data. Mol Biol Evol (2013) 0.89
Some considerations for analyzing biodiversity using integrative metagenomics and gene networks. Biol Direct (2010) 0.89
Horizontal gene transfer and the evolution of cnidarian stinging cells. Curr Biol (2008) 0.89
The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea. J Bacteriol (2009) 0.88
EGN: a wizard for construction of gene and genome similarity networks. BMC Evol Biol (2013) 0.87
Genetics. Paradigm for life. Science (2007) 0.87
Fibroblast growth factor receptor-3 expression in meningiomas with stimulation of proliferation by the phosphoinositide 3 kinase-Akt pathway. J Neurosurg (2010) 0.86
Molecular evidence for dim-light vision in the last common ancestor of the vertebrates. Curr Biol (2006) 0.86
Clanistics: a multi-level perspective for harvesting unrooted gene trees. Trends Microbiol (2010) 0.85
Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins. BMC Evol Biol (2010) 0.85
Revisiting the concept of lineage in prokaryotes: a phylogenetic perspective. Bioessays (2009) 0.85
Early detection and measurement of urothelial tumors in mice. Urology (2006) 0.85
MosaicFinder: identification of fused gene families in sequence similarity networks. Bioinformatics (2013) 0.84
Evaluating phylogenetic congruence in the post-genomic era. Genome Biol Evol (2011) 0.83
A case-by-case evolutionary analysis of four imprinted retrogenes. Evolution (2011) 0.83
Functional consequence of positive selection revealed through rational mutagenesis of human myeloperoxidase. Mol Biol Evol (2012) 0.83
Response to Teladorsagia circumcincta infection in Scottish Blackface lambs with divergent phenotypes for nematode resistance. Vet Parasitol (2014) 0.82
The shape of modern tree reconstruction methods. Syst Biol (2013) 0.81
Sequence comparative analysis using networks: software for evaluating de novo transcript assembly from next-generation sequencing. Mol Biol Evol (2013) 0.80
Investigating stagnation in morphological phylogenetics using consensus data. Syst Biol (2007) 0.80
Refuting phylogenetic relationships. Biol Direct (2006) 0.80
Colon cancer associated genes exhibit signatures of positive selection at functionally significant positions. BMC Evol Biol (2012) 0.80
Analysis of transforming growth factor β receptor expression and signaling in higher grade meningiomas. J Neurooncol (2010) 0.79
Bone morphogenetic protein 4 and its receptors are expressed in the leptomeninges and meningiomas and signal via the Smad pathway. J Neuropathol Exp Neurol (2009) 0.78
Cucurbitacin I blocks cerebrospinal fluid and platelet derived growth factor-BB stimulation of leptomeningeal and meningioma DNA synthesis. BMC Complement Altern Med (2013) 0.78
Grade progression and regression in recurrent urothelial cancer. J Urol (2003) 0.78
Consensus mutagenesis reveals that non-helical regions influence thermal stability of horseradish peroxidase. Biochimie (2008) 0.77
Mesothelin expression in the leptomeninges and meningiomas. J Histochem Cytochem (2008) 0.77
The genes encoding cAMP-dependent protein kinase catalytic subunit homologues of the microsporidia Encephalitozoon intestinalis and E. cuniculi: molecular characterisation and phylogenetic analysis. Parasitol Int (2004) 0.76
Molecular adaptation of telomere associated genes in mammals. BMC Evol Biol (2013) 0.76
Evolutionary relationships of the critically endangered frog Ericabatrachus baleensis Largen, 1991 with notes on incorporating previously unsampled taxa into large-scale phylogenetic analyses. BMC Evol Biol (2014) 0.76
The landscape for epigenetic/epigenomic biomedical resources. Epigenetics (2012) 0.75
Differential expression of somatostatin receptors, P44/42 MAPK, and mTOR activation in medulloblastomas and primitive neuroectodermal tumors. Appl Immunohistochem Mol Morphol (2013) 0.75
Prognostic role of salivary CD44sol levels in the follow-up of laryngeal carcinomas. J Oral Pathol Med (2014) 0.75
Mitochondrial data are not suitable for resolving placental mammal phylogeny. Mamm Genome (2014) 0.75