Published in Methods Mol Biol on January 01, 2009
MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol (2013) 34.34
A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res (2010) 11.42
A molecular phylogeny of living primates. PLoS Genet (2011) 5.61
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet (2011) 4.65
Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS. Nature (2013) 4.03
The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature (2012) 3.53
The hymenopteran tree of life: evidence from protein-coding genes and objectively aligned ribosomal data. PLoS One (2013) 3.14
A high-throughput DNA sequence aligner for microbial ecology studies. PLoS One (2009) 3.07
A class-wide phylogenetic assessment of Dothideomycetes. Stud Mycol (2009) 2.91
Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathog (2012) 2.66
Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc Natl Acad Sci U S A (2014) 2.48
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
Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics. Proc Natl Acad Sci U S A (2010) 1.99
Complete genome characterisation of a novel 26th bluetongue virus serotype from Kuwait. PLoS One (2011) 1.93
Hydrogen is an energy source for hydrothermal vent symbioses. Nature (2011) 1.86
High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences. Eur J Hum Genet (2011) 1.80
Nitrogen recycling and nutritional provisioning by Blattabacterium, the cockroach endosymbiont. Proc Natl Acad Sci U S A (2009) 1.80
Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing. PLoS One (2012) 1.77
Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation. Stud Mycol (2009) 1.74
Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites. PLoS Pathog (2013) 1.72
Genome sequencing of recent clinical Chlamydia trachomatis strains identifies loci associated with tissue tropism and regions of apparent recombination. Infect Immun (2010) 1.71
Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Mol Ecol (2010) 1.63
Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes. BMC Microbiol (2011) 1.58
Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. PLoS Pathog (2011) 1.57
High-throughput sequencing of complete human mtDNA genomes from the Philippines. Genome Res (2010) 1.56
Critical association of ncRNA with introns. Nucleic Acids Res (2010) 1.54
Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol (2010) 1.53
The Ras protein superfamily: evolutionary tree and role of conserved amino acids. J Cell Biol (2012) 1.50
Unity in variety--the pan-genome of the Chlamydiae. Mol Biol Evol (2011) 1.47
Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 Clade. Genes (Basel) (2011) 1.36
A study of the relationships of cultivated peanut (Arachis hypogaea) and its most closely related wild species using intron sequences and microsatellite markers. Ann Bot (2012) 1.34
Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics. Nucleic Acids Res (2010) 1.34
Chasing Jenner's vaccine: revisiting cowpox virus classification. PLoS One (2011) 1.33
The banana genome hub. Database (Oxford) (2013) 1.29
HmtDB, a genomic resource for mitochondrion-based human variability studies. Nucleic Acids Res (2011) 1.26
The evolution of novel fungal genes from non-retroviral RNA viruses. BMC Biol (2009) 1.24
Mitochondrial DNA and morphology show independent evolutionary histories of bedbug Cimex lectularius (Heteroptera: Cimicidae) on bats and humans. Parasitol Res (2012) 1.24
Genomic sequencing and comparative analysis of Epstein-Barr virus genome isolated from primary nasopharyngeal carcinoma biopsy. PLoS One (2012) 1.20
A taxonomic and phylogenetic revision of the Penicillium sclerotiorum complex. Stud Mycol (2011) 1.19
Cleaning up the 'Bigmessidae': molecular phylogeny of scleractinian corals from Faviidae, Merulinidae, Pectiniidae and Trachyphylliidae. BMC Evol Biol (2011) 1.16
Isolation and evaluation of oil-producing microalgae from subtropical coastal and brackish waters. PLoS One (2012) 1.15
Conserved repressive function of Krüppel homolog 1 on insect metamorphosis in hemimetabolous and holometabolous species. Sci Rep (2011) 1.12
Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization. G3 (Bethesda) (2012) 1.12
A mitogenomic phylogeny of living primates. PLoS One (2013) 1.10
Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals. BMC Genomics (2013) 1.07
Divergent evolution of norovirus GII/4 by genome recombination from May 2006 to February 2009 in Japan. J Virol (2010) 1.07
Phylogeographic analysis elucidates the influence of the ice ages on the disjunct distribution of relict dragonflies in Asia. PLoS One (2012) 1.06
Generating conformation-specific synthetic antibodies to trap proteins in selected functional states. Methods (2012) 1.06
Next-generation museomics disentangles one of the largest primate radiations. Syst Biol (2013) 1.05
The continuing debate on deep molluscan phylogeny: evidence for Serialia (Mollusca, Monoplacophora + Polyplacophora). Biomed Res Int (2013) 1.05
MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes. Appl Plant Sci (2015) 1.05
Expression of the R2R3-MYB transcription factor TaMYB14 from Trifolium arvense activates proanthocyanidin biosynthesis in the legumes Trifolium repens and Medicago sativa. Plant Physiol (2012) 1.05
Capnodiaceae. Fungal Divers (2011) 1.05
Chikungunya virus 3' untranslated region: adaptation to mosquitoes and a population bottleneck as major evolutionary forces. PLoS Pathog (2013) 1.04
Differential loss and retention of cytoglobin, myoglobin, and globin-E during the radiation of vertebrates. Genome Biol Evol (2011) 1.04
Dichotomy in the NRT gene families of dicots and grass species. PLoS One (2010) 1.04
Patterns of post-glacial genetic differentiation in marginal populations of a marine microalga. PLoS One (2012) 1.04
The biogeography of the yeti crabs (Kiwaidae) with notes on the phylogeny of the Chirostyloidea (Decapoda: Anomura). Proc Biol Sci (2013) 1.03
A reappraisal of Microthyriaceae. Fungal Divers (2011) 1.03
Expanded cocirculation of stable subtypes, emerging lineages, and new sporadic reassortants of porcine influenza viruses in swine populations in Northwest Germany. J Virol (2013) 1.03
Winding up the molecular clock in the genus Carabus (Coleoptera: Carabidae): assessment of methodological decisions on rate and node age estimation. BMC Evol Biol (2012) 1.03
Assessing phylogenetic relationships among galliformes: a multigene phylogeny with expanded taxon sampling in Phasianidae. PLoS One (2013) 1.02
Comparing the usefulness of distance, monophyly and character-based DNA barcoding methods in species identification: a case study of neogastropoda. PLoS One (2011) 1.02
Genome shrinkage and loss of nutrient-providing potential in the obligate symbiont of the primitive termite Mastotermes darwiniensis. Appl Environ Microbiol (2011) 1.01
Genomic diversity of Epstein-Barr virus genomes isolated from primary nasopharyngeal carcinoma biopsy samples. J Virol (2014) 1.01
Estimating tempo and mode of Y chromosome turnover: explaining Y chromosome loss with the fragile Y hypothesis. Genetics (2014) 1.00
PSAR: measuring multiple sequence alignment reliability by probabilistic sampling. Nucleic Acids Res (2011) 1.00
Comprehensive phylogenetic reconstruction of amoebozoa based on concatenated analyses of SSU-rDNA and actin genes. PLoS One (2011) 0.99
A molecular phylogenetic reappraisal of the Hysteriaceae, Mytilinidiaceae and Gloniaceae (Pleosporomycetidae, Dothideomycetes) with keys to world species. Stud Mycol (2009) 0.98
The Maize PIN Gene Family of Auxin Transporters. Front Plant Sci (2012) 0.98
Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data. Methods Ecol Evol (2014) 0.98
Circulation of different lineages of Dengue virus 2, genotype American/Asian in Brazil: dynamics and molecular and phylogenetic characterization. PLoS One (2013) 0.97
Three new additions to the genus Talaromyces isolated from Atlantis sandveld fynbos soils. Persoonia (2012) 0.97
Crystal structure of the conserved domain of the DC lysosomal associated membrane protein: implications for the lysosomal glycocalyx. BMC Biol (2012) 0.97
A naturally chimeric type IIA topoisomerase in Aquifex aeolicus highlights an evolutionary path for the emergence of functional paralogs. Proc Natl Acad Sci U S A (2010) 0.97
Genome scale evolution of myxoma virus reveals host-pathogen adaptation and rapid geographic spread. J Virol (2013) 0.96
Eukaryotic protein kinases (ePKs) of the helminth parasite Schistosoma mansoni. BMC Genomics (2011) 0.96
Laser capture microdissection assessment of virus compartmentalization in the central nervous systems of macaques infected with neurovirulent simian immunodeficiency virus. J Virol (2013) 0.95
Domain movement within a gene: a novel evolutionary mechanism for protein diversification. PLoS One (2011) 0.95
Detection and identification of the atypical bovine pestiviruses in commercial foetal bovine serum batches. PLoS One (2011) 0.95
Genomic and phenotypic characterization of in vitro-generated Chlamydia trachomatis recombinants. BMC Microbiol (2013) 0.95
Phylogenetic relationships and species delimitation in pinus section trifoliae inferrred from plastid DNA. PLoS One (2013) 0.95
Asynchronous origins of ectomycorrhizal clades of Agaricales. Proc Biol Sci (2011) 0.94
Interspecific sex in grass smuts and the genetic diversity of their pheromone-receptor system. PLoS Genet (2011) 0.94
Evolution of the globin gene family in deuterostomes: lineage-specific patterns of diversification and attrition. Mol Biol Evol (2012) 0.94
Genome sequencing of the plant pathogen Taphrina deformans, the causal agent of peach leaf curl. MBio (2013) 0.93
Diversification and Expression of the PIN, AUX/LAX, and ABCB Families of Putative Auxin Transporters in Populus. Front Plant Sci (2012) 0.93
Whole-genome duplication and the functional diversification of teleost fish hemoglobins. Mol Biol Evol (2012) 0.93
Insights into the CRISPR/Cas system of Gardnerella vaginalis. BMC Microbiol (2012) 0.92
The worldwide holoparasitic Apodanthaceae confidently placed in the Cucurbitales by nuclear and mitochondrial gene trees. BMC Evol Biol (2010) 0.92
Genome-wide identification, characterization and phylogenetic analysis of 50 catfish ATP-binding cassette (ABC) transporter genes. PLoS One (2013) 0.92
Cross-lineage influenza B and heterologous influenza A antibody responses in vaccinated mice: immunologic interactions and B/Yamagata dominance. PLoS One (2012) 0.92
Five new Penicillium species in section Sclerotiora: a tribute to the Dutch Royal family. Persoonia (2013) 0.91
Genome-wide analysis of Stowaway-like MITEs in wheat reveals high sequence conservation, gene association, and genomic diversification. Plant Physiol (2012) 0.91
Regulation of Schistosoma mansoni development and reproduction by the mitogen-activated protein kinase signaling pathway. PLoS Negl Trop Dis (2014) 0.91
Stelis zootrophionoides (Orchidaceae: Pleurothallidinae), a new species from Mexico. PLoS One (2012) 0.91
Molecular evolutionary analysis of ABCB5: the ancestral gene is a full transporter with potentially deleterious single nucleotide polymorphisms. PLoS One (2011) 0.91
Resistance analysis of baseline and treatment-emergent variants in hepatitis C virus genotype 1 in the AVIATOR study with paritaprevir-ritonavir, ombitasvir, and dasabuvir. Antimicrob Agents Chemother (2015) 0.90
Flooding greatly affects the diversity of arbuscular mycorrhizal fungi communities in the roots of wetland plants. PLoS One (2011) 0.90
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res (2005) 31.64
Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform (2008) 22.07
Distribution and intensity of constraint in mammalian genomic sequence. Genome Res (2005) 18.85
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05
Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics (2010) 4.61
PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. Bioinformatics (2006) 3.92
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinformatics (2008) 3.55
Identification of a new cryptochrome class. Structure, function, and evolution. Mol Cell (2003) 2.11
Archaeal-type rhodopsins in Chlamydomonas: model structure and intracellular localization. Biochem Biophys Res Commun (2003) 2.09
Improvement in the accuracy of multiple sequence alignment program MAFFT. Genome Inform (2005) 1.83
The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics (2005) 1.75
ASH structure alignment package: sensitivity and selectivity in domain classification. BMC Bioinformatics (2007) 1.73
GASH: an improved algorithm for maximizing the number of equivalent residues between two protein structures. BMC Bioinformatics (2005) 1.71
Detecting local structural similarity in proteins by maximizing number of equivalent residues. Proteins (2004) 1.61
Loss of FBXW7, a cell cycle regulating gene, in colorectal cancer: clinical significance. Int J Cancer (2010) 1.49
A novel representation of protein sequences for prediction of subcellular location using support vector machines. Protein Sci (2005) 1.38
Identification of cryptochrome DASH from vertebrates. Genes Cells (2004) 1.36
DROP: an SVM domain linker predictor trained with optimal features selected by random forest. Bioinformatics (2010) 1.31
Plastin3 is a novel marker for circulating tumor cells undergoing the epithelial-mesenchymal transition and is associated with colorectal cancer prognosis. Cancer Res (2013) 1.29
Identification of rDNA-specific non-LTR retrotransposons in Cnidaria. Mol Biol Evol (2006) 1.25
ASIAN: a web server for inferring a regulatory network framework from gene expression profiles. Nucleic Acids Res (2005) 1.25
Notch-Hes1 pathway is required for the development of IL-17-producing γδ T cells. Blood (2011) 1.14
Protective role of the leukotriene B4 receptor BLT2 in murine inflammatory colitis. FASEB J (2010) 1.04
Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions. Bioinformatics (2006) 1.03
Loop-length-dependent SVM prediction of domain linkers for high-throughput structural proteomics. Biopolymers (2009) 0.98
Analysis of membrane stereochemistry with homology modeling of sn-glycerol-1-phosphate dehydrogenase. Protein Eng (2002) 0.97
ASIAN: a website for network inference. Bioinformatics (2004) 0.95
Interaction between intrinsically disordered proteins frequently occurs in a human protein-protein interaction network. J Mol Biol (2009) 0.94
Membrane interactive alpha-helices in GPCRs as a novel drug target. Curr Protein Pept Sci (2006) 0.92
VCIP135 deubiquitinase and its binding protein, WAC, in p97ATPase-mediated membrane fusion. EMBO J (2011) 0.92
A comparative study of conservation and variation scores. BMC Bioinformatics (2010) 0.91
SeSAW: balancing sequence and structural information in protein functional mapping. Bioinformatics (2010) 0.90
Molecular characterization of a novel type of prostamide/prostaglandin F synthase, belonging to the thioredoxin-like superfamily. J Biol Chem (2007) 0.90
The rs6983267 SNP is associated with MYC transcription efficiency, which promotes progression and worsens prognosis of colorectal cancer. Ann Surg Oncol (2012) 0.90
A study of archaeal enzymes involved in polar lipid synthesis linking amino acid sequence information, genomic contexts and lipid composition. Archaea (2005) 0.90
Functional annotation by sequence-weighted structure alignments: statistical analysis and case studies from the Protein 3000 structural genomics project in Japan. Proteins (2008) 0.87
Copy number loss of FBXW7 is related to gene expression and poor prognosis in esophageal squamous cell carcinoma. Int J Oncol (2012) 0.87
GRIP: a server for predicting interfaces for GPCR oligomerization. J Recept Signal Transduct Res (2009) 0.85
Evolutionary Analysis of Functional Divergence among Chemokine Receptors, Decoy Receptors, and Viral Receptors. Front Microbiol (2012) 0.83
Prediction of interfaces for oligomerizations of G-protein coupled receptors. Proteins (2005) 0.82
Relative von Neumann entropy for evaluating amino acid conservation. J Bioinform Comput Biol (2010) 0.80
Positive selection in the ComC-ComD system of Streptococcal Species. J Bacteriol (2006) 0.80
Gtr1p differentially associates with Gtr2p and Ego1p. Gene (2009) 0.79
Functional region prediction with a set of appropriate homologous sequences--an index for sequence selection by integrating structure and sequence information with spatial statistics. BMC Struct Biol (2012) 0.79
Overexpression of SUGT1 in human colorectal cancer and its clinicopathological significance. Int J Oncol (2010) 0.78
Genomics and computational science for virus research. Front Microbiol (2013) 0.77
FANCD2 mRNA overexpression is a bona fide indicator of lymph node metastasis in human colorectal cancer. Ann Surg Oncol (2010) 0.77
Computational and experimental analyses of furcatin hydrolase for substrate specificity studies of disaccharide-specific glycosidases. J Biochem (2008) 0.77
Increased risk for CRC in diabetic patients with the nonrisk allele of SNPs at 8q24. Ann Surg Oncol (2012) 0.76
How does a topological inversion change the evolutionary constraints on membrane proteins? Protein Eng Des Sel (2004) 0.76
Two novel genes expressed in Xenopus germ line: characteristic features of putative protein structures, their gene expression profiles and their possible roles in gametogenesis and embryogenesis. Mol Reprod Dev (2002) 0.76
GRIPDB - G protein coupled Receptor Interaction Partners DataBase. J Recept Signal Transduct Res (2011) 0.76
Recruitment of thioredoxin-like domains into prostaglandin synthases. Biochem Biophys Res Commun (2008) 0.76
[Extraction of information about protein interaction using evolutionary trace]. Tanpakushitsu Kakusan Koso (2002) 0.75
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Functional expression of single-chain antibody to leukotriene C(4). Biochem Biophys Res Commun (2010) 0.75
[Interface re-engineering as an evolutionary mechanism of protein function]. Tanpakushitsu Kakusan Koso (2002) 0.75
[Interface prediction for class A GPCR oligomers]. Tanpakushitsu Kakusan Koso (2005) 0.75
[Structural bioinformatics]. Tanpakushitsu Kakusan Koso (2009) 0.75