Published in Bioinformatics on October 04, 2006
TimeTree2: species divergence times on the iPhone. Bioinformatics (2011) 14.23
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet (2009) 5.37
The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat Genet (2013) 4.40
Characterization of the proteome, diseases and evolution of the human postsynaptic density. Nat Neurosci (2010) 3.67
Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction. PLoS Genet (2010) 3.03
The evolutionary origin of orphan genes. Nat Rev Genet (2011) 2.98
The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature (2014) 2.93
Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature (2014) 2.15
Thermodynamic system drift in protein evolution. PLoS Biol (2014) 2.10
Local DNA hypomethylation activates genes in rice endosperm. Proc Natl Acad Sci U S A (2010) 1.99
Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the X chromosome. PLoS Biol (2010) 1.98
Tree of life reveals clock-like speciation and diversification. Mol Biol Evol (2015) 1.85
A role for host-parasite interactions in the horizontal transfer of transposons across phyla. Nature (2010) 1.83
Comparative genomics of the odorant-binding and chemosensory protein gene families across the Arthropoda: origin and evolutionary history of the chemosensory system. Genome Biol Evol (2011) 1.82
Exploiting diversity and synthetic biology for the production of algal biofuels. Nature (2012) 1.80
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biol (2013) 1.65
Nocturnality in synapsids predates the origin of mammals by over 100 million years. Proc Biol Sci (2014) 1.60
Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biol (2013) 1.59
Reassessing domain architecture evolution of metazoan proteins: major impact of gene prediction errors. Genes (Basel) (2011) 1.56
Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genet (2008) 1.52
The genome of Mesobuthus martensii reveals a unique adaptation model of arthropods. Nat Commun (2013) 1.50
Coevolution of retroelements and tandem zinc finger genes. Genome Res (2011) 1.46
Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. PLoS Pathog (2012) 1.44
The α1,6-fucosyltransferase gene (fut8) from the Sf9 lepidopteran insect cell line: insights into fut8 evolution. PLoS One (2014) 1.43
Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proc Natl Acad Sci U S A (2014) 1.36
RNA polymerase II C-terminal domain: Tethering transcription to transcript and template. Chem Rev (2013) 1.35
The probability of genetic parallelism and convergence in natural populations. Proc Biol Sci (2012) 1.35
Measuring the evolutionary rate of protein-protein interaction. Proc Natl Acad Sci U S A (2011) 1.32
Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations. Genome Res (2009) 1.26
Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life. BMC Evol Biol (2011) 1.25
Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. BMC Res Notes (2012) 1.24
HAMR: high-throughput annotation of modified ribonucleotides. RNA (2013) 1.24
Origin and evolution of SINEs in eukaryotic genomes. Heredity (Edinb) (2011) 1.23
Pervasive horizontal transfer of rolling-circle transposons among animals. Genome Biol Evol (2010) 1.21
Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms. PLoS One (2011) 1.20
Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms. BMC Evol Biol (2012) 1.18
Evolutionary history and metabolic insights of ancient mammalian uricases. Proc Natl Acad Sci U S A (2014) 1.18
Timing the origin of human malarias: the lemur puzzle. BMC Evol Biol (2011) 1.17
Mechanisms and dynamics of orphan gene emergence in insect genomes. Genome Biol Evol (2013) 1.13
The Ancient Evolutionary History of Polyomaviruses. PLoS Pathog (2016) 1.12
Daily magnesium fluxes regulate cellular timekeeping and energy balance. Nature (2016) 1.12
Lineage-specific patterns of functional diversification in the alpha- and beta-globin gene families of tetrapod vertebrates. Mol Biol Evol (2010) 1.11
The dispanins: a novel gene family of ancient origin that contains 14 human members. PLoS One (2012) 1.11
DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis. PLoS Genet (2013) 1.11
Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. Genome Biol Evol (2015) 1.11
The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks. PLoS One (2013) 1.11
Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos). BMC Genomics (2011) 1.10
Male-specific region of the bovine Y chromosome is gene rich with a high transcriptomic activity in testis development. Proc Natl Acad Sci U S A (2013) 1.10
Hybridisation is associated with increased fecundity and size in invasive taxa: meta-analytic support for the hybridisation-invasion hypothesis. Ecol Lett (2014) 1.10
Determinants of the rate of protein sequence evolution. Nat Rev Genet (2015) 1.09
Insights into the evolution of longevity from the bowhead whale genome. Cell Rep (2015) 1.09
Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans. Proc Natl Acad Sci U S A (2013) 1.09
Molecular cytogenetic map of the central bearded dragon, Pogona vitticeps (Squamata: Agamidae). Chromosome Res (2013) 1.09
The obesity gene, TMEM18, is of ancient origin, found in majority of neuronal cells in all major brain regions and associated with obesity in severely obese children. BMC Med Genet (2010) 1.09
Phylostratigraphic bias creates spurious patterns of genome evolution. Mol Biol Evol (2014) 1.09
Functional morphometric analysis of the furcula in mesozoic birds. PLoS One (2012) 1.08
Networks of bZIP protein-protein interactions diversified over a billion years of evolution. Science (2013) 1.08
When orthologs diverge between human and mouse. Brief Bioinform (2011) 1.07
Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants. Plant Cell (2012) 1.07
The human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer. Genome Res (2011) 1.07
Non-homologous sex chromosomes of birds and snakes share repetitive sequences. Chromosome Res (2010) 1.06
Metabolic rate and body size are linked with perception of temporal information. Anim Behav (2013) 1.06
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
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. J Biomed Semantics (2010) 1.04
Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects. Elife (2014) 1.03
Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication. Genome Res (2010) 1.03
Extreme expansion of the olfactory receptor gene repertoire in African elephants and evolutionary dynamics of orthologous gene groups in 13 placental mammals. Genome Res (2014) 1.03
An ancient history of gene duplications, fusions and losses in the evolution of APOBEC3 mutators in mammals. BMC Evol Biol (2012) 1.02
Maximum likelihood models and algorithms for gene tree evolution with duplications and losses. BMC Bioinformatics (2011) 1.02
Widespread horizontal transfer of retrotransposons. Proc Natl Acad Sci U S A (2012) 1.02
Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes. Nat Commun (2014) 1.01
On the origins of Mendelian disease genes in man: the impact of gene duplication. Mol Biol Evol (2011) 1.01
A quick guide for developing effective bioinformatics programming skills. PLoS Comput Biol (2009) 1.01
Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways. Elife (2014) 1.01
TIR domain-containing adaptor SARM is a late addition to the ongoing microbe-host dialog. Dev Comp Immunol (2010) 1.01
Massive expansion and functional divergence of innate immune genes in a protostome. Sci Rep (2015) 1.00
Endogenous lentiviruses in the ferret genome. J Virol (2012) 1.00
Mechanisms of intron gain and loss in Drosophila. BMC Evol Biol (2011) 1.00
Correcting for differential transcript coverage reveals a strong relationship between alternative splicing and organism complexity. Mol Biol Evol (2014) 1.00
Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles. Proc Biol Sci (2010) 0.99
Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution. Genome Biol Evol (2012) 0.99
Integration of new genes into cellular networks, and their structural maturation. Genetics (2013) 0.98
Scaffold nucleoporins Nup188 and Nup192 share structural and functional properties with nuclear transport receptors. Elife (2013) 0.98
Ultraconserved coding regions outside the homeobox of mammalian Hox genes. BMC Evol Biol (2008) 0.98
Phylogeny, life history, and ecology contribute to differences in amphibian susceptibility to ranaviruses. Ecohealth (2011) 0.98
ProteinHistorian: tools for the comparative analysis of eukaryote protein origin. PLoS Comput Biol (2012) 0.97
Conservation of transcription factor binding specificities across 600 million years of bilateria evolution. Elife (2015) 0.97
Inference of the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes from comparative gene mapping. PLoS One (2012) 0.97
Potential functional replacement of the plastidic acetyl-CoA carboxylase subunit (accD) gene by recent transfers to the nucleus in some angiosperm lineages. Plant Physiol (2013) 0.97
Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks. BMC Evol Biol (2012) 0.96
In silico prediction of physical protein interactions and characterization of interactome orphans. Nat Methods (2014) 0.96
The dynamics and evolutionary potential of domain loss and emergence. Mol Biol Evol (2011) 0.95
The evolution of the ribosome biogenesis pathway from a yeast perspective. Nucleic Acids Res (2013) 0.95
Integrated syntenic and phylogenomic analyses reveal an ancient genome duplication in monocots. Plant Cell (2014) 0.94
Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites. Nucleic Acids Res (2012) 0.94
Sex chromosome-to-autosome transposition events counter Y-chromosome gene loss in mammals. Genome Biol (2015) 0.93
Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes. Genome Biol (2013) 0.93
The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution. PLoS Genet (2013) 0.93
Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes. Proc Natl Acad Sci U S A (2015) 0.93
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
MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform (2008) 24.69
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
Bioinformatics software for biologists in the genomics era. Bioinformatics (2007) 10.70
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
Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. J Exp Zool B Mol Dev Evol (2005) 2.22
Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. Genome Res (2003) 1.94
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
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
FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. Genome Biol (2008) 1.58
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
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
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
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
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
Developmental Stage Annotation of Drosophila Gene Expression Pattern Images via an Entire Solution Path for LDA. ACM Trans Knowl Discov Data (2008) 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
Magnetic resonance evaluation of tubercular lesion in spine. Int Orthop (2011) 1.01
Isolated bilateral ptosis as the presentation of midbrain tuberculoma. Neurol India (2008) 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
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
Drosophila gene expression pattern annotation through multi-instance multi-label learning. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.95
Kaempferol has osteogenic effect in ovariectomized adult Sprague-Dawley rats. Mol Cell Endocrinol (2008) 0.95
Structural dynamics flexibility informs function and evolution at a proteome scale. Evol Appl (2013) 0.95
Amniote phylogeny and the position of turtles. BMC Biol (2012) 0.95
Reversible electrophysiological abnormalities in hypokalemic periodic paralysis. Indian Pediatr (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
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
Effect of dust aerosol in patients with asthma. J Asthma (2012) 0.87
Awake fibreoptic intubation in the sitting position in a patient with a huge goitre. Case Rep Anesthesiol (2011) 0.87
Interlaminar discectomy and selective foraminotomy in lumbar disc herniation. J Orthop Surg (Hong Kong) (2001) 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
Genome-wide profiling of human cap-independent translation-enhancing elements. Nat Methods (2013) 0.84
Guillain-Barre syndrome occurring in the course of dengue fever. Neurol India (2005) 0.84
A case study: biomedical waste management practices at city hospital in Himachal Pradesh. Waste Manag Res (2011) 0.84
Phylogenetic placement of metagenomic reads using the minimum evolution principle. BMC Genomics (2015) 0.83