Published in Proc Natl Acad Sci U S A on December 27, 2010
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol (2012) 62.36
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience (2012) 20.89
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol (2013) 16.13
FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics (2011) 13.71
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
A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics (2012) 9.97
Initial impact of the sequencing of the human genome. Nature (2011) 9.18
An integrated pipeline for de novo assembly of microbial genomes. PLoS One (2012) 8.97
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
Genome structural variation discovery and genotyping. Nat Rev Genet (2011) 7.34
Efficient de novo assembly of large genomes using compressed data structures. Genome Res (2011) 6.05
De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat Genet (2012) 5.61
Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet (2011) 5.58
Modernizing reference genome assemblies. PLoS Biol (2011) 5.23
The MaSuRCA genome assembler. Bioinformatics (2013) 5.07
Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One (2014) 4.94
Characterizing and measuring bias in sequence data. Genome Biol (2013) 4.39
Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res (2014) 4.29
Molecular diagnosis of infantile mitochondrial disease with targeted next-generation sequencing. Sci Transl Med (2012) 4.02
Finished bacterial genomes from shotgun sequence data. Genome Res (2012) 3.86
Experimental and analytical tools for studying the human microbiome. Nat Rev Genet (2011) 3.30
Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. Proc Natl Acad Sci U S A (2012) 3.10
REAPR: a universal tool for genome assembly evaluation. Genome Biol (2013) 3.05
Pacific biosciences sequencing technology for genotyping and variation discovery in human data. BMC Genomics (2012) 2.92
Exploiting sparseness in de novo genome assembly. BMC Bioinformatics (2012) 2.88
Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol (2012) 2.82
The African coelacanth genome provides insights into tetrapod evolution. Nature (2013) 2.78
GapFiller: a de novo assembly approach to fill the gap within paired reads. BMC Bioinformatics (2012) 2.72
Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proc Natl Acad Sci U S A (2011) 2.67
Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathog (2012) 2.66
The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line. Nature (2013) 2.65
The expanding scope of DNA sequencing. Nat Biotechnol (2012) 2.57
A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies. PLoS One (2011) 2.55
Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics (2012) 2.46
Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nat Biotechnol (2011) 2.45
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol (2014) 2.44
The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum. Nat Genet (2012) 2.43
Comparing de novo genome assembly: the long and short of it. PLoS One (2011) 2.37
GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics (2013) 2.24
Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science (2014) 2.21
Sequence assembly demystified. Nat Rev Genet (2013) 2.09
Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads--a baiting and iterative mapping approach. Nucleic Acids Res (2013) 2.08
Improving PacBio long read accuracy by short read alignment. PLoS One (2012) 2.06
Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. Nat Biotechnol (2013) 2.05
A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains. Genome Biol (2013) 2.04
Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J (2013) 2.02
Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proc Natl Acad Sci U S A (2011) 1.99
From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics. PLoS One (2015) 1.95
De novo assembly of highly diverse viral populations. BMC Genomics (2012) 1.87
Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods (2015) 1.83
Efficient counting of k-mers in DNA sequences using a bloom filter. BMC Bioinformatics (2011) 1.76
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol (2013) 1.74
Draft genome of the kiwifruit Actinidia chinensis. Nat Commun (2013) 1.72
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Brief Bioinform (2011) 1.70
Current challenges in de novo plant genome sequencing and assembly. Genome Biol (2012) 1.69
An extensive evaluation of read trimming effects on Illumina NGS data analysis. PLoS One (2013) 1.66
Genome sequence of mungbean and insights into evolution within Vigna species. Nat Commun (2014) 1.62
Fast scaffolding with small independent mixed integer programs. Bioinformatics (2011) 1.59
The genome of Chenopodium quinoa. Nature (2017) 1.58
Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora. Proc Natl Acad Sci U S A (2014) 1.56
Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science (2014) 1.55
The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet (2016) 1.54
FastUniq: a fast de novo duplicates removal tool for paired short reads. PLoS One (2012) 1.54
High-throughput genome scaffolding from in vivo DNA interaction frequency. Nat Biotechnol (2013) 1.53
Paired-end sequencing of Fosmid libraries by Illumina. Genome Res (2012) 1.52
GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers. PLoS One (2014) 1.49
Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes. PLoS Genet (2015) 1.49
Graph accordance of next-generation sequence assemblies. Bioinformatics (2011) 1.47
Sequencing and assembly of the 22-gb loblolly pine genome. Genetics (2014) 1.46
Single haplotype assembly of the human genome from a hydatidiform mole. Genome Res (2014) 1.44
proovread: large-scale high-accuracy PacBio correction through iterative short read consensus. Bioinformatics (2014) 1.43
Staphylococcal enterotoxin P predicts bacteremia in hospitalized patients colonized with methicillin-resistant Staphylococcus aureus. J Infect Dis (2013) 1.43
The Genome of the "Great Speciator" Provides Insights into Bird Diversification. Genome Biol Evol (2015) 1.43
Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. Genome Biol (2017) 1.43
The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species. Genome Biol (2016) 1.42
Permanent draft genome of Thermithiobaclillus tepidarius DSM 3134(T), a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia. Stand Genomic Sci (2016) 1.41
A new transcriptome and transcriptome profiling of adult and larval tissue in the box jellyfish Alatina alata: an emerging model for studying venom, vision and sex. BMC Genomics (2016) 1.39
Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species. BMC Biol (2017) 1.39
Inferring the global structure of chromosomes from structural variations. BMC Genomics (2015) 1.37
Draft genome sequence of adzuki bean, Vigna angularis. Sci Rep (2015) 1.37
LoRDEC: accurate and efficient long read error correction. Bioinformatics (2014) 1.36
Using population admixture to help complete maps of the human genome. Nat Genet (2013) 1.35
Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biol (2012) 1.33
Complete genomes of two dipteran-associated spiroplasmas provided insights into the origin, dynamics, and impacts of viral invasion in spiroplasma. Genome Biol Evol (2013) 1.32
An improved genome release (version Mt4.0) for the model legume Medicago truncatula. BMC Genomics (2014) 1.32
Draft Genome Sequence of Frankia sp. Strain BCU110501, a Nitrogen-Fixing Actinobacterium Isolated from Nodules of Discaria trinevis. Genome Announc (2013) 1.27
Next-generation sequencing and large genome assemblies. Pharmacogenomics (2012) 1.27
Reference-assisted chromosome assembly. Proc Natl Acad Sci U S A (2013) 1.26
Draft Genome Sequence of Frankia sp. Strain CcI6, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodule of Casuarina cunninghamiana. Genome Announc (2014) 1.26
Genetic variation and the de novo assembly of human genomes. Nat Rev Genet (2015) 1.24
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
Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction. Brief Bioinform (2015) 1.22
A vertebrate case study of the quality of assemblies derived from next-generation sequences. Genome Biol (2011) 1.22
Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton. ISME J (2012) 1.21
Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. Elife (2014) 1.21
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res (2016) 1.20
Comparative genomics of recent Shiga toxin-producing Escherichia coli O104:H4: short-term evolution of an emerging pathogen. MBio (2013) 1.19
Comprehensive variation discovery in single human genomes. Nat Genet (2014) 1.18
FGAP: an automated gap closing tool. BMC Res Notes (2014) 1.18
Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16
A map of human genome variation from population-scale sequencing. Nature (2010) 121.13
Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res (1998) 106.16
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91
The diploid genome sequence of an individual human. PLoS Biol (2007) 44.80
ABySS: a parallel assembler for short read sequence data. Genome Res (2009) 43.20
Finishing the euchromatic sequence of the human genome. Nature (2004) 41.40
An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci U S A (2001) 31.51
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04
ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods (2009) 10.41
Complete Khoisan and Bantu genomes from southern Africa. Nature (2010) 9.06
Limitations of next-generation genome sequence assembly. Nat Methods (2010) 9.04
Directional cloning of DNA fragments at a large distance from an initial probe: a circularization method. Proc Natl Acad Sci U S A (1984) 7.38
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biol (2009) 6.76
Genome analysis of the platypus reveals unique signatures of evolution. Nature (2008) 5.74
Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol (2009) 5.45
Mouse segmental duplication and copy number variation. Nat Genet (2008) 4.24
A burst of segmental duplications in the genome of the African great ape ancestor. Nature (2009) 3.63
De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. PLoS Genet (2010) 2.77
10,000 genomes to come. Nature (2009) 1.65
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
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
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
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
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
Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1. Proc Natl Acad Sci U S A (2003) 17.10
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
Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell (2006) 15.12
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
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res (2006) 13.32
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
Structural and functional bases for broad-spectrum neutralization of avian and human influenza A viruses. Nat Struct Mol Biol (2009) 12.13
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