Published in Bioinformatics on January 12, 2010
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform (2012) 23.58
A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform (2010) 18.05
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics (2011) 4.31
Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics (2012) 2.20
Studying bacterial transcriptomes using RNA-seq. Curr Opin Microbiol (2010) 2.06
MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation. Nucleic Acids Res (2010) 1.49
Next-generation sequencing techniques for eukaryotic microorganisms: sequencing-based solutions to biological problems. Eukaryot Cell (2010) 1.18
Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome. Microbiology (2011) 1.10
BamView: visualizing and interpretation of next-generation sequencing read alignments. Brief Bioinform (2012) 1.08
Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux. PLoS Pathog (2011) 1.05
Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces. BMC Genomics (2014) 0.89
Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans. PLoS One (2011) 0.84
A novel application of pattern recognition for accurate SNP and indel discovery from high-throughput data: targeted resequencing of the glucocorticoid receptor co-chaperone FKBP5 in a Caucasian population. Mol Genet Metab (2011) 0.83
Streptococcal collagen-like protein A and general stress protein 24 are immunomodulating virulence factors of group A Streptococcus. FASEB J (2013) 0.82
Draft Genome Sequence of Bacillus pumilus ku-bf1 Isolated from the Gut Contents of Wood Boring Mesomorphus sp. Front Microbiol (2016) 0.79
Geno viewer, a SAM/BAM viewer tool. Bioinformation (2012) 0.79
Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files. Cancer Inform (2015) 0.78
Comparative genomics of drug resistance in Trypanosoma brucei rhodesiense. Cell Mol Life Sci (2016) 0.76
Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC). BMC Genomics (2016) 0.76
Lineage-specific SoxR-mediated regulation of an endoribonuclease protects non-enteric bacteria from redox-active compounds. J Biol Chem (2016) 0.75
Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory RNA RyhB and a peptide, RyhP. BMC Genomics (2017) 0.75
Brucella abortus Strain 2308 Wisconsin Genome: Importance of the Definition of Reference Strains. Front Microbiol (2016) 0.75
Incorporating computational resources in a cancer research program. Hum Genet (2014) 0.75
CRCDA--Comprehensive resources for cancer NGS data analysis. Database (Oxford) (2015) 0.75
Draft genome sequence of type strain HBR26(T) and description of Rhizobium aethiopicum sp. nov. Stand Genomic Sci (2017) 0.75
From next-generation resequencing reads to a high-quality variant data set. Heredity (Edinb) (2016) 0.75
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
SSAHA: a fast search method for large DNA databases. Genome Res (2001) 48.64
Artemis: sequence visualization and annotation. Bioinformatics (2000) 46.68
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics (2008) 9.17
New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. Mol Microbiol (2010) 2.76
LookSeq: a browser-based viewer for deep sequencing data. Genome Res (2009) 2.70
HI: haplotype improver using paired-end short reads. Bioinformatics (2009) 1.20
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
Enterotypes of the human gut microbiome. Nature (2011) 24.36
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet (2008) 19.97
ACT: the Artemis Comparison Tool. Bioinformatics (2005) 17.91
Evolution of MRSA during hospital transmission and intercontinental spread. Science (2010) 13.34
Prepublication data sharing. Nature (2009) 12.24
The genome of the African trypanosome Trypanosoma brucei. Science (2005) 11.48
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods (2009) 10.41
A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics (2012) 9.97
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics (2008) 9.17
Rapid pneumococcal evolution in response to clinical interventions. Science (2011) 9.09
Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci U S A (2004) 8.95
The genome of the kinetoplastid parasite, Leishmania major. Science (2005) 8.64
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature (2005) 8.55
The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet (2006) 8.02
Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol (2007) 7.58
Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei. Proc Natl Acad Sci U S A (2004) 7.30
Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis (2012) 7.18
The complete genome sequence of Mycobacterium bovis. Proc Natl Acad Sci U S A (2003) 6.79
Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis (2012) 6.64
Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes. PLoS Genet (2006) 6.43
Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med (2012) 6.36
GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res (2004) 6.30
Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study. Lancet Infect Dis (2011) 6.08
A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science (2005) 5.99
The genome of the blood fluke Schistosoma mansoni. Nature (2009) 5.94
Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature (2009) 5.90
Multidrug-resistant Salmonella enterica serovar paratyphi A harbors IncHI1 plasmids similar to those found in serovar typhi. J Bacteriol (2007) 5.88
Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol (2010) 5.79
Evidence for several waves of global transmission in the seventh cholera pandemic. Nature (2011) 5.62
DNAPlotter: circular and linear interactive genome visualization. Bioinformatics (2008) 5.49
Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J (2010) 5.43
Comparative genomics of trypanosomatid parasitic protozoa. Science (2005) 5.37
Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia. Nat Genet (2013) 5.22
Microevolution and history of the plague bacillus, Yersinia pestis. Proc Natl Acad Sci U S A (2004) 5.04
ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics (2009) 4.98
Microbiology in the post-genomic era. Nat Rev Microbiol (2008) 4.88
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics (2004) 4.76
Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. Lancet (2013) 4.75
Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog (2012) 4.69
Comparative genomic analysis of three Leishmania species that cause diverse human disease. Nat Genet (2007) 4.58
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol (2014) 4.39
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature (2012) 4.37
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics (2011) 4.31
Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics (2006) 4.27
Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics (2010) 4.18
Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res (2009) 4.12
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11
Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nat Genet (2012) 4.10
High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome. Genome Res (2011) 4.09
Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. Genome Res (2009) 3.99
Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet (2013) 3.89
WormBase 2012: more genomes, more data, new website. Nucleic Acids Res (2011) 3.87
The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants. Genome Biol (2008) 3.85
Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS Pathog (2012) 3.81
TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Res (2009) 3.79
Genome plasticity of BCG and impact on vaccine efficacy. Proc Natl Acad Sci U S A (2007) 3.73
Genome variation and evolution of the malaria parasite Plasmodium falciparum. Nat Genet (2006) 3.68
Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium. Genome Biol (2009) 3.66
Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol (2009) 3.63
Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome. J Bacteriol (2007) 3.62
Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways. Genome Res (2008) 3.54
Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer. Genome Res (2007) 3.45
Antibiotic treatment of clostridium difficile carrier mice triggers a supershedder state, spore-mediated transmission, and severe disease in immunocompromised hosts. Infect Immun (2009) 3.36
Comparative genomic structure of prokaryotes. Annu Rev Genet (2004) 3.34
The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081. PLoS Genet (2006) 3.33
Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei. Lancet (2003) 3.30
RATT: Rapid Annotation Transfer Tool. Nucleic Acids Res (2011) 3.29
Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis. Genome Res (2008) 3.26
Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat Genet (2012) 3.22
Optimal enzymes for amplifying sequencing libraries. Nat Methods (2011) 3.21
Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc Natl Acad Sci U S A (2010) 3.18
A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat Protoc (2012) 3.17
High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol (2011) 3.11
Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69. J Bacteriol (2008) 3.10
Extensive DNA inversions in the B. fragilis genome control variable gene expression. Science (2005) 3.08
An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm. Proc Natl Acad Sci U S A (2005) 3.06
REAPR: a universal tool for genome assembly evaluation. Genome Biol (2013) 3.05
A human-curated annotation of the Candida albicans genome. PLoS Genet (2005) 3.04
Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa. Genome Res (2008) 3.03
Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nat Genet (2013) 3.03
The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol (2006) 2.93
A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet (2009) 2.87
Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat Genet (2012) 2.86
Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science (2005) 2.86
Genome sequence of a recently emerged, highly transmissible, multi-antibiotic- and antiseptic-resistant variant of methicillin-resistant Staphylococcus aureus, sequence type 239 (TW). J Bacteriol (2009) 2.81