Published in Proc Natl Acad Sci U S A on July 13, 2006
Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol (2007) 23.64
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Assembly algorithms for next-generation sequencing data. Genomics (2010) 8.56
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454 sequencing put to the test using the complex genome of barley. BMC Genomics (2006) 6.12
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Bioinformatics challenges of new sequencing technology. Trends Genet (2008) 5.34
Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Plant Biol (2006) 4.85
New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev (2007) 4.62
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A bioinformatician's guide to metagenomics. Microbiol Mol Biol Rev (2008) 4.33
From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing. Nucleic Acids Res (2007) 4.26
Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet (2007) 4.25
Multigene amplification and massively parallel sequencing for cancer mutation discovery. Proc Natl Acad Sci U S A (2007) 3.93
Metagenomics: read length matters. Appl Environ Microbiol (2008) 3.51
Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions. PLoS Genet (2012) 3.46
De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res (2008) 3.41
Experimental and analytical tools for studying the human microbiome. Nat Rev Genet (2011) 3.30
A hybrid approach for the automated finishing of bacterial genomes. Nat Biotechnol (2012) 3.29
SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. BMC Bioinformatics (2014) 3.26
Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature (2010) 2.93
Metagenomic pyrosequencing and microbial identification. Clin Chem (2009) 2.81
Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLoS One (2009) 2.67
Scaffolding and validation of bacterial genome assemblies using optical restriction maps. Bioinformatics (2008) 2.61
Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics (2009) 2.60
Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12. J Bacteriol (2009) 2.51
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol (2010) 2.36
DNA sequencing: bench to bedside and beyond. Nucleic Acids Res (2007) 2.25
High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies. BMC Genomics (2008) 2.21
Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria). Proc Natl Acad Sci U S A (2008) 2.20
De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J (2011) 2.14
Gene-boosted assembly of a novel bacterial genome from very short reads. PLoS Comput Biol (2008) 2.04
A probabilistic method for small RNA flowgram matching. Pac Symp Biocomput (2008) 2.03
Next-generation gap. Nat Methods (2009) 2.01
Photosystem I gene cassettes are present in marine virus genomes. Nature (2009) 1.95
The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity. PLoS One (2012) 1.84
Conservation and divergence of microRNAs in Populus. BMC Genomics (2007) 1.78
Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation. PLoS Biol (2010) 1.77
Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing. Genetica (2008) 1.74
The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PLoS One (2010) 1.71
Integrating genome assemblies with MAIA. Bioinformatics (2010) 1.70
Metagenomic analysis of RNA viruses in a fresh water lake. PLoS One (2009) 1.69
Analysis of high-throughput sequencing and annotation strategies for phage genomes. PLoS One (2010) 1.64
Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA. Genome Res (2007) 1.62
Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches. BMC Genomics (2008) 1.62
Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment. PLoS One (2008) 1.60
The next-generation sequencing technology and application. Protein Cell (2010) 1.52
Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis. Proc Natl Acad Sci U S A (2007) 1.51
Prokaryotic lifestyles in deep sea habitats. Extremophiles (2007) 1.49
Unlocking the transcriptomes of two carcinogenic parasites, Clonorchis sinensis and Opisthorchis viverrini. PLoS Negl Trop Dis (2010) 1.46
Definition of the zebrafish genome using flow cytometry and cytogenetic mapping. BMC Genomics (2007) 1.46
Genome characterization of the oleaginous fungus Mortierella alpina. PLoS One (2011) 1.43
Mariprofundus ferrooxydans PV-1 the first genome of a marine Fe(II) oxidizing Zetaproteobacterium. PLoS One (2011) 1.40
The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing. BMC Genomics (2010) 1.33
Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS One (2013) 1.32
Perspective on optical biosensors and integrated sensor systems. Anal Chem (2009) 1.31
The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms). PLoS One (2009) 1.28
Complete and draft genome sequences of six members of the Aquificales. J Bacteriol (2009) 1.27
A vertebrate case study of the quality of assemblies derived from next-generation sequences. Genome Biol (2011) 1.22
Complete genomic sequence and mass spectrometric analysis of highly diverse, atypical Bacillus thuringiensis phage 0305phi8-36. Virology (2007) 1.21
Massively parallel sequencing identifies the gene Megf8 with ENU-induced mutation causing heterotaxy. Proc Natl Acad Sci U S A (2009) 1.19
Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants. PLoS Comput Biol (2009) 1.18
Engineering proteinase K using machine learning and synthetic genes. BMC Biotechnol (2007) 1.17
Complete genome sequence of a beneficial plant root-associated bacterium, Pseudomonas brassicacearum. J Bacteriol (2011) 1.16
Scanning the human genome at kilobase resolution. Genome Res (2008) 1.13
Genomes and virulence factors of novel bacterial pathogens causing bleaching disease in the marine red alga Delisea pulchra. PLoS One (2011) 1.11
Using 454 technology for long-PCR based sequencing of the complete mitochondrial genome from single Haemonchus contortus (Nematoda). BMC Genomics (2008) 1.06
The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants. PLoS One (2011) 1.06
Reconstructing phylogenies and phenotypes: a molecular view of human evolution. J Anat (2008) 1.01
Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. strain MED134. Appl Environ Microbiol (2011) 0.98
The glycobiome of the rumen bacterium Butyrivibrio proteoclasticus B316(T) highlights adaptation to a polysaccharide-rich environment. PLoS One (2010) 0.97
Metagenomic analysis of a stable trichloroethene-degrading microbial community. ISME J (2012) 0.97
Genome sequence and transcriptome analysis of the radioresistant bacterium Deinococcus gobiensis: insights into the extreme environmental adaptations. PLoS One (2012) 0.95
Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm. BMC Bioinformatics (2008) 0.95
Two Strains of Crocosphaera watsonii with Highly Conserved Genomes are Distinguished by Strain-Specific Features. Front Microbiol (2011) 0.91
Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME J (2013) 0.90
Genome sequence of strain HIMB624, a cultured representative from the OM43 clade of marine Betaproteobacteria. Stand Genomic Sci (2012) 0.90
Insights into the physiology and ecology of the brackish-water-adapted Cyanobacterium Nodularia spumigena CCY9414 based on a genome-transcriptome analysis. PLoS One (2013) 0.89
Genomic DNA sequence comparison between two inbred soybean cyst nematode biotypes facilitated by massively parallel 454 micro-bead sequencing. Mol Genet Genomics (2008) 0.88
Genome sequence of the Marine Janibacter Sp. Strain HTCC2649. J Bacteriol (2010) 0.87
Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant. Ann Bot (2010) 0.87
Genome sequence of the marine photoheterotrophic bacterium Erythrobacter sp. strain NAP1. J Bacteriol (2011) 0.86
A guided tour of large genome size in animals: what we know and where we are heading. Chromosome Res (2011) 0.85
Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes. BMC Genomics (2011) 0.84
Draft genome sequence of Caminibacter mediatlanticus strain TB-2, an epsilonproteobacterium isolated from a deep-sea hydrothermal vent. Stand Genomic Sci (2011) 0.83
Bioenergy research: a new paradigm in multidisciplinary research. J R Soc Interface (2010) 0.82
Using RNase sequence specificity to refine the identification of RNA-protein binding regions. BMC Genomics (2008) 0.82
Pyrosequencing reveals fungal communities in the rhizosphere of Xinjiang Jujube. Biomed Res Int (2015) 0.80
Genome sequence of Corynebacterium casei UCMA 3821, isolated from a smear-ripened cheese. J Bacteriol (2012) 0.80
Complete Genome Sequence of the Deep-Sea Bacterium Psychromonas Strain CNPT3. Genome Announc (2013) 0.79
From bacterial genomics to metagenomics: concept, tools and recent advances. Indian J Microbiol (2008) 0.79
Recent advances and future perspectives in microbial phototrophy in antarctic sea ice. Biology (Basel) (2012) 0.78
Ecotype diversity and conversion in Photobacterium profundum strains. PLoS One (2014) 0.78
Structural peculiarities of linear megaplasmid, pLMA1, from Micrococcus luteus interfere with pyrosequencing reads assembly. Biotechnol Lett (2010) 0.77
BAC-pool sequencing and analysis of large segments of A12 and D12 homoeologous chromosomes in upland cotton. PLoS One (2013) 0.77
Computational biology methods and their application to the comparative genomics of endocellular symbiotic bacteria of insects. Biol Proced Online (2009) 0.76
Determination of complete nucleotide sequence of the genome of hyperthermophilic microorganism. Dokl Biochem Biophys (2008) 0.75
DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A (1977) 790.54
Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21
A sequencing method based on real-time pyrophosphate. Science (1998) 21.21
Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem (1996) 12.94
Design of a compartmentalized shotgun assembler for the human genome. Bioinformatics (2001) 3.55
Environmental genome shotgun sequencing of the Sargasso Sea. Science (2004) 45.23
The diploid genome sequence of an individual human. PLoS Biol (2007) 44.80
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
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol (2007) 23.58
Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods (2009) 22.47
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A (2005) 14.59
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
Creation of a bacterial cell controlled by a chemically synthesized genome. Science (2010) 13.45
Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature (2005) 11.99
The genome of the African trypanosome Trypanosoma brucei. Science (2005) 11.48
Aggressive assembly of pyrosequencing reads with mates. Bioinformatics (2008) 11.01
Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science (2008) 10.90
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59
Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science (2003) 9.20
Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature (2002) 8.92
Assembly algorithms for next-generation sequencing data. Genomics (2010) 8.56
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature (2005) 8.55
A catalog of reference genomes from the human microbiome. Science (2010) 8.10
Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol (2002) 8.07
Shotgun sequence assembly and recent segmental duplications within the human genome. Nature (2004) 7.91
The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science (2005) 7.61
Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat Biotechnol (2002) 6.96
Genetic variation in an individual human exome. PLoS Genet (2008) 6.68
CAMERA: a community resource for metagenomics. PLoS Biol (2007) 6.49
Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature (2012) 6.37
Essential genes of a minimal bacterium. Proc Natl Acad Sci U S A (2006) 6.31
Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A (2004) 6.08
The dog genome: survey sequencing and comparative analysis. Science (2003) 5.84
The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci U S A (2003) 5.62
Draft genome of the filarial nematode parasite Brugia malayi. Science (2007) 5.28
Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proc Natl Acad Sci U S A (2002) 5.28
Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci U S A (2003) 5.10
Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol (2002) 5.09
A physical map of the mouse genome. Nature (2002) 4.97
Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic Acids Res (2004) 4.97
Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. PLoS Biol (2006) 4.92
Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat Biotechnol (2005) 4.65
Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83. J Bacteriol (2003) 4.41
Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet (2007) 4.25
Comparative genomics of emerging human ehrlichiosis agents. PLoS Genet (2006) 4.23
An agenda for personalized medicine. Nature (2009) 4.14
Structural flexibility in the Burkholderia mallei genome. Proc Natl Acad Sci U S A (2004) 4.13
The dynamic genome of Hydra. Nature (2010) 4.00
Genome transplantation in bacteria: changing one species to another. Science (2007) 3.95
Structural and functional diversity of the microbial kinome. PLoS Biol (2007) 3.74
The genomic basis of trophic strategy in marine bacteria. Proc Natl Acad Sci U S A (2009) 3.72
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SNP500Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes. Nucleic Acids Res (2004) 3.47
The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nat Biotechnol (2004) 3.43
Plasmodium, human and Anopheles genomics and malaria. Nature (2002) 3.42
Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades. J Bacteriol (2006) 3.33
Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoa. PLoS Pathog (2007) 3.27
Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet (2008) 3.23
The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc Natl Acad Sci U S A (2002) 3.19