Published in PLoS Biol on January 01, 2006
Diet rapidly and reproducibly alters the human gut microbiome. Nature (2013) 11.04
The marine viromes of four oceanic regions. PLoS Biol (2006) 10.19
Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature (2010) 5.92
A bioinformatician's guide to metagenomics. Microbiol Mol Biol Rev (2008) 4.33
Metagenomic analysis of human diarrhea: viral detection and discovery. PLoS Pathog (2008) 4.29
Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis. J Virol (2009) 4.14
Viral genome sequencing by random priming methods. BMC Genomics (2008) 3.48
Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS One (2009) 3.41
Laboratory procedures to generate viral metagenomes. Nat Protoc (2009) 3.20
A highly prevalent and genetically diversified Picornaviridae genus in South Asian children. Proc Natl Acad Sci U S A (2008) 3.12
Bat guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses. J Virol (2010) 3.03
Complete genome sequence of a highly divergent astrovirus isolated from a child with acute diarrhea. Virol J (2008) 2.72
Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. J Virol (2009) 2.70
Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLoS One (2009) 2.67
Rapid evolution of the human gut virome. Proc Natl Acad Sci U S A (2013) 2.53
Metagenomic characterization of Chesapeake Bay virioplankton. Appl Environ Microbiol (2007) 2.22
Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS One (2011) 2.14
Do symbiotic bacteria subvert host immunity? Nat Rev Microbiol (2009) 2.07
The fecal viral flora of California sea lions. J Virol (2011) 2.06
The fecal virome of pigs on a high-density farm. J Virol (2011) 2.03
High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage. J Virol (2012) 2.03
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
Human picobirnaviruses identified by molecular screening of diarrhea samples. J Clin Microbiol (2010) 1.86
Fever from the forest: prospects for the continued emergence of sylvatic dengue virus and its impact on public health. Nat Rev Microbiol (2011) 1.86
Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes. PLoS One (2011) 1.75
Metagenomic analysis of RNA viruses in a fresh water lake. PLoS One (2009) 1.69
Spatial organization of intestinal microbiota in the mouse ascending colon. ISME J (2010) 1.66
Viral communities associated with healthy and bleaching corals. Environ Microbiol (2008) 1.64
Discovering the phylodynamics of RNA viruses. PLoS Comput Biol (2009) 1.63
Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. Appl Environ Microbiol (2011) 1.62
Discovery of a novel single-stranded DNA virus from a sea turtle fibropapilloma by using viral metagenomics. J Virol (2008) 1.59
Resident viruses and their interactions with the immune system. Nat Immunol (2013) 1.58
Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing. PLoS One (2012) 1.54
CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome. Genome Res (2012) 1.52
Raw sewage harbors diverse viral populations. MBio (2011) 1.50
Healthy human gut phageome. Proc Natl Acad Sci U S A (2016) 1.47
Novel circular DNA viruses in stool samples of wild-living chimpanzees. J Gen Virol (2009) 1.46
The dynamic genetic repertoire of microbial communities. FEMS Microbiol Rev (2008) 1.42
Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. Nat Rev Microbiol (2015) 1.41
Recent advances and remaining gaps in our knowledge of associations between gut microbiota and human health. World J Gastroenterol (2009) 1.36
A third gyrovirus species in human faeces. J Gen Virol (2012) 1.36
Diversity and abundance of single-stranded DNA viruses in human feces. Appl Environ Microbiol (2011) 1.27
Utility of DNA microarrays for detection of viruses in acute respiratory tract infections in children. J Pediatr (2008) 1.26
Characterization of a novel gyrovirus in human stool and chicken meat. J Clin Virol (2012) 1.26
Eukaryotic viruses in wastewater samples from the United States. Appl Environ Microbiol (2009) 1.25
Use of nucleotide composition analysis to infer hosts for three novel picorna-like viruses. J Virol (2010) 1.25
Conclusive evidence of replication of a plant virus in honeybees is lacking. MBio (2014) 1.24
Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities. J Cyst Fibros (2012) 1.23
RNA virus genomics: a world of possibilities. J Clin Invest (2009) 1.23
Pepper mild mottle virus, a plant virus associated with specific immune responses, Fever, abdominal pains, and pruritus in humans. PLoS One (2010) 1.21
Commensal Clostridia: leading players in the maintenance of gut homeostasis. Gut Pathog (2013) 1.19
Optimization and clinical validation of a pathogen detection microarray. Genome Biol (2007) 1.18
Emerging view of the human virome. Transl Res (2012) 1.17
Virome profiling of bats from Myanmar by metagenomic analysis of tissue samples reveals more novel Mammalian viruses. PLoS One (2013) 1.16
Kingdom-agnostic metagenomics and the importance of complete characterization of enteric microbial communities. Gastroenterology (2014) 1.16
Pepper mild mottle virus as an indicator of fecal pollution. Appl Environ Microbiol (2009) 1.13
Metagenomic analysis of the turkey gut RNA virus community. Virol J (2010) 1.12
Metagenomic analysis of viral communities in (hado)pelagic sediments. PLoS One (2013) 1.10
Simultaneous identification of DNA and RNA viruses present in pig faeces using process-controlled deep sequencing. PLoS One (2012) 1.09
Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch. Proc Natl Acad Sci U S A (2014) 1.08
Classification and quantification of bacteriophage taxa in human gut metagenomes. ISME J (2014) 1.08
Study of the viral and microbial communities associated with Crohn's disease: a metagenomic approach. Clin Transl Gastroenterol (2013) 1.06
Functional viral metagenomics and the next generation of molecular tools. Trends Microbiol (2009) 1.06
Movers and shakers: influence of bacteriophages in shaping the mammalian gut microbiota. Gut Microbes (2012) 1.06
Metagenomic analysis of double-stranded DNA viruses in healthy adults. BMC Biol (2014) 1.05
A roadmap to the human virome. PLoS Pathog (2013) 1.04
Metagenomic analysis of the viral communities in fermented foods. Appl Environ Microbiol (2010) 0.99
Functional dynamics of the gut microbiome in elderly people during probiotic consumption. MBio (2015) 0.99
Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara. ISME J (2012) 0.99
Seasonal dynamics and metagenomic characterization of estuarine viriobenthos assemblages by randomly amplified polymorphic DNA PCR. Appl Environ Microbiol (2009) 0.97
Is there still room for novel viral pathogens in pediatric respiratory tract infections? PLoS One (2014) 0.97
The molecular basis for flexibility in the flexible filamentous plant viruses. Nat Struct Mol Biol (2015) 0.97
Comparative (meta)genomic analysis and ecological profiling of human gut-specific bacteriophage φB124-14. PLoS One (2012) 0.96
The human gut virome: a multifaceted majority. Front Microbiol (2015) 0.95
TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data. Stand Genomic Sci (2011) 0.94
Temporal dynamics and decay of putatively allochthonous and autochthonous viral genotypes in contrasting freshwater lakes. Appl Environ Microbiol (2012) 0.94
Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea. Front Microbiol (2013) 0.93
The virome in host health and disease. Immunity (2015) 0.92
Origin of hepatitis delta virus. Future Microbiol (2010) 0.91
Prevalence of classic, MLB-clade and VA-clade Astroviruses in Kenya and The Gambia. Virol J (2015) 0.90
Occupancy modeling, maximum contig size probabilities and designing metagenomics experiments. PLoS One (2010) 0.90
From orphan virus to pathogen: the path to the clinical lab. Curr Opin Virol (2011) 0.90
Development and validation of a microarray for the investigation of the CAZymes encoded by the human gut microbiome. PLoS One (2013) 0.88
Geographic variation in the eukaryotic virome of human diarrhea. Virology (2014) 0.88
Viral metagenome analysis to guide human pathogen monitoring in environmental samples. Lett Appl Microbiol (2011) 0.88
Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation. MBio (2016) 0.88
Reverse transcriptase droplet digital PCR shows high resilience to PCR inhibitors from plant, soil and water samples. Plant Methods (2014) 0.87
Gut inflammation and immunity: what is the role of the human gut virome? Mediators Inflamm (2015) 0.87
Epithelial cells augment barrier function via activation of the Toll-like receptor 2/phosphatidylinositol 3-kinase pathway upon recognition of Salmonella enterica serovar Typhimurium curli fibrils in the gut. Infect Immun (2012) 0.86
The general composition of the faecal virome of pigs depends on age, but not on feeding with a probiotic bacterium. PLoS One (2014) 0.86
Metagenomic analysis of viruses in feces from unsolved outbreaks of gastroenteritis in humans. J Clin Microbiol (2014) 0.85
Genogroup I picobirnavirus in diarrhoeic foals: can the horse serve as a natural reservoir for human infection? Vet Res (2011) 0.84
Evaluation of a new disinfection approach: efficacy of chlorine and bromine halogenated contact disinfection for reduction of viruses and microcystin toxin. Am J Trop Med Hyg (2010) 0.84
Calicivirus from novel Recovirus genogroup in human diarrhea, Bangladesh. Emerg Infect Dis (2012) 0.83
Occurrence of pepper mild mottle virus in drinking water sources in Japan. Appl Environ Microbiol (2013) 0.82
Simian genogroup I picobirnaviruses: prevalence, genetic diversity, and zoonotic potential. J Clin Microbiol (2012) 0.82
Metagenomic analysis of microbiome in colon tissue from subjects with inflammatory bowel diseases reveals interplay of viruses and bacteria. Inflamm Bowel Dis (2015) 0.82
Animal picobirnavirus. Virusdisease (2014) 0.81
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Basic local alignment search tool. J Mol Biol (1990) 659.07
Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res (1998) 106.16
Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res (1998) 96.63
Environmental genome shotgun sequencing of the Sargasso Sea. Science (2004) 45.23
Host-bacterial mutualism in the human intestine. Science (2005) 26.39
Comparative metagenomics of microbial communities. Science (2005) 25.88
Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature (2004) 20.20
Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A (2002) 9.21
Interactions between commensal intestinal bacteria and the immune system. Nat Rev Immunol (2004) 8.45
Ecology of prokaryotic viruses. FEMS Microbiol Rev (2004) 7.64
Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol (2003) 6.65
The Phage Proteomic Tree: a genome-based taxonomy for phage. J Bacteriol (2002) 6.09
Norwalk virus genome cloning and characterization. Science (1990) 5.83
Honor thy symbionts. Proc Natl Acad Sci U S A (2003) 5.72
Gut microorganisms, mammalian metabolism and personalized health care. Nat Rev Microbiol (2005) 5.35
Transmission of acute infectious nonbacterial gastroenteritis to volunteers by oral administration of stool filtrates. J Infect Dis (1971) 3.88
Biological properties of Norwalk agent of acute infectious nonbacterial gastroenteritis. Proc Soc Exp Biol Med (1972) 2.94
Distribution of ribonucleic acid coliphages in animals. Appl Environ Microbiol (1981) 2.39
Long-term association of tomato yellow leaf curl virus with its whitefly vector Bemisia tabaci: effect on the insect transmission capacity, longevity and fecundity. J Gen Virol (1997) 2.17
A review of viral gastroenteritis. Curr Opin Infect Dis (2004) 2.13
Viruses causing gastroenteritis. Clin Microbiol Infect (2003) 1.99
Gastroenteritis viruses: an overview. Novartis Found Symp (2001) 1.63
Pathogenic human viruses in coastal waters. Clin Microbiol Rev (2003) 1.57
Usefulness of the stomacher in a microbiological regulatory laboratory. Appl Environ Microbiol (1978) 1.53
Development of a strand-specific RT-PCR based assay to detect the replicative form of hepatitis C virus RNA. J Virol Methods (2001) 1.43
Cloning of human picobirnavirus genomic segments and development of an RT-PCR detection assay. Virology (2000) 1.37
The potential role of endogenous bacteriophages in controlling invading pathogens. Cell Mol Life Sci (2005) 1.28
Insect transmission of plant viruses: a constraint on virus variability. Curr Opin Plant Biol (2000) 1.26
Plant and animal rhabdovirus host range: a bug's view. Trends Microbiol (2003) 1.25
Sequence heterogeneity among human picobirnaviruses detected in a gastroenteritis outbreak. Arch Virol (2003) 1.25
Novel viruses in human faeces. Lancet (1988) 1.21
Expression in plants and immunogenicity of plant virus-based experimental rabies vaccine. Vaccine (2002) 1.20
Evidence for in vitro falsely-primed cDNAs that prevent specific detection of virus negative strand RNAs in dengue-infected cells: improvement by tagged RT-PCR. J Virol Methods (2003) 1.12
Recycling of pathogenic microbes through survival in ice. Med Hypotheses (2004) 1.12
Expression of tobacco mosaic virus coat protein and assembly of pseudovirus particles in Escherichia coli. Proc Natl Acad Sci U S A (1994) 1.09
Picobirnavirus, a novel group of undescribed viruses of mammals and birds: a minireview. Acta Virol (1997) 1.03
Site-directed mutagenesis of a potyvirus coat protein and its assembly in Escherichia coli. J Gen Virol (1993) 1.01
Viruses that multiply in the gut and cause endemic and epidemic gastroenteritis. Clin Diagn Virol (1996) 0.91
Comparison of bacterial counts obtained from naturally contaminated foods by means of Stomacher and blender. Can J Microbiol (1987) 0.84
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell (2008) 28.29
The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet (2006) 20.76
A global map of p53 transcription-factor binding sites in the human genome. Cell (2006) 20.65
International network of cancer genome projects. Nature (2010) 20.35
Landscape of transcription in human cells. Nature (2012) 20.18
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41
An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci U S A (2005) 13.54
Breast cancer classification and prognosis based on gene expression profiles from a population-based study. Proc Natl Acad Sci U S A (2003) 13.00
An oestrogen-receptor-alpha-bound human chromatin interactome. Nature (2009) 12.16
Functional metagenomic profiling of nine biomes. Nature (2008) 11.00
The marine viromes of four oceanic regions. PLoS Biol (2006) 10.19
Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A (2002) 9.21
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
Baselines and degradation of coral reefs in the Northern Line Islands. PLoS One (2008) 9.10
Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res (2005) 8.73
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
Genomewide association study of leprosy. N Engl J Med (2009) 8.17
Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Cancer Res (2006) 8.08
Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat Methods (2005) 7.87
Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics (2006) 7.65
Mapping human genetic diversity in Asia. Science (2009) 7.40
Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell (2007) 7.05
Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells. Genes Dev (2007) 6.71
Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol (2003) 6.65
CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet (2011) 6.55
Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet (2009) 6.39
An application of statistics to comparative metagenomics. BMC Bioinformatics (2006) 6.29
Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci U S A (2011) 6.16
Viral metagenomics. Nat Rev Microbiol (2005) 6.04
Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection. Lancet (2003) 5.99
Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature (2010) 5.92
Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet (2007) 5.85
Global mapping of c-Myc binding sites and target gene networks in human B cells. Proc Natl Acad Sci U S A (2006) 5.27
Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res (2008) 5.12
A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer. Nat Med (2012) 4.90
Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes. Nat Genet (2012) 4.82
Diversity and population structure of a near-shore marine-sediment viral community. Proc Biol Sci (2004) 4.79
Genome-wide association identifies multiple ulcerative colitis susceptibility loci. Nat Genet (2010) 4.65
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res (2007) 4.59
Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS Biol (2005) 4.55
Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes. Nucleic Acids Res (2006) 4.51
Microbial ecology of four coral atolls in the Northern Line Islands. PLoS One (2008) 4.48
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res (2009) 4.47
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. BMC Bioinformatics (2010) 4.32
Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol (2007) 4.32
Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ Microbiol (2007) 4.21
Here a virus, there a virus, everywhere the same virus? Trends Microbiol (2005) 3.90
Explaining microbial population genomics through phage predation. Nat Rev Microbiol (2009) 3.87
Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc Natl Acad Sci U S A (2013) 3.86
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res (2007) 3.82
Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res (2008) 3.76
FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries. BMC Bioinformatics (2006) 3.65
Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS One (2009) 3.41
Gene expression profiles of BRCA1-linked, BRCA2-linked, and sporadic ovarian cancers. J Natl Cancer Inst (2002) 3.40
Transfer of photosynthesis genes to and from Prochlorococcus viruses. Proc Natl Acad Sci U S A (2004) 3.38
Metagenomic signatures of 86 microbial and viral metagenomes. Environ Microbiol (2009) 3.30
ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol (2010) 3.24
Laboratory procedures to generate viral metagenomes. Nat Protoc (2009) 3.20
Transcriptome profiling of human and murine ESCs identifies divergent paths required to maintain the stem cell state. Stem Cells (2005) 3.16
Viral and microbial community dynamics in four aquatic environments. ISME J (2010) 2.95
PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics (2005) 2.94
Metagenomics and future perspectives in virus discovery. Curr Opin Virol (2012) 2.92
The epidemiology of respiratory syncytial virus lower respiratory tract infections in children less than 5 years of age in Indonesia. Pediatr Infect Dis J (2011) 2.82
The draft genome of sweet orange (Citrus sinensis). Nat Genet (2012) 2.81
Discovery of estrogen receptor alpha target genes and response elements in breast tumor cells. Genome Biol (2004) 2.77
Genomic epidemiology of a dengue virus epidemic in urban Singapore. J Virol (2009) 2.74
Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature (2008) 2.70
Intrinsic molecular signature of breast cancer in a population-based cohort of 412 patients. Breast Cancer Res (2006) 2.69
Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res (2012) 2.66
Viral diversity and dynamics in an infant gut. Res Microbiol (2008) 2.63
Metagenomic analysis of stressed coral holobionts. Environ Microbiol (2009) 2.62
A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loci. Nat Genet (2010) 2.62
The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol (2009) 2.61
Finding novel genes in bacterial communities isolated from the environment. Bioinformatics (2006) 2.55
Conservation of gene expression signatures between zebrafish and human liver tumors and tumor progression. Nat Biotechnol (2005) 2.51