Published in J Mol Evol on August 17, 2014
A phylogenomic data-driven exploration of viral origins and evolution. Sci Adv (2015) 0.91
Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology. Comput Struct Biotechnol J (2015) 0.82
A phylogenomic census of molecular functions identifies modern thermophilic archaea as the most ancient form of cellular life. Archaea (2014) 0.76
Eliciting the Functional Taxonomy from protein annotations and taxa. Sci Rep (2016) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol (1987) 266.90
MODELTEST: testing the model of DNA substitution. Bioinformatics (1998) 101.19
Bacterial evolution. Microbiol Rev (1987) 85.63
SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A (1990) 50.63
CATH--a hierarchic classification of protein domain structures. Structure (1997) 29.95
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res (2005) 29.61
Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A (1977) 26.08
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res (2012) 19.48
The uncultured microbial majority. Annu Rev Microbiol (2003) 17.33
Toward automatic reconstruction of a highly resolved tree of life. Science (2006) 14.96
Phylogenetic classification and the universal tree. Science (1999) 14.28
Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformatics (2007) 11.03
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res (2009) 9.98
SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics (1998) 9.87
Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol (2003) 8.51
Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol (2001) 8.14
Genome streamlining in a cosmopolitan oceanic bacterium. Science (2005) 8.11
Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci U S A (1999) 7.65
Enzyme recruitment in evolution of new function. Annu Rev Microbiol (1976) 6.95
Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet (2005) 6.47
Phylogenetic analysis of the mycoplasmas. Proc Natl Acad Sci U S A (1980) 6.06
A molecular phylogeny of living primates. PLoS Genet (2011) 5.61
Use and misuse of the gene ontology annotations. Nat Rev Genet (2008) 5.01
Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu Rev Biochem (2010) 4.41
Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol (2003) 3.59
HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res (2003) 3.41
Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature (2004) 3.29
Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol (2005) 2.95
The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol (2002) 2.93
Protein family expansions and biological complexity. PLoS Comput Biol (2006) 2.69
The major evolutionary transitions. Nature (1995) 2.46
Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. Proc Natl Acad Sci U S A (1992) 2.25
Reverse gyrase: a helicase-like domain and a type I topoisomerase in the same polypeptide. Proc Natl Acad Sci U S A (1993) 2.04
Testing the hypothesis of common ancestry. J Theor Biol (2002) 2.03
Hot spots for allosteric regulation on protein surfaces. Cell (2011) 1.89
Mapping the tree of life: progress and prospects. Microbiol Mol Biol Rev (2009) 1.87
High frequency of horizontal gene transfer in the oceans. Science (2010) 1.84
Comparison of the genomes of human and mouse lays the foundation of genome zoology. Hum Mol Genet (2003) 1.83
The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev (2000) 1.82
Phylogeny: a non-hyperthermophilic ancestor for bacteria. Nature (2002) 1.78
Convergent evolution of domain architectures (is rare). Bioinformatics (2004) 1.77
Hyperthermus butylicus, a hyperthermophilic sulfur-reducing archaebacterium that ferments peptides. J Bacteriol (1990) 1.76
Transfer RNA paralogs: evidence for genetic code-amino acid biosynthesis coevolution and an archaeal root of life. Gene (2003) 1.71
Phylogeny and evolution of the Archaea: one hundred genomes later. Curr Opin Microbiol (2011) 1.68
Orthologs, paralogs and genome comparisons. Curr Opin Genet Dev (1999) 1.65
The origin, evolution and structure of the protein world. Biochem J (2009) 1.65
A genealogical approach to quantifying lineage divergence. Evolution (2008) 1.62
An evolutionarily structured universe of protein architecture. Genome Res (2003) 1.61
The origin and evolution of Archaea: a state of the art. Philos Trans R Soc Lond B Biol Sci (2006) 1.54
Where is the root of the universal tree of life? Bioessays (1999) 1.53
Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea. ISME J (2010) 1.52
Estimating species trees using multiple-allele DNA sequence data. Evolution (2008) 1.50
Structure is three to ten times more conserved than sequence--a study of structural response in protein cores. Proteins (2009) 1.48
The unique DNA topology and DNA topoisomerases of hyperthermophilic archaea. FEMS Microbiol Rev (1996) 1.48
The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world. Structure (2009) 1.47
Domain tree-based analysis of protein architecture evolution. Mol Biol Evol (2007) 1.46
Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths. Mol Biol Evol (2010) 1.42
Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census. Proteins (1998) 1.40
Horizontal gene exchange in environmental microbiota. Front Microbiol (2011) 1.39
Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world. Genome Res (2007) 1.31
Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. J Bacteriol (2008) 1.27
Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis. J Bacteriol (2008) 1.23
A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation. Mol Biol Evol (2010) 1.23
Delta plots: a tool for analyzing phylogenetic distance data. Mol Biol Evol (2002) 1.22
Global phylogeny determined by the combination of protein domains in proteomes. Mol Biol Evol (2006) 1.21
Ribosomal history reveals origins of modern protein synthesis. PLoS One (2012) 1.19
Reductive evolution of proteomes and protein structures. Proc Natl Acad Sci U S A (2011) 1.18
Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya. BMC Evol Biol (2012) 1.18
The origin and evolution of tRNA inferred from phylogenetic analysis of structure. J Mol Evol (2007) 1.18
Genome phylogenetic analysis based on extended gene contents. Mol Biol Evol (2004) 1.10
The evolutionary history of protein domains viewed by species phylogeny. PLoS One (2009) 1.09
Genome beginnings: rooting the tree of life. Philos Trans R Soc Lond B Biol Sci (2009) 1.08
The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota. BMC Genomics (2009) 1.07
Reverse gyrase from hyperthermophiles: probable transfer of a thermoadaptation trait from archaea to bacteria. Trends Genet (2000) 1.07
The evolutionary history of the structure of 5S ribosomal RNA. J Mol Evol (2009) 1.05
The nature of the last universal common ancestor. Curr Opin Genet Dev (1999) 1.05
Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species. Bioinformatics (2004) 1.02
Genome networks root the tree of life between prokaryotic domains. Genome Biol Evol (2010) 1.02
Signature sequences in diverse proteins provide evidence for the late divergence of the Order Aquificales. Int Microbiol (2004) 1.01
The proteomic complexity and rise of the primordial ancestor of diversified life. BMC Evol Biol (2011) 1.00
The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms. BMC Evol Biol (2012) 1.00
Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility. PLoS One (2013) 0.97
A phase transition for a random cluster model on phylogenetic trees. Math Biosci (2004) 0.97
Standard maximum likelihood analyses of alignments with gaps can be statistically inconsistent. PLoS Curr (2012) 0.97
Emergence and evolution of modern molecular functions inferred from phylogenomic analysis of ontological data. Mol Biol Evol (2010) 0.96
The ancient history of the structure of ribonuclease P and the early origins of Archaea. BMC Bioinformatics (2010) 0.96
Not so old Archaea - the antiquity of biogeochemical processes in the archaeal domain of life. Geobiology (2009) 0.95
Evolutionary patterns in the sequence and structure of transfer RNA: early origins of archaea and viruses. PLoS Comput Biol (2008) 0.95
Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms. Genes (Basel) (2011) 0.94
The contest between parsimony and likelihood. Syst Biol (2004) 0.94
The evolution of information in the major transitions. J Theor Biol (2005) 0.94
Global patterns of protein domain gain and loss in superkingdoms. PLoS Comput Biol (2014) 0.92
Benefits of using molecular structure and abundance in phylogenomic analysis. Front Genet (2012) 0.89
The tree of life might be rooted in the branch leading to Nanoarchaeota. Gene (2007) 0.88
Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes. PLoS Comput Biol (2013) 0.88
Polyphasic evidence delineating the root of life and roots of biological domains. Gene (2007) 0.86
On the conceptual difficulties in rooting the tree of life. Trends Microbiol (2004) 0.86
History of biological metal utilization inferred through phylogenomic analysis of protein structures. Proc Natl Acad Sci U S A (2010) 1.71
Protein domain structure uncovers the origin of aerobic metabolism and the rise of planetary oxygen. Structure (2012) 1.53
The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world. Structure (2009) 1.47
Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world. Genome Res (2007) 1.31
A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation. Mol Biol Evol (2010) 1.23
Global phylogeny determined by the combination of protein domains in proteomes. Mol Biol Evol (2006) 1.21
Ribosomal history reveals origins of modern protein synthesis. PLoS One (2012) 1.19
Reductive evolution of proteomes and protein structures. Proc Natl Acad Sci U S A (2011) 1.18
The origin and evolution of tRNA inferred from phylogenetic analysis of structure. J Mol Evol (2007) 1.18
The evolutionary history of the structure of 5S ribosomal RNA. J Mol Evol (2009) 1.05
Proteome evolution and the metabolic origins of translation and cellular life. J Mol Evol (2010) 1.02
Common evolutionary trends for SINE RNA structures. Trends Genet (2006) 1.01
The proteomic complexity and rise of the primordial ancestor of diversified life. BMC Evol Biol (2011) 1.00
An approach of orthology detection from homologous sequences under minimum evolution. Nucleic Acids Res (2008) 1.00
The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms. BMC Evol Biol (2012) 1.00
MANET: tracing evolution of protein architecture in metabolic networks. BMC Bioinformatics (2006) 1.00
Emergence and evolution of modern molecular functions inferred from phylogenomic analysis of ontological data. Mol Biol Evol (2010) 0.96
The ancient history of the structure of ribonuclease P and the early origins of Archaea. BMC Bioinformatics (2010) 0.96
Evolutionary patterns in the sequence and structure of transfer RNA: early origins of archaea and viruses. PLoS Comput Biol (2008) 0.95
Benefits of using molecular structure and abundance in phylogenomic analysis. Front Genet (2012) 0.89
NOBAI: a web server for character coding of geometrical and statistical features in RNA structure. Nucleic Acids Res (2008) 0.88
Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes. PLoS Comput Biol (2013) 0.88
Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome. Biol Direct (2011) 0.88
Structural phylogenomics reveals gradual evolutionary replacement of abiotic chemistries by protein enzymes in purine metabolism. PLoS One (2013) 0.86
The impact of oxygen on metabolic evolution: a chemoinformatic investigation. PLoS Comput Biol (2012) 0.86
Evolutionary optimization of protein folding. PLoS Comput Biol (2013) 0.86
Transfer RNA and the origins of diversified life. Sci Prog (2008) 0.85
Biphasic patterns of diversification and the emergence of modules. Front Genet (2012) 0.85
Evolutionary patterns in the sequence and structure of transfer RNA: a window into early translation and the genetic code. PLoS One (2008) 0.84
Widespread recruitment of ancient domain structures in modern enzymes during metabolic evolution. J Integr Bioinform (2013) 0.84
CLUSTOM: a novel method for clustering 16S rRNA next generation sequences by overlap minimization. PLoS One (2013) 0.83
A general framework of persistence strategies for biological systems helps explain domains of life. Front Genet (2013) 0.83
Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: are they proof of an ancient genome duplication event? Biol Direct (2007) 0.81
Viral evolution: Primordial cellular origins and late adaptation to parasitism. Mob Genet Elements (2012) 0.80
The origin of modern 5S rRNA: a case of relating models of structural history to phylogenetic data. J Mol Evol (2010) 0.79
Structural phylogenomics uncovers the early and concurrent origins of cysteine biosynthesis and iron-sulfur proteins. J Biomol Struct Dyn (2012) 0.79
Population genetics and spatial structure of the fairy ring fungus Marasmius oreades in a Norwegian sand dune ecosystem. Mycologia (2010) 0.79
Comparative genomic and phylogenetic analyses reveal the evolution of the core two-component signal transduction systems in enterobacteria. J Mol Evol (2010) 0.79
Computational analysis reveals abundance of potential glycoproteins in Archaea, Bacteria and Eukarya. Bioinformation (2011) 0.77
Phylogenomics supports a cellularly structured urancestor. J Mol Microbiol Biotechnol (2013) 0.77
Untangling the origin of viruses and their impact on cellular evolution. Ann N Y Acad Sci (2015) 0.77
Comparative analysis of barophily-related amino acid content in protein domains of Pyrococcus abyssi and Pyrococcus furiosus. Archaea (2013) 0.75
Analysis of glycosylation motifs and glycosyltransferases in Bacteria and Archaea. Bioinformation (2011) 0.75
Comparative analysis of organophosphate degrading enzymes from diverse species. Bioinformation (2010) 0.75