Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins.
暂无分享,去创建一个
Nicholas D. Youngblut | T. Spector | J. Bell | R. Ley | I. Hewson | Julia Goodrich | J. L. Moreno-Gallego | Sara C. Di Rienzi | A. Reyes | Shao-Pei Chou | S. C. D. Rienzi | Alejandro Reyes
[1] R. P. Ross,et al. ΦCrAss001, a member of the most abundant bacteriophage family in the human gut, infects Bacteroides , 2018, bioRxiv.
[2] J. Weitz,et al. A virus or more in (nearly) every cell: ubiquitous networks of virus–host interactions in extreme environments , 2018, The ISME Journal.
[3] Evelien M. Adriaenssens,et al. Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Bacteriophages , 2018 .
[4] L. Ogilvie,et al. The human gut virome: form and function. , 2017, Emerging topics in life sciences.
[5] Xing-Ming Zhao,et al. MVP: a microbe–phage interaction database , 2017, Nucleic Acids Res..
[6] R. Edwards,et al. Genomic, proteomic, and phylogenetic analysis of spounaviruses indicates paraphyly of the order Caudovirales , 2017, bioRxiv.
[7] Robert A Edwards,et al. Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut , 2017, Nature Microbiology.
[8] Emiley A. Eloe-Fadrosh,et al. Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity , 2017, PeerJ.
[9] P. Rice,et al. Transposable phages, DNA reorganization and transfer. , 2017, Current opinion in microbiology.
[10] M. Young,et al. The Human Gut Phage Community and Its Implications for Health and Disease , 2017, Viruses.
[11] Alexander V. Tyakht,et al. Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses , 2017, PloS one.
[12] Benjamin Bolduc,et al. Healthy human gut phageome , 2016, Proceedings of the National Academy of Sciences.
[13] C. Desnues,et al. Viral metagenomics: are we missing the giants? , 2016, Current opinion in microbiology.
[14] S. Salzberg,et al. Centrifuge: rapid and sensitive classification of metagenomic sequences , 2016, bioRxiv.
[15] Emily R. Davenport,et al. Genetic Determinants of the Gut Microbiome in UK Twins. , 2016, Cell host & microbe.
[16] Barbara A. Bailey,et al. Lytic to temperate switching of viral communities , 2016, Nature.
[17] I. Hewson,et al. Comparative Metagenomics of Viral Assemblages Inhabiting Four Phyla of Marine Invertebrates , 2016, Front. Mar. Sci..
[18] A. Gruber,et al. GenSeed-HMM: A Tool for Progressive Assembly Using Profile HMMs as Seeds and its Application in Alpavirinae Viral Discovery from Metagenomic Data , 2016, Front. Microbiol..
[19] M. Breitbart,et al. Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology. , 2016, FEMS microbiology letters.
[20] Ron Milo,et al. Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans , 2016, Cell.
[21] Tim D Spector,et al. Proton pump inhibitors alter the composition of the gut microbiota , 2015, Gut.
[22] H. Neve,et al. Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut , 2015, Microbiome.
[23] Yanjiao Zhou,et al. Early life dynamics of the human gut virome and bacterial microbiome in infants , 2015, Nature Medicine.
[24] Forest Rohwer,et al. Gut DNA viromes of Malawian twins discordant for severe acute malnutrition , 2015, Proceedings of the National Academy of Sciences.
[25] Huaiqiu Zhu,et al. InteMAP: Integrated metagenomic assembly pipeline for NGS short reads , 2015, BMC Bioinformatics.
[26] J. Sanderson,et al. Characterization of virus-like particles associated with the human faecal and caecal microbiota. , 2014, Research in microbiology.
[27] Chao Xie,et al. Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.
[28] Angela C. Poole,et al. Human Genetics Shape the Gut Microbiome , 2014, Cell.
[29] Eric J Alm,et al. Host lifestyle affects human microbiota on daily timescales , 2014, Genome Biology.
[30] R. Edwards,et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes , 2014, Nature Communications.
[31] Jens Roat Kultima,et al. An integrated catalog of reference genes in the human gut microbiome , 2014, Nature Biotechnology.
[32] Julia E. Storesund,et al. A theoretical analysis of how strain-specific viruses can control microbial species diversity , 2014, Proceedings of the National Academy of Sciences.
[33] I. Hewson,et al. Discovery of urchin-associated densoviruses (family Parvoviridae) in coastal waters of the Big Island, Hawaii. , 2014, The Journal of general virology.
[34] Alexandros Stamatakis,et al. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..
[35] S. Chisholm,et al. Bacterial Vesicles in Marine Ecosystems , 2014, Science.
[36] François Enault,et al. Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences , 2013, Open Biology.
[37] J. Gordon,et al. Gnotobiotic mouse model of phage–bacterial host dynamics in the human gut , 2013, Proceedings of the National Academy of Sciences.
[38] Mathieu Almeida,et al. Dietary intervention impact on gut microbial gene richness , 2013, Nature.
[39] Frederic D Bushman,et al. Rapid evolution of the human gut virome , 2013, Proceedings of the National Academy of Sciences.
[40] C. Desnues,et al. Evidence of the megavirome in humans. , 2013, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.
[41] W. Shi,et al. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote , 2013, Nucleic acids research.
[42] S. Tims,et al. Microbiota conservation and BMI signatures in adult monozygotic twins , 2012, The ISME Journal.
[43] Forest Rohwer,et al. Going viral: next-generation sequencing applied to phage populations in the human gut , 2012, Nature Reviews Microbiology.
[44] D. Sinderen,et al. Gut microbiota composition correlates with diet and health in the elderly , 2012, Nature.
[45] Axel Poulet,et al. Evolution and Diversity of the Microviridae Viral Family through a Collection of 81 New Complete Genomes Assembled from Virome Reads , 2012, PloS one.
[46] Olga Golosova,et al. Unipro UGENE: a unified bioinformatics toolkit , 2012, Bioinform..
[47] J. Clemente,et al. Human gut microbiome viewed across age and geography , 2012, Nature.
[48] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[49] F. Bushman,et al. Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes , 2011, Science.
[50] F. Bushman,et al. The human gut virome: inter-individual variation and dynamic response to diet. , 2011, Genome research.
[51] S. Schuster,et al. Integrative analysis of environmental sequences using MEGAN4. , 2011, Genome research.
[52] J. Sung,et al. Comparison of the Gut Microbiotas of Healthy Adult Twins Living in South Korea and the United States , 2011, Applied and Environmental Microbiology.
[53] P. Forterre,et al. Microviridae Goes Temperate: Microvirus-Related Proviruses Reside in the Genomes of Bacteroidetes , 2011, PloS one.
[54] Ramón Doallo,et al. ProtTest 3: fast selection of best-fit models of protein evolution , 2011, Bioinform..
[55] M. Frith,et al. Adaptive seeds tame genomic sequence comparison. , 2011, Genome research.
[56] Amos Bairoch,et al. ViralZone: a knowledge resource to understand virus diversity , 2010, Nucleic Acids Res..
[57] L. Mcdaniel,et al. High Frequency of Horizontal Gene Transfer in the Oceans , 2010, Science.
[58] S. Massart,et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa , 2010, Proceedings of the National Academy of Sciences.
[59] Forest Rohwer,et al. Viruses in the fecal microbiota of monozygotic twins and their mothers , 2010, Nature.
[60] William A. Walters,et al. QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.
[61] Peter Salamon,et al. Viral and microbial community dynamics in four aquatic environments , 2010, The ISME Journal.
[62] R. Barrangou,et al. CRISPR/Cas, the Immune System of Bacteria and Archaea , 2010, Science.
[63] Ning Ma,et al. BLAST+: architecture and applications , 2009, BMC Bioinformatics.
[64] F. Rohwer,et al. Explaining microbial population genomics through phage predation , 2009, Nature Reviews Microbiology.
[65] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[66] B. Roe,et al. A core gut microbiome in obese and lean twins , 2008, Nature.
[67] Florent E. Angly,et al. Viral diversity and dynamics in an infant gut. , 2008, Research in microbiology.
[68] J. Dushoff,et al. Alternative stable states in host–phage dynamics , 2008, Theoretical Ecology.
[69] C. Suttle. Marine viruses — major players in the global ecosystem , 2007, Nature Reviews Microbiology.
[70] Daniel B. DiGiulio,et al. Development of the Human Infant Intestinal Microbiota , 2007, PLoS biology.
[71] Robert C. Edgar,et al. PILER-CR: Fast and accurate identification of CRISPR repeats , 2007, BMC Bioinformatics.
[72] R. Knight,et al. Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities , 2007, Applied and Environmental Microbiology.
[73] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[74] P. Salamon,et al. Metagenomic Analyses of an Uncultured Viral Community from Human Feces , 2003, Journal of bacteriology.
[75] M. Borodovsky,et al. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. , 2001, Nucleic acids research.
[76] T. Thingstad. Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems , 2000 .
[77] A. L. Taylor. BACTERIOPHAGE-INDUCED MUTATION IN ESCHERICHIA COLI. , 1963, Proceedings of the National Academy of Sciences of the United States of America.
[78] J. T. Curtis,et al. An Ordination of the Upland Forest Communities of Southern Wisconsin , 1957 .
[79] Sean R. Eddy,et al. Profile hidden Markov models , 1998, Bioinform..