Published in BMC Res Notes on October 22, 2012
Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proc Natl Acad Sci U S A (2015) 1.96
Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies. PLoS One (2014) 1.31
Lost branches on the tree of life. PLoS Biol (2013) 1.26
The dawn of open access to phylogenetic data. PLoS One (2014) 1.18
Best practices for data sharing in phylogenetic research. PLoS Curr (2014) 1.04
Phylesystem: a git-based data store for community-curated phylogenetic estimates. Bioinformatics (2015) 1.00
An open future for ecological and evolutionary data? BMC Ecol (2014) 0.91
Advancing data reuse in phyloinformatics using an ontology-driven Semantic Web approach. BMC Med Genomics (2013) 0.89
Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies. Syst Biol (2015) 0.89
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC Bioinformatics (2013) 0.87
A tale of two drug targets: the evolutionary history of BACE1 and BACE2. Front Genet (2013) 0.81
An open future for ecological and evolutionary data? BMC Evol Biol (2014) 0.75
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
The Pfam protein families database. Nucleic Acids Res (2009) 37.98
The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics (2002) 29.41
bold: The Barcode of Life Data System (http://www.barcodinglife.org). Mol Ecol Notes (2007) 25.13
The worldwide leaf economics spectrum. Nature (2004) 20.42
The delayed rise of present-day mammals. Nature (2007) 15.98
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res (2008) 12.72
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2010) 10.97
NEXUS: an extensible file format for systematic information. Syst Biol (1997) 10.63
TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics (2006) 10.24
BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res (2004) 8.21
Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples. Zookeys (2010) 6.64
TreeFam: 2008 Update. Nucleic Acids Res (2007) 6.63
Biodiversity informatics: the challenge of linking data and the role of shared identifiers. Brief Bioinform (2008) 6.07
phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics (2009) 6.02
Darwin's abominable mystery: Insights from a supertree of the angiosperms. Proc Natl Acad Sci U S A (2004) 5.41
The poor availability of psychological research data for reanalysis. Am Psychol (2006) 5.21
Globally distributed object identification for biological knowledgebases. Brief Bioinform (2004) 4.72
Adventures in semantic publishing: exemplar semantic enhancements of a research article. PLoS Comput Biol (2009) 4.72
Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol (2009) 4.65
A new dawn for the naming of fungi: impacts of decisions made in Melbourne in July 2011 on the future publication and regulation of fungal names. IMA Fungus (2011) 4.14
Empirical study of data sharing by authors publishing in PLoS journals. PLoS One (2009) 4.09
Preserving the evolutionary potential of floras in biodiversity hotspots. Nature (2007) 3.93
Names are key to the big new biology. Trends Ecol Evol (2010) 3.86
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics (2005) 3.62
Data archiving is a good investment. Nature (2011) 3.53
Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules. Acta Crystallogr D Biol Crystallogr (1998) 3.35
Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS (2006) 2.57
On the persistence of supplementary resources in biomedical publications. BMC Bioinformatics (2006) 2.27
Visualising very large phylogenetic trees in three dimensional hyperbolic space. BMC Bioinformatics (2004) 2.26
Evolutionary informatics: unifying knowledge about the diversity of life. Trends Ecol Evol (2011) 1.93
NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Syst Biol (2012) 1.86
Understanding angiosperm diversification using small and large phylogenetic trees. Am J Bot (2011) 1.77
Relative rates of gene fusion and fission in multi-domain proteins. Trends Genet (2005) 1.75
More closely related species are more ecologically similar in an experimental test. Proc Natl Acad Sci U S A (2011) 1.68
PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nucleic Acids Res (2006) 1.58
Data archiving in ecology and evolution: best practices. Trends Ecol Evol (2010) 1.46
Spatial patterns of phylogenetic diversity. Ecol Lett (2010) 1.45
Data sharing: how much doesn't get submitted to GenBank? PLoS Biol (2006) 1.37
Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees. Syst Biol (2010) 1.36
Shark tales: a molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes). Mol Phylogenet Evol (2010) 1.35
Linking big: the continuing promise of evolutionary synthesis. Evolution (2009) 1.33
Deriving phylogenetic trees from the similarity analysis of metabolic pathways. Bioinformatics (2003) 1.31
The impact of multiple protein sequence alignment on phylogenetic estimation. IEEE/ACM Trans Comput Biol Bioinform (2011) 1.31
The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics. Nucleic Acids Res (2005) 1.27
Animal and human pathogenic Escherichia coli strains share common genetic backgrounds. Infect Genet Evol (2011) 1.23
TreeSnatcher: coding trees from images. Bioinformatics (2007) 1.20
Angiosperm leaf vein patterns are linked to leaf functions in a global-scale data set. Am J Bot (2011) 1.03
TreeRipper web application: towards a fully automated optical tree recognition software. BMC Bioinformatics (2011) 1.03
Correlated evolution of female neoteny and flightlessness with male spermatophore production in fireflies (Coleoptera: Lampyridae). Evolution (2010) 0.99
Phylogenetic utility of nuclear introns in interfamilial relationships of Caniformia (order Carnivora). Syst Biol (2011) 0.95
Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data. BMC Bioinformatics (2007) 0.93
Phylogenomic analysis of kinetoplastids supports that trypanosomatids arose from within bodonids. Mol Biol Evol (2010) 0.87
Searching NCBI databases using Entrez. Curr Protoc Bioinformatics (2011) 0.85
Phylogenetic signals and ecotoxicological responses: potential implications for aquatic biomonitoring. Ecotoxicology (2011) 0.84
Oogonial biometry and phylogenetic analyses of the Pythium vexans species group from woody agricultural hosts in South Africa reveal distinct groups within this taxon. Fungal Biol (2010) 0.83
Lacustrine radiations in African Synodontis catfish. J Evol Biol (2009) 0.83
Conservative coevolution of Müllerian mimicry in a group of rift lake catfish. Evolution (2010) 0.82
Ecology and evolution of the diaspore "burial syndrome". Evolution (2010) 0.82
Comparing chromosomal and mitochondrial phylogenies of the Indriidae (Primates, Lemuriformes). Chromosome Res (2011) 0.80
Ancient colonization predicts recent naturalization in Anolis lizards. Evolution (2011) 0.78
On the artefactual parasitic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations. BMC Evol Biol (2010) 0.78
A methodological investigation of hominoid craniodental morphology and phylogenetics. J Hum Evol (2010) 0.77
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
The delayed rise of present-day mammals. Nature (2007) 15.98
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
The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Front Plant Sci (2011) 4.16
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
The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proc Natl Acad Sci U S A (2013) 1.68
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
Nurturing the use of evolutionary diversity in nature conservation. Trends Ecol Evol (2013) 1.52
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
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. J Biomed Semantics (2013) 1.44
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
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
Higher intensity of purifying selection on >90% of the human genes revealed by the intrinsic replacement mutation rates. Mol Biol Evol (2006) 1.12
Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous. Mol Biol Evol (2005) 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 DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. J Biomed Semantics (2010) 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
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
Structural dynamics flexibility informs function and evolution at a proteome scale. Evol Appl (2013) 0.95
Reversible electrophysiological abnormalities in hypokalemic periodic paralysis. Indian Pediatr (2008) 0.95
Kaempferol has osteogenic effect in ovariectomized adult Sprague-Dawley rats. Mol Cell Endocrinol (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
IPS multicentric study: Antidepressant prescription patterns. Indian J Psychiatry (2013) 0.90
A survey of prescribing pattern for osteoarticular tuberculosis: orthopaedic surgeons' and infectious disease experts' perspective. Indian J Tuberc (2009) 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
Advancing data reuse in phyloinformatics using an ontology-driven Semantic Web approach. BMC Med Genomics (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
Energy-dependent modulation of glucagon-like signaling in Drosophila via the AMP-activated protein kinase. Genetics (2012) 0.89
Differential diagnosis of scrub typhus meningitis from bacterial meningitis using clinical and laboratory features. Neurol India (2013) 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
Assessment of health risks with reference to oxidative stress and DNA damage in chromium exposed population. Sci Total Environ (2012) 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
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
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC Bioinformatics (2013) 0.87
Interlaminar discectomy and selective foraminotomy in lumbar disc herniation. J Orthop Surg (Hong Kong) (2001) 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