What Lies Beneath? Taking the Plunge into the Murky Waters of Phage Biology
暂无分享,去创建一个
[1] C. Hill,et al. Viral biogeography of the mammalian gut and parenchymal organs , 2022, Nature Microbiology.
[2] B. Dutilh,et al. iPHoP: an integrated machine-learning framework to maximize host prediction for metagenome-assembled virus genomes , 2022, bioRxiv.
[3] B. Warner,et al. Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants , 2022, Nature Microbiology.
[4] Andrew Millard,et al. Phage Genome Annotation: Where to Begin and End. , 2021, PHAGE.
[5] Martha R. J. Clokie,et al. INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes. , 2021, PHAGE.
[6] C. Hill,et al. Viral biogeography of gastrointestinal tract and parenchymal organs in two representative species of mammals , 2021 .
[7] T. Hackl,et al. Genetic engineering of marine cyanophages reveals integration but not lysogeny in T7-like cyanophages , 2021, The ISME journal.
[8] Evan A. Eskew,et al. The Global Virome in One Network (VIRION): an Atlas of Vertebrate-Virus Associations , 2021, bioRxiv.
[9] Natalia N. Ivanova,et al. Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome , 2021, Nature Microbiology.
[10] Christine L. Sun,et al. Accurate viral genome reconstruction and host assignment with proximity-ligation sequencing , 2021, bioRxiv.
[11] F. Rohwer,et al. The landscape of lysogeny across microbial community density, diversity, and energetics. , 2021, Environmental microbiology.
[12] S. Roux,et al. Global overview and major challenges of host prediction methods for uncultivated phages. , 2021, Current opinion in virology.
[13] C. Silveira,et al. Prophage Genomics and Ecology in the Family Rhodobacteraceae , 2021, Microorganisms.
[14] Ayal B. Gussow,et al. Thousands of previously unknown phages discovered in whole-community human gut metagenomes , 2021, Microbiome.
[15] S. Sunagawa,et al. High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains , 2021, Microbiome.
[16] R. P. Ross,et al. Probing the “Dark Matter” of the Human Gut Phageome: Culture Assisted Metagenomics Enables Rapid Discovery and Host-Linking for Novel Bacteriophages , 2021, Frontiers in Cellular and Infection Microbiology.
[17] A. Thierry,et al. MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut , 2021, eLife.
[18] Tom O. Delmont,et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses , 2021, Microbiome.
[19] Karthik Anantharaman,et al. Deciphering Active Prophages from Metagenomes , 2021, bioRxiv.
[20] B. De Baets,et al. Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins , 2021, Scientific Reports.
[21] I-Min A. Chen,et al. IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses , 2020, Nucleic Acids Res..
[22] R. Finn,et al. Massive expansion of human gut bacteriophage diversity , 2020, Cell.
[23] S. Hallam,et al. Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages , 2020, Nature Communications.
[24] N. Kyrpides,et al. CheckV assesses the quality and completeness of metagenome-assembled viral genomes , 2020, Nature Biotechnology.
[25] Ayal B. Gussow,et al. Thousands of previously unknown phages discovered in whole-community human gut metagenomes , 2020, Microbiome.
[26] Matthew B. Sullivan,et al. Cenote-Taker 2 Democratizes Virus Discovery and Sequence Annotation , 2020, bioRxiv.
[27] M. Sullivan,et al. The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut , 2020, Cell Host & Microbe.
[28] Stan J. J. Brouns,et al. Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts , 2020, iScience.
[29] J. Söding,et al. SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts , 2020, bioRxiv.
[30] Dmitry Antipov,et al. Metaviral SPAdes: assembly of viruses from metagenomic data , 2020, Bioinform..
[31] G. Cochrane,et al. Tara Oceans: towards global ocean ecosystems biology , 2020, Nature Reviews Microbiology.
[32] Vito Adrian Cantu,et al. PhANNs, a fast and accurate tool and web server to classify phage structural proteins , 2020, bioRxiv.
[33] Karthik Anantharaman,et al. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences , 2020, Microbiome.
[34] H. Ochman,et al. Resurrection of a global, metagenomically defined gokushovirus , 2020, eLife.
[35] Chao Deng,et al. Identifying viruses from metagenomic data using deep learning , 2020, Quantitative Biology.
[36] B. Andreopoulos,et al. Phage-specific metabolic reprogramming of virocells , 2020, The ISME Journal.
[37] A. Maresso,et al. Constructing and Characterizing Bacteriophage Libraries for Phage Therapy of Human Infections , 2019, Front. Microbiol..
[38] T. Sutton,et al. The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific. , 2019, Cell host & microbe.
[39] P. Turnbaugh,et al. CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog. , 2019, Cell host & microbe.
[40] M. Touchon,et al. A simple, reproducible and cost-effective procedure to analyse gut phageome: from phage isolation to bioinformatic approach , 2019, Scientific Reports.
[41] A. Franks,et al. Bacteriophages in Natural and Artificial Environments , 2019, Pathogens.
[42] Dan Wang,et al. Prophage Hunter: an integrative hunting tool for active prophages , 2019, Nucleic Acids Res..
[43] Daniel A. Cuevas,et al. Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information , 2019, mBio.
[44] Edoardo Pasolli,et al. Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle , 2019, Cell.
[45] Brian Bushnell,et al. Murine colitis reveals a disease-associated bacteriophage community , 2018, Nature Microbiology.
[46] M. Breitbart,et al. Phage puppet masters of the marine microbial realm , 2018, Nature Microbiology.
[47] B. Blasdel,et al. From Host to Phage Metabolism: Hot Tales of Phage T4’s Takeover of E. coli , 2018, Viruses.
[48] J. Bae,et al. Lysogeny is prevalent and widely distributed in the murine gut microbiota , 2018, The ISME Journal.
[49] Ana Rodríguez,et al. Phage or foe: an insight into the impact of viral predation on microbial communities , 2018, The ISME Journal.
[50] M. Shi,et al. Meta-transcriptomics and the evolutionary biology of RNA viruses , 2017, Virus Research.
[51] F. Bushman,et al. Viral communities of the human gut: metagenomic analysis of composition and dynamics , 2017, Mobile DNA.
[52] Yang Young Lu,et al. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data , 2017, Microbiome.
[53] S. Abedon,et al. Lysogeny in nature: mechanisms, impact and ecology of temperate phages , 2017, The ISME Journal.
[54] S. Schreiber,et al. Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection. , 2017, Gastroenterology.
[55] Lyam Baudry,et al. Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay , 2017, Science Advances.
[56] U. Sauer,et al. Next-Generation “-omics” Approaches Reveal a Massive Alteration of Host RNA Metabolism during Bacteriophage Infection of Pseudomonas aeruginosa , 2016, PLoS genetics.
[57] J. D. Elsas,et al. The Significance of Mutualistic Phages for Bacterial Ecology and Evolution. , 2016, Trends in microbiology.
[58] B. Hurwitz,et al. Computational prospecting the great viral unknown. , 2016, FEMS microbiology letters.
[59] U. Sauer,et al. High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection , 2016, The ISME Journal.
[60] Bas E. Dutilh,et al. Computational approaches to predict bacteriophage–host relationships , 2015, FEMS microbiology reviews.
[61] P. Forterre,et al. Single‐stranded DNA viruses employ a variety of mechanisms for integration into host genomes , 2015, Annals of the New York Academy of Sciences.
[62] Matthew B. Sullivan,et al. Rising to the challenge: accelerated pace of discovery transforms marine virology , 2015, Nature Reviews Microbiology.
[63] M. Sullivan. Viromes, Not Gene Markers, for Studying Double-Stranded DNA Virus Communities , 2014, Journal of Virology.
[64] J. Derisi,et al. Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data , 2014, PloS one.
[65] R. Edwards,et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes , 2014, Nature Communications.
[66] Peer Bork,et al. Classification and quantification of bacteriophage taxa in human gut metagenomes , 2014, The ISME Journal.
[67] S. Sarker,et al. Coverage of diarrhoea-associated Escherichia coli isolates from different origins with two types of phage cocktails , 2014, Microbial biotechnology.
[68] B. Hurwitz,et al. Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics , 2013, Environmental microbiology.
[69] Sergey I. Nikolenko,et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..
[70] Kyoung-Ho Kim,et al. Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded and Double-Stranded DNA Viruses , 2011, Applied and Environmental Microbiology.
[71] F. Rohwer,et al. Consider something viral in your research , 2011, Nature Reviews Microbiology.
[72] E. Holmes,et al. Rates of evolutionary change in viruses: patterns and determinants , 2008, Nature Reviews Genetics.
[73] C. Suttle. Marine viruses — major players in the global ecosystem , 2007, Nature Reviews Microbiology.
[74] Curtis A. Suttle,et al. Exploring the Vast Diversity of Marine Viruses , 2007 .
[75] Sean R. Eddy,et al. Profile hidden Markov models , 1998, Bioinform..
[76] R. Contreras,et al. Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene , 1976, Nature.