Published in Methods Mol Biol on January 01, 2000
Savant: genome browser for high-throughput sequencing data. Bioinformatics (2010) 6.51
Genome assembly forensics: finding the elusive mis-assembly. Genome Biol (2008) 4.91
Complete nucleotide sequence of a 92-kilobase plasmid harboring the CTX-M-15 extended-spectrum beta-lactamase involved in an outbreak in long-term-care facilities in Toronto, Canada. Antimicrob Agents Chemother (2004) 4.46
RePS: a sequence assembler that masks exact repeats identified from the shotgun data. Genome Res (2002) 4.35
A bioinformatician's guide to metagenomics. Microbiol Mol Biol Rev (2008) 4.33
Complete genome sequence of the marine planctomycete Pirellula sp. strain 1. Proc Natl Acad Sci U S A (2003) 4.16
Long-range heterogeneity at the 3' ends of human mRNAs. Genome Res (2002) 3.91
Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. J Bacteriol (2007) 3.43
High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak. BMC Genomics (2010) 3.09
Usefulness of multilocus sequence typing for characterization of clinical isolates of Candida albicans. J Clin Microbiol (2002) 3.01
The genome sequence of Clostridium tetani, the causative agent of tetanus disease. Proc Natl Acad Sci U S A (2003) 2.88
Analysis of the genome structure of the nonpathogenic probiotic Escherichia coli strain Nissle 1917. J Bacteriol (2004) 2.80
Use of sequence analysis of the NS5B region for routine genotyping of hepatitis C virus with reference to C/E1 and 5' untranslated region sequences. J Clin Microbiol (2007) 2.55
The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. J Bacteriol (2006) 2.50
The genome of Aeromonas salmonicida subsp. salmonicida A449: insights into the evolution of a fish pathogen. BMC Genomics (2008) 2.40
A transposon-induced epigenetic change leads to sex determination in melon. Nature (2009) 2.39
Genetic structure and distribution of four pathogenicity islands (PAI I(536) to PAI IV(536)) of uropathogenic Escherichia coli strain 536. Infect Immun (2002) 2.36
DNA sequencing: bench to bedside and beyond. Nucleic Acids Res (2007) 2.25
Diversity and seasonal dynamics of bacterial community in indoor environment. BMC Microbiol (2008) 2.22
Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging. Proc Natl Acad Sci U S A (2010) 2.14
Gene islands integrated into tRNA(Gly) genes confer genome diversity on a Pseudomonas aeruginosa clone. J Bacteriol (2002) 2.14
CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes. BMC Bioinformatics (2002) 2.13
The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features. Proc Natl Acad Sci U S A (2008) 2.12
Cystin, a novel cilia-associated protein, is disrupted in the cpk mouse model of polycystic kidney disease. J Clin Invest (2002) 2.07
Longitudinal study of Finnish Campylobacter jejuni and C. coli isolates from humans, using multilocus sequence typing, including comparison with epidemiological data and isolates from poultry and cattle. Appl Environ Microbiol (2006) 2.01
Structural and functional characterization of gene clusters directing nonribosomal synthesis of bioactive cyclic lipopeptides in Bacillus amyloliquefaciens strain FZB42. J Bacteriol (2004) 1.99
S-Fimbria-encoding determinant sfa(I) is located on pathogenicity island III(536) of uropathogenic Escherichia coli strain 536. Infect Immun (2001) 1.89
Identification of the fertility restoration locus, Rfo, in radish, as a member of the pentatricopeptide-repeat protein family. EMBO Rep (2003) 1.87
Human leptospirosis caused by a new, antigenically unique Leptospira associated with a Rattus species reservoir in the Peruvian Amazon. PLoS Negl Trop Dis (2008) 1.87
GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database. Nucleic Acids Res (2011) 1.86
Characterization of a spontaneous nonmagnetic mutant of Magnetospirillum gryphiswaldense reveals a large deletion comprising a putative magnetosome island. J Bacteriol (2003) 1.85
Analysis of fungal flora in indoor dust by ribosomal DNA sequence analysis, quantitative PCR, and culture. Appl Environ Microbiol (2007) 1.80
Exome sequencing of index patients with retinal dystrophies as a tool for molecular diagnosis. PLoS One (2013) 1.77
Microbial community analysis reveals high level phylogenetic alterations in the overall gastrointestinal microbiota of diarrhoea-predominant irritable bowel syndrome sufferers. BMC Gastroenterol (2009) 1.76
A dense single-nucleotide polymorphism-based genetic linkage map of grapevine (Vitis vinifera L.) anchoring Pinot Noir bacterial artificial chromosome contigs. Genetics (2007) 1.75
The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PLoS One (2010) 1.71
The nucleotide sequence of Shiga toxin (Stx) 2e-encoding phage phiP27 is not related to other Stx phage genomes, but the modular genetic structure is conserved. Infect Immun (2002) 1.71
Mitochondrial DNA analysis of field populations of Helicoverpa armigera (Lepidoptera: Noctuidae) and of its relationship to H. zea. BMC Evol Biol (2007) 1.68
Identification of novel imprinted genes in a genome-wide screen for maternal methylation. Genome Res (2003) 1.67
A single nucleotide exchange in the wzy gene is responsible for the semirough O6 lipopolysaccharide phenotype and serum sensitivity of Escherichia coli strain Nissle 1917. J Bacteriol (2002) 1.66
The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity. PLoS Genet (2009) 1.64
The clc element of Pseudomonas sp. strain B13, a genomic island with various catabolic properties. J Bacteriol (2006) 1.61
Host imprints on bacterial genomes--rapid, divergent evolution in individual patients. PLoS Pathog (2010) 1.54
Characterization of a shiga toxin 2e-converting bacteriophage from an Escherichia coli strain of human origin. Infect Immun (2000) 1.53
Identification of candidate genome regions controlling disease resistance in Arachis. BMC Plant Biol (2009) 1.51
Genome sequence of Picrophilus torridus and its implications for life around pH 0. Proc Natl Acad Sci U S A (2004) 1.51
A Stenotrophomonas maltophilia multilocus sequence typing scheme for inferring population structure. J Bacteriol (2009) 1.44
The Complete Genome Sequence of Clostridium aceticum: a Missing Link between Rnf- and Cytochrome-Containing Autotrophic Acetogens. MBio (2015) 1.43
First Insights into the Genome of the Gram-Negative, Endospore-Forming Organism Sporomusa ovata Strain H1 DSM 2662. Genome Announc (2013) 1.40
Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens. J Gen Virol (2009) 1.39
Evolutionary convergence and nitrogen metabolism in Blattabacterium strain Bge, primary endosymbiont of the cockroach Blattella germanica. PLoS Genet (2009) 1.38
Signatures of selection among sex-determining alleles of the honey bee. Proc Natl Acad Sci U S A (2004) 1.37
Conserved footprints of APOBEC3G on Hypermutated human immunodeficiency virus type 1 and human endogenous retrovirus HERV-K(HML2) sequences. J Virol (2008) 1.36
Evolution and diversity in human herpes simplex virus genomes. J Virol (2013) 1.35
Serratia symbiotica from the aphid Cinara cedri: a missing link from facultative to obligate insect endosymbiont. PLoS Genet (2011) 1.34
The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae. BMC Genomics (2008) 1.34
SNP high-throughput screening in grapevine using the SNPlex genotyping system. BMC Plant Biol (2008) 1.33
How to kill the honey bee larva: genomic potential and virulence mechanisms of Paenibacillus larvae. PLoS One (2014) 1.32
Complete genome sequences of elephant endotheliotropic herpesviruses 1A and 1B determined directly from fatal cases. J Virol (2013) 1.31
Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light. Proc Natl Acad Sci U S A (2008) 1.30
The complex repeats of Dictyostelium discoideum. Genome Res (2001) 1.27
Genome-wide association study identifies novel restless legs syndrome susceptibility loci on 2p14 and 16q12.1. PLoS Genet (2011) 1.27
Decoding of superimposed traces produced by direct sequencing of heterozygous indels. PLoS Comput Biol (2008) 1.27
Genetic linkage map of the guppy, Poecilia reticulata, and quantitative trait loci analysis of male size and colour variation. Proc Biol Sci (2009) 1.24
Persistence of adenovirus nucleic acids in nasopharyngeal secretions: a diagnostic conundrum. Pediatr Infect Dis J (2010) 1.24
Two distinct Triatoma dimidiata (Latreille, 1811) taxa are found in sympatry in Guatemala and Mexico. PLoS Negl Trop Dis (2009) 1.23
A "repertoire for repertoire" hypothesis: repertoires of type three effectors are candidate determinants of host specificity in Xanthomonas. PLoS One (2009) 1.23
Evolution of the secondary symbiont "Candidatus serratia symbiotica" in aphid species of the subfamily lachninae. Appl Environ Microbiol (2008) 1.22
Assessing gut microbial diversity from feces and rectal mucosa. Microb Ecol (2010) 1.21
Multiple quantitative trait locus analysis of bovine chromosome 6 in the Israeli Holstein population by a daughter design. Genetics (2001) 1.18
Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8. BMC Genomics (2010) 1.18
DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions. BMC Bioinformatics (2006) 1.18
The pathogenicity island-associated K15 capsule determinant exhibits a novel genetic structure and correlates with virulence in uropathogenic Escherichia coli strain 536. Infect Immun (2004) 1.18
The mouse homeobox gene Not is required for caudal notochord development and affected by the truncate mutation. Genes Dev (2004) 1.17
Flagellin diversity in Clostridium botulinum groups I and II: a new strategy for strain identification. Appl Environ Microbiol (2007) 1.16
Rapid Leptospira identification by direct sequencing of the diagnostic PCR products in New Caledonia. BMC Microbiol (2010) 1.16
Whole-genome sequence of Stenotrophomonas maltophilia D457, a clinical isolate and a model strain. J Bacteriol (2012) 1.16
Bacterial diversity at different stages of the composting process. BMC Microbiol (2010) 1.16
Involvement of two latex-clearing proteins during rubber degradation and insights into the subsequent degradation pathway revealed by the genome sequence of Gordonia polyisoprenivorans strain VH2. Appl Environ Microbiol (2012) 1.15
Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein. PLoS One (2013) 1.14
Type three effector gene distribution and sequence analysis provide new insights into the pathogenicity of plant-pathogenic Xanthomonas arboricola. Appl Environ Microbiol (2011) 1.14
Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide. Environ Microbiol (2009) 1.14
Transcript- and tissue-specific imprinting of a tumour suppressor gene. Hum Mol Genet (2008) 1.13
Complete Genome Sequence of Mannheimia haemolytica Strain 42548 from a Case of Bovine Respiratory Disease. Genome Announc (2013) 1.13
Multilocus sequence types of Finnish bovine Campylobacter jejuni isolates and their attribution to human infections. BMC Microbiol (2010) 1.12
The genomic sequence and comparative analysis of the rat major histocompatibility complex. Genome Res (2004) 1.11
Complete Genome Sequence of Amino Acid-Utilizing Eubacterium acidaminophilum al-2 (DSM 3953). Genome Announc (2014) 1.10
SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects. BMC Bioinformatics (2011) 1.10
A SNP transferability survey within the genus Vitis. BMC Plant Biol (2008) 1.09
Tn1546 is part of a larger plasmid-encoded genetic unit horizontally disseminated among clonal Enterococcus faecium lineages. J Antimicrob Chemother (2010) 1.06
Exome sequencing reveals novel rare variants in the ryanodine receptor and calcium channel genes in malignant hyperthermia families. Anesthesiology (2013) 1.06
Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae). BMC Evol Biol (2011) 1.05
Complete genome sequence of "Candidatus Tremblaya princeps" strain PCVAL, an intriguing translational machine below the living-cell status. J Bacteriol (2011) 1.05
Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs. Database (Oxford) (2009) 1.05
The fragmented mitochondrial ribosomal RNAs of Plasmodium falciparum. PLoS One (2012) 1.04
Genotypic analysis of two hypervariable human cytomegalovirus genes. J Med Virol (2008) 1.04
New, closely related haloarchaeal viral elements with different nucleic Acid types. J Virol (2010) 1.03
Sequence analysis of percent G+C fraction libraries of human faecal bacterial DNA reveals a high number of Actinobacteria. BMC Microbiol (2009) 1.03
Staden: searching for motifs in nucleic acid sequences. Methods Mol Biol (1994) 4.65
Methods for calculating the probabilities of finding patterns in sequences. Comput Appl Biosci (1989) 3.64
Experiment files and their application during large-scale sequencing projects. DNA Seq (1996) 2.48
An improved sequence handling package that runs on the Apple Macintosh. Comput Appl Biosci (1990) 1.96
Methods for discovering novel motifs in nucleic acid sequences. Comput Appl Biosci (1989) 1.79
Sequence assembly and finishing methods. Methods Biochem Anal (2001) 1.28
Staden: managing sequence projects. Methods Mol Biol (1994) 1.02
Staden: introduction. Methods Mol Biol (1994) 0.91
Staden: statistical and structural analysis of nucleotide sequences. Methods Mol Biol (1994) 0.79
Staden: searching for restriction sites. Methods Mol Biol (1994) 0.78
Staden: comparing sequences. Methods Mol Biol (1994) 0.78
Staden: translating and listing nucleic acid sequences. Methods Mol Biol (1994) 0.75
Screening protein and nucleic acid sequences against libraries of patterns. DNA Seq (1991) 0.75
Staden: using patterns to analyze nucleic acid sequences. Methods Mol Biol (1994) 0.75
Indexing the sequence libraries: software providing a common indexing system for all the standard sequence libraries. DNA Seq (1992) 0.75
Staden: sequence input, editing, and sequence library use. Methods Mol Biol (1994) 0.75
Staden: analyzing sequences to find genes. Methods Mol Biol (1994) 0.75
Staden: using patterns to analyze protein sequences. Methods Mol Biol (1994) 0.75
Staden: searching for motifs in protein sequences. Methods Mol Biol (1994) 0.75
Staden: statistical and structural analysis of protein sequences. Methods Mol Biol (1994) 0.75