Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut
出版年份 2019 全文链接
标题
Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut
作者
关键词
-
出版物
Microbiome
Volume 7, Issue 1, Pages -
出版商
Springer Science and Business Media LLC
发表日期
2019-08-27
DOI
10.1186/s40168-019-0737-z
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures
- (2018) Pawel S Krawczyk et al. NUCLEIC ACIDS RESEARCH
- Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
- (2018) Robert D. Stewart et al. Nature Communications
- Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes
- (2018) Jeffrey K. Cornuault et al. Microbiome
- Reproducible protocols for metagenomic analysis of human faecal phageomes
- (2018) Andrey N. Shkoporov et al. Microbiome
- Evolution of Plasmid-Mediated Antibiotic Resistance in the Clinical Context
- (2018) Alvaro San Millan TRENDS IN MICROBIOLOGY
- Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut
- (2018) Emma Guerin et al. Cell Host & Microbe
- High-quality genome sequences of uncultured microbes by assembly of read clouds
- (2018) Alex Bishara et al. NATURE BIOTECHNOLOGY
- Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation
- (2017) John Beaulaurier et al. NATURE BIOTECHNOLOGY
- MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach
- (2017) Bonnie L. Brown et al. GigaScience
- Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission
- (2017) Sabrina Duranti et al. Microbiome
- The gut microbiome of healthy Japanese and its microbial and functional uniqueness
- (2016) Suguru Nishijima et al. DNA RESEARCH
- Mobile genes in the human microbiome are structured from global to individual scales
- (2016) I. L. Brito et al. NATURE
- Uncovering Earth’s virome
- (2016) David Paez-Espino et al. NATURE
- Phased diploid genome assembly with single-molecule real-time sequencing
- (2016) Chen-Shan Chin et al. NATURE METHODS
- IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses
- (2016) David Paez-Espino et al. NUCLEIC ACIDS RESEARCH
- Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
- (2016) Ivica Letunic et al. NUCLEIC ACIDS RESEARCH
- Healthy human gut phageome
- (2016) Pilar Manrique et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing
- (2016) Yu-Chih Tsai et al. mBio
- Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data
- (2016) J. A. Frank et al. Scientific Reports
- The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences
- (2016) Nirav Merchant et al. PLOS BIOLOGY
- MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
- (2015) Dinghua Li et al. BIOINFORMATICS
- Roary: rapid large-scale prokaryote pan genome analysis
- (2015) Andrew J. Page et al. BIOINFORMATICS
- Accurate, multi-kb reads resolve complex populations and detect rare microorganisms
- (2015) Itai Sharon et al. GENOME RESEARCH
- CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- (2015) Donovan H. Parks et al. GENOME RESEARCH
- Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome
- (2015) Volodymyr Kuleshov et al. NATURE BIOTECHNOLOGY
- Viral dark matter and virus–host interactions resolved from publicly available microbial genomes
- (2015) Simon Roux et al. eLife
- Strategies and approaches in plasmidome studies—uncovering plasmid diversity disregarding of linear elements?
- (2015) Julián R. Dib et al. Frontiers in Microbiology
- VirSorter: mining viral signal from microbial genomic data
- (2015) Simon Roux et al. PeerJ
- MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
- (2015) Dongwan D. Kang et al. PeerJ
- Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut
- (2015) Josué L. Castro-Mejía et al. Microbiome
- Prokka: rapid prokaryotic genome annotation
- (2014) T. Seemann BIOINFORMATICS
- The Virome in Mammalian Physiology and Disease
- (2014) Herbert W. Virgin CELL
- Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology
- (2014) Molly K Gibson et al. ISME Journal
- An integrated catalog of reference genes in the human gut microbiome
- (2014) Junhua Li et al. NATURE BIOTECHNOLOGY
- Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
- (2014) H Bjørn Nielsen et al. NATURE BIOTECHNOLOGY
- Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
- (2014) Bruce J. Walker et al. PLoS One
- Evidence of Extensive DNA Transfer between Bacteroidales Species within the Human Gut
- (2014) M. J. Coyne et al. mBio
- A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
- (2014) Bas E. Dutilh et al. Nature Communications
- Robustness of Gut Microbiota of Healthy Adults in Response to Probiotic Intervention Revealed by High-Throughput Pyrosequencing
- (2013) S.-W. Kim et al. DNA RESEARCH
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
- (2013) K. Katoh et al. MOLECULAR BIOLOGY AND EVOLUTION
- MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
- (2013) Koichiro Tamura et al. MOLECULAR BIOLOGY AND EVOLUTION
- Richness of human gut microbiome correlates with metabolic markers
- (2013) Emmanuelle Le Chatelier et al. NATURE
- Accurate and universal delineation of prokaryotic species
- (2013) Daniel R Mende et al. NATURE METHODS
- 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
- Expanding the Marine Virosphere Using Metagenomics
- (2013) Carolina Megumi Mizuno et al. PLoS Genetics
- Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
- (2012) H. Thorvaldsdottir et al. BRIEFINGS IN BIOINFORMATICS
- CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome
- (2012) A. Stern et al. GENOME RESEARCH
- A metagenome-wide association study of gut microbiota in type 2 diabetes
- (2012) Junjie Qin et al. NATURE
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Going viral: next-generation sequencing applied to phage populations in the human gut
- (2012) Alejandro Reyes et al. NATURE REVIEWS MICROBIOLOGY
- Hypervariable loci in the human gut virome
- (2012) S. Minot et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces
- (2011) Min-Soo Kim et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- The human gut virome: Inter-individual variation and dynamic response to diet
- (2011) S. Minot et al. GENOME RESEARCH
- Evolutionarily Conserved Orthologous Families in Phages Are Relatively Rare in Their Prokaryotic Hosts
- (2011) D. M. Kristensen et al. JOURNAL OF BACTERIOLOGY
- Enterotypes of the human gut microbiome
- (2011) Manimozhiyan Arumugam et al. NATURE
- HMMER web server: interactive sequence similarity searching
- (2011) R. D. Finn et al. NUCLEIC ACIDS RESEARCH
- genoPlotR: comparative gene and genome visualization in R
- (2010) L. Guy et al. BIOINFORMATICS
- Prodigal: prokaryotic gene recognition and translation initiation site identification
- (2010) Doug Hyatt et al. BMC BIOINFORMATICS
- Mobility of Plasmids
- (2010) C. Smillie et al. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
- 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
- Ab initio gene identification in metagenomic sequences
- (2010) Wenhan Zhu et al. NUCLEIC ACIDS RESEARCH
- Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world
- (2008) E. V. Koonin et al. NUCLEIC ACIDS RESEARCH
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