Strain-level microbial epidemiology and population genomics from shotgun metagenomics
Published 2016 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Strain-level microbial epidemiology and population genomics from shotgun metagenomics
Authors
Keywords
-
Journal
NATURE METHODS
Volume 13, Issue 5, Pages 435-438
Publisher
Springer Nature
Online
2016-03-22
DOI
10.1038/nmeth.3802
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- 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
- ConStrains identifies microbial strains in metagenomic datasets
- (2015) Chengwei Luo et al. NATURE BIOTECHNOLOGY
- MetaPhlAn2 for enhanced metagenomic taxonomic profiling
- (2015) Duy Tin Truong et al. NATURE METHODS
- Prokka: rapid prokaryotic genome annotation
- (2014) T. Seemann BIOINFORMATICS
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- (2014) Alexandros Stamatakis BIOINFORMATICS
- Potential of fecal microbiota for early-stage detection of colorectal cancer
- (2014) G. Zeller et al. Molecular Systems Biology
- Alterations of the human gut microbiome in liver cirrhosis
- (2014) Nan Qin et al. NATURE
- Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
- (2014) H Bjørn Nielsen et al. NATURE BIOTECHNOLOGY
- Relating the metatranscriptome and metagenome of the human gut
- (2014) E. A. Franzosa et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Kraken: ultrafast metagenomic sequence classification using exact alignments
- (2014) Derrick E Wood et al. GENOME BIOLOGY
- Culture-independent detection and characterisation ofMycobacterium tuberculosisandM. africanumin sputum samples using shotgun metagenomics on a benchtop sequencer
- (2014) Emma L. Doughty et al. PeerJ
- The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes
- (2014) Jason W. Sahl et al. PeerJ
- Pathoscope: Species identification and strain attribution with unassembled sequencing data
- (2013) O. E. Francis et al. GENOME RESEARCH
- A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4
- (2013) Nicholas J. Loman et al. JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
- Richness of human gut microbiome correlates with metabolic markers
- (2013) Emmanuelle Le Chatelier et al. NATURE
- Bacterial colonization factors control specificity and stability of the gut microbiota
- (2013) S. Melanie Lee et al. NATURE
- Gut metagenome in European women with normal, impaired and diabetic glucose control
- (2013) Fredrik H. Karlsson et al. NATURE
- Metagenomic species profiling using universal phylogenetic marker genes
- (2013) Shinichi Sunagawa et al. NATURE METHODS
- Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity
- (2013) A. Everard et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes
- (2013) Nicola Segata et al. Nature Communications
- Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis
- (2013) Jose U Scher et al. eLife
- Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants
- (2013) Ardythe L Morrow et al. Microbiome
- GemSIM: general, error-model based simulator of next-generation sequencing data
- (2012) Kerensa E McElroy et al. BMC GENOMICS
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
- (2012) Anton Bankevich et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- A metagenome-wide association study of gut microbiota in type 2 diabetes
- (2012) Junjie Qin et al. NATURE
- Metagenomic microbial community profiling using unique clade-specific marker genes
- (2012) Nicola Segata et al. NATURE METHODS
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak
- (2012) Claudio U. Köser et al. NEW ENGLAND JOURNAL OF MEDICINE
- PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species
- (2012) Derrick E. Fouts et al. NUCLEIC ACIDS RESEARCH
- Genomic Comparison of Escherichia coli O104:H4 Isolates from 2009 and 2011 Reveals Plasmid, and Prophage Heterogeneity, Including Shiga Toxin Encoding Phage stx2
- (2012) Sanaa A. Ahmed et al. PLoS One
- Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
- (2012) Sahar Abubucker et al. PLoS Computational Biology
- Origins of theE. coliStrain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany
- (2011) David A. Rasko et al. NEW ENGLAND JOURNAL OF MEDICINE
- Search and clustering orders of magnitude faster than BLAST
- (2010) Robert C. Edgar BIOINFORMATICS
- A human gut microbial gene catalogue established by metagenomic sequencing
- (2010) Junjie Qin et al. NATURE
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients
- (2008) H. Sokol et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExplorePublish 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 More