Published in Nucleic Acids Res on February 18, 2011
Deciphering a global network of functionally associated post-translational modifications. Mol Syst Biol (2012) 1.86
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data. Mol Biol Evol (2016) 1.41
New metrics for comparison of taxonomies reveal striking discrepancies among species delimitation methods in Madascincus lizards. PLoS One (2013) 1.12
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. Nucleic Acids Res (2014) 1.01
Comparative transcriptomics of early dipteran development. BMC Genomics (2013) 0.99
Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics. Mol Biol Evol (2014) 0.92
Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life. Methods Mol Biol (2012) 0.81
PhyBin: binning trees by topology. PeerJ (2013) 0.79
Evolution of bluetongue virus serotype 1 in northern Australia over 30 years. J Virol (2014) 0.78
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Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family. BMC Bioinformatics (2017) 0.75
Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol (1996) 6.99
Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol (2009) 4.91
Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol (2009) 4.65
ETE: a python Environment for Tree Exploration. BMC Bioinformatics (2010) 4.17
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol (2006) 4.03
Phylogenetic analysis using PHYLIP. Methods Mol Biol (2000) 3.27
A phylogenomic approach to microbial evolution. Nucleic Acids Res (2001) 3.06
Phylogenetic identification of lateral genetic transfer events. BMC Evol Biol (2006) 2.43
GeneTree: comparing gene and species phylogenies using reconciled trees. Bioinformatics (1998) 2.41
A congruence index for testing topological similarity between trees. Bioinformatics (2007) 2.35
Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome. PLoS Genet (2009) 2.32
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. Nucleic Acids Res (2010) 2.22
Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Syst Biol (2007) 1.69
A fungal phylogeny based on 82 complete genomes using the composition vector method. BMC Evol Biol (2009) 1.61
Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes. Genome Res (2007) 1.57
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics (2008) 1.53
The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome. PLoS One (2009) 1.53
TOPD/FMTS: a new software to compare phylogenetic trees. Bioinformatics (2007) 1.49
Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees. Syst Biol (2010) 1.36
The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees. Bioinformatics (2007) 1.35
PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees. BMC Bioinformatics (2009) 1.32
A practical method for exact computation of subtree prune and regraft distance. Bioinformatics (2008) 1.14
Supertree construction in the genomic age. Methods Enzymol (2005) 1.13
Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models. BMC Bioinformatics (2010) 1.05
Topological variation in single-gene phylogenetic trees. Genome Biol (2007) 1.02
Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes. Bioinformatics (2005) 1.01
Trees from trees: construction of phylogenetic supertrees using clann. Methods Mol Biol (2009) 0.84
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics (2009) 9.81
ETE: a python Environment for Tree Exploration. BMC Bioinformatics (2010) 4.17
The human phylome. Genome Biol (2007) 3.81
eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res (2013) 3.77
PhylomeDB: a database for genome-wide collections of gene phylogenies. Nucleic Acids Res (2007) 3.30
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics. Nucleic Acids Res (2007) 3.09
The genome of melon (Cucumis melo L.). Proc Natl Acad Sci U S A (2012) 2.24
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. Nucleic Acids Res (2010) 2.22
Immunity and other defenses in pea aphids, Acyrthosiphon pisum. Genome Biol (2010) 2.09
Joining forces in the quest for orthologs. Genome Biol (2009) 1.96
Acquisition of prokaryotic genes by fungal genomes. Trends Genet (2009) 1.72
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. Nucleic Acids Res (2013) 1.69
An anaerobic mitochondrion that produces hydrogen. Nature (2005) 1.64
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score. Nucleic Acids Res (2010) 1.59
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. Nucleic Acids Res (2011) 1.53
The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome. PLoS One (2009) 1.53
2x genomes--depth does matter. Genome Biol (2010) 1.47
Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi. BMC Biol (2012) 1.45
Toward community standards in the quest for orthologs. Bioinformatics (2012) 1.36
Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida. Proc Natl Acad Sci U S A (2013) 1.36
PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome. Nucleic Acids Res (2009) 1.24
Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxin. FEBS Lett (2005) 1.21
A midzone-based ruler adjusts chromosome compaction to anaphase spindle length. Science (2011) 1.19
Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes. Genome Biol (2013) 1.18
Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains. ISME J (2010) 1.17
Ancient dispersal of the human fungal pathogen Cryptococcus gattii from the Amazon rainforest. PLoS One (2013) 1.15
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. Brief Bioinform (2011) 1.15
Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus. BMC Genomics (2012) 1.14
Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression. Bioessays (2010) 1.10
Assigning duplication events to relative temporal scales in genome-wide studies. Bioinformatics (2010) 1.09
From Saccharomyces cerevisiae to Candida glabratain a few easy steps: important adaptations for an opportunistic pathogen. FEMS Microbiol Lett (2010) 1.08
PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease. Nucleic Acids Res (2006) 1.08
The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties. Int J Food Microbiol (2012) 1.04
Comparative transcriptomics of early dipteran development. BMC Genomics (2013) 0.99
YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors. RNA (2010) 0.99
Variation and evolution of biomolecular systems: searching for functional relevance. FEBS Lett (2005) 0.96
The kinomes of apicomplexan parasites. Microbes Infect (2012) 0.96
Genome comparison of Candida orthopsilosis clinical strains reveals the existence of hybrids between two distinct subspecies. Genome Biol Evol (2014) 0.93
Unexpected genomic variability in clinical and environmental strains of the pathogenic yeast Candida parapsilosis. Genome Biol Evol (2013) 0.91
Inferring gene function from evolutionary change in signatures of translation efficiency. Genome Biol (2014) 0.91
Genome, Transcriptome, and Functional Analyses of Penicillium expansum Provide New Insights Into Secondary Metabolism and Pathogenicity. Mol Plant Microbe Interact (2015) 0.91
The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite's biology. BMC Genomics (2012) 0.89
Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence. BMC Evol Biol (2009) 0.89
High variability of mitochondrial gene order among fungi. Genome Biol Evol (2014) 0.88
Mitochondrial genome variability within the Candida parapsilosis species complex. Mitochondrion (2012) 0.87
Predicting phenotypic traits of prokaryotes from protein domain frequencies. BMC Bioinformatics (2010) 0.87
Measuring guide-tree dependency of inferred gaps in progressive aligners. Bioinformatics (2013) 0.87
Regulation of Candida glabrata oxidative stress resistance is adapted to host environment. FEBS Lett (2010) 0.87
A phylogenomics approach for selecting robust sets of phylogenetic markers. Nucleic Acids Res (2014) 0.86
TACC3-TSC2 maintains nuclear envelope structure and controls cell division. Cell Cycle (2010) 0.85
Lack of phylogenetic support for a supposed actinobacterial origin of peroxisomes. Gene (2010) 0.84
Pathogenic mutations in the 5' untranslated region of BCS1L mRNA in mitochondrial complex III deficiency. Mitochondrion (2009) 0.84
Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi. BMC Genomics (2014) 0.83
CycADS: an annotation database system to ease the development and update of BioCyc databases. Database (Oxford) (2011) 0.81
Evolution of spliceosomal introns following endosymbiotic gene transfer. BMC Evol Biol (2010) 0.81
Evolutionary histories of expanded peptidase families in Schistosoma mansoni. Mem Inst Oswaldo Cruz (2011) 0.80
Phylogenetic analyses uncover a novel clade of transferrin in nonmammalian vertebrates. Mol Biol Evol (2012) 0.78
Selection of marker genes using whole-genome DNA polymorphism analysis. Evol Bioinform Online (2012) 0.77
Correction: The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis. PLoS Genet (2016) 0.75
Perceptions about postdocs. EMBO Rep (2004) 0.75
Correction: Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina). PLoS Genet (2016) 0.75
FUNGALOXPHOS: an integrated database for oxidative phosphorylation in fungi. Mitochondrion (2013) 0.75
Corrigendum: Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. Sci Rep (2015) 0.75
The Case of the Missing Ancient Fungal Polyploids. Am Nat (2016) 0.75