Published in J Exp Zool B Mol Dev Evol on January 15, 2005
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol (2006) 4.03
Discordance of species trees with their most likely gene trees. PLoS Genet (2006) 3.58
Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genet (2006) 3.01
Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects. Genome Res (2006) 2.42
AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses. BMC Bioinformatics (2009) 2.17
Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs. J Mol Evol (2006) 1.91
Evolution of box jellyfish (Cnidaria: Cubozoa), a group of highly toxic invertebrates. Proc Biol Sci (2009) 1.77
Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes. Genome Res (2007) 1.57
Molecular phylogeny of beetle associated diplogastrid nematodes suggests host switching rather than nematode-beetle coevolution. BMC Evol Biol (2009) 1.53
Diversity and evolution of phycobilisomes in marine Synechococcus spp.: a comparative genomics study. Genome Biol (2007) 1.47
Searching for species in haloarchaea. Proc Natl Acad Sci U S A (2007) 1.46
Phylogeny of the nematode genus Pristionchus and implications for biodiversity, biogeography and the evolution of hermaphroditism. BMC Evol Biol (2007) 1.34
Rooting the eutherian tree: the power and pitfalls of phylogenomics. Genome Biol (2007) 1.31
Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PLoS One (2013) 1.23
The ompA gene in Chlamydia trachomatis differs in phylogeny and rate of evolution from other regions of the genome. Infect Immun (2006) 1.22
Phylogenetic inference under varying proportions of indel-induced alignment gaps. BMC Evol Biol (2009) 1.17
Accuracy of phylogeny reconstruction methods combining overlapping gene data sets. Algorithms Mol Biol (2010) 1.17
Statistics and truth in phylogenomics. Mol Biol Evol (2011) 1.12
The performance of the Congruence Among Distance Matrices (CADM) test in phylogenetic analysis. BMC Evol Biol (2011) 1.11
Chlamydia trachomatis diversity viewed as a tissue-specific coevolutionary arms race. Genome Biol (2008) 1.10
Fast and consistent estimation of species trees using supermatrix rooted triples. Mol Biol Evol (2009) 1.03
Carbon and arsenic metabolism in Thiomonas strains: differences revealed diverse adaptation processes. BMC Microbiol (2009) 1.02
MySSP: non-stationary evolutionary sequence simulation, including indels. Evol Bioinform Online (2007) 0.97
Evolutionary sequence analysis of complete eukaryote genomes. BMC Bioinformatics (2005) 0.97
Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics. Mol Biol Evol (2012) 0.96
A tribal level phylogeny of Lake Tanganyika cichlid fishes based on a genomic multi-marker approach. Mol Phylogenet Evol (2014) 0.92
Simultaneous analysis of multiple enzymes increases accuracy of pulsed-field gel electrophoresis in assigning genetic relationships among homogeneous Salmonella strains. J Clin Microbiol (2010) 0.91
The Influence of Hepatitis C Virus Genetic Region on Phylogenetic Clustering Analysis. PLoS One (2015) 0.90
The Diversity and Molecular Evolution of B-Cell Receptors during Infection. Mol Biol Evol (2016) 0.89
Gene order phylogeny of the genus Prochlorococcus. PLoS One (2008) 0.89
Comparative genomics of Mycoplasma: analysis of conserved essential genes and diversity of the pan-genome. PLoS One (2012) 0.88
Molecular phylogenetics of eimeriid coccidia (Eimeriidae, Eimeriorina, Apicomplexa, Alveolata): A preliminary multi-gene and multi-genome approach. Parasitol Res (2015) 0.87
Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line. Mol Biol Evol (2008) 0.84
Assessing meiofaunal variation among individuals utilising morphological and molecular approaches: an example using the Tardigrada. BMC Ecol (2008) 0.84
Phylogeny and biogeography of cyanobacteria and their produced toxins. Mar Drugs (2013) 0.84
Detection of Low-Level Cardinium and Wolbachia Infections in Culicoides. Appl Environ Microbiol (2015) 0.82
A Genomic Island in Salmonella enterica ssp. salamae provides new insights on the genealogy of the locus of enterocyte effacement. PLoS One (2012) 0.82
Molecular characterization and phylogeny of anisakid nematodes from cetaceans from southeastern Atlantic coasts of USA, Gulf of Mexico, and Caribbean Sea. Parasitol Res (2011) 0.82
A new effective method for estimating missing values in the sequence data prior to phylogenetic analysis. Evol Bioinform Online (2007) 0.80
Networks, trees, and treeshrews: assessing support and identifying conflict with multiple loci and a problematic root. Syst Biol (2009) 0.80
An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines. BMC Evol Biol (2014) 0.80
PoMo: An Allele Frequency-Based Approach for Species Tree Estimation. Syst Biol (2015) 0.80
Functional Annotation and Comparative Analysis of a Zygopteran Transcriptome. G3 (Bethesda) (2013) 0.78
Evolutionary diversification of banded tube-dwelling anemones (Cnidaria; Ceriantharia; Isarachnanthus) in the Atlantic Ocean. PLoS One (2012) 0.78
African origin and europe-mediated global dispersal of the cyanobacterium Microcystis aeruginosa. Curr Microbiol (2014) 0.78
Concatenated alignments and the case of the disappearing tree. BMC Evol Biol (2014) 0.78
A Primer on Infectious Disease Bacterial Genomics. Clin Microbiol Rev (2016) 0.78
Analyses of mitochondrial genes reveal two sympatric but genetically divergent lineages of Rhipicephalus appendiculatus in Kenya. Parasit Vectors (2016) 0.77
Phylogenetic analysis of genome rearrangements among five mammalian orders. Mol Phylogenet Evol (2012) 0.77
An application of supertree methods to Mammalian mitogenomic sequences. Evol Bioinform Online (2010) 0.77
Maximum gene-support tree. Evol Bioinform Online (2008) 0.77
High prevalence of trypanosomes in European badgers detected using ITS-PCR. Parasit Vectors (2015) 0.77
Phylogenomics of asexual Epichloë fungal endophytes forming associations with perennial ryegrass. BMC Evol Biol (2015) 0.76
Population-based resequencing revealed an ancestral winter group of cultivated flax: implication for flax domestication processes. Ecol Evol (2012) 0.76
Ortholog-Finder: A Tool for Constructing an Ortholog Data Set. Genome Biol Evol (2016) 0.76
The Origin of Land Plants: A Phylogenomic Perspective. Evol Bioinform Online (2015) 0.76
Virulence Markers and Phylogenetic Analysis of Escherichia coli Strains with Hybrid EAEC/UPEC Genotypes Recovered from Sporadic Cases of Extraintestinal Infections. Front Microbiol (2017) 0.75
Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe. PeerJ (2017) 0.75
Gene and whole genome analyses reveal that the mycobacterial strain JS623 is not a member of the species Mycobacterium smegmatis. Microb Biotechnol (2016) 0.75
Comparative genomics analysis of pKF3-94 in Klebsiella pneumoniae reveals plasmid compatibility and horizontal gene transfer. Front Microbiol (2015) 0.75
Conventional simulation of biological sequences leads to a biased assessment of multi-Loci phylogenetic analysis. Evol Bioinform Online (2013) 0.75
Phylogenetic Diversity, Distribution, and Cophylogeny of Giant Bacteria (Epulopiscium) with their Surgeonfish Hosts in the Red Sea. Front Microbiol (2016) 0.75
Mitochondrial data are not suitable for resolving placental mammal phylogeny. Mamm Genome (2014) 0.75
Integrated gene mapping and synteny studies give insights into the evolution of a sex proto-chromosome in Solea senegalensis. Chromosoma (2016) 0.75
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol (2011) 220.97
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol (2007) 168.76
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol (2013) 112.81
Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A (2004) 20.53
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Precision of molecular time estimates. Trends Genet (2004) 15.94
Estimating divergence times in large molecular phylogenies. Proc Natl Acad Sci U S A (2012) 13.49
TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics (2006) 10.24
Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Mol Biol Evol (2003) 7.78
Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence times. Mol Biol Evol (2011) 6.93
Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol (2003) 5.30
Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals. Mol Biol Evol (2010) 5.13
Evolutionary diagnosis method for variants in personal exomes. Nat Methods (2012) 3.32
Constraint and turnover in sex-biased gene expression in the genus Drosophila. Nature (2007) 3.04
Genomic clocks and evolutionary timescales. Trends Genet (2003) 2.83
Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics (2004) 2.63
Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Mol Biol Evol (2002) 2.23
Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. Genome Res (2003) 1.94
Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP*. Syst Biol (2007) 1.90
Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genome. BMC Genomics (2006) 1.87
Bone and Joint day - India. Indian J Orthop (2013) 1.84
Multiple sequence alignment accuracy and phylogenetic inference. Syst Biol (2006) 1.73
Nullomers: really a matter of natural selection? PLoS One (2007) 1.67
Clinical and laboratory features and response to treatment in patients presenting with vitamin B12 deficiency-related neurological syndromes. Neurol India (2005) 1.66
Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations. BMC Bioinformatics (2004) 1.64
Genomics. Vertebrate genomes compared. Science (2002) 1.57
Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders. Mol Biol Evol (2011) 1.55
Zinc oxide nanoparticles selectively induce apoptosis in human cancer cells through reactive oxygen species. Int J Nanomedicine (2012) 1.54
Considering spatial and temporal scale in landscape-genetic studies of gene flow. Mol Ecol (2010) 1.50
Automated annotation of Drosophila gene expression patterns using a controlled vocabulary. Bioinformatics (2008) 1.50
Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations. Bioinformatics (2012) 1.46
Decompressive surgery for severe cerebral venous sinus thrombosis. Neurol India (2010) 1.46
Drosophila Gene Expression Pattern Annotation Using Sparse Features and Term-Term Interactions. KDD (2009) 1.45
Taxon sampling, bioinformatics, and phylogenomics. Syst Biol (2003) 1.44
Improved lignocellulose conversion to biofuels with thermophilic bacteria and thermostable enzymes. Bioresour Technol (2012) 1.40
Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PLoS Biol (2010) 1.40
Bilateral anterior shoulder dislocation: a case report. Eur J Emerg Med (2005) 1.35
A bag-of-words approach for Drosophila gene expression pattern annotation. BMC Bioinformatics (2009) 1.34
Classification of Drosophila embryonic developmental stage range based on gene expression pattern images. Comput Syst Bioinformatics Conf (2006) 1.33
Recombination and its impact on the genome of the haplodiploid parasitoid wasp Nasonia. PLoS One (2010) 1.31
Comparison of embryonic expression within multigene families using the FlyExpress discovery platform reveals more spatial than temporal divergence. Dev Dyn (2011) 1.27
Genomic sequence of a ranavirus (family Iridoviridae) associated with salamander mortalities in North America. Virology (2003) 1.27
Utility of computer simulations in landscape genetics. Mol Ecol (2010) 1.26
Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. BMC Res Notes (2012) 1.24
Local or general anesthesia for open hernia repair: a randomized trial. Ann Surg (2003) 1.20
The origin of Metazoa: a transition from temporal to spatial cell differentiation. Bioessays (2009) 1.16
Patterns of transitional mutation biases within and among mammalian genomes. Mol Biol Evol (2003) 1.13
Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous. Mol Biol Evol (2005) 1.12
Higher intensity of purifying selection on >90% of the human genes revealed by the intrinsic replacement mutation rates. Mol Biol Evol (2006) 1.12
Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field. Mol Ecol (2010) 1.11
Signatures of ecological resource availability in the animal and plant proteomes. Mol Biol Evol (2006) 1.10
Outcome of laparoscopic cholecystectomy in patients 80 years and older. World J Surg (2004) 1.09
Branding: a harmful practice. Indian Pediatr (2005) 1.07
More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure. Philos Trans R Soc Lond B Biol Sci (2010) 1.05
Nanotoxicity of pure silica mediated through oxidant generation rather than glutathione depletion in human lung epithelial cells. Toxicology (2010) 1.05
Contamination levels and spatial distribution of organochlorine pesticides in soils from India. Ecotoxicol Environ Saf (2011) 1.04
The spectrum of human rhodopsin disease mutations through the lens of interspecific variation. Gene (2004) 1.04
Human genomic disease variants: a neutral evolutionary explanation. Genome Res (2012) 1.02
Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster. Bioinformatics (2009) 1.02
Isolated dorsal dislocation of the intermediate cunieform: a case report and review of the literature. Arch Orthop Trauma Surg (2003) 1.02
Developmental Stage Annotation of Drosophila Gene Expression Pattern Images via an Entire Solution Path for LDA. ACM Trans Knowl Discov Data (2008) 1.02
Magnetic resonance evaluation of tubercular lesion in spine. Int Orthop (2011) 1.01
The role of simultaneous gap arthroplasty and distraction osteogenesis in the management of temporo-mandibular joint ankylosis with mandibular deformity in children. J Craniomaxillofac Surg (2004) 1.01
Isolated bilateral ptosis as the presentation of midbrain tuberculoma. Neurol India (2008) 1.01
DNA vaccines encoding viral envelope proteins confer protective immunity against WSSV in black tiger shrimp. Vaccine (2007) 1.01
Ecological nitrogen limitation shapes the DNA composition of plant genomes. Mol Biol Evol (2009) 1.00
Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label Learning. IJCAI (U S) (2009) 0.99
Evolutionary balancing is critical for correctly forecasting disease-associated amino acid variants. Mol Biol Evol (2013) 0.99
Multifocal skeletal tuberculosis in children: a retrospective study of 18 cases. Scand J Infect Dis (2003) 0.97
Kaempferol has osteogenic effect in ovariectomized adult Sprague-Dawley rats. Mol Cell Endocrinol (2008) 0.95
Reversible electrophysiological abnormalities in hypokalemic periodic paralysis. Indian Pediatr (2008) 0.95
Structural dynamics flexibility informs function and evolution at a proteome scale. Evol Appl (2013) 0.95
Drosophila gene expression pattern annotation through multi-instance multi-label learning. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.95
Confident intraoperative decision making during percutaneous nephrolithotomy: does this patient need a second look? Urology (2008) 0.95
Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition. Trends Ecol Evol (2010) 0.94
Effects of Egb 761 on bone mineral density, bone microstructure, and osteoblast function: Possible roles of quercetin and kaempferol. Mol Cell Endocrinol (2009) 0.92
Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery. Mol Biol Evol (2012) 0.92
How should gaps be treated in parsimony? A comparison of approaches using simulation. Mol Phylogenet Evol (2006) 0.92
Behaviour problems in children and adolescents with seizure disorder: associations and risk factors. Seizure (2005) 0.91
Rampant purifying selection conserves positions with posttranslational modifications in human proteins. Mol Biol Evol (2011) 0.91
A survey of prescribing pattern for osteoarticular tuberculosis: orthopaedic surgeons' and infectious disease experts' perspective. Indian J Tuberc (2009) 0.90
IPS multicentric study: Antidepressant prescription patterns. Indian J Psychiatry (2013) 0.90
Gsdma3(I359N) is a novel ENU-induced mutant mouse line for studying the function of Gasdermin A3 in the hair follicle and epidermis. J Dermatol Sci (2012) 0.90
Snake venom: a potent anticancer agent. Asian Pac J Cancer Prev (2012) 0.90
Differential diagnosis of scrub typhus meningitis from bacterial meningitis using clinical and laboratory features. Neurol India (2013) 0.89
Efficacy of extended DOTS category I chemotherapy in spinal tuberculosis based on MRI-based healed status. Indian J Orthop (2012) 0.89
Genotoxicity assessment of acute exposure of chlorpyrifos to freshwater fish Channa punctatus (Bloch) using micronucleus assay and alkaline single-cell gel electrophoresis. Chemosphere (2008) 0.88
Laparoscopic totally extraperitoneal mesh repair for femoral hernia. J Laparoendosc Adv Surg Tech A (2004) 0.88
Purifying selection modulates the estimates of population differentiation and confounds genome-wide comparisons across single-nucleotide polymorphisms. Mol Biol Evol (2012) 0.88
Assessment of health risks with reference to oxidative stress and DNA damage in chromium exposed population. Sci Total Environ (2012) 0.88
Y Chromosome microdeletion and altered sperm quality in human males with high concentration of seminal hexachlorocyclohexane (HCH). Chemosphere (2010) 0.88
POSSUM scoring for laparoscopic cholecystectomy in the elderly. ANZ J Surg (2005) 0.88
Macrophage migration inhibitory factor: a potential marker for cancer diagnosis and therapy. Asian Pac J Cancer Prev (2012) 0.87
MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation. Bioinformatics (2014) 0.87
Interlaminar discectomy and selective foraminotomy in lumbar disc herniation. J Orthop Surg (Hong Kong) (2001) 0.87
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC Bioinformatics (2013) 0.87
Awake fibreoptic intubation in the sitting position in a patient with a huge goitre. Case Rep Anesthesiol (2011) 0.87
Effect of dust aerosol in patients with asthma. J Asthma (2012) 0.87
Learning sparse representations for fruit-fly gene expression pattern image annotation and retrieval. BMC Bioinformatics (2012) 0.86
Constraining fossil calibrations for molecular clocks. Bioessays (2006) 0.85