Published in Nat Methods on December 14, 2008
Sequencing technologies - the next generation. Nat Rev Genet (2009) 40.57
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol (2011) 9.18
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biol (2009) 6.76
Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog (2012) 4.69
Simultaneous alignment of short reads against multiple genomes. Genome Biol (2009) 2.79
Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics. Proc Natl Acad Sci U S A (2010) 2.43
Inviability of a DNA2 deletion mutant is due to the DNA damage checkpoint. Cell Cycle (2011) 2.25
Serine/threonine phosphatase Stp1 contributes to reduced susceptibility to vancomycin and virulence in Staphylococcus aureus. J Infect Dis (2012) 1.78
Whole genome characterization of the mechanisms of daptomycin resistance in clinical and laboratory derived isolates of Staphylococcus aureus. PLoS One (2012) 1.59
Distinct signatures of diversifying selection revealed by genome analysis of respiratory tract and invasive bacterial populations. Proc Natl Acad Sci U S A (2011) 1.39
PBP2a mutations causing high-level Ceftaroline resistance in clinical methicillin-resistant Staphylococcus aureus isolates. Antimicrob Agents Chemother (2014) 1.31
Using small molecules to dissect mechanisms of microbial pathogenesis. ACS Chem Biol (2009) 1.14
Bi-modal distribution of the second messenger c-di-GMP controls cell fate and asymmetry during the caulobacter cell cycle. PLoS Genet (2013) 1.12
Absence of patient-to-patient intrahospital transmission of Staphylococcus aureus as determined by whole-genome sequencing. MBio (2014) 1.12
Aminoglycoside cross-resistance in Mycobacterium tuberculosis due to mutations in the 5' untranslated region of whiB7. Antimicrob Agents Chemother (2013) 1.09
Population structure and antimicrobial resistance of invasive serotype IV group B Streptococcus, Toronto, Ontario, Canada. Emerg Infect Dis (2015) 1.04
Site-specific mobilization of vinyl chloride respiration islands by a mechanism common in Dehalococcoides. BMC Genomics (2011) 1.03
Sequence type 1 group B Streptococcus, an emerging cause of invasive disease in adults, evolves by small genetic changes. Proc Natl Acad Sci U S A (2015) 1.01
LOCAS--a low coverage assembly tool for resequencing projects. PLoS One (2011) 0.99
Characterization of invasive group B streptococcus strains from the greater Toronto area, Canada. J Clin Microbiol (2014) 0.99
High Incidence of Invasive Group A Streptococcus Disease Caused by Strains of Uncommon emm Types in Thunder Bay, Ontario, Canada. J Clin Microbiol (2015) 0.95
Whole-genome sequencing reveals distinct mutational patterns in closely related laboratory and naturally propagated Francisella tularensis strains. PLoS One (2010) 0.92
Emergence of Serotype IV Group B Streptococcus Adult Invasive Disease in Manitoba and Saskatchewan, Canada, Is Driven by Clonal Sequence Type 459 Strains. J Clin Microbiol (2015) 0.91
A Zn-dependent metallopeptidase is responsible for sensitivity to LsbB, a class II leaderless bacteriocin of Lactococcus lactis subsp. lactis BGMN1-5. J Bacteriol (2013) 0.89
Integrated whole-genome sequencing and temporospatial analysis of a continuing Group A Streptococcus epidemic. Emerg Microbes Infect (2013) 0.87
The role of clonal interference in the evolutionary dynamics of plasmid-host adaptation. MBio (2012) 0.86
Complex Population Structure and Virulence Differences among Serotype 2 Streptococcus suis Strains Belonging to Sequence Type 28. PLoS One (2015) 0.86
Clonal Complex 17 Group B Streptococcus strains causing invasive disease in neonates and adults originate from the same genetic pool. Sci Rep (2016) 0.83
Serotype distribution, population structure and antimicrobial resistance of Group B Streptococcus strains recovered from colonized pregnant women. J Clin Microbiol (2016) 0.80
Isolation of Salmonella enterica serovar Kentucky strain ST 198 and its H2S-negative variant from a patient: implications for diagnosis. J Clin Microbiol (2014) 0.80
Population Structure and Antimicrobial Resistance Profiles of Streptococcus suis Serotype 2 Sequence Type 25 Strains. PLoS One (2016) 0.80
Whole-genome sequencing of the Mycobacterium tuberculosis Manila sublineage results in less clustering and better resolution than mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing and spoligotyping. J Clin Microbiol (2014) 0.79
The Majority of 9,729 Group A Streptococcus Strains Causing Disease Secrete SpeB Cysteine Protease: Pathogenesis Implications. Infect Immun (2015) 0.79
A putative amino acid transporter determines sensitivity to the two-peptide bacteriocin plantaricin JK. Microbiologyopen (2016) 0.78
Genomic Characterization of a Pattern D Streptococcus pyogenes emm53 Isolate Reveals a Genetic Rationale for Invasive Skin Tropicity. J Bacteriol (2016) 0.78
Genomic Recombination Leading to Decreased Virulence of Group B Streptococcus in a Mouse Model of Adult Invasive Disease. Pathogens (2016) 0.75
Phenotypic differentiation of Streptococcus pyogenes populations is induced by recombination-driven gene-specific sweeps. Sci Rep (2016) 0.75
Capsular Switching and Other Large-Scale Recombination Events in Invasive Sequence Type 1 Group B Streptococcus. Emerg Infect Dis (2016) 0.75
Fluoroquinolone Resistance among Clonal Complex 1 Group B Streptococcus Strains. Can J Infect Dis Med Microbiol (2016) 0.75
Whole-genome sequencing of mutants with increased resistance against the two-peptide bacteriocin plantaricin JK reveals a putative receptor and potential docking site. PLoS One (2017) 0.75
Antibacterial small molecules targeting the conserved TOPRIM domain of DNA gyrase. PLoS One (2017) 0.75
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
Whole-genome sequencing and variant discovery in C. elegans. Nat Methods (2008) 31.92
An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci U S A (2001) 31.51
Accurate multiplex polony sequencing of an evolved bacterial genome. Science (2005) 20.91
ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet (2008) 19.97
Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature (1999) 19.34
Single-molecule DNA sequencing of a viral genome. Science (2008) 11.66
Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res (2008) 10.49
Gene sequencing. The race for the $1000 genome. Science (2006) 6.76
Mutation discovery in bacterial genomes: metronidazole resistance in Helicobacter pylori. Nat Methods (2005) 3.19
Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor. Proc Natl Acad Sci U S A (2006) 2.00
Genomics and microbiology. Microbial forensics--"cross-examining pathogens". Science (2002) 1.47
Microbiology. TB--a new target, a new drug. Science (2005) 1.18
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18
Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (2011) 53.86
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59
The structure of haplotype blocks in the human genome. Science (2002) 50.88
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell (2006) 48.80
Integrative genomics viewer. Nat Biotechnol (2011) 42.83
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48
The landscape of somatic copy-number alteration across human cancers. Nature (2010) 31.88
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29
Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) 30.02
Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 29.83
Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature (2003) 29.16
Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol (2009) 27.17
The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science (2006) 25.99
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04
High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97
ARACHNE: a whole-genome shotgun assembler. Genome Res (2002) 22.72
Detecting recent positive selection in the human genome from haplotype structure. Nature (2002) 22.00
A molecular signature of metastasis in primary solid tumors. Nat Genet (2002) 21.36
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A (2009) 20.66
ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61
International network of cancer genome projects. Nature (2010) 20.35
Genomic maps and comparative analysis of histone modifications in human and mouse. Cell (2005) 18.96
Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A (2007) 18.83
A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell (2006) 18.81
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
The mammalian epigenome. Cell (2007) 18.13
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Initial genome sequencing and analysis of multiple myeloma. Nature (2011) 17.28
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res (2011) 17.21
Risk alleles for multiple sclerosis identified by a genomewide study. N Engl J Med (2007) 17.06
The mutational landscape of head and neck squamous cell carcinoma. Science (2011) 16.88
Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat Genet (2003) 16.51
Characterizing the cancer genome in lung adenocarcinoma. Nature (2007) 16.48
Dissecting direct reprogramming through integrative genomic analysis. Nature (2008) 16.47
Assessing the impact of population stratification on genetic association studies. Nat Genet (2004) 16.28
Gene expression correlates of clinical prostate cancer behavior. Cancer Cell (2002) 16.27
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol (2013) 16.13
Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature (2002) 15.36
Genetic mapping in human disease. Science (2008) 15.12
The genomic complexity of primary human prostate cancer. Nature (2011) 14.06
Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med (2002) 14.01
The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99
MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat Genet (2001) 13.79
A landscape of driver mutations in melanoma. Cell (2012) 12.61
High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods (2008) 12.56
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature (2004) 12.32
Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res (2003) 12.30
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell (2010) 12.27
Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell (2012) 11.69
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature (2009) 11.46
The genome sequence of the filamentous fungus Neurospora crassa. Nature (2003) 11.39
lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature (2011) 11.31
The mystery of missing heritability: Genetic interactions create phantom heritability. Proc Natl Acad Sci U S A (2012) 11.23
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17
SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med (2011) 11.07
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03
Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol (2012) 10.87
Genetic screens in human cells using the CRISPR-Cas9 system. Science (2013) 10.75
Detecting novel associations in large data sets. Science (2011) 10.60
Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res (2008) 10.49
Reactive oxygen species have a causal role in multiple forms of insulin resistance. Nature (2006) 10.07
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet (2012) 9.93
Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell (2013) 9.24
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol (2011) 9.18
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res (2005) 8.69
A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011) 8.67
Integrative analysis of the melanoma transcriptome. Genome Res (2010) 8.46
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
Lessons from the cancer genome. Cell (2013) 8.12
A catalog of reference genomes from the human microbiome. Science (2010) 8.10
Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci U S A (2007) 8.00
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
Loss of E-cadherin promotes metastasis via multiple downstream transcriptional pathways. Cancer Res (2008) 7.91
Melanoma genome sequencing reveals frequent PREX2 mutations. Nature (2012) 7.77
Sequence analysis of mutations and translocations across breast cancer subtypes. Nature (2012) 7.76