Published in PLoS One on January 19, 2009
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. BMC Bioinformatics (2010) 4.32
Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS One (2009) 3.41
Bat guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses. J Virol (2010) 3.03
Viral quasispecies evolution. Microbiol Mol Biol Rev (2012) 2.69
Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time. Genome Res (2010) 2.46
A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America. PLoS One (2010) 1.99
Going viral: next-generation sequencing applied to phage populations in the human gut. Nat Rev Microbiol (2012) 1.89
A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun (2014) 1.88
Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur J Clin Microbiol Infect Dis (2012) 1.73
Metagenomic analysis of RNA viruses in a fresh water lake. PLoS One (2009) 1.69
Applications of next-generation sequencing technologies to diagnostic virology. Int J Mol Sci (2011) 1.64
Chlorovirus ATCV-1 is part of the human oropharyngeal virome and is associated with changes in cognitive functions in humans and mice. Proc Natl Acad Sci U S A (2014) 1.60
Characterization of quasispecies of pandemic 2009 influenza A virus (A/H1N1/2009) by de novo sequencing using a next-generation DNA sequencer. PLoS One (2010) 1.56
Sequence analysis of the human virome in febrile and afebrile children. PLoS One (2012) 1.56
Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. ISME J (2011) 1.55
Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity. Proc Natl Acad Sci U S A (2010) 1.53
Virus identification in unknown tropical febrile illness cases using deep sequencing. PLoS Negl Trop Dis (2012) 1.52
Novel circular DNA viruses in stool samples of wild-living chimpanzees. J Gen Virol (2009) 1.46
The feasibility of using high resolution genome sequencing of influenza A viruses to detect mixed infections and quasispecies. PLoS One (2009) 1.46
A comparison of single molecule and amplification based sequencing of cancer transcriptomes. PLoS One (2011) 1.44
Unbiased parallel detection of viral pathogens in clinical samples by use of a metagenomic approach. J Clin Microbiol (2011) 1.41
Finding the lost treasures in exome sequencing data. Trends Genet (2013) 1.36
A microbial detection array (MDA) for viral and bacterial detection. BMC Genomics (2010) 1.35
Host RNAs, including transposons, are encapsidated by a eukaryotic single-stranded RNA virus. Proc Natl Acad Sci U S A (2012) 1.27
Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities. J Cyst Fibros (2012) 1.23
Testing and validation of high density resequencing microarray for broad range biothreat agents detection. PLoS One (2009) 1.22
Use of illumina deep sequencing technology to differentiate hepatitis C virus variants. J Clin Microbiol (2012) 1.19
The key role of genomics in modern vaccine and drug design for emerging infectious diseases. PLoS Genet (2009) 1.18
The impact of multiple infections on wild animal hosts: a review. Infect Ecol Epidemiol (2011) 1.17
Using populations of human and microbial genomes for organism detection in metagenomes. Genome Res (2015) 1.12
Deep sequencing evidence from single grapevine plants reveals a virome dominated by mycoviruses. Arch Virol (2010) 1.10
High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic. J Pathol (2013) 1.09
A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples. PLoS One (2013) 1.07
Study of the viral and microbial communities associated with Crohn's disease: a metagenomic approach. Clin Transl Gastroenterol (2013) 1.06
Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel. J Clin Microbiol (2016) 1.05
Defining the causes of diarrhea: novel approaches. Curr Opin Infect Dis (2011) 1.03
Evolution of mosquito-based arbovirus surveillance systems in Australia. J Biomed Biotechnol (2012) 1.02
Multiplex primer prediction software for divergent targets. Nucleic Acids Res (2009) 0.99
Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections. Parasitology (2014) 0.99
Protocol for metagenomic virus detection in clinical specimens. Emerg Infect Dis (2015) 0.99
Reference-independent comparative metagenomics using cross-assembly: crAss. Bioinformatics (2012) 0.95
Viruses in a 14th-century coprolite. Appl Environ Microbiol (2014) 0.94
MinION nanopore sequencing of an influenza genome. Front Microbiol (2015) 0.93
Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza. PLoS One (2013) 0.91
Norovirus Whole-Genome Sequencing by SureSelect Target Enrichment: a Robust and Sensitive Method. J Clin Microbiol (2016) 0.90
Pathogenic characterization of a cervical lymph node derived from a patient with Kawasaki disease. Int J Clin Exp Pathol (2012) 0.88
Geographic variation in the eukaryotic virome of human diarrhea. Virology (2014) 0.88
Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. PLoS One (2012) 0.87
Alternative applications for distinct RNA sequencing strategies. Brief Bioinform (2014) 0.85
Viral communities associated with human pericardial fluids in idiopathic pericarditis. PLoS One (2014) 0.85
Translational research in infectious disease: current paradigms and challenges ahead. Transl Res (2012) 0.83
ViromeScan: a new tool for metagenomic viral community profiling. BMC Genomics (2016) 0.83
Next-generation sequencing in clinical virology: Discovery of new viruses. World J Virol (2015) 0.82
A microfluidic DNA library preparation platform for next-generation sequencing. PLoS One (2013) 0.82
Tropism of Pandemic 2009 H1N1 Influenza a Virus. Front Microbiol (2012) 0.81
Viral metagenomics: a tool for virus discovery and diversity in aquaculture. Indian J Virol (2012) 0.80
Tobacco mosaic virus in the lungs of mice following intra-tracheal inoculation. PLoS One (2013) 0.80
Detection of bovine group a rotavirus using rapid antigen detection kits, rt-PCR and next-generation DNA sequencing. J Vet Med Sci (2013) 0.80
Using high-throughput sequencing to leverage surveillance of genetic diversity and oseltamivir resistance: a pilot study during the 2009 influenza A(H1N1) pandemic. PLoS One (2013) 0.79
Large-scale sequencing and the natural history of model human RNA viruses. Future Virol (2012) 0.79
Evaluation of the human host range of bovine and porcine viruses that may contaminate bovine serum and porcine trypsin used in the manufacture of biological products. Biologicals (2011) 0.79
Can plant viruses cross the kingdom border and be pathogenic to humans? Viruses (2015) 0.79
Concentration and diversity of noroviruses detected in Luxembourg wastewaters in 2008-2009. Appl Environ Microbiol (2011) 0.78
Genomic library screening for viruses from the human dental plaque revealed pathogen-specific lytic phage sequences. Curr Microbiol (2011) 0.78
The Fecal Virome of Children with Hand, Foot, and Mouth Disease that Tested PCR Negative for Pathogenic Enteroviruses. PLoS One (2015) 0.78
Next-generation sequencing diagnostics of bacteremia in septic patients. Genome Med (2016) 0.78
A novel species of torque teno mini virus (TTMV) in gingival tissue from chronic periodontitis patients. Sci Rep (2016) 0.78
An easy operating pathogen microarray (EOPM) platform for rapid screening of vertebrate pathogens. BMC Infect Dis (2013) 0.77
Emergence of infectious malignant thrombocytopenia in Japanese macaques (Macaca fuscata) by SRV-4 after transmission to a novel host. Sci Rep (2015) 0.77
Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome. Biol Direct (2016) 0.77
Rapid Microbiome Changes in Freshly Deposited Cow Feces under Field Conditions. Front Microbiol (2016) 0.75
First report of human salivirus/klassevirus in respiratory specimens of a child with fatal adenovirus infection. Virus Genes (2016) 0.75
Virome characterisation from Guthrie cards in children who later developed acute lymphoblastic leukaemia. Br J Cancer (2016) 0.75
Molecular Diagnostic Methods for Detection and Characterization of Human Noroviruses. Open Microbiol J (2016) 0.75
Complete Genome Sequence of a Salivirus in Respiratory Specimens from a Child with Adenovirus Infection. Genome Announc (2016) 0.75
Enteric Infections Circulating during Hajj Seasons, 2011-2013. Emerg Infect Dis (2017) 0.75
Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21
The Bioperl toolkit: Perl modules for the life sciences. Genome Res (2002) 58.63
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res (2007) 35.65
Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science (2008) 16.60
A metagenomic survey of microbes in honey bee colony collapse disorder. Science (2007) 11.72
The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One (2007) 9.17
Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J Virol (2005) 9.13
Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol (2008) 9.09
Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci U S A (2008) 8.38
Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science (2005) 8.14
Identification of a novel polyomavirus from patients with acute respiratory tract infections. PLoS Pathog (2007) 8.01
A new arenavirus in a cluster of fatal transplant-associated diseases. N Engl J Med (2008) 7.73
A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad Sci U S A (2006) 7.17
Identification of a third human polyomavirus. J Virol (2007) 7.06
Gene expression profiling by massively parallel sequencing. Genome Res (2007) 6.69
454 sequencing put to the test using the complex genome of barley. BMC Genomics (2006) 6.12
RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol (2006) 4.93
Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Plant Biol (2006) 4.85
Mechanisms of GII.4 norovirus persistence in human populations. PLoS Med (2008) 4.57
Metagenomic analysis of human diarrhea: viral detection and discovery. PLoS Pathog (2008) 4.29
Parallel tagged sequencing on the 454 platform. Nat Protoc (2008) 3.49
Coronavirus HKU1 and other coronavirus infections in Hong Kong. J Clin Microbiol (2006) 2.44
Clinical and molecular epidemiological features of coronavirus HKU1-associated community-acquired pneumonia. J Infect Dis (2005) 2.43
Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays. Genome Res (2006) 2.11
No evidence for an association between infections with WU and KI polyomaviruses and respiratory disease. J Clin Virol (2007) 1.96
Metagenomic diagnosis of bacterial infections. Emerg Infect Dis (2008) 1.74
Detection of respiratory viruses and subtype identification of influenza A viruses by GreeneChipResp oligonucleotide microarray. J Clin Microbiol (2007) 1.59
Detection of the new human coronavirus HKU1: a report of 6 cases. Clin Infect Dis (2006) 1.51
Nucleic acid amplification tests for detection of respiratory viruses. J Clin Virol (2007) 1.43
Laboratory diagnosis of SARS. Emerg Infect Dis (2004) 1.41
Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. PLoS Pathog (2008) 1.37
The evolution of norovirus, the "gastric flu". PLoS Med (2008) 1.32
A newly reported human polyomavirus, KI virus, is present in the respiratory tract of Australian children. J Clin Virol (2007) 1.28
Adding pathogens by genomic subtraction. Nat Genet (2008) 1.21
The human endogenous retrovirus K Rev response element coincides with a predicted RNA folding region. RNA (2000) 1.04
Ligation-mediated amplification for effective rapid determination of viral RNA sequences (RDV). J Clin Virol (2008) 0.98
Norovirus storm in Osaka, Japan, last winter (2006/2007). Jpn J Infect Dis (2007) 0.97
Identification of upper respiratory tract pathogens using electrochemical detection on an oligonucleotide microarray. PLoS One (2007) 0.94
Sequence determination of a mildly virulent strain (CU-2) of Gallid herpesvirus type 2 using 454 pyrosequencing. Virus Genes (2008) 0.93
THOR: targeted high-throughput ortholog reconstructor. Bioinformatics (2006) 0.84
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
Landscape of transcription in human cells. Nature (2012) 20.18
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
In vitro and in vivo characterization of new swine-origin H1N1 influenza viruses. Nature (2009) 14.59
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res (2009) 12.09
Empirical analysis of transcriptional activity in the Arabidopsis genome. Science (2003) 11.62
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A (2003) 8.73
Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science (2003) 8.65
Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J (2002) 7.70
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae. Lancet (2003) 6.95
The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes. Genome Res (2002) 6.61
A promoter-level mammalian expression atlas. Nature (2014) 6.25
An atlas of combinatorial transcriptional regulation in mouse and man. Cell (2010) 6.24
Functional annotation of a full-length Arabidopsis cDNA collection. Science (2002) 6.15
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02
The regulated retrotransposon transcriptome of mammalian cells. Nat Genet (2009) 5.79
Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat Rev Genet (2007) 5.75
High-throughput mapping of a dynamic signaling network in mammalian cells. Science (2005) 5.21
CAGE: cap analysis of gene expression. Nat Methods (2006) 5.04
The first identification and retrospective study of Severe Fever with Thrombocytopenia Syndrome in Japan. J Infect Dis (2013) 4.92
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res (2005) 4.86
Newcastle disease virus (NDV)-based assay demonstrates interferon-antagonist activity for the NDV V protein and the Nipah virus V, W, and C proteins. J Virol (2003) 4.45
Biodiversity of vibrios. Microbiol Mol Biol Rev (2004) 4.25
Tiny RNAs associated with transcription start sites in animals. Nat Genet (2009) 4.19
Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. DNA Res (2003) 4.01
Toll-like receptor 9 mediates innate immune activation by the malaria pigment hemozoin. J Exp Med (2005) 3.85
Complex Loci in human and mouse genomes. PLoS Genet (2006) 3.74
TagDust--a program to eliminate artifacts from next generation sequencing data. Bioinformatics (2009) 3.64
Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Genome Res (2003) 3.50
The reality of pervasive transcription. PLoS Biol (2011) 3.41
Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res (2003) 3.40
Hidden layers of human small RNAs. BMC Genomics (2008) 3.31
Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res (2003) 3.21
The lipid mediator protectin D1 inhibits influenza virus replication and improves severe influenza. Cell (2013) 3.19
A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics (2008) 3.19
Small RNAs derived from snoRNAs. RNA (2009) 3.04
An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA. Nature (2009) 3.04
Rapid detection of epidermal growth factor receptor mutations in lung cancer by the SMart-Amplification Process. Clin Cancer Res (2007) 3.02
Cytotoxic T lymphocyte-based control of simian immunodeficiency virus replication in a preclinical AIDS vaccine trial. J Exp Med (2004) 2.99
Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution. Genome Res (2003) 2.96
Functional characterization of two type III secretion systems of Vibrio parahaemolyticus. Infect Immun (2004) 2.92
Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature (2010) 2.91
A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness. Genome Res (2010) 2.87
Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biol (2009) 2.86
RNAdb--a comprehensive mammalian noncoding RNA database. Nucleic Acids Res (2005) 2.84
A code for transcription initiation in mammalian genomes. Genome Res (2007) 2.71
Genome-wide analysis of cancer/testis gene expression. Proc Natl Acad Sci U S A (2008) 2.66
Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res (2003) 2.63
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res (2008) 2.60
Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray. Funct Integr Genomics (2002) 2.59
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. Nucleic Acids Res (2006) 2.54
Human atrial natriuretic peptide and nicorandil as adjuncts to reperfusion treatment for acute myocardial infarction (J-WIND): two randomised trials. Lancet (2007) 2.48
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet (2006) 2.48
Acquisition of human-type receptor binding specificity by new H5N1 influenza virus sublineages during their emergence in birds in Egypt. PLoS Pathog (2011) 2.45
Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution. Proc Natl Acad Sci U S A (2003) 2.33
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat Methods (2010) 2.30
A rapid and efficient single-cell manipulation method for screening antigen-specific antibody-secreting cells from human peripheral blood. Nat Med (2009) 2.24
Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin. RNA Biol (2011) 2.18
Development and evaluation of an automated annotation pipeline and cDNA annotation system. Genome Res (2003) 2.15
Impaired processing and presentation of cytotoxic-T-lymphocyte (CTL) epitopes are major escape mechanisms from CTL immune pressure in human immunodeficiency virus type 1 infection. J Virol (2004) 2.12
Transcriptome analysis of the aphid bacteriocyte, the symbiotic host cell that harbors an endocellular mutualistic bacterium, Buchnera. Proc Natl Acad Sci U S A (2005) 2.09
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res (2007) 2.07
Immunogenicity of whole-parasite vaccines against Plasmodium falciparum involves malarial hemozoin and host TLR9. Cell Host Microbe (2010) 2.03
A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes. Proc Natl Acad Sci U S A (2006) 2.02
Vibrios commonly possess two chromosomes. J Bacteriol (2005) 1.99
Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays. Genome Res (2003) 1.98
Mutations in EFHC1 cause juvenile myoclonic epilepsy. Nat Genet (2004) 1.98
Roles of toll-like receptors in C-C chemokine production by renal tubular epithelial cells. J Immunol (2002) 1.98