Published in Nucleic Acids Res on October 02, 2008
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Genomic characterization of the Yersinia genus. Genome Biol (2010) 1.63
ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria. Nucleic Acids Res (2011) 1.62
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Klebsiella: a long way to go towards understanding this enigmatic jet-setter. F1000Prime Rep (2014) 1.43
Plasmid metagenome reveals high levels of antibiotic resistance genes and mobile genetic elements in activated sludge. PLoS One (2011) 1.41
Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates. Genome Biol (2012) 1.38
BacMet: antibacterial biocide and metal resistance genes database. Nucleic Acids Res (2013) 1.35
Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. Nucleic Acids Res (2015) 1.35
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The multifaceted roles of antibiotics and antibiotic resistance in nature. Front Microbiol (2013) 1.21
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Extensive microbial and functional diversity within the chicken cecal microbiome. PLoS One (2014) 1.16
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res (2016) 1.14
Comparative genomic analysis of rapid evolution of an extreme-drug-resistant Acinetobacter baumannii clone. Genome Biol Evol (2013) 1.12
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res (2016) 1.12
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Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis. J Clin Microbiol (2013) 1.10
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Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces. MBio (2015) 1.05
The impact of triclosan on the spread of antibiotic resistance in the environment. Front Microbiol (2015) 1.04
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Draft genome sequence of Serratia marcescens strain LCT-SM213. J Bacteriol (2012) 1.01
Rapid identification of genetic modifications in Bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing. PLoS One (2010) 0.99
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The evolution of plasmid-carried antibiotic resistance. BMC Evol Biol (2011) 0.98
Draft genome sequence of an Acinetobacter genomic species 3 strain harboring a bla(NDM-1) gene. J Bacteriol (2012) 0.97
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Genomic analysis of the emergence of 20th century epidemic dysentery. BMC Genomics (2014) 0.97
Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences. Nat Commun (2013) 0.97
How bioinformatics influences health informatics: usage of biomolecular sequences, expression profiles and automated microscopic image analyses for clinical needs and public health. Health Inf Sci Syst (2013) 0.96
A metagenomic framework for the study of airborne microbial communities. PLoS One (2013) 0.96
Evidence for Elizabethkingia anophelis transmission from mother to infant, Hong Kong. Emerg Infect Dis (2015) 0.95
Metagenomic frameworks for monitoring antibiotic resistance in aquatic environments. Environ Health Perspect (2013) 0.95
Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment. mSystems (2016) 0.95
Protein-protein interaction networks suggest different targets have different propensities for triggering drug resistance. Syst Synth Biol (2011) 0.94
Viruses in a 14th-century coprolite. Appl Environ Microbiol (2014) 0.94
Chlortetracycline-resistant intestinal bacteria in organically raised and feral Swine. Appl Environ Microbiol (2011) 0.94
What It Takes to Be a Pseudomonas aeruginosa? The Core Genome of the Opportunistic Pathogen Updated. PLoS One (2015) 0.93
Whole-genome sequence of a multidrug-resistant clinical isolate of Acinetobacter lwoffii. J Bacteriol (2011) 0.93
Functional profiling of the gut microbiome in disease-associated inflammation. Genome Med (2013) 0.93
In silico analysis of antibiotic resistance genes in the gut microflora of individuals from diverse geographies and age-groups. PLoS One (2013) 0.93
Marine sediment bacteria harbor antibiotic resistance genes highly similar to those found in human pathogens. Microb Ecol (2013) 0.92
Genomic epidemiology of Klebsiella pneumoniae in Italy and novel insights into the origin and global evolution of its resistance to carbapenem antibiotics. Antimicrob Agents Chemother (2014) 0.92
mBLAST: Keeping up with the sequencing explosion for (meta)genome analysis. J Data Mining Genomics Proteomics (2013) 0.92
Stepwise evolution of pandrug-resistance in Klebsiella pneumoniae. Sci Rep (2015) 0.91
Metagenomic profiling of antibiotic resistance genes and mobile genetic elements in a tannery wastewater treatment plant. PLoS One (2013) 0.91
Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes. Infect Drug Resist (2014) 0.91
Whole-Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter spp. Appl Environ Microbiol (2015) 0.91
The extant World War 1 dysentery bacillus NCTC1: a genomic analysis. Lancet (2014) 0.90
Thousands of missed genes found in bacterial genomes and their analysis with COMBREX. Biol Direct (2012) 0.90
The initial state of the human gut microbiome determines its reshaping by antibiotics. ISME J (2015) 0.90
A review on computational systems biology of pathogen-host interactions. Front Microbiol (2015) 0.88
Metagenomic profiling of microbial composition and antibiotic resistance determinants in Puget Sound. PLoS One (2012) 0.88
Functional metagenomics reveals previously unrecognized diversity of antibiotic resistance genes in gulls. Front Microbiol (2011) 0.88
Genome sequencing and genomic characterization of a tigecycline-resistant Klebsiella pneumoniae strain isolated from the bile samples of a cholangiocarcinoma patient. Gut Pathog (2014) 0.88
Genomic insights into intrinsic and acquired drug resistance mechanisms in Achromobacter xylosoxidans. Antimicrob Agents Chemother (2014) 0.88
Metagenomic insights into tetracycline effects on microbial community and antibiotic resistance of mouse gut. Ecotoxicology (2015) 0.88
Metagenomic Analysis of Antibiotic Resistance Genes in Dairy Cow Feces following Therapeutic Administration of Third Generation Cephalosporin. PLoS One (2015) 0.87
Acquired genetic mechanisms of a multiresistant bacterium isolated from a treatment plant receiving wastewater from antibiotic production. Appl Environ Microbiol (2013) 0.87
Comparative genomics study of multi-drug-resistance mechanisms in the antibiotic-resistant Streptococcus suis R61 strain. PLoS One (2011) 0.87
Exploring antibiotic resistance genes and metal resistance genes in plasmid metagenomes from wastewater treatment plants. Front Microbiol (2015) 0.87
Draft Genome Sequences of Two Multidrug Resistant Klebsiella pneumoniae ST258 Isolates Resistant to Colistin. Genome Announc (2013) 0.86
Nonclinical and clinical Enterococcus faecium strains, but not Enterococcus faecalis strains, have distinct structural and functional genomic features. Appl Environ Microbiol (2013) 0.86
Complete genome assembly and characterization of an outbreak strain of the causative agent of swine erysipelas--Erysipelothrix rhusiopathiae SY1027. BMC Microbiol (2014) 0.86
Synergistic effects of honey and propolis toward drug multi-resistant Staphylococcus aureus, Escherichia coli and Candida albicans isolates in single and polymicrobial cultures. Int J Med Sci (2012) 0.86
An approach to identifying drug resistance associated mutations in bacterial strains. BMC Genomics (2012) 0.86
Prevalence of antibiotic resistance genes and bacterial community composition in a river influenced by a wastewater treatment plant. PLoS One (2013) 0.85
Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses. ISME J (2016) 0.85
Safety of the surrogate microorganism Enterococcus faecium NRRL B-2354 for use in thermal process validation. Appl Environ Microbiol (2014) 0.84
Draft Genome of Klebsiella pneumoniae Sequence Type 512, a Multidrug-Resistant Strain Isolated during a Recent KPC Outbreak in Italy. Genome Announc (2013) 0.84
The Bacterial Mobile Resistome Transfer Network Connecting the Animal and Human Microbiomes. Appl Environ Microbiol (2016) 0.84
Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities. Front Microbiol (2015) 0.84
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
KEGG for linking genomes to life and the environment. Nucleic Acids Res (2007) 49.37
Extensively drug-resistant tuberculosis as a cause of death in patients co-infected with tuberculosis and HIV in a rural area of South Africa. Lancet (2006) 21.60
CDD: a Conserved Domain Database for protein classification. Nucleic Acids Res (2005) 18.85
GenBank. Nucleic Acids Res (2007) 16.92
The universal protein resource (UniProt). Nucleic Acids Res (2007) 16.33
Methicillin-resistant staphylococci. J Clin Pathol (1961) 6.42
Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing. Proc Natl Acad Sci U S A (2007) 6.14
Molecular mechanisms of antibacterial multidrug resistance. Cell (2007) 5.32
Vancomycin resistance in gram-positive cocci. Clin Infect Dis (2006) 4.95
Multiple molecular mechanisms for multidrug resistance transporters. Nature (2007) 3.96
MvirDB--a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications. Nucleic Acids Res (2006) 2.76
Porins, efflux pumps and multidrug resistance in Acinetobacter baumannii. J Antimicrob Chemother (2007) 2.27
Detection of multidrug resistance in Mycobacterium tuberculosis. J Clin Microbiol (2006) 2.06
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A double mutation in the gyrA gene is necessary to produce high levels of resistance to moxifloxacin in Campylobacter spp. clinical isolates. Int J Antimicrob Agents (2005) 1.20
Mortality after infection with methicillin-resistant Staphylococcus aureus (MRSA) diagnosed in the community. BMC Med (2008) 1.18
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
Metagenomic analysis of the human distal gut microbiome. Science (2006) 29.76
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res (2012) 11.33
The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature (2003) 10.38
Searching for SNPs with cloud computing. Genome Biol (2009) 10.12
Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science (2002) 9.83
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature (2002) 8.92
Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol (2009) 8.06
Minimus: a fast, lightweight genome assembler. BMC Bioinformatics (2007) 7.65
The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science (2005) 7.61
The dog genome: survey sequencing and comparative analysis. Science (2003) 5.84
The genome of the protist parasite Entamoeba histolytica. Nature (2005) 5.33
Draft genome of the filarial nematode parasite Brugia malayi. Science (2007) 5.28
Genome assembly forensics: finding the elusive mis-assembly. Genome Biol (2008) 4.91
Differential abundance analysis for microbial marker-gene surveys. Nat Methods (2013) 4.49
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biol (2005) 4.42
Next generation sequence assembly with AMOS. Curr Protoc Bioinformatics (2011) 3.60
Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics (2010) 3.45
Exploiting sparseness in de novo genome assembly. BMC Bioinformatics (2012) 2.88
Figaro: a novel statistical method for vector sequence removal. Bioinformatics (2008) 2.81
Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proc Natl Acad Sci U S A (2011) 2.62
Scaffolding and validation of bacterial genome assemblies using optical restriction maps. Bioinformatics (2008) 2.61
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics (2011) 2.55
Bambus 2: scaffolding metagenomes. Bioinformatics (2011) 2.24
Parametric complexity of sequence assembly: theory and applications to next generation sequencing. J Comput Biol (2009) 2.10
Sequence assembly demystified. Nat Rev Genet (2013) 2.09
Alignment and clustering of phylogenetic markers--implications for microbial diversity studies. BMC Bioinformatics (2010) 2.01
An optimized system for expression and purification of secreted bacterial proteins. Protein Expr Purif (2005) 1.96
Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS One (2012) 1.96
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol (2013) 1.74
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Brief Bioinform (2011) 1.70
DNACLUST: accurate and efficient clustering of phylogenetic marker genes. BMC Bioinformatics (2011) 1.66
Genomic characterization of the Yersinia genus. Genome Biol (2010) 1.63
Automated ensemble assembly and validation of microbial genomes. BMC Bioinformatics (2014) 1.33
Characterization of Ehp, a secreted complement inhibitory protein from Staphylococcus aureus. J Biol Chem (2007) 1.32
Finishing genomes with limited resources: lessons from an ensemble of microbial genomes. BMC Genomics (2010) 1.31
Quantitative PCR for detection of Shigella improves ascertainment of Shigella burden in children with moderate-to-severe diarrhea in low-income countries. J Clin Microbiol (2013) 1.30
Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. Genome Biol (2014) 1.24
Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Res (2011) 1.17
Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biol (2005) 1.16
Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information. J Comput Biol (2010) 1.15
Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC Bioinformatics (2011) 1.13
De novo likelihood-based measures for comparing genome assemblies. BMC Res Notes (2013) 1.07
AGORA: Assembly Guided by Optical Restriction Alignment. BMC Bioinformatics (2012) 1.06
Sequencing and genome assembly using next-generation technologies. Methods Mol Biol (2010) 1.05
3-day treatment with azithromycin 1.5% eye drops versus 7-day treatment with tobramycin 0.3% for purulent bacterial conjunctivitis: multicentre, randomised and controlled trial in adults and children. Br J Ophthalmol (2006) 1.04
MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasets. BMC Proc (2011) 1.00
Bioinformatics for the Human Microbiome Project. PLoS Comput Biol (2012) 0.97
Identification of Coli Surface Antigen 23, a novel adhesin of enterotoxigenic Escherichia coli. Infect Immun (2012) 0.92
Complete genome sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700. J Bacteriol (2009) 0.88
Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold. Bioinformatics (2013) 0.88
Survey of culture, goldengate assay, universal biosensor assay, and 16S rRNA Gene sequencing as alternative methods of bacterial pathogen detection. J Clin Microbiol (2013) 0.87
The Theory and Practice of Genome Sequence Assembly. Annu Rev Genomics Hum Genet (2015) 0.85
Microbiota that affect risk for shigellosis in children in low-income countries. Emerg Infect Dis (2015) 0.84
Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products. BMC Genomics (2014) 0.84
Inexact Local Alignment Search over Suffix Arrays. Proceedings (IEEE Int Conf Bioinformatics Biomed) (2009) 0.81
Genome Sequencing of Four Strains of Rickettsia prowazekii, the Causative Agent of Epidemic Typhus, Including One Flying Squirrel Isolate. Genome Announc (2013) 0.77
Comparison of 360-Degree Circumferential Trabeculotomy and Conventional Trabeculotomy in Primary Pediatric Glaucoma Surgery: Part 1. J Pediatr Ophthalmol Strabismus (2016) 0.75
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes. Brief Bioinform (2017) 0.75
This special issue includes a selection of papers presented at the 2nd IEEE International Conference. Introduction. Int J Bioinform Res Appl (2014) 0.75
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