Published in Nucleic Acids Res on January 01, 2006
Reordering contigs of draft genomes using the Mauve aligner. Bioinformatics (2009) 6.97
MicroScope: a platform for microbial genome annotation and comparative genomics. Database (Oxford) (2009) 3.87
National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. Infect Immun (2007) 3.02
The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J Bacteriol (2008) 2.97
Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics (2008) 2.62
Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria. Nucleic Acids Res (2007) 2.25
EcoGene 3.0. Nucleic Acids Res (2012) 1.75
Solving the Problem: Genome Annotation Standards before the Data Deluge. Stand Genomic Sci (2011) 1.54
Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: focus on point miscalls and artefactual expansions. BMC Genomics (2008) 1.39
The evolution of metabolic networks of E. coli. BMC Syst Biol (2011) 1.32
G-InforBIO: integrated system for microbial genomics. BMC Bioinformatics (2006) 1.22
Insight into the transmission biology and species-specific functional capabilities of tsetse (Diptera: glossinidae) obligate symbiont Wigglesworthia. MBio (2012) 1.12
Using comparative genomics for inquiry-based learning to dissect virulence of Escherichia coli O157:H7 and Yersinia pestis. CBE Life Sci Educ (2012) 1.11
PSAT: a web tool to compare genomic neighborhoods of multiple prokaryotic genomes. BMC Bioinformatics (2008) 1.03
The 3-hydroxy-2-butanone pathway is required for Pectobacterium carotovorum pathogenesis. PLoS One (2011) 0.95
Mosquito transcriptome profiles and filarial worm susceptibility in Armigeres subalbatus. PLoS Negl Trop Dis (2010) 0.93
Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens. BMC Bioinformatics (2009) 0.91
Technologies and approaches to elucidate and model the virulence program of salmonella. Front Microbiol (2011) 0.88
The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes. Database (Oxford) (2011) 0.87
Inferring ancient metabolism using ancestral core metabolic models of enterobacteria. BMC Syst Biol (2013) 0.83
Biochemical and Genetic Characterization of PspE and GlpE, Two Single-domain Sulfurtransferases of Escherichia coli. Open Microbiol J (2008) 0.83
GenoBase: comprehensive resource database of Escherichia coli K-12. Nucleic Acids Res (2014) 0.79
Predicting Essential Metabolic Genome Content of Niche-Specific Enterobacterial Human Pathogens during Simulation of Host Environments. PLoS One (2016) 0.76
Identification of host-microbe interaction factors in the genomes of soft rot-associated pathogens Dickeya dadantii 3937 and Pectobacterium carotovorum WPP14 with supervised machine learning. BMC Genomics (2014) 0.75
Databases for Microbiologists. J Bacteriol (2015) 0.75
Siderophore-mediated iron acquisition influences motility and is required for full virulence of the xylem-dwelling bacterial phytopathogen Pantoea stewartii subsp. stewartii. Appl Environ Microbiol (2014) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res (2004) 54.37
Versatile and open software for comparing large genomes. Genome Biol (2004) 49.45
Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res (2004) 28.63
InterProScan: protein domains identifier. Nucleic Acids Res (2005) 18.82
ACT: the Artemis Comparison Tool. Bioinformatics (2005) 17.91
PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics (2004) 7.15
MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products. Microb Comp Genomics (2000) 4.60
Viewing and annotating sequence data with Artemis. Brief Bioinform (2003) 4.38
ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res (2003) 3.99
Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol (2005) 3.96
coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics. Nucleic Acids Res (2004) 2.75
Description of the transcriptomes of immune response-activated hemocytes from the mosquito vectors Aedes aegypti and Armigeres subalbatus. Infect Immun (2004) 1.62
Genome-wide identification of plant-upregulated genes of Erwinia chrysanthemi 3937 using a GFP-based IVET leaf array. Mol Plant Microbe Interact (2004) 1.21
GenColors: accelerated comparative analysis and annotation of prokaryotic genomes at various stages of completeness. Bioinformatics (2005) 1.07
MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol (2012) 40.23
Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res (2004) 28.63
progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One (2010) 24.31
The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature (2012) 9.89
Insights into the phylogeny and coding potential of microbial dark matter. Nature (2013) 8.55
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res (2006) 7.93
Genome sequence of Yersinia pestis KIM. J Bacteriol (2002) 7.14
Reordering contigs of draft genomes using the Mauve aligner. Bioinformatics (2009) 6.97
Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J Bacteriol (2003) 5.45
BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Syst Biol (2011) 5.40
Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N Engl J Med (2014) 5.37
The Amphimedon queenslandica genome and the evolution of animal complexity. Nature (2010) 5.11
A novel retinoblastoma therapy from genomic and epigenetic analyses. Nature (2012) 5.02
Novel mutations target distinct subgroups of medulloblastoma. Nature (2012) 4.82
ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res (2003) 3.99
Emergent properties of reduced-genome Escherichia coli. Science (2006) 3.88
Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas. Nat Genet (2013) 3.51
The genomic landscape of hypodiploid acute lymphoblastic leukemia. Nat Genet (2013) 3.43
The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J Bacteriol (2008) 2.97
Kinetics and mechanism of the reaction of cysteine and hydrogen peroxide in aqueous solution. J Pharm Sci (2005) 2.42
Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria. Nucleic Acids Res (2007) 2.25
Identification and characterization of lpfABCC'DE, a fimbrial operon of enterohemorrhagic Escherichia coli O157:H7. Infect Immun (2002) 2.18
Engineering a reduced Escherichia coli genome. Genome Res (2002) 2.16
Genome of bacteriophage P1. J Bacteriol (2004) 2.15
GRIL: genome rearrangement and inversion locator. Bioinformatics (2004) 1.95
Inference of homologous recombination in bacteria using whole-genome sequences. Genetics (2010) 1.85
Host range and molecular phylogenies of the soft rot enterobacterial genera pectobacterium and dickeya. Phytopathology (2007) 1.81
Strains of Escherichia coli O157:H7 differ primarily by insertions or deletions, not single-nucleotide polymorphisms. J Bacteriol (2002) 1.68
A whole-genome shotgun optical map of Yersinia pestis strain KIM. Appl Environ Microbiol (2002) 1.68
Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli. Genome Biol (2006) 1.66
Genomic variability of O islands encoding tellurite resistance in enterohemorrhagic Escherichia coli O157:H7 isolates. J Bacteriol (2002) 1.63
Description of the transcriptomes of immune response-activated hemocytes from the mosquito vectors Aedes aegypti and Armigeres subalbatus. Infect Immun (2004) 1.62
An Inv(16)(p13.3q24.3)-encoded CBFA2T3-GLIS2 fusion protein defines an aggressive subtype of pediatric acute megakaryoblastic leukemia. Cancer Cell (2012) 1.61
Directed evolution of ionizing radiation resistance in Escherichia coli. J Bacteriol (2009) 1.60
Enhanced active liposomal loading of a poorly soluble ionizable drug using supersaturated drug solutions. J Control Release (2012) 1.52
Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation. BMC Genomics (2012) 1.42
Annotation and overview of the Pseudomonas savastanoi pv. savastanoi NCPPB 3335 draft genome reveals the virulence gene complement of a tumour-inducing pathogen of woody hosts. Environ Microbiol (2010) 1.34
Patterns of gene flow define species of thermophilic Archaea. PLoS Biol (2012) 1.33
Analyzing patterns of microbial evolution using the mauve genome alignment system. Methods Mol Biol (2007) 1.32
The evolution of metabolic networks of E. coli. BMC Syst Biol (2011) 1.32
Characterization of Cah, a calcium-binding and heat-extractable autotransporter protein of enterohaemorrhagic Escherichia coli. Mol Microbiol (2002) 1.32
Inferring genomic flux in bacteria. Genome Res (2008) 1.25
Evolution of extreme resistance to ionizing radiation via genetic adaptation of DNA repair. Elife (2014) 1.22
Genome-wide identification of plant-upregulated genes of Erwinia chrysanthemi 3937 using a GFP-based IVET leaf array. Mol Plant Microbe Interact (2004) 1.21
Genome sequence of the plant-pathogenic bacterium Dickeya dadantii 3937. J Bacteriol (2011) 1.18
Phylogeny and virulence of naturally occurring type III secretion system-deficient Pectobacterium strains. Appl Environ Microbiol (2009) 1.12
Insight into the transmission biology and species-specific functional capabilities of tsetse (Diptera: glossinidae) obligate symbiont Wigglesworthia. MBio (2012) 1.12
hrp genes of Erwinia chrysanthemi 3937 are important virulence factors. Mol Plant Microbe Interact (2002) 1.12
Using comparative genomics for inquiry-based learning to dissect virulence of Escherichia coli O157:H7 and Yersinia pestis. CBE Life Sci Educ (2012) 1.11
Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence. BMC Genomics (2013) 1.09
Gene Ontology annotation highlights shared and divergent pathogenic strategies of type III effector proteins deployed by the plant pathogen Pseudomonas syringae pv tomato DC3000 and animal pathogenic Escherichia coli strains. BMC Microbiol (2009) 1.09
Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. PLoS One (2012) 1.07
Liposomal drug transport: a molecular perspective from molecular dynamics simulations in lipid bilayers. Adv Drug Deliv Rev (2006) 1.06
Identification and characterization of Escherichia coli RS218-derived islands in the pathogenesis of E. coli meningitis. J Infect Dis (2006) 1.05
Phylogenetic and molecular analysis of hydrogen-producing green algae. J Exp Bot (2009) 1.05
In silico identification of genes in bacteriophage DNA. Methods Mol Biol (2009) 1.04
Integrated cross-species transcriptional network analysis of metastatic susceptibility. Proc Natl Acad Sci U S A (2012) 1.03
Escherichia coli K1-specific bacteriophage CUS-3 distribution and function in phase-variable capsular polysialic acid O acetylation. J Bacteriol (2007) 1.01
What determines drug solubility in lipid vehicles: is it predictable? Adv Drug Deliv Rev (2007) 0.99
Urease of enterohemorrhagic Escherichia coli: evidence for regulation by fur and a trans-acting factor. Infect Immun (2002) 0.98
Multiplex sequencing of seven ocular herpes simplex virus type-1 genomes: phylogeny, sequence variability, and SNP distribution. Invest Ophthalmol Vis Sci (2011) 0.97
Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data. Genome Biol (2012) 0.95
Insertions, deletions, and single-nucleotide polymorphisms at rare restriction enzyme sites enhance discriminatory power of polymorphic amplified typing sequences, a novel strain typing system for Escherichia coli O157:H7. J Clin Microbiol (2004) 0.94
Inhibition of P-glycoprotein activity at the primate blood-brain barrier increases the distribution of nelfinavir into the brain but not into the cerebrospinal fluid. Drug Metab Dispos (2007) 0.94
Polymorphic amplified typing sequences provide a novel approach to Escherichia coli O157:H7 strain typing. J Clin Microbiol (2002) 0.92
Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens. BMC Bioinformatics (2009) 0.91
Acquisition of stcE, a C1 esterase inhibitor-specific metalloprotease, during the evolution of Escherichia coli O157:H7. J Infect Dis (2003) 0.91
Determination of drug release kinetics from nanoparticles: overcoming pitfalls of the dynamic dialysis method. Mol Pharm (2013) 0.90
Epimer interconversion, isomerization, and hydrolysis of tetrahydrouridine: implications for cytidine deaminase inhibition. J Pharm Sci (2003) 0.89
Indigenous Vibrio cholerae strains from a non-endemic region are pathogenic. Open Biol (2013) 0.89
Microarray profiling of Erwinia chrysanthemi 3937 genes that are regulated during plant infection. Mol Plant Microbe Interact (2002) 0.89
A shift in energy metabolism anticipates the onset of sarcopenia in rhesus monkeys. Aging Cell (2013) 0.89
Liposomal delivery of hydrophobic weak acids: enhancement of drug retention using a high intraliposomal pH. J Pharm Sci (2008) 0.89
chipD: a web tool to design oligonucleotide probes for high-density tiling arrays. Nucleic Acids Res (2010) 0.88
Effects of a P-glycoprotein inhibitor on brain and plasma concentrations of anti-human immunodeficiency virus drugs administered in combination in rats. Drug Metab Dispos (2002) 0.87
The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes. Database (Oxford) (2011) 0.87
Liposome transport of hydrophobic drugs: gel phase lipid bilayer permeability and partitioning of the lactone form of a hydrophobic camptothecin, DB-67. J Pharm Sci (2008) 0.86