标题
virMine: automated detection of viral sequences from complex metagenomic samples
作者
关键词
-
出版物
PeerJ
Volume 7, Issue -, Pages e6695
出版商
PeerJ
发表日期
2019-04-10
DOI
10.7717/peerj.6695
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Bacteriophages of the Urinary Microbiome
- (2018) Taylor Miller-Ensminger et al. JOURNAL OF BACTERIOLOGY
- Detecting viral genomes in the female urinary microbiome
- (2018) Andrea Garretto et al. JOURNAL OF GENERAL VIROLOGY
- Close Encounters of Three Kinds: Bacteriophages, Commensal Bacteria, and Host Immunity
- (2018) Eric C. Keen et al. TRENDS IN MICROBIOLOGY
- The ‘Neglected’ Soil Virome – Potential Role and Impact
- (2018) Akbar Adjie Pratama et al. TRENDS IN MICROBIOLOGY
- Phage hunters: Computational strategies for finding phages in large-scale ‘omics datasets
- (2018) Bonnie L. Hurwitz et al. VIRUS RESEARCH
- Pseudomonas PB1-Like Phages: Whole Genomes from Metagenomes Offer Insight into an Abundant Group of Bacteriophages
- (2018) Siobhan Watkins et al. Viruses-Basel
- Microbial metagenome of urinary tract infection
- (2018) Ahmed Moustafa et al. Scientific Reports
- Overview of Virus Metagenomic Classification Methods and Their Biological Applications
- (2018) Sam Nooij et al. Frontiers in Microbiology
- FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data
- (2018) Saima Sultana Tithi et al. PeerJ
- Phage puppet masters of the marine microbial realm
- (2018) Mya Breitbart et al. Nature Microbiology
- MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins
- (2018) Deyvid Amgarten et al. Frontiers in Genetics
- Minimum Information about an Uncultivated Virus Genome (MIUViG)
- (2018) Simon Roux et al. NATURE BIOTECHNOLOGY
- Quantitative CrAssphage PCR Assays for Human Fecal Pollution Measurement
- (2017) Elyse Stachler et al. ENVIRONMENTAL SCIENCE & TECHNOLOGY
- Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples
- (2017) Jakob Thannesberger et al. FASEB JOURNAL
- metaSPAdes: a new versatile metagenomic assembler
- (2017) Sergey Nurk et al. GENOME RESEARCH
- A bacteriophages journey through the human body
- (2017) Jeremy J. Barr IMMUNOLOGICAL REVIEWS
- High abundance and expression of transposases in bacteria from the Baltic Sea
- (2017) Theoden Vigil-Stenman et al. ISME Journal
- Virus taxonomy in the age of metagenomics
- (2017) Peter Simmonds et al. NATURE REVIEWS MICROBIOLOGY
- VirusSeeker, a computational pipeline for virus discovery and virome composition analysis
- (2017) Guoyan Zhao et al. VIROLOGY
- Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches
- (2017) Stephen Hayes et al. Viruses-Basel
- Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans
- (2017) Felipe H. Coutinho et al. Nature Communications
- Editorial: Virus Discovery by Metagenomics: The (Im)possibilities
- (2017) Bas E. Dutilh et al. Frontiers in Microbiology
- Environmental drivers of viral community composition in Antarctic soils identified by viromics
- (2017) Evelien M. Adriaenssens et al. Microbiome
- VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
- (2017) Jie Ren et al. Microbiome
- Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples
- (2017) Dagmara W. Lewandowska et al. Microbiome
- The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses
- (2017) Lisa Zeigler Allen et al. mSystems
- Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies
- (2016) Bryan D. Merrill et al. BMC GENOMICS
- Toward Accurate and Quantitative Comparative Metagenomics
- (2016) Stephen Nayfach et al. CELL
- Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges
- (2016) Katherine Bruder et al. Evolutionary Bioinformatics
- Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria
- (2016) Rohit Ghai et al. ISME Journal
- Assessment of a metaviromic dataset generated from nearshore Lake Michigan
- (2016) Siobhan C. Watkins et al. MARINE AND FRESHWATER RESEARCH
- MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices
- (2016) Dinghua Li et al. METHODS
- Uncovering Earth’s virome
- (2016) David Paez-Espino et al. NATURE
- VirusTAP: Viral Genome-Targeted Assembly Pipeline
- (2016) Akifumi Yamashita et al. Frontiers in Microbiology
- Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes
- (2016) Branko Rihtman et al. PeerJ
- Recovering complete and draft population genomes from metagenome datasets
- (2016) Naseer Sangwan et al. Microbiome
- A new view of the tree of life
- (2016) Laura A. Hug et al. Nature Microbiology
- Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland
- (2016) Timofey Skvortsov et al. PLoS One
- MetaPhinder—Identifying Bacteriophage Sequences in Metagenomic Data Sets
- (2016) Vanessa Isabell Jurtz et al. PLoS One
- VIP: an integrated pipeline for metagenomics of virus identification and discovery
- (2016) Yang Li et al. Scientific Reports
- A diverse virome in kidney transplant patients contains multiple viral subtypes with distinct polymorphisms
- (2016) Asha Rani et al. Scientific Reports
- From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems
- (2015) Daniel R. Garza et al. CELLULAR AND MOLECULAR LIFE SCIENCES
- Ecological and genetic interactions between cyanobacteria and viruses in a low-oxygen mat community inferred through metagenomics and metatranscriptomics
- (2015) Alexander A. Voorhies et al. ENVIRONMENTAL MICROBIOLOGY
- Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake
- (2015) A. López-Bueno et al. MOLECULAR ECOLOGY
- Rising to the challenge: accelerated pace of discovery transforms marine virology
- (2015) Jennifer R. Brum et al. NATURE REVIEWS MICROBIOLOGY
- Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
- (2015) Nuala A. O'Leary et al. NUCLEIC ACIDS RESEARCH
- Patterns and ecological drivers of ocean viral communities
- (2015) J. R. Brum et al. SCIENCE
- The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome
- (2015) Geoffrey D. Hannigan et al. mBio
- Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis
- (2015) Nádia Conceição-Neto et al. Scientific Reports
- Four novel algal virus genomes discovered from Yellowstone Lake metagenomes
- (2015) Weijia Zhang et al. Scientific Reports
- Recovering full-length viral genomes from metagenomes
- (2015) Saskia L. Smits et al. Frontiers in Microbiology
- Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins
- (2015) Karyna Rosario et al. Frontiers in Microbiology
- The human urine virome in association with urinary tract infections
- (2015) Tasha M. Santiago-Rodriguez et al. Frontiers in Microbiology
- Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions
- (2015) Christopher M. Bellas et al. Frontiers in Microbiology
- VirSorter: mining viral signal from microbial genomic data
- (2015) Simon Roux et al. PeerJ
- VirAmp: a galaxy-based viral genome assembly pipeline
- (2015) Yinan Wan et al. GigaScience
- High-Level Diversity of Tailed Phages, Eukaryote-Associated Viruses, and Virophage-Like Elements in the Metaviromes of Antarctic Soils
- (2014) Olivier Zablocki et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Metavir 2: new tools for viral metagenome comparison and assembled virome analysis
- (2014) Simon Roux et al. BMC BIOINFORMATICS
- Molecular Bases and Role of Viruses in the Human Microbiome
- (2014) Shira R. Abeles et al. JOURNAL OF MOLECULAR BIOLOGY
- Expanded microbial genome coverage and improved protein family annotation in the COG database
- (2014) Michael Y. Galperin et al. NUCLEIC ACIDS RESEARCH
- Development of a virus detection and discovery pipeline using next generation sequencing
- (2014) Thien Ho et al. VIROLOGY
- A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
- (2014) Bas E. Dutilh et al. Nature Communications
- Assembly of viral genomes from metagenomes
- (2014) Saskia L. Smits et al. Frontiers in Microbiology
- Previously unknown and highly divergent ssDNA viruses populate the oceans
- (2013) Jessica M Labonté et al. ISME Journal
- The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology
- (2013) Bonnie L. Hurwitz et al. PLoS One
- Rapid evolution of the human gut virome
- (2013) S. Minot et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Genomes from Metagenomics
- (2013) I. Sharon et al. SCIENCE
- Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry
- (2013) William P. Inskeep et al. Frontiers in Microbiology
- IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
- (2012) Y. Peng et al. BIOINFORMATICS
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
- (2012) Anton Bankevich et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics
- (2012) Simon Roux et al. PLoS One
- VIROME: a standard operating procedure for analysis of viral metagenome sequences
- (2012) K. Eric Wommack et al. Standards in Genomic Sciences
- Phage Eco-Locator: a web tool for visualization and analysis of phage genomes in metagenomic data sets
- (2011) Ramy K Aziz et al. BMC BIOINFORMATICS
- The human gut virome: Inter-individual variation and dynamic response to diet
- (2011) S. Minot et al. GENOME RESEARCH
- Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome
- (2011) David T Pride et al. ISME Journal
- Viruses in the faecal microbiota of monozygotic twins and their mothers
- (2010) Alejandro Reyes et al. NATURE
- A human gut microbial gene catalogue established by metagenomic sequencing
- (2010) Junjie Qin et al. NATURE
- Transposases are the most abundant, most ubiquitous genes in nature
- (2010) Ramy K. Aziz et al. NUCLEIC ACIDS RESEARCH
- Why genes overlap in viruses
- (2010) N. Chirico et al. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Biopython: freely available Python tools for computational molecular biology and bioinformatics
- (2009) P. J. A. Cock et al. BIOINFORMATICS
- BLAST+: architecture and applications
- (2009) Christiam Camacho et al. BMC BIOINFORMATICS
- Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm
- (2009) William J Brazelton et al. ISME Journal
- High Diversity of the Viral Community from an Antarctic Lake
- (2009) A. Lopez-Bueno et al. SCIENCE
- The RAST Server: Rapid Annotations using Subsystems Technology
- (2008) Ramy K Aziz et al. BMC GENOMICS
- Bacteriophage genomics
- (2008) Graham F Hatfull CURRENT OPINION IN MICROBIOLOGY
- MetaSim—A Sequencing Simulator for Genomics and Metagenomics
- (2008) Daniel C. Richter et al. PLoS One
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreFind the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
Search