Published in Proc Natl Acad Sci U S A on February 21, 2012
Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc Natl Acad Sci U S A (2013) 3.86
Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell (2015) 3.13
Rapid evolution of the human gut virome. Proc Natl Acad Sci U S A (2013) 2.53
The virome in mammalian physiology and disease. Cell (2014) 2.00
Genomic approaches to studying the human microbiota. Nature (2012) 2.00
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
Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. Elife (2015) 1.79
Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS One (2013) 1.64
Resident viruses and their interactions with the immune system. Nat Immunol (2013) 1.58
Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut. Proc Natl Acad Sci U S A (2013) 1.35
Metavir 2: new tools for viral metagenome comparison and assembled virome analysis. BMC Bioinformatics (2014) 1.32
Gut DNA viromes of Malawian twins discordant for severe acute malnutrition. Proc Natl Acad Sci U S A (2015) 1.08
Gut and root microbiota commonalities. Appl Environ Microbiol (2012) 1.07
Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. Appl Environ Microbiol (2012) 1.06
The intestinal microbiome in type 1 diabetes. Clin Exp Immunol (2014) 1.02
Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome. Comput Struct Biotechnol J (2015) 1.00
Viral immunity. Transkingdom control of viral infection and immunity in the mammalian intestine. Science (2016) 0.97
Conservation of gene cassettes among diverse viruses of the human gut. PLoS One (2012) 0.96
The human gut virome: a multifaceted majority. Front Microbiol (2015) 0.95
Structure of the essential diversity-generating retroelement protein bAvd and its functionally important interaction with reverse transcriptase. Structure (2012) 0.91
Identification of hepatotropic viruses from plasma using deep sequencing: a next generation diagnostic tool. PLoS One (2013) 0.90
The human urine virome in association with urinary tract infections. Front Microbiol (2015) 0.90
Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation. MBio (2016) 0.88
Innate and acquired bacteriophage-mediated immunity. Bacteriophage (2013) 0.87
Gut inflammation and immunity: what is the role of the human gut virome? Mediators Inflamm (2015) 0.87
Tradeoffs in bacteriophage life histories. Bacteriophage (2014) 0.86
New approaches indicate constant viral diversity despite shifts in assemblage structure in an Australian hypersaline lake. Appl Environ Microbiol (2013) 0.85
Mechanisms of viral mutation. Cell Mol Life Sci (2016) 0.85
The intersection of microbiome and host at the skin interface: genomic- and metagenomic-based insights. Genome Res (2015) 0.85
Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses. ISME J (2016) 0.85
Characterization of bacteriophage communities and CRISPR profiles from dental plaque. BMC Microbiol (2014) 0.83
Targeted diversity generation by intraterrestrial archaea and archaeal viruses. Nat Commun (2015) 0.82
Identification of diversity-generating retroelements in human microbiomes. Int J Mol Sci (2014) 0.81
Diversity-generating Retroelements in Phage and Bacterial Genomes. Microbiol Spectr (2014) 0.80
Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice. ISME J (2015) 0.80
Risperidone-induced weight gain is mediated through shifts in the gut microbiome and suppression of energy expenditure. EBioMedicine (2015) 0.80
Hyperexpansion of RNA Bacteriophage Diversity. PLoS Biol (2016) 0.79
Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages. Front Microbiol (2015) 0.79
Finding and identifying the viral needle in the metagenomic haystack: trends and challenges. Front Microbiol (2015) 0.78
Genomic and Metagenomic Analysis of Diversity-Generating Retroelements Associated with Treponema denticola. Front Microbiol (2016) 0.77
Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution. Microbiol Spectr (2015) 0.77
Conservation of the C-type lectin fold for accommodating massive sequence variation in archaeal diversity-generating retroelements. BMC Struct Biol (2016) 0.76
Direct sequencing of human gut virome fractions obtained by flow cytometry. Front Microbiol (2015) 0.76
Pharmacometabolomics Informs Viromics toward Precision Medicine. Front Pharmacol (2016) 0.75
Evolutionary and functional implications of hypervariable loci within the skin virome. PeerJ (2017) 0.75
Viruses and the origin of microbiome selection and immunity. ISME J (2016) 0.75
Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea. Nat Microbiol (2017) 0.75
Viral communities of the human gut: metagenomic analysis of composition and dynamics. Mob DNA (2017) 0.75
De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91
Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc (2009) 32.64
Linking long-term dietary patterns with gut microbial enterotypes. Science (2011) 17.30
The V(D)J recombination activating gene, RAG-1. Cell (1989) 9.79
Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature (2010) 5.92
The human gut virome: inter-individual variation and dynamic response to diet. Genome Res (2011) 3.32
Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage. Science (2002) 2.62
Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements. Nature (2004) 2.59
The C-type lectin fold as an evolutionary solution for massive sequence variation. Nat Struct Mol Biol (2005) 2.13
Bacteriophage genomics. Curr Opin Microbiol (2008) 2.06
Ig-like domains on bacteriophages: a tale of promiscuity and deceit. J Mol Biol (2006) 1.99
A common evolutionary origin for tailed-bacteriophage functional modules and bacterial machineries. Microbiol Mol Biol Rev (2011) 1.92
AID targeting in antibody diversity. Adv Immunol (2011) 1.78
Immunoglobulin-like domains on bacteriophage: weapons of modest damage? Curr Opin Microbiol (2007) 1.33
Three-dimensional structure of tropism-switching Bordetella bacteriophage. Proc Natl Acad Sci U S A (2010) 1.20
A diversity of uncharacterized reverse transcriptases in bacteria. Nucleic Acids Res (2008) 1.19
Selective ligand recognition by a diversity-generating retroelement variable protein. PLoS Biol (2008) 1.17
Diversity-generating retroelement homing regenerates target sequences for repeated rounds of codon rewriting and protein diversification. Mol Cell (2008) 1.14
Structure of the three N-terminal immunoglobulin domains of the highly immunogenic outer capsid protein from a T4-like bacteriophage. J Virol (2011) 1.10
The solution structure of the C-terminal Ig-like domain of the bacteriophage λ tail tube protein. J Mol Biol (2010) 1.04
Target site recognition by a diversity-generating retroelement. PLoS Genet (2011) 0.97
Purification of phage display-modified bacteriophage T4 by affinity chromatography. BMC Biotechnol (2011) 0.96
QIIME allows analysis of high-throughput community sequencing data. Nat Methods (2010) 85.34
Linking long-term dietary patterns with gut microbial enterotypes. Science (2011) 17.30
PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics (2009) 15.93
Long-term proton pump inhibitor therapy and risk of hip fracture. JAMA (2006) 9.53
Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med (2013) 9.44
Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1. J Clin Invest (2008) 9.42
Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res (2007) 9.15
Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell (2008) 8.41
Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol (2004) 8.27
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res (2007) 6.89
The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. PLoS Pathog (2008) 5.28
High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology (2009) 5.08
The association between hepatitis C infection and survival after orthotopic liver transplantation. Gastroenterology (2002) 4.98
Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol (2010) 4.97
In vivo genome editing restores haemostasis in a mouse model of haemophilia. Nature (2011) 4.81
Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med (2011) 4.78
HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Res (2007) 4.72
Gene transfer in humans using a conditionally replicating lentiviral vector. Proc Natl Acad Sci U S A (2006) 4.23
Innate lymphoid cells promote anatomical containment of lymphoid-resident commensal bacteria. Science (2012) 4.20
Bayesian community-wide culture-independent microbial source tracking. Nat Methods (2011) 3.88
Global landscape of HIV-human protein complexes. Nature (2011) 3.70
Retroviral DNA integration: viral and cellular determinants of target-site selection. PLoS Pathog (2006) 3.67
Initiation of tumor necrosis factor-α antagonists and the risk of hospitalization for infection in patients with autoimmune diseases. JAMA (2011) 3.58
Insulin therapy and colorectal cancer risk among type 2 diabetes mellitus patients. Gastroenterology (2004) 3.57
Efficacy of gene therapy for X-linked severe combined immunodeficiency. N Engl J Med (2010) 3.54
Human immunodeficiency virus cDNA metabolism: notable stability of two-long terminal repeat circles. J Virol (2002) 3.46
The human gut virome: inter-individual variation and dynamic response to diet. Genome Res (2011) 3.32
Decade-long safety and function of retroviral-modified chimeric antigen receptor T cells. Sci Transl Med (2012) 3.29
Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria. Nature (2013) 3.21
Selection of target sites for mobile DNA integration in the human genome. PLoS Comput Biol (2006) 3.21
RELMbeta/FIZZ2 is a goblet cell-specific immune-effector molecule in the gastrointestinal tract. Proc Natl Acad Sci U S A (2004) 3.05
Efficacy of anti-tumor necrosis factor therapy in patients with ulcerative colitis. Am J Gastroenterol (2002) 3.01
Mortality associated with medical therapy versus elective colectomy in ulcerative colitis: a cohort study. Ann Intern Med (2014) 2.73
HIV-1 capsid-cyclophilin interactions determine nuclear import pathway, integration targeting and replication efficiency. PLoS Pathog (2011) 2.68
DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer. Nucleic Acids Res (2008) 2.64
Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS One (2010) 2.60
Rosiglitazone for active ulcerative colitis: a randomized placebo-controlled trial. Gastroenterology (2007) 2.55
Rapid evolution of the human gut virome. Proc Natl Acad Sci U S A (2013) 2.53
Association between vaccination for herpes zoster and risk of herpes zoster infection among older patients with selected immune-mediated diseases. JAMA (2012) 2.51
Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation. Nat Med (2012) 2.49
Assessing the potential for AAV vector genotoxicity in a murine model. Blood (2010) 2.48
Role of PSIP1/LEDGF/p75 in lentiviral infectivity and integration targeting. PLoS One (2007) 2.48
Hepatitis C virus transmission bottlenecks analyzed by deep sequencing. J Virol (2010) 2.45
Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells. Nat Biotechnol (2010) 2.43
Use of abdominopelvic computed tomography in emergency departments and rates of urgent diagnoses in Crohn's disease. Clin Gastroenterol Hepatol (2011) 2.40
The risk of mortality in patients with psoriasis: results from a population-based study. Arch Dermatol (2007) 2.32
Incidence and mortality of colorectal adenocarcinoma in persons with inflammatory bowel disease from 1998 to 2010. Gastroenterology (2012) 2.26
Development of an internet-based cohort of patients with inflammatory bowel diseases (CCFA Partners): methodology and initial results. Inflamm Bowel Dis (2012) 2.23
Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics (2012) 2.19
Cxcr2 and Cxcl5 regulate the IL-17/G-CSF axis and neutrophil homeostasis in mice. J Clin Invest (2012) 2.18
Incidence and risk factors for herpes zoster among patients with inflammatory bowel disease. Clin Gastroenterol Hepatol (2006) 2.16
Increased risk for demyelinating diseases in patients with inflammatory bowel disease. Gastroenterology (2005) 2.15
Rates of malignancy associated with juvenile idiopathic arthritis and its treatment. Arthritis Rheum (2012) 2.15
Association of 6-thioguanine nucleotide levels and inflammatory bowel disease activity: a meta-analysis. Gastroenterology (2006) 2.14
Initiation of anti-TNF therapy and the risk of optic neuritis: from the safety assessment of biologic ThERapy (SABER) Study. Am J Ophthalmol (2012) 2.14
The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones. Blood (2011) 2.11
The IL-27 receptor (WSX-1) is an inhibitor of innate and adaptive elements of type 2 immunity. J Immunol (2004) 2.09
AGA medical position statement on the diagnosis and management of colorectal neoplasia in inflammatory bowel disease. Gastroenterology (2010) 2.09
The interferon response inhibits HIV particle production by induction of TRIM22. PLoS Pathog (2008) 2.06
An optimized patient-reported ulcerative colitis disease activity measure derived from the Mayo score and the simple clinical colitis activity index. Inflamm Bowel Dis (2014) 2.05
Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial. Blood (2010) 2.05
Risks of herpes zoster in patients with rheumatoid arthritis according to biologic disease-modifying therapy. Arthritis Care Res (Hoboken) (2015) 2.03
HIV integration targeting: a pathway involving Transportin-3 and the nuclear pore protein RanBP2. PLoS Pathog (2011) 2.00
Analysis of lentiviral vector integration in HIV+ study subjects receiving autologous infusions of gene modified CD4+ T cells. Mol Ther (2009) 1.97
Corticosteroids and immunomodulators: postoperative infectious complication risk in inflammatory bowel disease patients. Gastroenterology (2003) 1.94
Trends in the use of biologic agents among rheumatoid arthritis patients enrolled in the US medicare program. Arthritis Care Res (Hoboken) (2013) 1.92
Risk of kidney injury following oral phosphosoda bowel preparations. J Am Soc Nephrol (2007) 1.89
Renal function after orthotopic liver transplantation is predicted by duration of pretransplantation creatinine elevation. Liver Transpl (2005) 1.87
Integration site selection by HIV-based vectors in dividing and growth-arrested IMR-90 lung fibroblasts. Mol Ther (2005) 1.85
Cohort study of pioglitazone and cancer incidence in patients with diabetes. Diabetes Care (2011) 1.83
HIV integration site selection: targeting in macrophages and the effects of different routes of viral entry. Mol Ther (2006) 1.75
Time trends in therapies and outcomes for adult inflammatory bowel disease, Northern California, 1998-2005. Gastroenterology (2009) 1.74
HIV DNA integration. Cold Spring Harb Perspect Med (2012) 1.73
Incidence and prevalence of inflammatory bowel disease in a Northern California managed care organization, 1996-2002. Am J Gastroenterol (2008) 1.72
LEDGF hybrids efficiently retarget lentiviral integration into heterochromatin. Mol Ther (2010) 1.72
Inhibition of retroviral pathogenesis by RNA interference. Curr Biol (2002) 1.70
Association between longer therapy with thiazolidinediones and risk of bladder cancer: a cohort study. J Natl Cancer Inst (2012) 1.69
Safe harbours for the integration of new DNA in the human genome. Nat Rev Cancer (2011) 1.67
Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Am J Respir Crit Care Med (2013) 1.66
Absence of bacterially induced RELMbeta reduces injury in the dextran sodium sulfate model of colitis. J Clin Invest (2006) 1.66
Retroviral DNA integration--mechanism and consequences. Adv Genet (2005) 1.66
Cancer incidence in The Health Improvement Network. Pharmacoepidemiol Drug Saf (2009) 1.65
Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS One (2013) 1.64
Antiviral effects of autologous CD4 T cells genetically modified with a conditionally replicating lentiviral vector expressing long antisense to HIV. Blood (2012) 1.64