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An integrated phylogenomic approach toward pinpointing the origin of mitochondria. Sci Rep (2015) 0.90

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Ancient horizontal gene transfer and the last common ancestors. BMC Evol Biol (2015) 0.84

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Evolutionary, molecular and genetic analyses of Tic22 homologues in Arabidopsis thaliana chloroplasts. PLoS One (2013) 0.80

Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus. Front Microbiol (2016) 0.79

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Structural and functional analysis of the finished genome of the recently isolated toxic Anabaena sp. WA102. BMC Genomics (2016) 0.78

A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction. Syst Biol (2014) 0.78

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Unnoticed in the tropics: phylogenomic resolution of the poorly known arachnid order Ricinulei (Arachnida). R Soc Open Sci (2015) 0.76

Genomic Patterns of Positive Selection at the Origin of Rust Fungi. PLoS One (2015) 0.76

PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories. PLoS Comput Biol (2016) 0.75

Indel reliability in indel-based phylogenetic inference. Genome Biol Evol (2014) 0.75

Burrowers from the past: mitochondrial signatures of Ordovician bivalve infaunalization. Genome Biol Evol (2017) 0.75

The Cytochrome P450 superfamily complement (CYPome) in the annelid Capitella teleta. PLoS One (2014) 0.75

MARS: improving multiple circular sequence alignment using refined sequences. BMC Genomics (2017) 0.75

A large 28S rDNA-based phylogeny confirms the limitations of established morphological characters for classification of proteocephalidean tapeworms (Platyhelminthes, Cestoda). Zookeys (2015) 0.75

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SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter. MBio (2017) 0.75

The genome of the emerging barley pathogen Ramularia collo-cygni. BMC Genomics (2016) 0.75

String kernels for protein sequence comparisons: improved fold recognition. BMC Bioinformatics (2017) 0.75

High-Resolution Identification of Specificity Determining Positions in the LacI Protein Family Using Ensembles of Sub-Sampled Alignments. PLoS One (2016) 0.75

In silico approach to designing rational metagenomic libraries for functional studies. BMC Bioinformatics (2017) 0.75

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A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol (2003) 102.57

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MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res (2002) 47.62

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Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol (2007) 14.96

A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res (1999) 12.56

DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics (1999) 12.22

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Fast statistical alignment. PLoS Comput Biol (2009) 5.92

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Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics (2002) 4.54

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PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics (2001) 3.34

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An alignment confidence score capturing robustness to guide tree uncertainty. Mol Biol Evol (2010) 2.39

Phylogenetic assessment of alignments reveals neglected tree signal in gaps. Genome Biol (2010) 2.27

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Heads or tails: a simple reliability check for multiple sequence alignments. Mol Biol Evol (2007) 2.04

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SOAP, cleaning multiple alignments from unstable blocks. Bioinformatics (2001) 1.73

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Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? BMC Evol Biol (2008) 1.45

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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

Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40

The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol (2007) 23.58

Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01

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

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

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

Prediction of Saccharomyces cerevisiae replication origins. Genome Biol (2004) 1.81

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

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

Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts. Appl Environ Microbiol (2006) 1.53

An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS One (2008) 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

Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255). Stand Genomic Sci (2009) 1.34

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

Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PLoS One (2013) 1.23

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

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

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 Sulfurimonas autotrophica type strain (OK10). Stand Genomic Sci (2010) 1.00

Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575). Stand Genomic Sci (2009) 1.00

Complete genome sequence of Dyadobacter fermentans type strain (NS114). Stand Genomic Sci (2009) 0.99

A cut above: discovery of an alternative excision repair pathway in bacteria. Proc Natl Acad Sci U S A (2002) 0.99

Complete genome sequence of Cellulophaga lytica type strain (LIM-21). Stand Genomic Sci (2011) 0.99

Complete genome sequence of Aminobacterium colombiense type strain (ALA-1). Stand Genomic Sci (2010) 0.99

Complete genome sequence of Arcobacter nitrofigilis type strain (CI). Stand Genomic Sci (2010) 0.99

Complete genome sequence of Planctomyces limnophilus type strain (Mü 290). Stand Genomic Sci (2010) 0.98

Complete genome sequence of Anaerococcus prevotii type strain (PC1). Stand Genomic Sci (2009) 0.97

Complete genome sequence of Desulfomicrobium baculatum type strain (X). Stand Genomic Sci (2009) 0.97