Published in PLoS One on April 25, 2013
PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ (2014) 5.52
Variation, evolution, and correlation analysis of C+G content and genome or chromosome size in different kingdoms and phyla. PLoS One (2014) 0.96
How reticulated are species? Bioessays (2015) 0.96
Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production. ISME J (2014) 0.90
Marine extremophiles: a source of hydrolases for biotechnological applications. Mar Drugs (2015) 0.90
The candidate phylum Poribacteria by single-cell genomics: new insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features. PLoS One (2014) 0.88
Ribosome reinitiation at leader peptides increases translation of bacterial proteins. Biol Direct (2016) 0.85
Evolutionary origins and diversification of proteobacterial mutualists. Proc Biol Sci (2013) 0.84
Aquifer environment selects for microbial species cohorts in sediment and groundwater. ISME J (2015) 0.81
Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage. ISME J (2015) 0.80
Evolution of the methyl directed mismatch repair system in Escherichia coli. DNA Repair (Amst) (2015) 0.80
A cytoplasmic peptidoglycan amidase homologue controls mycobacterial cell wall synthesis. Elife (2016) 0.80
Evolution of the F0F1 ATP synthase complex in light of the patchy distribution of different bioenergetic pathways across prokaryotes. PLoS Comput Biol (2014) 0.79
Mechanisms of bacterial morphogenesis: evolutionary cell biology approaches provide new insights. Bioessays (2015) 0.78
A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction. Syst Biol (2014) 0.78
Phylogenetics and the human microbiome. Syst Biol (2014) 0.78
Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream. Genome Biol Evol (2015) 0.77
Phylogenetic Analysis of the Bifidobacterium Genus Using Glycolysis Enzyme Sequences. Front Microbiol (2016) 0.77
Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer. PLoS Comput Biol (2016) 0.76
Draft genome sequences of 24 microbial strains assembled from direct sequencing from 4 stool samples. Genome Announc (2015) 0.76
A phylogenetic analysis of macroevolutionary patterns in fermentative yeasts. Ecol Evol (2016) 0.75
Genome-wide gene order distances support clustering the gram-positive bacteria. Front Microbiol (2015) 0.75
Computational prediction shines light on type III secretion origins. Sci Rep (2016) 0.75
Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers. Nucleic Acids Res (2014) 0.75
Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay. Sci Adv (2017) 0.75
SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter. MBio (2017) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (2006) 87.59
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol (2009) 77.55
UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol (2005) 49.76
MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol (2012) 40.23
A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol (2008) 38.22
Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol (2012) 32.00
Construction of phylogenetic trees. Science (1967) 23.69
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol (2009) 15.15
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature (2009) 15.06
Toward automatic reconstruction of a highly resolved tree of life. Science (2006) 14.96
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J (2011) 13.64
Infernal 1.0: inference of RNA alignments. Bioinformatics (2009) 12.98
IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res (2012) 12.03
Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformatics (2007) 11.03
The origin of the Haitian cholera outbreak strain. N Engl J Med (2010) 9.85
Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med (2011) 9.37
A new generation of homology search tools based on probabilistic inference. Genome Inform (2009) 8.93
ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics (2011) 8.68
Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol (2004) 7.98
A simple, fast, and accurate method of phylogenomic inference. Genome Biol (2008) 5.47
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res (2008) 4.78
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol (2006) 4.03
Independent origins and horizontal transfer of bacterial symbionts of aphids. Mol Ecol (2001) 3.84
Speciation durations and Pleistocene effects on vertebrate phylogeography. Proc Biol Sci (1998) 3.66
Phylogenetic analysis using PHYLIP. Methods Mol Biol (2000) 3.27
The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr Opin Biotechnol (2006) 3.21
Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci U S A (2008) 2.97
STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics (2009) 2.70
Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS Biol (2007) 2.69
Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol (2009) 2.66
The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. J Mol Evol (1995) 2.59
PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Comput Biol (2011) 2.54
The supermatrix approach to systematics. Trends Ecol Evol (2006) 2.44
Phylogeny of gammaproteobacteria. J Bacteriol (2010) 2.35
Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. J Exp Zool B Mol Dev Evol (2005) 2.22
Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genet (2005) 2.21
Do orthologous gene phylogenies really support tree-thinking? BMC Evol Biol (2005) 2.10
Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. J Bacteriol (2001) 2.05
BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics (2010) 1.91
Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function. Nat Rev Microbiol (2011) 1.88
Phylogenomics of prokaryotic ribosomal proteins. PLoS One (2012) 1.82
Assessment of the accuracy of matrix representation with parsimony analysis supertree construction. Syst Biol (2001) 1.76
Horizontal transfer of ATPase genes--the tree of life becomes a net of life. Biosystems (1993) 1.73
Humans and evolutionary and ecological forces shaped the phylogeography of recently emerged diseases. Nat Rev Microbiol (2009) 1.72
Phylogenetic diversity and the greedy algorithm. Syst Biol (2005) 1.70
Phylogeny and evolution of the Archaea: one hundred genomes later. Curr Opin Microbiol (2011) 1.68
Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J (2010) 1.66
Estimating species trees using multiple-allele DNA sequence data. Evolution (2008) 1.50
Characterization of a new thermophilic sulfate-reducing bacterium Thermodesulfovibrio yellowstonii, gen. nov. and sp. nov.: its phylogenetic relationship to Thermodesulfobacterium commune and their origins deep within the bacterial domain. Arch Microbiol (1994) 1.47
Matrix representation with parsimony, taxonomic congruence, and total evidence. Syst Biol (2002) 1.28
Hidden likelihood support in genomic data: can forty-five wrongs make a right? Syst Biol (2005) 1.27
Bacterial molecular phylogeny using supertree approach. Genome Inform (2001) 1.24
The phylogenetic diversity of metagenomes. PLoS One (2011) 1.21
Cospeciation in the triplex symbiosis of termite gut protists (Pseudotrichonympha spp.), their hosts, and their bacterial endosymbionts. Mol Ecol (2007) 1.21
Accuracy of phylogeny reconstruction methods combining overlapping gene data sets. Algorithms Mol Biol (2010) 1.17
Phylogeny and palaeoecology of Polyommatus blue butterflies show Beringia was a climate-regulated gateway to the New World. Proc Biol Sci (2011) 1.09
An AT mutational bias in the tiny GC-rich endosymbiont genome of Hodgkinia. Genome Biol Evol (2011) 1.09
Fast and accurate methods for phylogenomic analyses. BMC Bioinformatics (2011) 1.07
Telling the whole story in a 10,000-genome world. Biol Direct (2011) 1.01
A novel lineage of sulfate-reducing microorganisms: Thermodesulfobiaceae fam. nov., Thermodesulfobium narugense, gen. nov., sp. nov., a new thermophilic isolate from a hot spring. Extremophiles (2003) 1.01
Imputing supertrees and supernetworks from quartets. Syst Biol (2007) 1.00
Long branch effects distort maximum likelihood phylogenies in simulations despite selection of the correct model. PLoS One (2012) 0.98
Thermodesulfatator indicus gen. nov., sp. nov., a novel thermophilic chemolithoautotrophic sulfate-reducing bacterium isolated from the Central Indian Ridge. Int J Syst Evol Microbiol (2004) 0.96
Uncovering rate variation of lateral gene transfer during bacterial genome evolution. BMC Genomics (2008) 0.96
Phylogenetic inference via sequential Monte Carlo. Syst Biol (2012) 0.95
A likelihood look at the supermatrix-supertree controversy. Gene (2008) 0.94
Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae. Genomics (2011) 0.91
Let them fall where they may: congruence analysis in massive phylogenetically messy data sets. Mol Biol Evol (2011) 0.91
Phylogenetic analysis of vertically transmitted psyllid endosymbionts (Candidatus Carsonella ruddii) based on atpAGD and rpoC: comparisons with 16S-23S rDNA-derived phylogeny. Curr Microbiol (2001) 0.90
Complete genome sequences of two hemotropic mycoplasmas, Mycoplasma haemofelis strain Ohio2 and Mycoplasma suis Strain Illinois. J Bacteriol (2011) 0.86
Hippea maritima gen. nov., sp. nov., a new genus of thermophilic, sulfur-reducing bacterium from submarine hot vents. Int J Syst Bacteriol (1999) 0.84
Total evidence, average consensus and matrix representation with parsimony: what a difference distances make. Evol Bioinform Online (2007) 0.83
Phylogenomics-based reconstruction of protozoan species tree. Evol Bioinform Online (2011) 0.78
Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2)). Stand Genomic Sci (2011) 0.78
Environmental genome shotgun sequencing of the Sargasso Sea. Science (2004) 45.23
Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol (2007) 23.58
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature (2009) 15.06
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature (2003) 10.38
An integrated pipeline for de novo assembly of microbial genomes. PLoS One (2012) 8.97
Insights into the phylogeny and coding potential of microbial dark matter. Nature (2013) 8.55
Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol (2004) 7.95
Reordering contigs of draft genomes using the Mauve aligner. Bioinformatics (2009) 6.97
Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat Biotechnol (2002) 6.96
A simple, fast, and accurate method of phylogenomic inference. Genome Biol (2008) 5.47
Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proc Natl Acad Sci U S A (2002) 5.28
The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A (2002) 5.28
Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella. Proc Natl Acad Sci U S A (2005) 5.02
Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature (2004) 5.00
Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. PLoS Biol (2006) 4.92
Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci (2010) 4.70
Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83. J Bacteriol (2003) 4.41
Comparative genomics of emerging human ehrlichiosis agents. PLoS Genet (2006) 4.23
Complete genome sequence of the Q-fever pathogen Coxiella burnetii. Proc Natl Acad Sci U S A (2003) 4.20
Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature (2002) 4.14
Assembling the marine metagenome, one cell at a time. PLoS One (2009) 4.10
The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nat Biotechnol (2004) 3.43
Complete genome sequence of Kytococcus sedentarius type strain (541). Stand Genomic Sci (2009) 3.30
Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc Natl Acad Sci U S A (2012) 3.26
Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science (2005) 3.10
Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PLoS One (2013) 2.91
The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS One (2010) 2.84
Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics (2008) 2.64
Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proc Natl Acad Sci U S A (2004) 2.60
The value of complete microbial genome sequencing (you get what you pay for). J Bacteriol (2002) 2.58
Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS (2006) 2.57
Bacterial communities of diverse Drosophila species: ecological context of a host-microbe model system. PLoS Genet (2011) 2.55
Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis. J Bacteriol (2003) 2.54
PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Comput Biol (2011) 2.54
Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage. J Bacteriol (2003) 2.51
Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Comput Biol (2012) 2.50
Metagenomic sequencing of an in vitro-simulated microbial community. PLoS One (2010) 2.40
Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol (2004) 2.36
Mauve assembly metrics. Bioinformatics (2011) 2.25
Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria. Nucleic Acids Res (2007) 2.25
Drivers of bacterial beta-diversity depend on spatial scale. Proc Natl Acad Sci U S A (2011) 2.24
Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genet (2005) 2.21
BioTorrents: a file sharing service for scientific data. PLoS One (2010) 2.15
Human gut microbiome adopts an alternative state following small bowel transplantation. Proc Natl Acad Sci U S A (2009) 2.08
Complete genome sequence of Meiothermus ruber type strain (21). Stand Genomic Sci (2010) 1.96
Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS One (2009) 1.83
Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3). Stand Genomic Sci (2009) 1.82
Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance. Genetics (2004) 1.80
Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun (2013) 1.80
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol (2013) 1.74
Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli. Genome Biol (2006) 1.66
Genetic and physical mapping of DNA replication origins in Haloferax volcanii. PLoS Genet (2007) 1.60
A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biol (2008) 1.60
Comparative studies of resistin expression and phylogenomics in human and mouse. Biochem Biophys Res Commun (2003) 1.59
Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. PLoS One (2011) 1.56
An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS One (2008) 1.53
Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts. Appl Environ Microbiol (2006) 1.53
The age of the Arabidopsis thaliana genome duplication. Plant Mol Biol (2003) 1.52
Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. PLoS Genet (2009) 1.48
Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure. BMC Genomics (2008) 1.40
Progressive genome-wide introgression in agricultural Campylobacter coli. Mol Ecol (2012) 1.37
Accounting for alignment uncertainty in phylogenomics. PLoS One (2012) 1.35
Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255). Stand Genomic Sci (2009) 1.34
Analyzing patterns of microbial evolution using the mauve genome alignment system. Methods Mol Biol (2007) 1.32
Complete genome sequence of Spirosoma linguale type strain (1). Stand Genomic Sci (2010) 1.32
The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms). PLoS One (2009) 1.28
Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli. BMC Genomics (2012) 1.23
A novel heuristic for local multiple alignment of interspersed DNA repeats. IEEE/ACM Trans Comput Biol Bioinform (2009) 1.22
The phylogenetic diversity of metagenomes. PLoS One (2011) 1.21
Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034). Stand Genomic Sci (2010) 1.21
Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10). Stand Genomic Sci (2009) 1.17
Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophila. G3 (Bethesda) (2011) 1.16
Lateral transfer of genes and gene fragments in prokaryotes. Genome Biol Evol (2009) 1.16
Complete genome sequence of Segniliparus rotundus type strain (CDC 1076). Stand Genomic Sci (2010) 1.15
Complete genome sequence of Atopobium parvulum type strain (IPP 1246). Stand Genomic Sci (2009) 1.14
Complete genome sequence of Cryptobacterium curtum type strain (12-3). Stand Genomic Sci (2009) 1.12
Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales. Int J Syst Evol Microbiol (2005) 1.12
Identification of a fourth family of lycopene cyclases in photosynthetic bacteria. Proc Natl Acad Sci U S A (2007) 1.10
Complete genome sequence of Streptosporangium roseum type strain (NI 9100). Stand Genomic Sci (2010) 1.10
Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence. BMC Genomics (2013) 1.09
Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845). Stand Genomic Sci (2011) 1.08
Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. PLoS One (2012) 1.07
Are protein domains modules of lateral genetic transfer? PLoS One (2009) 1.07
Complete genome sequence of Saccharomonospora viridis type strain (P101). Stand Genomic Sci (2009) 1.07
Complete genome sequence of Haloterrigena turkmenica type strain (4k). Stand Genomic Sci (2010) 1.06
Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21). Stand Genomic Sci (2011) 1.06
Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges. Environ Microbiol (2011) 1.06
MicrobeDB: a locally maintainable database of microbial genomic sequences. Bioinformatics (2012) 1.05
Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta. Stand Genomic Sci (2012) 1.05
Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1). Stand Genomic Sci (2009) 1.04
Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences. BMC Bioinformatics (2010) 1.04
Complete genome sequence of Desulfobulbus propionicus type strain (1pr3). Stand Genomic Sci (2011) 1.01
Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122). Stand Genomic Sci (2009) 1.00
Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575). Stand Genomic Sci (2009) 1.00
Complete genome sequence of Sulfurimonas autotrophica type strain (OK10). Stand Genomic Sci (2010) 1.00
A cut above: discovery of an alternative excision repair pathway in bacteria. Proc Natl Acad Sci U S A (2002) 0.99