Published in Genome Biol on July 03, 2013
Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae. Sci Transl Med (2014) 2.87
Standards for sequencing viral genomes in the era of high-throughput sequencing. MBio (2014) 1.85
Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements. PLoS One (2014) 1.74
Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences. Bioinformatics (2014) 1.73
The role of replicates for error mitigation in next-generation sequencing. Nat Rev Genet (2013) 1.66
Quantifying genome-editing outcomes at endogenous loci with SMRT sequencing. Cell Rep (2014) 1.50
Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet (2016) 1.49
Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia. Biotechnol Biofuels (2014) 1.47
Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes. Nat Biotechnol (2015) 1.47
proovread: large-scale high-accuracy PacBio correction through iterative short read consensus. Bioinformatics (2014) 1.43
Long-read, whole-genome shotgun sequence data for five model organisms. Sci Data (2014) 1.30
Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol (2014) 1.24
Breast cancer intra-tumor heterogeneity. Breast Cancer Res (2014) 1.16
Characterizing 5-methylcytosine in the mammalian epitranscriptome. Genome Biol (2013) 1.11
Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies. Sci Data (2015) 1.06
SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips. Bioinformatics (2014) 1.04
Whole-genome sequencing in outbreak analysis. Clin Microbiol Rev (2015) 1.03
Validation of high throughput sequencing and microbial forensics applications. Investig Genet (2014) 1.02
Metassembler: merging and optimizing de novo genome assemblies. Genome Biol (2015) 0.98
Accurate typing of short tandem repeats from genome-wide sequencing data and its applications. Genome Res (2015) 0.96
Characterization of structural variants with single molecule and hybrid sequencing approaches. Bioinformatics (2014) 0.92
A precise chloroplast genome of Nelumbo nucifera (Nelumbonaceae) evaluated with Sanger, Illumina MiSeq, and PacBio RS II sequencing platforms: insight into the plastid evolution of basal eudicots. BMC Plant Biol (2014) 0.91
Exome Sequencing: Current and Future Perspectives. G3 (Bethesda) (2015) 0.91
Next-generation sequencing and epigenomics research: a hammer in search of nails. Genomics Inform (2014) 0.89
The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms. BMC Genomics (2014) 0.89
Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing. Sci Rep (2015) 0.87
Quality scores for 32,000 genomes. Stand Genomic Sci (2014) 0.85
Epigenetic regulation by heritable RNA. PLoS Genet (2014) 0.85
Chloroplast genome of Aconitum barbatum var. puberulum (Ranunculaceae) derived from CCS reads using the PacBio RS platform. Front Plant Sci (2015) 0.85
Structural variation discovery in the cancer genome using next generation sequencing: computational solutions and perspectives. Oncotarget (2015) 0.85
Complete Genome Sequence of Pseudomonas aeruginosa PA1, Isolated from a Patient with a Respiratory Tract Infection. Genome Announc (2015) 0.83
An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. BMC Genomics (2017) 0.82
Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research. BMC Genomics (2015) 0.82
HIV-1 interacts with human endogenous retrovirus K (HML-2) envelopes derived from human primary lymphocytes. J Virol (2014) 0.82
Towards Better Precision Medicine: PacBio Single-Molecule Long Reads Resolve the Interpretation of HIV Drug Resistant Mutation Profiles at Explicit Quasispecies (Haplotype) Level. J Data Mining Genomics Proteomics (2015) 0.82
Genome Sequence of "Candidatus Thioglobus autotrophica" Strain EF1, a Chemoautotroph from the SUP05 Clade of Marine Gammaproteobacteria. Genome Announc (2015) 0.81
Global Identification of the Full-Length Transcripts and Alternative Splicing Related to Phenolic Acid Biosynthetic Genes in Salvia miltiorrhiza. Front Plant Sci (2016) 0.81
A fault-tolerant method for HLA typing with PacBio data. BMC Bioinformatics (2014) 0.81
Next-Generation Sequencing Approaches in Cancer: Where Have They Brought Us and Where Will They Take Us? Cancers (Basel) (2015) 0.80
Population Structure and Antimicrobial Resistance Profiles of Streptococcus suis Serotype 2 Sequence Type 25 Strains. PLoS One (2016) 0.80
Profiling genome-wide DNA methylation. Epigenetics Chromatin (2016) 0.79
Mappability and read length. Front Genet (2014) 0.79
Insights on virulence from the complete genome of Staphylococcus capitis. Front Microbiol (2015) 0.78
The RBPome: where the brains meet the brawn. Genome Biol (2014) 0.78
Cancer genomics just got personal. Genome Biol (2014) 0.78
Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing. BMC Cancer (2015) 0.78
A comprehensive approach to expression of L1 loci. Nucleic Acids Res (2016) 0.77
A vast genomic deletion in the C56BL/6 genome affects different genes within the Ifi200 cluster on chromosome 1 and mediates obesity and insulin resistance. BMC Genomics (2017) 0.77
Cultivation of a chemoautotroph from the SUP05 clade of marine bacteria that produces nitrite and consumes ammonium. ISME J (2016) 0.77
Refined Pichia pastoris reference genome sequence. J Biotechnol (2016) 0.77
Complete Genome Sequence of Pseudomonas aeruginosa Phage-Resistant Variant PA1RG. Genome Announc (2016) 0.76
Non-coding RNA gene families in the genomes of anopheline mosquitoes. BMC Genomics (2014) 0.76
Comparative genomics reveals Lysinibacillus sphaericus group comprises a novel species. BMC Genomics (2016) 0.76
Plant exomics: concepts, applications and methodologies in crop improvement. Plant Signal Behav (2015) 0.75
Complete Genome Sequence of Hemolysin-Containing Carnobacterium sp. Strain CP1 Isolated from the Antarctic. Genome Announc (2016) 0.75
Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads. BioData Min (2016) 0.75
High Throughput Random Mutagenesis and Single Molecule Real Time Sequencing of the Muscle Nicotinic Acetylcholine Receptor. PLoS One (2016) 0.75
PWHATSHAP: efficient haplotyping for future generation sequencing. BMC Bioinformatics (2016) 0.75
Evolution of multi-drug resistant HCV clones from pre-existing resistant-associated variants during direct-acting antiviral therapy determined by third-generation sequencing. Sci Rep (2017) 0.75
The impact of "omic" and imaging technologies on assessing the host immune response to biodefence agents. J Immunol Res (2014) 0.75
A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes. PLoS One (2016) 0.75
Genome of Cnaphalocrocis medinalis Granulovirus, the First Crambidae-Infecting Betabaculovirus Isolated from Rice Leaffolder to Sequenced. PLoS One (2016) 0.75
Next generation sequencing data of a defined microbial mock community. Sci Data (2016) 0.75
Higher-order organisation of extremely amplified, potentially functional and massively methylated 5S rDNA in European pikes (Esox sp.). BMC Genomics (2017) 0.75
Genome-wide analysis of complex wheat gliadins, the dominant carriers of celiac disease epitopes. Sci Rep (2017) 0.75
The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features. Sci Rep (2016) 0.75
The Lysobacter capsici AZ78 Genome Has a Gene Pool Enabling it to Interact Successfully with Phytopathogenic Microorganisms and Environmental Factors. Front Microbiol (2016) 0.75
A Simple Thermoplastic Substrate Containing Hierarchical Silica Lamellae for High-Molecular-Weight DNA Extraction. Adv Mater (2016) 0.75
Complete Genome Sequence of Rhodococcus sp. B7740, a Carotenoid-Producing Bacterium Isolated from the Arctic Sea. Genome Announc (2015) 0.75
The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity. BMC Genomics (2017) 0.75
Single-Molecule Sequencing (PacBio) of the Staphylococcus capitis NRCS-A Clone Reveals the Basis of Multidrug Resistance and Adaptation to the Neonatal Intensive Care Unit Environment. Front Microbiol (2016) 0.75
Elastic proteins in the flight muscle of Manduca sexta. Arch Biochem Biophys (2015) 0.75
SNP Mining in Functional Genes from Nonmodel Species by Next-Generation Sequencing: A Case of Flowering, Pre-Harvest Sprouting, and Dehydration Resistant Genes in Wheat. Biomed Res Int (2016) 0.75
DNA Methylation Assessed by SMRT Sequencing Is Linked to Mutations in Neisseria meningitidis Isolates. PLoS One (2015) 0.75
SMRT genome assembly corrects reference errors, resolving the genetic basis of virulence in Mycobacterium tuberculosis. BMC Genomics (2017) 0.75
Technological advances in precision medicine and drug development. Expert Rev Precis Med Drug Dev (2016) 0.75
EasyCluster2: an improved tool for clustering and assembling long transcriptome reads. BMC Bioinformatics (2014) 0.75
Organelle_PBA, a pipeline for assembling chloroplast and mitochondrial genomes from PacBio DNA sequencing data. BMC Genomics (2017) 0.75
Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue. BMC Vet Res (2017) 0.75
Analysis of single nucleic acid molecules in micro- and nano-fluidics. Lab Chip (2016) 0.75
Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human. BMC Genomics (2017) 0.75
Extensive Mobilome-Driven Genome Diversification in Mouse Gut-Associated Bacteroides vulgatus mpk. Genome Biol Evol (2016) 0.75
Complete Genome Sequence of Enterobacter sp. Strain ODB01, a Bacterium That Degrades Crude Oil. Genome Announc (2017) 0.75
Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage. Algorithms Mol Biol (2016) 0.75
Analyses of Compact Trichinella Kinomes Reveal a MOS-Like Protein Kinase with a Unique N-Terminal Domain. G3 (Bethesda) (2016) 0.75
Complete Genome Sequence of Brevibacterium linens SMQ-1335. Genome Announc (2016) 0.75
TeloPCR-seq: a high-throughput sequencing approach for telomeres. FEBS Lett (2016) 0.75
Erratum to: The advantages of SMRT sequencing. Genome Biol (2017) 0.75
De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads. Gigascience (2017) 0.75
Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition. Mycorrhiza (2016) 0.75
A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies. Front Microbiol (2017) 0.75
Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species. Sci Rep (2017) 0.75
Hybrid assembly with long and short reads improves discovery of gene family expansions. BMC Genomics (2017) 0.75
Genome Sequence of Pseudomonas stutzeri 273 and Identification of the Exopolysaccharide EPS273 Biosynthesis Locus. Mar Drugs (2017) 0.75
Sample Size Estimation for Detection of Splicing Events in Transcriptome Sequencing Data. Int J Mol Sci (2017) 0.75
Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome. Genes (Basel) (2017) 0.75
A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet (2011) 59.36
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods (2013) 31.15
Real-time DNA sequencing from single polymerase molecules. Science (2008) 29.53
Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol (2012) 10.31
Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods (2010) 9.75
Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biol (2013) 4.55
A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res (2010) 4.48
Real-time tRNA transit on single translating ribosomes at codon resolution. Nature (2010) 3.87
Finished bacterial genomes from shotgun sequence data. Genome Res (2012) 3.86
Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics (2010) 3.45
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nat Biotechnol (2012) 3.39
A hybrid approach for the automated finishing of bacterial genomes. Nat Biotechnol (2012) 3.29
The methylomes of six bacteria. Nucleic Acids Res (2012) 3.19
Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res (2011) 3.18
Pacific biosciences sequencing technology for genotyping and variation discovery in human data. BMC Genomics (2012) 2.92
The birth of the Epitranscriptome: deciphering the function of RNA modifications. Genome Biol (2012) 1.96
Aluminum tolerance in maize is associated with higher MATE1 gene copy number. Proc Natl Acad Sci U S A (2013) 1.63
Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription. J Nanobiotechnology (2013) 1.19
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Quake: quality-aware detection and correction of sequencing errors. Genome Biol (2010) 12.52
GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res (2012) 11.33
Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol (2012) 10.31
Searching for SNPs with cloud computing. Genome Biol (2009) 10.12
De novo gene disruptions in children on the autistic spectrum. Neuron (2012) 9.69
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol (2009) 5.93
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39
Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations. Nature (2012) 5.23
Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS Biol (2005) 5.22
Genome assembly forensics: finding the elusive mis-assembly. Genome Biol (2008) 4.91
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11
NEBcutter: A program to cleave DNA with restriction enzymes. Nucleic Acids Res (2003) 3.68
Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics (2010) 3.45
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nat Biotechnol (2012) 3.39
The methylomes of six bacteria. Nucleic Acids Res (2012) 3.19
Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res (2011) 3.18
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics (2008) 2.51
Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases. EMBO J (2002) 2.40
Computational identification of operons in microbial genomes. Genome Res (2002) 2.35
Save your notes, drafts and printouts: today's work is tomorrow's history. Nature (2007) 2.19
Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees. PLoS Pathog (2009) 1.97
Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. J Bacteriol (2011) 1.80
Genomic functional annotation using co-evolution profiles of gene clusters. Genome Biol (2002) 1.76
Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score. Bioinformatics (2012) 1.64
Aluminum tolerance in maize is associated with higher MATE1 gene copy number. Proc Natl Acad Sci U S A (2013) 1.63
Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biol (2013) 1.59
A unique family of Mrr-like modification-dependent restriction endonucleases. Nucleic Acids Res (2010) 1.53
The human proteins MBD5 and MBD6 associate with heterochromatin but they do not bind methylated DNA. PLoS One (2010) 1.37
Using shotgun sequence data to find active restriction enzyme genes. Nucleic Acids Res (2008) 1.34
Rate of meristem maturation determines inflorescence architecture in tomato. Proc Natl Acad Sci U S A (2011) 1.34
Characterization of RimO, a new member of the methylthiotransferase subclass of the radical SAM superfamily. Biochemistry (2009) 1.33
RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli. Proc Natl Acad Sci U S A (2008) 1.27
Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis. Proc Natl Acad Sci U S A (2011) 1.25
The MspJI family of modification-dependent restriction endonucleases for epigenetic studies. Proc Natl Acad Sci U S A (2011) 1.25
The complex methylome of the human gastric pathogen Helicobacter pylori. Nucleic Acids Res (2013) 1.25
Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol (2014) 1.24
The COMBREX project: design, methodology, and initial results. PLoS Biol (2013) 1.24
Complete Genome Sequence of a Multidrug-Resistant Salmonella enterica Serovar Typhimurium var. 5- Strain Isolated from Chicken Breast. Genome Announc (2013) 1.23
Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera. BMC Genomics (2010) 1.23
DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion. Nucleic Acids Res (2006) 1.20
The DNA Data Deluge: Fast, efficient genome sequencing machines are spewing out more data than geneticists can analyze. IEEE Spectr (2013) 1.18
Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps. Genome Biol (2008) 1.17
Extending reference assembly models. Genome Biol (2015) 1.06
Revealing biological modules via graph summarization. J Comput Biol (2009) 1.06
Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine. Nucleic Acids Res (2011) 1.05
An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site. Structure (2004) 1.02
Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI. Nucleic Acids Res (2005) 0.98
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Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus. BMC Microbiol (2007) 0.97
Phylogenetic detection of conserved gene clusters in microbial genomes. BMC Bioinformatics (2005) 0.97
Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase. J Mol Biol (2004) 0.97
Convergence in a mechanically complex phenotype: detecting structural adaptations for crushing in cichlid fish. Evolution (2008) 0.95
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International guidelines for effective control of head louse infestations. J Drugs Dermatol (2007) 0.94
Segmentally variable genes: a new perspective on adaptation. PLoS Biol (2004) 0.91
Identification of genes with fast-evolving regions in microbial genomes. Nucleic Acids Res (2004) 0.91
Vero cytotoxin-producing Escherichia coli O157 gastroenteritis in farm visitors, North Wales. Emerg Infect Dis (2003) 0.90
Selection of restriction endonucleases using artificial cells. Nucleic Acids Res (2007) 0.90
Genotyping in the cloud with Crossbow. Curr Protoc Bioinformatics (2012) 0.89
Computational thinking in the era of big data biology. Genome Biol (2012) 0.89
An open letter to Colonel Muammar al-Gaddafi. Nature (2006) 0.89
Functional characterization of the YmcB and YqeV tRNA methylthiotransferases of Bacillus subtilis. Nucleic Acids Res (2010) 0.86
Sequence-specific cleavage of RNA by Type II restriction enzymes. Nucleic Acids Res (2010) 0.86
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Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions. Biol Chem (2004) 0.85
Two crystal forms of the restriction enzyme MspI-DNA complex show the same novel structure. Protein Sci (2005) 0.85
Sixty years of genome biology. Genome Biol (2013) 0.85
Optimizing Data Intensive GPGPU Computations for DNA Sequence Alignment. Parallel Comput (2009) 0.84
Crystallization and preliminary crystallographic analysis of the type IIL restriction enzyme MmeI in complex with DNA. Acta Crystallogr Sect F Struct Biol Cryst Commun (2011) 0.82
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The BsaHI restriction-modification system: cloning, sequencing and analysis of conserved motifs. BMC Mol Biol (2008) 0.79
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Semiconductor-based DNA sequencing of histone modification states. Nat Commun (2013) 0.78
Teenage booster vaccine: factors affecting uptake. J Public Health (Oxf) (2012) 0.77
Training the next generation of biomedical investigators in glycosciences. J Clin Invest (2016) 0.76
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Correction: Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet (2016) 0.75
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Complete Genome Sequence of a Multidrug-Resistant Salmonella enterica Serovar Typhimurium var. 5- Strain Isolated from Chicken Breast. Genome Announc (2014) 0.75
Libya should stop denying scientific evidence on HIV. Nature (2007) 0.75
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Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region. medRxiv (2020) 0.75
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Fully Assembled Genome Sequence for Salmonella enterica subsp. enterica Serovar Javiana CFSAN001992. Genome Announc (2014) 0.75