Published in Bioinformatics on January 22, 2004
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol (2013) 11.05
Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet (2009) 8.51
Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet (2010) 7.67
The evolution of gene expression levels in mammalian organs. Nature (2011) 7.16
An atlas of active enhancers across human cell types and tissues. Nature (2014) 6.57
The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell. Bioinformatics (2010) 6.42
Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc Natl Acad Sci U S A (2009) 5.57
A DNA-based registry for all animal species: the barcode index number (BIN) system. PLoS One (2013) 5.10
Phylogeography takes a relaxed random walk in continuous space and time. Mol Biol Evol (2010) 4.82
phangorn: phylogenetic analysis in R. Bioinformatics (2010) 4.57
The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Front Plant Sci (2011) 4.16
LASER: a maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies. Evol Bioinform Online (2007) 3.40
Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat Genet (2012) 3.22
Absence of putative artemisinin resistance mutations among Plasmodium falciparum in Sub-Saharan Africa: a molecular epidemiologic study. J Infect Dis (2014) 3.21
Gene expression divergence recapitulates the developmental hourglass model. Nature (2010) 3.20
adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics (2011) 3.18
The hymenopteran tree of life: evidence from protein-coding genes and objectively aligned ribosomal data. PLoS One (2013) 3.14
Independently evolving species in asexual bdelloid rotifers. PLoS Biol (2007) 3.05
Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing. PLoS One (2010) 3.02
Prions are a common mechanism for phenotypic inheritance in wild yeasts. Nature (2012) 2.89
Comparative genomic and phylogeographic analysis of Mycobacterium leprae. Nat Genet (2009) 2.76
Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol (2010) 2.60
A comparison of bats and rodents as reservoirs of zoonotic viruses: are bats special? Proc Biol Sci (2013) 2.56
PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Comput Biol (2011) 2.54
Plant extinctions and introductions lead to phylogenetic and taxonomic homogenization of the European flora. Proc Natl Acad Sci U S A (2009) 2.51
Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc Natl Acad Sci U S A (2012) 2.40
Mitochondrial cox1 sequence data reliably uncover patterns of insect diversity but suffer from high lineage-idiosyncratic error rates. PLoS One (2010) 2.38
Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets. Syst Biol (2013) 2.36
Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence. Curr Biol (2009) 2.35
Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana. Nature (2010) 2.34
Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis. PLoS Med (2015) 2.28
A universal scaling relationship between body mass and proximal limb bone dimensions in quadrupedal terrestrial tetrapods. BMC Biol (2012) 2.27
The effect of geographical scale of sampling on DNA barcoding. Syst Biol (2012) 2.22
An extreme case of plant-insect codiversification: figs and fig-pollinating wasps. Syst Biol (2012) 2.20
Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environ Microbiol (2009) 2.20
Coinfection. Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation. Science (2014) 2.19
Both social and ecological factors predict ungulate brain size. Proc Biol Sci (2006) 2.17
Historical collections reveal patterns of diffusion of sweet potato in Oceania obscured by modern plant movements and recombination. Proc Natl Acad Sci U S A (2013) 2.08
A timescale for evolution, population expansion, and spatial spread of an emerging clone of methicillin-resistant Staphylococcus aureus. PLoS Pathog (2010) 2.04
Advancing our understanding of the human microbiome using QIIME. Methods Enzymol (2013) 2.04
Disease associations between honeybees and bumblebees as a threat to wild pollinators. Nature (2014) 2.01
Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ (2014) 2.01
The evolution of the social brain: anthropoid primates contrast with other vertebrates. Proc Biol Sci (2007) 2.01
Divergent, coexisting Pseudomonas aeruginosa lineages in chronic cystic fibrosis lung infections. Am J Respir Crit Care Med (2015) 2.00
Transmission network parameters estimated from HIV sequences for a nationwide epidemic. J Infect Dis (2011) 1.98
Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science (2014) 1.94
Phylogenetic conservatism of functional traits in microorganisms. ISME J (2012) 1.92
EvolView, an online tool for visualizing, annotating and managing phylogenetic trees. Nucleic Acids Res (2012) 1.90
DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors. Cancer Cell (2015) 1.87
Reconstructing disease outbreaks from genetic data: a graph approach. Heredity (Edinb) (2010) 1.86
An adaptive threshold in mammalian neocortical evolution. PLoS Biol (2014) 1.84
Climate change, body size evolution, and Cope's Rule in deep-sea ostracodes. Proc Natl Acad Sci U S A (2006) 1.81
A comparative analysis of the evolution of imperfect mimicry. Nature (2012) 1.77
The roles of time and ecology in the continental radiation of the Old World leaf warblers (Phylloscopus and Seicercus). Philos Trans R Soc Lond B Biol Sci (2010) 1.77
Viral phylodynamics and the search for an 'effective number of infections'. Philos Trans R Soc Lond B Biol Sci (2010) 1.76
Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence. BMC Genomics (2010) 1.75
Unexpected patterns of fisheries collapse in the world's oceans. Proc Natl Acad Sci U S A (2011) 1.75
Brain size and resource specialization predict long-term population trends in British birds. Proc Biol Sci (2005) 1.73
Genomic diversity and evolution of the head crest in the rock pigeon. Science (2013) 1.68
Hibernation is associated with increased survival and the evolution of slow life histories among mammals. Proc Biol Sci (2011) 1.67
A whole genome Bayesian scan for adaptive genetic divergence in West African cattle. BMC Genomics (2009) 1.65
Selective pressure of antibiotic pollution on bacteria of importance to public health. Environ Health Perspect (2012) 1.65
Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster. Mol Ecol (2016) 1.65
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biol (2013) 1.65
Epiphytic leafy liverworts diversified in angiosperm-dominated forests. Sci Rep (2014) 1.63
Space versus phylogeny: disentangling phylogenetic and spatial signals in comparative data. Proc Biol Sci (2009) 1.63
Avoidance of protein fold disruption in natural virus recombinants. PLoS Pathog (2007) 1.62
Cooperative breeding and monogamy in mammalian societies. Proc Biol Sci (2012) 1.62
Nocturnality in synapsids predates the origin of mammals by over 100 million years. Proc Biol Sci (2014) 1.60
Phylogenetic trait conservatism and the evolution of functional trade-offs in arbuscular mycorrhizal fungi. Proc Biol Sci (2009) 1.60
The mode and tempo of genome size evolution in eukaryotes. Genome Res (2007) 1.59
The inconstant gut microbiota of Drosophila species revealed by 16S rRNA gene analysis. ISME J (2013) 1.58
Niche filling slows the diversification of Himalayan songbirds. Nature (2014) 1.58
The evolution of intron size in amniotes: a role for powered flight? Genome Biol Evol (2012) 1.57
Inference of demographic history from genealogical trees using reversible jump Markov chain Monte Carlo. BMC Evol Biol (2005) 1.56
Towards a comprehensive barcode library for arctic life - Ephemeroptera, Plecoptera, and Trichoptera of Churchill, Manitoba, Canada. Front Zool (2009) 1.55
Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection. MBio (2012) 1.55
A comparison of worldwide phonemic and genetic variation in human populations. Proc Natl Acad Sci U S A (2015) 1.54
Domestication selected for deceleration of the circadian clock in cultivated tomato. Nat Genet (2015) 1.53
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
Diversity versus disparity and the radiation of modern cetaceans. Proc Biol Sci (2010) 1.53
Phylogenetic and trait similarity to a native species predict herbivory on non-native oaks. Proc Natl Acad Sci U S A (2009) 1.52
Insights into the genetic history of French cattle from dense SNP data on 47 worldwide breeds. PLoS One (2010) 1.51
Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila. PLoS Genet (2014) 1.50
DNA barcode analysis: a comparison of phylogenetic and statistical classification methods. BMC Bioinformatics (2009) 1.50
Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds. Ecol Lett (2011) 1.49
The scaling of frontal cortex in primates and carnivores. Proc Natl Acad Sci U S A (2004) 1.48
Low Prevalence of Conjunctival Infection with Chlamydia trachomatis in a Treatment-Naïve Trachoma-Endemic Region of the Solomon Islands. PLoS Negl Trop Dis (2016) 1.47
African origin of the malaria parasite Plasmodium vivax. Nat Commun (2014) 1.47
Functional traits explain variation in plant life history strategies. Proc Natl Acad Sci U S A (2013) 1.47
Daily torpor and hibernation in birds and mammals. Biol Rev Camb Philos Soc (2014) 1.46
Determination of mitochondrial genetic diversity in mammals. Genetics (2008) 1.46
Social fishes and single mothers: brain evolution in African cichlids. Proc Biol Sci (2009) 1.45
A Highly Conserved Bacterial D-Serine Uptake System Links Host Metabolism and Virulence. PLoS Pathog (2016) 1.45
How does cognition evolve? Phylogenetic comparative psychology. Anim Cogn (2011) 1.45
Abundant occurrence of basal radial glia in the subventricular zone of embryonic neocortex of a lissencephalic primate, the common marmoset Callithrix jacchus. Cereb Cortex (2011) 1.45
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Res (2008) 1.45
Genome-Based Infection Tracking Reveals Dynamics of Clostridium difficile Transmission and Disease Recurrence. Clin Infect Dis (2015) 1.45
Comparative transcriptomics reveals the conserved building blocks involved in parallel evolution of diverse phenotypic traits in ants. Genome Biol (2016) 1.44
Dissecting the phenotypic components of crop plant growth and drought responses based on high-throughput image analysis. Plant Cell (2014) 1.43
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics (2002) 19.27
A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Stat Appl Genet Mol Biol (2005) 9.57
Retracted TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol (2004) 8.78
An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics (2004) 7.85
Identifying periodically expressed transcripts in microarray time series data. Bioinformatics (2004) 4.62
A general modular framework for gene set enrichment analysis. BMC Bioinformatics (2009) 3.92
From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data. BMC Syst Biol (2007) 3.56
Partial least squares: a versatile tool for the analysis of high-dimensional genomic data. Brief Bioinform (2006) 3.16
Learning causal networks from systems biology time course data: an effective model selection procedure for the vector autoregressive process. BMC Bioinformatics (2007) 2.39
Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach. Stat Appl Genet Mol Biol (2007) 2.31
Analysis of comparative data using generalized estimating equations. J Theor Biol (2002) 1.89
Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach. Theor Biol Med Model (2005) 1.76
Over-optimism in bioinformatics: an illustration. Bioinformatics (2010) 1.67
Inference of demographic history from genealogical trees using reversible jump Markov chain Monte Carlo. BMC Evol Biol (2005) 1.56
MALDIquant: a versatile R package for the analysis of mass spectrometry data. Bioinformatics (2012) 1.52
Dating cryptodiran nodes: origin and diversification of the turtle superfamily Testudinoidea. Mol Phylogenet Evol (2011) 1.28
Gene ranking and biomarker discovery under correlation. Bioinformatics (2009) 1.26
A unifying model for the analysis of phenotypic, genetic, and geographic data. Syst Biol (2012) 0.96
A CART-based approach to discover emerging patterns in microarray data. Bioinformatics (2003) 0.95
Morphometrics parallel genetics in a newly discovered and endangered taxon of Galápagos tortoise. PLoS One (2009) 0.91
Study of the carapace shape and growth in two Galápagos tortoise lineages. J Morphol (2011) 0.85
A novel algorithm for simultaneous SNP selection in high-dimensional genome-wide association studies. BMC Bioinformatics (2012) 0.85
Cytonuclear discordance among Southeast Asian black rats (Rattus rattus complex). Mol Ecol (2012) 0.85
Incorporating parasite systematics in comparative analyses of variation in spleen mass and testes sizes of rodents. Parasitology (2011) 0.85
Height and body mass influence on human body outlines: a quantitative approach using an elliptic Fourier analysis. Am J Phys Anthropol (2010) 0.84
Gavialis from the Pleistocene of Thailand and its relevance for drainage connections from India to Java. PLoS One (2012) 0.82
Signal identification for rare and weak features: higher criticism or false discovery rates? Biostatistics (2012) 0.80
Morphometric identification of individuals when there are more shape variables than reference specimens: a case study in Galápagos tortoises. C R Biol (2011) 0.78
Therapeutic vaccination reduces HIV sequence variability. FASEB J (2007) 0.77
Non-random occurrence of Robertsonian translocations in the house mouse (Mus musculus domesticus): is it related to quantitative variation in the minor satellite? Cytogenet Genome Res (2014) 0.75