Published in Syst Biol on October 01, 2005
Many-core algorithms for statistical phylogenetics. Bioinformatics (2009) 6.70
Assessment of substitution model adequacy using frequentist and Bayesian methods. Mol Biol Evol (2010) 6.51
Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genet (2006) 3.01
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol (2010) 2.58
Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades. BMC Evol Biol (2009) 1.80
CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models. Mol Biol Evol (2013) 1.37
Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes. Philos Trans R Soc Lond B Biol Sci (2008) 1.29
A molecular phylogeny for yponomeutoidea (insecta, Lepidoptera, ditrysia) and its implications for classification, biogeography and the evolution of host plant use. PLoS One (2013) 1.23
Integration of molecules and new fossils supports a Triassic origin for Lepidosauria (lizards, snakes, and tuatara). BMC Evol Biol (2013) 1.21
Phylogenetic incongruence arising from fragmented speciation in enteric bacteria. Proc Natl Acad Sci U S A (2010) 1.20
Long branch effects distort maximum likelihood phylogenies in simulations despite selection of the correct model. PLoS One (2012) 0.98
Resolving discrepancy between nucleotides and amino acids in deep-level arthropod phylogenomics: differentiating serine codons in 21-amino-acid models. PLoS One (2012) 0.97
Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data. BMC Evol Biol (2007) 0.87
Estimating empirical codon hidden Markov models. Mol Biol Evol (2012) 0.85
Markovian and non-Markovian protein sequence evolution: aggregated Markov process models. J Mol Biol (2011) 0.84
Phylogenetic inference with weighted codon evolutionary distances. J Mol Evol (2009) 0.83
The impact of modelling rate heterogeneity among sites on phylogenetic estimates of intraspecific evolutionary rates and timescales. PLoS One (2014) 0.81
Mitogenomic sequences effectively recover relationships within brush-footed butterflies (Lepidoptera: Nymphalidae). BMC Genomics (2014) 0.80
Human alpha and beta papillomaviruses use different synonymous codon profiles. Virus Genes (2010) 0.79
Influenza viruses with receptor-binding N1 neuraminidases occur sporadically in several lineages and show no attenuation in cell culture or mice. J Virol (2015) 0.78
Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes. BMC Evol Biol (2011) 0.76
State aggregation for fast likelihood computations in molecular evolution. Bioinformatics (2017) 0.75
Phylogenetic stochastic mapping without matrix exponentiation. J Comput Biol (2014) 0.75
Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants. Genome Biol Evol (2017) 0.75
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol (2005) 8.74
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics (2003) 7.05
A promoter-level mammalian expression atlas. Nature (2014) 6.25
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics (2004) 4.22
Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa. Mol Biol Evol (2003) 4.10
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics (2003) 3.89
Inferring speciation times under an episodic molecular clock. Syst Biol (2007) 3.85
Loss of Keap1 function activates Nrf2 and provides advantages for lung cancer cell growth. Cancer Res (2008) 3.56
INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol (2009) 3.29
Accuracy and power of bayes prediction of amino acid sites under positive selection. Mol Biol Evol (2002) 3.26
Early infection of scutellum tissue with Agrobacterium allows high-speed transformation of rice. Plant J (2006) 3.09
The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Syst Biol (2009) 3.04
Phylogenetic inference using whole genomes. Annu Rev Genomics Hum Genet (2008) 2.98
A new time-scale for ray-finned fish evolution. Proc Biol Sci (2007) 2.92
Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol Biol Evol (2008) 2.90
Erect leaves caused by brassinosteroid deficiency increase biomass production and grain yield in rice. Nat Biotechnol (2005) 2.89
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc Biol Sci (2012) 2.68
Best practices for justifying fossil calibrations. Syst Biol (2011) 2.51
Integral role of Noxa in p53-mediated apoptotic response. Genes Dev (2003) 2.50
Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol Biol Evol (2003) 2.29
Efficacy of moderate hypothermia in patients with severe head injury and intracranial hypertension refractory to mild hypothermia. J Neurosurg (2003) 2.27
Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Syst Biol (2002) 2.15
Genome-wide association study identifies three new susceptibility loci for adult asthma in the Japanese population. Nat Genet (2011) 2.10
Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context. Mol Ecol (2004) 2.01
Abnormal dimercapto-succinic acid scan is a predictive factor of breakthrough urinary tract infection in children with primary vesicoureteral reflux. J Urol (2009) 2.01
The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Mol Biol Evol (2010) 2.01
The analysis of efficacy for AutoPulse™ system in flying helicopter. Resuscitation (2013) 1.98
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science (2015) 1.91
Dating primate divergences through an integrated analysis of palaeontological and molecular data. Syst Biol (2010) 1.85
Genetic manipulation of gibberellin metabolism in transgenic rice. Nat Biotechnol (2003) 1.83
On experiences of i2b2 (Informatics for integrating biology and the bedside) database with Japanese clinical patients' data. Bioinformation (2011) 1.82
Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Mol Biol Evol (2007) 1.77
Exploring uncertainty in the calibration of the molecular clock. Biol Lett (2011) 1.74
Alternative splicing of CD44 mRNA by ESRP1 enhances lung colonization of metastatic cancer cell. Nat Commun (2012) 1.71
A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. J Mol Evol (2004) 1.70
Disease-associated CIAS1 mutations induce monocyte death, revealing low-level mosaicism in mutation-negative cryopyrin-associated periodic syndrome patients. Blood (2007) 1.69
Diffusion-weighted magnetic resonance imaging in the differentiation of angiomyolipoma with minimal fat from clear cell renal cell carcinoma. Int J Urol (2011) 1.68
Altered gut flora and environment in patients with severe SIRS. J Trauma (2006) 1.67
Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales. Curr Biol (2015) 1.66
Maximum likelihood methods for detecting adaptive evolution after gene duplication. J Struct Funct Genomics (2003) 1.61
Immortalized neural stem cells transplanted into the injured spinal cord promote recovery of voiding function in the rat. J Urol (2003) 1.61
Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Mol Biol Evol (2011) 1.58
Depletion of radio-resistant regulatory T cells enhances antitumor immunity during recovery from lymphopenia. Blood (2012) 1.54
The duration of signaling through CD40 directs biological ability of dendritic cells to induce antitumor immunity. J Immunol (2003) 1.54
Evolving arch surgery using integrated antegrade selective cerebral perfusion: impact of axillary artery perfusion. J Thorac Cardiovasc Surg (2008) 1.53
Evolving selective cerebral perfusion for aortic arch replacement: high flow rate with moderate hypothermic circulatory arrest. Ann Thorac Surg (2008) 1.53
Initial experience of diffusion-weighted magnetic resonance imaging to assess therapeutic response to induction chemoradiotherapy against muscle-invasive bladder cancer. Urology (2009) 1.53
Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes. Nucleic Acids Res (2007) 1.52
Multidisciplinary approach to prevent spinal cord ischemia after thoracic endovascular aneurysm repair for distal descending aorta. Ann Thorac Surg (2010) 1.51
Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J Mol Evol (2003) 1.49
Predictive model for estimating risk of crush syndrome: a data mining approach. J Trauma (2007) 1.48
Effectiveness of the new 'Mobile AED Map' to find and retrieve an AED: A randomised controlled trial. Resuscitation (2010) 1.47
Impact of Elevated D-Dimer on Diagnosis of Acute Aortic Dissection With Isolated Neurological Symptoms in Ischemic Stroke. Circ J (2015) 1.46
Function, intracellular localization and the importance in salt tolerance of a vacuolar Na(+)/H(+) antiporter from rice. Plant Cell Physiol (2004) 1.46
Host-symbiont conflicts: positive selection on an outer membrane protein of parasitic but not mutualistic Rickettsiaceae. Mol Biol Evol (2002) 1.46
Occult spinal canal stenosis due to C-1 hypoplasia in children with Down syndrome. J Neurosurg (2007) 1.44
Clinical responses to EGFR-tyrosine kinase inhibitor retreatment in non-small cell lung cancer patients who benefited from prior effective gefitinib therapy: a retrospective analysis. BMC Cancer (2011) 1.44
Steroid responsiveness and frequency of relapse in adult-onset minimal change nephrotic syndrome. Am J Kidney Dis (2002) 1.42
Clinical implication of idiopathic plasmacytic lymphadenopathy with polyclonal hypergammaglobulinemia: a report of 16 cases. Int J Surg Pathol (2004) 1.40
Long-term outcome of vaginoplasty with the bilateral labioscrotal flap. J Urol (2009) 1.40
Overview of late outcome of medical and surgical treatment for Takayasu arteritis. Circulation (2008) 1.40
A simple alternative method to confirm lung separation. Anesth Analg (2012) 1.38
Spinal cord malperfusion caused by using the segmental clamp technique during descending aortic repair for chronic type B aortic dissection. Interact Cardiovasc Thorac Surg (2007) 1.38
Changes in CSF S100B and cytokine concentrations in early-phase severe traumatic brain injury. Shock (2004) 1.36
Human mesenchymal stem cells in synovial fluid increase in the knee with degenerated cartilage and osteoarthritis. J Orthop Res (2011) 1.35
Evaluation of a bayesian coalescent method of species delimitation. Syst Biol (2011) 1.34
PAMLX: a graphical user interface for PAML. Mol Biol Evol (2013) 1.30
Dialysis-related hypotension as a cause of progressive frontal lobe atrophy in chronic hemodialysis patients: a 3-year prospective study. Nephron Clin Pract (2004) 1.30
Recombinant human soluble thrombomodulin in sepsis-induced disseminated intravascular coagulation: a multicenter propensity score analysis. Intensive Care Med (2013) 1.29
Diverse characteristics of the CagA gene of Helicobacter pylori strains collected from patients from southern vietnam with gastric cancer and peptic ulcer. J Clin Microbiol (2009) 1.25
Quantitative analysis of bronchial wall vascularity in the medium and small airways of patients with asthma and COPD. Chest (2005) 1.22
Characterization of Neisseria meningitidis isolates collected from 1974 to 2003 in Japan by multilocus sequence typing. J Med Microbiol (2004) 1.22
Inhibitory effects of macrolide antibiotics on exacerbations and hospitalization in chronic obstructive pulmonary disease in Japan: a retrospective multicenter analysis. J Am Geriatr Soc (2008) 1.19
Detecting site-specific physicochemical selective pressures: applications to the Class I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system. J Mol Evol (2005) 1.19
Both regulatory T cells and antitumor effector T cells are primed in the same draining lymph nodes during tumor progression. J Immunol (2005) 1.18
Intersigmoid hernia: Report of a case. Surg Today (2010) 1.18
Mutation of ACTA2 gene as an important cause of familial and nonfamilial nonsyndromatic thoracic aortic aneurysm and/or dissection (TAAD). Hum Mutat (2009) 1.18
Genomewide linkage and linkage disequilibrium analyses identify COL6A1, on chromosome 21, as the locus for ossification of the posterior longitudinal ligament of the spine. Am J Hum Genet (2003) 1.15
Structure of protein interaction networks and their implications on drug design. PLoS Comput Biol (2009) 1.15
Expression of novel rice gibberellin 2-oxidase gene is under homeostatic regulation by biologically active gibberellins. J Plant Res (2003) 1.15
Controlled, prospective trial of steroid treatment in IgA nephropathy: a limitation of low-dose prednisolone therapy. Am J Kidney Dis (2003) 1.14
Phylogenomic analysis of natural selection pressure in Streptococcus genomes. BMC Evol Biol (2007) 1.14
AlzPathway: a comprehensive map of signaling pathways of Alzheimer's disease. BMC Syst Biol (2012) 1.13
Clinical significance of osteoprotegerin expression in human colorectal cancer. Clin Cancer Res (2011) 1.11
The role of positive selection in determining the molecular cause of species differences in disease. BMC Evol Biol (2008) 1.11
MtZoa: a general mitochondrial amino acid substitutions model for animal evolutionary studies. Mol Phylogenet Evol (2009) 1.10
Reciprocal CD4+ T-cell balance of effector CD62Llow CD4+ and CD62LhighCD25+ CD4+ regulatory T cells in small cell lung cancer reflects disease stage. Clin Cancer Res (2008) 1.09
Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals. Biol Lett (2014) 1.08
Synergistic tumour suppressor activity of E-cadherin and p53 in a conditional mouse model for metastatic diffuse-type gastric cancer. Gut (2011) 1.08
The Tohoku Medical Megabank Project: Design and Mission. J Epidemiol (2016) 1.08
Enhanced production of endothelial microparticles with increased binding to leukocytes in patients with severe systemic inflammatory response syndrome. J Trauma (2004) 1.07
[Visualization of the airway using ultrasound]. Masui (2014) 1.07
Efficacy of multislice computed tomography for the detection of acute coronary syndrome in the emergency department. Circ J (2005) 1.07
Classification of acute pancreatitis based on retroperitoneal extension: application of the concept of interfascial planes. Eur J Radiol (2006) 1.07
Diagnostic performance of diffusion-weighted magnetic resonance imaging in bladder cancer: potential utility of apparent diffusion coefficient values as a biomarker to predict clinical aggressiveness. Eur Radiol (2011) 1.07
Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference. Mol Biol Evol (2011) 1.06
Isolation from a healthy carrier and characterization of a Neisseria meningitidis strain that is deficient in gamma-Glutamyl aminopeptidase activity. J Clin Microbiol (2002) 1.06
Nuclear receptor-mediated transcriptional regulation in Phase I, II, and III xenobiotic metabolizing systems. Drug Metab Pharmacokinet (2006) 1.05
MUC12 mRNA expression is an independent marker of prognosis in stage II and stage III colorectal cancer. Int J Cancer (2010) 1.05