Published in Genome Biol on October 01, 2009
High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97
FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics (2011) 13.71
Toward almost closed genomes with GapFiller. Genome Biol (2012) 10.92
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol (2011) 9.18
Assembly algorithms for next-generation sequencing data. Genomics (2010) 8.56
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
Visualizing genomes: techniques and challenges. Nat Methods (2010) 6.66
Assembly of large genomes using second-generation sequencing. Genome Res (2010) 5.94
Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol (2010) 5.79
PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics (2013) 5.61
Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res (2010) 4.18
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
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res (2012) 3.52
Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. J Comput Biol (2011) 2.85
A computational genomics pipeline for prokaryotic sequencing projects. Bioinformatics (2010) 2.63
Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proc Natl Acad Sci U S A (2014) 2.42
Studying bacterial transcriptomes using RNA-seq. Curr Opin Microbiol (2010) 2.06
De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology. PLoS One (2010) 1.95
Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods (2015) 1.83
Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences. Bioinformatics (2014) 1.73
Deep evolutionary comparison of gene expression identifies parallel recruitment of trans-factors in two independent origins of C4 photosynthesis. PLoS Genet (2014) 1.70
Integrating genome assemblies with MAIA. Bioinformatics (2010) 1.70
Hi-C: a method to study the three-dimensional architecture of genomes. J Vis Exp (2010) 1.67
Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem. Appl Environ Microbiol (2011) 1.64
Paired-end sequencing of Fosmid libraries by Illumina. Genome Res (2012) 1.52
State of the art de novo assembly of human genomes from massively parallel sequencing data. Hum Genomics (2010) 1.51
Evaluating the fidelity of de novo short read metagenomic assembly using simulated data. PLoS One (2011) 1.39
Meraculous: de novo genome assembly with short paired-end reads. PLoS One (2011) 1.37
Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts. Nat Commun (2016) 1.13
Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. Bioinform Biol Insights (2015) 1.13
Effects of GC bias in next-generation-sequencing data on de novo genome assembly. PLoS One (2013) 1.13
Telescoper: de novo assembly of highly repetitive regions. Bioinformatics (2012) 1.08
Next-generation sequence assembly: four stages of data processing and computational challenges. PLoS Comput Biol (2013) 1.07
VSEARCH: a versatile open source tool for metagenomics. PeerJ (2016) 1.07
AGORA: Assembly Guided by Optical Restriction Alignment. BMC Bioinformatics (2012) 1.06
Adaptin evolution in kinetoplastids and emergence of the variant surface glycoprotein coat in African trypanosomatids. Mol Phylogenet Evol (2013) 1.02
Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies. PLoS One (2010) 0.98
Sequencing and characterization of the complete mitochondrial genomes of three Pneumocystis species provide new insights into divergence between human and rodent Pneumocystis. FASEB J (2013) 0.97
Genomics reveals new landscapes for crop improvement. Genome Biol (2013) 0.93
Fine de novo sequencing of a fungal genome using only SOLiD short read data: verification on Aspergillus oryzae RIB40. PLoS One (2013) 0.93
The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. Nat Genet (2016) 0.92
BESST--efficient scaffolding of large fragmented assemblies. BMC Bioinformatics (2014) 0.91
Draft genome of Myxosarcina sp. strain GI1, a baeocytous cyanobacterium associated with the marine sponge Terpios hoshinota. Stand Genomic Sci (2015) 0.86
Improving transcriptome assembly through error correction of high-throughput sequence reads. PeerJ (2013) 0.84
Nuclear pore complex evolution: a trypanosome Mlp analogue functions in chromosomal segregation but lacks transcriptional barrier activity. Mol Biol Cell (2014) 0.83
A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes. Methods (2012) 0.82
Optimal assembly for high throughput shotgun sequencing. BMC Bioinformatics (2013) 0.81
Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences. Bioinformatics (2016) 0.79
Comparative transcriptome analysis within the Lolium/Festuca species complex reveals high sequence conservation. BMC Genomics (2015) 0.78
Hybrid De Novo Genome Assembly Using MiSeq and SOLiD Short Read Data. PLoS One (2015) 0.78
High throughput sequencing approaches to mutation discovery in the mouse. Mamm Genome (2012) 0.76
C4 Photosynthesis in the Rice Paddy: Insights from the Noxious Weed Echinochloa glabrescens. Plant Physiol (2015) 0.76
Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland. Stand Genomic Sci (2016) 0.75
Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range. BMC Genomics (2017) 0.75
An unusual strategy for the anoxic biodegradation of phthalate. ISME J (2016) 0.75
High quality draft genome sequences of Pseudomonas fulva DSM 17717(T), Pseudomonas parafulva DSM 17004(T) and Pseudomonas cremoricolorata DSM 17059(T) type strains. Stand Genomic Sci (2016) 0.75
Permanent Draft Genome Sequence of Desulfurococcus amylolyticus Strain Z-533(T), a Peptide and Starch Degrader Isolated from Thermal Springs in the Kamchatka Peninsula and Kunashir Island, Russia. Genome Announc (2017) 0.75
Arapan-S: a fast and highly accurate whole-genome assembly software for viruses and small genomes. BMC Res Notes (2012) 0.75
Transcriptome-based investigation of cirrus development and identifying microsatellite markers in rattan (Daemonorops jenkinsiana). Sci Rep (2017) 0.75
A comparative study of k-spectrum-based error correction methods for next-generation sequencing data analysis. Hum Genomics (2016) 0.75
Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16
Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21
Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res (1998) 106.16
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
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
Assembling millions of short DNA sequences using SSAKE. Bioinformatics (2006) 18.71
SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res (2007) 16.20
A large genome center's improvements to the Illumina sequencing system. Nat Methods (2008) 15.56
Short read fragment assembly of bacterial genomes. Genome Res (2007) 15.40
De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res (2008) 14.90
Extending assembly of short DNA sequences to handle error. Bioinformatics (2007) 14.46
Single-molecule DNA sequencing of a viral genome. Science (2008) 11.66
The genome sequence of the filamentous fungus Neurospora crassa. Nature (2003) 11.39
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods (2009) 10.41
Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science (2002) 9.83
De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Res (2008) 7.66
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
Gene sequencing. The race for the $1000 genome. Science (2006) 6.76
Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nat Methods (2008) 2.61
De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads. FEMS Microbiol Lett (2008) 2.50
Quality assessment of the human genome sequence. Nature (2004) 2.29
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
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
Integrating common and rare genetic variation in diverse human populations. Nature (2010) 32.30
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29
Mapping and sequencing of structural variation from eight human genomes. Nature (2008) 30.28
Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 29.83
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol (2009) 27.17
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
ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell (2006) 15.12
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res (2006) 13.32
High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods (2008) 12.56
Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res (2003) 12.30
The genome sequence of the filamentous fungus Neurospora crassa. Nature (2003) 11.39
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03
Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res (2008) 10.49
Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol (2011) 9.18
Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods (2010) 9.09
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
Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell (2011) 8.21
A catalog of reference genomes from the human microbiome. Science (2010) 8.10
A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res (2008) 7.77
Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol (2006) 7.64
Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev (2010) 7.14
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00
The genome sequence of the rice blast fungus Magnaporthe grisea. Nature (2005) 6.95
Genetic evidence for complex speciation of humans and chimpanzees. Nature (2006) 6.66
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature (2013) 6.50
The genome of the model beetle and pest Tribolium castaneum. Nature (2008) 6.50
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature (2009) 6.44
A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature (2012) 6.34
Development of personalized tumor biomarkers using massively parallel sequencing. Sci Transl Med (2010) 6.08
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A (2009) 6.01
Comparative functional genomics of the fission yeasts. Science (2011) 6.00
Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol (2010) 5.96
Charting a dynamic DNA methylation landscape of the human genome. Nature (2013) 5.80
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature (2010) 5.79
A composite of multiple signals distinguishes causal variants in regions of positive selection. Science (2010) 5.61
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature (2006) 5.52
The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A (2002) 5.28
The genomic basis of adaptive evolution in threespine sticklebacks. Nature (2012) 5.20
A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol (2011) 5.11