Published in Bioinformatics on October 11, 2006
Comparative analysis of Acinetobacters: three genomes for three lifestyles. PLoS One (2008) 3.94
Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet (2011) 3.70
Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti. PLoS Genet (2009) 1.50
ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Res (2011) 1.33
A tribute to disorder in the genome of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa. PLoS One (2013) 1.15
Predicting phenotypic variation in yeast from individual genome sequences. Nat Genet (2011) 1.12
Identification of repeat structure in large genomes using repeat probability clouds. Anal Biochem (2008) 1.07
Swelfe: a detector of internal repeats in sequences and structures. Bioinformatics (2008) 1.06
RepARK--de novo creation of repeat libraries from whole-genome NGS reads. Nucleic Acids Res (2014) 1.01
Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes. Chromosome Res (2011) 0.96
Reductive genome evolution in chemoautotrophic intracellular symbionts of deep-sea Calyptogena clams. Extremophiles (2008) 0.96
Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome. Genome Res (2013) 0.94
The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes. Plant Methods (2009) 0.89
REMiner-II: a tool for rapid identification and configuration of repetitive element arrays from large mammalian chromosomes as a single query. Genomics (2012) 0.88
Plastic architecture of bacterial genome revealed by comparative genomics of Photorhabdus variants. Genome Biol (2008) 0.86
Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale. BMC Bioinformatics (2015) 0.78
Intronic and plasmid-derived regions contribute to the large mitochondrial genome sizes of Agaricomycetes. Curr Genet (2014) 0.78
MsDetector: toward a standard computational tool for DNA microsatellites detection. Nucleic Acids Res (2012) 0.77
Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates. Front Microbiol (2016) 0.76
Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps. Int J Bioinform Res Appl (2014) 0.76
How the Sequence of a Gene Specifies Structural Symmetry in Proteins. PLoS One (2015) 0.75
Understanding the evolution of holoparasitic plants: the complete plastid genome of the holoparasite Cytinus hypocistis (Cytinaceae). Ann Bot (2016) 0.75
Elevated Rate of Genome Rearrangements in Radiation-Resistant Bacteria. Genetics (2017) 0.75
Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue. Sci Rep (2017) 0.75
Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet (2009) 8.51
Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res (2006) 5.31
Burkholderia type VI secretion systems have distinct roles in eukaryotic and bacterial cell interactions. PLoS Pathog (2010) 3.15
ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol (2010) 2.95
Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. Genome Res (2005) 2.89
The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. J Bacteriol (2008) 2.71
Mobility of plasmids. Microbiol Mol Biol Rev (2010) 2.63
New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach. Mol Ecol Resour (2008) 2.58
Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet (2011) 2.54
UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res (2011) 2.45
Towards next-generation biodiversity assessment using DNA metabarcoding. Mol Ecol (2012) 2.43
Environmental DNA. Mol Ecol (2012) 2.36
Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence. Curr Biol (2009) 2.35
Glacial survival of boreal trees in northern Scandinavia. Science (2012) 2.28
The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation. PLoS Genet (2011) 2.01
An in silico approach for the evaluation of DNA barcodes. BMC Genomics (2010) 1.99
Causes of insertion sequences abundance in prokaryotic genomes. Mol Biol Evol (2007) 1.98
The systemic imprint of growth and its uses in ecological (meta)genomics. PLoS Genet (2010) 1.94
The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PLoS One (2010) 1.84
Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes. Mol Microbiol (2006) 1.80
Prey preference of snow leopard (Panthera uncia) in South Gobi, Mongolia. PLoS One (2012) 1.76
Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures. Front Zool (2009) 1.68
Genesis, effects and fates of repeats in prokaryotic genomes. FEMS Microbiol Rev (2009) 1.67
Universal DNA-based methods for assessing the diet of grazing livestock and wildlife from feces. J Agric Food Chem (2009) 1.67
Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan. Mol Ecol (2012) 1.65
Associations between inverted repeats and the structural evolution of bacterial genomes. Genetics (2003) 1.65
CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection. J Bacteriol (2011) 1.54
Microprocessor, Setx, Xrn2, and Rrp6 co-operate to induce premature termination of transcription by RNAPII. Cell (2012) 1.49
Intrastrain heterogeneity of the mgpB gene in Mycoplasma genitalium is extensive in vitro and in vivo and suggests that variation is generated via recombination with repetitive chromosomal sequences. Infect Immun (2006) 1.49
The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems. PLoS Genet (2012) 1.43
Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages. PLoS Genet (2006) 1.40
After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection. Genome Res (2012) 1.38
Persistence drives gene clustering in bacterial genomes. BMC Genomics (2008) 1.37
The temporal dynamics of slightly deleterious mutations in Escherichia coli and Shigella spp. Mol Biol Evol (2008) 1.35
Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction. Genome Res (2007) 1.34
ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Res (2011) 1.33
The impact of the neisserial DNA uptake sequences on genome evolution and stability. Genome Biol (2008) 1.31
Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data. Bioinformatics (2005) 1.30
Transcriptome response to pollutants and insecticides in the dengue vector Aedes aegypti using next-generation sequencing technology. BMC Genomics (2010) 1.27
Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data. Mol Ecol Resour (2014) 1.27
Comparative genomic analysis of three strains of Ehrlichia ruminantium reveals an active process of genome size plasticity. J Bacteriol (2006) 1.23
An integrative method for accurate comparative genome mapping. PLoS Comput Biol (2006) 1.22
A novel heuristic for local multiple alignment of interspersed DNA repeats. IEEE/ACM Trans Comput Biol Bioinform (2009) 1.22
A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability. Mol Ecol (2012) 1.20
New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Mol Ecol (2012) 1.18
Conservation genetics of cattle, sheep, and goats. C R Biol (2011) 1.18
Evolution of conjugation and type IV secretion systems. Mol Biol Evol (2012) 1.14
Dynamic of H5N1 virus in Cambodia and emergence of a novel endemic sub-clade. Infect Genet Evol (2012) 1.13
The adaptation of temperate bacteriophages to their host genomes. Mol Biol Evol (2012) 1.13
Complete genome sequence of the fish pathogen Flavobacterium branchiophilum. Appl Environ Microbiol (2011) 1.12
Calpain is a major cell death effector in selective striatal degeneration induced in vivo by 3-nitropropionate: implications for Huntington's disease. J Neurosci (2003) 1.12
Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA. Mol Ecol (2011) 1.10
Integration of data and methods for genome analysis. Curr Opin Drug Discov Devel (2003) 1.09
Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies. Mol Ecol (2012) 1.09
Conservation of the prion properties of Ure2p through evolution. Mol Biol Cell (2003) 1.07
Swelfe: a detector of internal repeats in sequences and structures. Bioinformatics (2008) 1.06
The unusually large Plasmodium telomerase reverse-transcriptase localizes in a discrete compartment associated with the nucleolus. Nucleic Acids Res (2005) 1.06
An ABC transporter and an outer membrane lipoprotein participate in posttranslational activation of type VI secretion in Pseudomonas aeruginosa. Environ Microbiol (2012) 1.04
The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes. PLoS Comput Biol (2012) 0.99
Alternative to homo-oligomerisation: the creation of local symmetry in proteins by internal amplification. J Mol Biol (2009) 0.97
Protein evolution: causes of trends in amino-acid gain and loss. Nature (2006) 0.97
From GC skews to wavelets: a gentle guide to the analysis of compositional asymmetries in genomic data. Biochimie (2007) 0.97
Assessment of the food habits of the Moroccan dorcas gazelle in M'Sabih Talaa, west central Morocco, using the trnL approach. PLoS One (2012) 0.97
Tracking earthworm communities from soil DNA. Mol Ecol (2012) 0.94
Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens. PLoS Pathog (2012) 0.94
PepLine: a software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences. J Proteome Res (2008) 0.93
Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements. Microbiology (2012) 0.92
Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family. Mol Ecol Resour (2014) 0.92
Plant functional traits reveal the relative contribution of habitat and food preferences to the diet of grasshoppers. Oecologia (2013) 0.90
Erosion of interaction networks in reduced and degraded genomes. J Exp Zool B Mol Dev Evol (2007) 0.90
An assessment of the impacts of molecular oxygen on the evolution of proteomes. Mol Biol Evol (2008) 0.90
Ab initio reconstruction of metabolic pathways. Bioinformatics (2003) 0.89
Neuroprotective effect of zVAD against the neurotoxin 3-nitropropionic acid involves inhibition of calpain. Neuropharmacology (2005) 0.89
Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost. Environ Microbiol (2012) 0.88
Potential involvement of cannabinoid receptors in 3-nitropropionic acid toxicity in vivo. Neuroreport (2004) 0.88
Complex dynamic of dengue virus serotypes 2 and 3 in Cambodia following series of climate disasters. Infect Genet Evol (2012) 0.88
Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding. Mol Ecol (2011) 0.88
Natural genome diversity of AI-2 quorum sensing in Escherichia coli: conserved signal production but labile signal reception. Genome Biol Evol (2013) 0.88
No evidence for elemental-based streamlining of prokaryotic genomes. Trends Ecol Evol (2010) 0.88
Effects of cannabinoids in the rat model of Huntington's disease generated by an intrastriatal injection of malonate. Neuroreport (2003) 0.87
Transcription profiling of resistance to Bti toxins in the mosquito Aedes aegypti using next-generation sequencing. J Invertebr Pathol (2011) 0.87
Genome-wide analysis of DNA repeats in Burkholderia cenocepacia J2315 identifies a novel adhesin-like gene unique to epidemic-associated strains of the ET-12 lineage. Microbiology (2009) 0.86
Bacterial syntenies: an exact approach with gene quorum. BMC Bioinformatics (2011) 0.84
Manipulating or superseding host recombination functions: a dilemma that shapes phage evolvability. PLoS Genet (2013) 0.84
Ehrlichia ruminantium: genomic and evolutionary features. Trends Parasitol (2007) 0.84
Characterization of novel phages isolated in coagulase-negative staphylococci reveals evolutionary relationships with Staphylococcus aureus phages. J Bacteriol (2012) 0.83
Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia. Infect Genet Evol (2011) 0.83
Innovative approach for transcriptomic analysis of obligate intracellular pathogen: selective capture of transcribed sequences of Ehrlichia ruminantium. BMC Mol Biol (2009) 0.83
Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria. PLoS One (2012) 0.83
IGF-1 exacerbates the neurotoxicity of the mitochondrial inhibitor 3NP in rats. Neurosci Lett (2007) 0.82
Natural selection for operons depends on genome size. Genome Biol Evol (2013) 0.82
Cytosine methylation is not the major factor inducing CpG dinucleotide deficiency in bacterial genomes. J Mol Evol (2004) 0.82
Comparative genomics of three strains of Ehrlichia ruminantium: a review. Ann N Y Acad Sci (2006) 0.81