标题
Best practices for analysing microbiomes
作者
关键词
-
出版物
NATURE REVIEWS MICROBIOLOGY
Volume 16, Issue 7, Pages 410-422
出版商
Springer Nature
发表日期
2018-05-23
DOI
10.1038/s41579-018-0029-9
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。- The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish
- (2017) Keaton Stagaman et al. ISME Journal
- Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
- (2017) Benjamin J Callahan et al. ISME Journal
- Human embryos: Collect reliable data on embryo selection
- (2017) Charis Thompson NATURE
- Shotgun metagenomics, from sampling to analysis
- (2017) Christopher Quince et al. NATURE BIOTECHNOLOGY
- 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
- (2017) Supratim Mukherjee et al. NATURE BIOTECHNOLOGY
- Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
- (2017) Alexander Sczyrba et al. NATURE METHODS
- Systems biology guided by XCMS Online metabolomics
- (2017) Tao Huan et al. NATURE METHODS
- 3D molecular cartography using LC–MS facilitated by Optimus and 'ili software
- (2017) Ivan Protsyuk et al. Nature Protocols
- Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!
- (2017) John Vollmers et al. PLoS One
- A Bayesian method for detecting pairwise associations in compositional data
- (2017) Emma Schwager et al. PLoS Computational Biology
- A phylogenetic transform enhances analysis of compositional microbiota data
- (2017) Justin D Silverman et al. eLife
- Resolving Species Level Changes in a Representative Soil Bacterial Community Using Microfluidic Quantitative PCR
- (2017) Hannah Kleyer et al. Frontiers in Microbiology
- Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets
- (2017) Alex D. Washburne et al. PeerJ
- Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems
- (2017) Joanne B. Emerson et al. Microbiome
- Normalization and microbial differential abundance strategies depend upon data characteristics
- (2017) Sophie Weiss et al. Microbiome
- Dynamics of the human gut microbiome in inflammatory bowel disease
- (2017) Jonas Halfvarson et al. Nature Microbiology
- Opinion: Hijacking exogenous signals to generate new secondary metabolites during symbiotic interactions
- (2017) Rurun Wang et al. Nature Reviews Chemistry
- Robust sparse canonical correlation analysis
- (2016) Ines Wilms et al. BMC Systems Biology
- Centrifuge: rapid and sensitive classification of metagenomic sequences
- (2016) Daehwan Kim et al. GENOME RESEARCH
- Correlation detection strategies in microbial data sets vary widely in sensitivity and precision
- (2016) Sophie Weiss et al. ISME Journal
- Skin Microbiome Surveys Are Strongly Influenced by Experimental Design
- (2016) Jacquelyn S. Meisel et al. JOURNAL OF INVESTIGATIVE DERMATOLOGY
- Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
- (2016) Mingxun Wang et al. NATURE BIOTECHNOLOGY
- Strain-level microbial epidemiology and population genomics from shotgun metagenomics
- (2016) Matthias Scholz et al. NATURE METHODS
- DADA2: High-resolution sample inference from Illumina amplicon data
- (2016) Benjamin J Callahan et al. NATURE METHODS
- PHASTER: a better, faster version of the PHAST phage search tool
- (2016) David Arndt et al. NUCLEIC ACIDS RESEARCH
- Immunization with a heat-killed preparation of the environmental bacteriumMycobacterium vaccaepromotes stress resilience in mice
- (2016) Stefan O. Reber et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Population-level analysis of gut microbiome variation
- (2016) Gwen Falony et al. SCIENCE
- MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
- (2016) Daniel H. Huson et al. PLoS Computational Biology
- Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health
- (2016) David Ríos-Covián et al. Frontiers in Microbiology
- Recovering complete and draft population genomes from metagenome datasets
- (2016) Naseer Sangwan et al. Microbiome
- Relic DNA is abundant in soil and obscures estimates of soil microbial diversity
- (2016) Paul Carini et al. Nature Microbiology
- Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome
- (2016) Antoine M. Snijders et al. Nature Microbiology
- A new view of the tree of life
- (2016) Laura A. Hug et al. Nature Microbiology
- Gut Microbiota Linked to Sexual Preference and HIV Infection
- (2016) Marc Noguera-Julian et al. EBioMedicine
- MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
- (2015) Yu-Wei Wu et al. BIOINFORMATICS
- Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.
- (2015) Kathrin P. Aßhauer et al. BIOINFORMATICS
- CCLasso: correlation inference for compositional data through Lasso
- (2015) Huaying Fang et al. BIOINFORMATICS
- Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis
- (2015) Yuzhen Ye et al. BIOINFORMATICS
- Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA
- (2015) Brendan J. Kelly et al. BIOINFORMATICS
- MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
- (2015) Dinghua Li et al. BIOINFORMATICS
- Metabolome searcher: a high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and using genome restriction
- (2015) A Ranjitha Dhanasekaran et al. BMC BIOINFORMATICS
- Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota
- (2015) Fei Teng et al. Cell Host & Microbe
- CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- (2015) Donovan H. Parks et al. GENOME RESEARCH
- Proton pump inhibitors alter the composition of the gut microbiota
- (2015) Matthew A Jackson et al. GUT
- Measuring β-diversity with species abundance data
- (2015) Louise J. Barwell et al. JOURNAL OF ANIMAL ECOLOGY
- Colibactin: understanding an elusive gut bacterial genotoxin
- (2015) Emily P. Balskus NATURAL PRODUCT REPORTS
- Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes
- (2015) Jenni Hultman et al. NATURE
- Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
- (2015) Kristoffer Forslund et al. NATURE
- A catalog of the mouse gut metagenome
- (2015) Liang Xiao et al. NATURE BIOTECHNOLOGY
- MetaPhlAn2 for enhanced metagenomic taxonomic profiling
- (2015) Duy Tin Truong et al. NATURE METHODS
- Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
- (2015) Nuala A. O'Leary et al. NUCLEIC ACIDS RESEARCH
- The Pfam protein families database: towards a more sustainable future
- (2015) Robert D. Finn et al. NUCLEIC ACIDS RESEARCH
- Metaproteomic analysis using the Galaxy framework
- (2015) Pratik D. Jagtap et al. PROTEOMICS
- Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples
- (2015) T. Korem et al. SCIENCE
- Microbial community assembly and metabolic function during mammalian corpse decomposition
- (2015) J. L. Metcalf et al. SCIENCE
- Structure and function of the global ocean microbiome
- (2015) S. Sunagawa et al. SCIENCE
- Sparse and Compositionally Robust Inference of Microbial Ecological Networks
- (2015) Zachary D. Kurtz et al. PLoS Computational Biology
- Proportionality: A Valid Alternative to Correlation for Relative Data
- (2015) David Lovell et al. PLoS Computational Biology
- 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice
- (2015) Alan W. Walker et al. Microbiome
- Context and the human microbiome
- (2015) Daniel McDonald et al. Microbiome
- VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data
- (2015) Cedric C Laczny et al. Microbiome
- Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome
- (2015) Shirley Bikel et al. Computational and Structural Biotechnology Journal
- The Effects of Freezing on Faecal Microbiota as Determined Using MiSeq Sequencing and Culture-Based Investigations
- (2015) Fiona Fouhy et al. PLoS One
- Metatranscriptomic Analysis of Arctic Peat Soil Microbiota
- (2014) Alexander T. Tveit et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- TIPP: taxonomic identification and phylogenetic profiling
- (2014) Nam-phuong Nguyen et al. BIOINFORMATICS
- UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
- (2014) B. E. Suzek et al. BIOINFORMATICS
- Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
- (2014) Susannah J Salter et al. BMC BIOLOGY
- Influence of RNA extraction methods and library selection schemes on RNA-seq data
- (2014) Marc Sultan et al. BMC GENOMICS
- The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease
- (2014) Cell Host & Microbe
- Predictive modeling of gingivitis severity and susceptibility via oral microbiota
- (2014) Shi Huang et al. ISME Journal
- Breath gas metabolites and bacterial metagenomes from cystic fibrosis airways indicate active pH neutral 2,3-butanedione fermentation
- (2014) Katrine L Whiteson et al. ISME Journal
- Persistent gut microbiota immaturity in malnourished Bangladeshi children
- (2014) Sathish Subramanian et al. NATURE
- Binning metagenomic contigs by coverage and composition
- (2014) Johannes Alneberg et al. NATURE METHODS
- FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus
- (2014) Emmanuel Prestat et al. NUCLEIC ACIDS RESEARCH
- 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
- Tackling soil diversity with the assembly of large, complex metagenomes
- (2014) Adina Chuang Howe et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Longitudinal analysis of microbial interaction between humans and the indoor environment
- (2014) S. Lax et al. SCIENCE
- Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection
- (2014) Casey M. Theriot et al. Nature Communications
- Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
- (2014) Paul J. McMurdie et al. PLoS Computational Biology
- Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome
- (2013) Corinne Ferrier Maurice et al. CELL
- PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing?
- (2013) Marti J. Anderson et al. ECOLOGICAL MONOGRAPHS
- Exploring host-microbiota interactions in animal models and humans
- (2013) A. D. Kostic et al. GENES & DEVELOPMENT
- Meta-analyses of studies of the human microbiota
- (2013) C. A. Lozupone et al. GENOME RESEARCH
- Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
- (2013) Morgan G I Langille et al. NATURE BIOTECHNOLOGY
- Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice
- (2013) V. K. Ridaura et al. SCIENCE
- Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data
- (2013) A. Murat Eren et al. Methods in Ecology and Evolution
- MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
- (2013) Todd J Treangen et al. GENOME BIOLOGY
- EMPeror: a tool for visualizing high-throughput microbial community data
- (2013) Yoshiki Vázquez-Baeza et al. GigaScience
- Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences
- (2012) David A W Soergel et al. ISME Journal
- A biomolecular isolation framework for eco-systems biology
- (2012) Hugo Roume et al. ISME Journal
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
- (2012) Anton Bankevich et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Extraction of Bacterial RNA from Soil: Challenges and Solutions
- (2012) Yong Wang et al. MICROBES AND ENVIRONMENTS
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Virtual metagenome reconstruction from 16S rRNA gene sequences
- (2012) Shujiro Okuda et al. Nature Communications
- Inferring Correlation Networks from Genomic Survey Data
- (2012) Jonathan Friedman et al. PLoS Computational Biology
- Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
- (2012) Georgia Giannoukos et al. GENOME BIOLOGY
- PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
- (2011) William A. Walters et al. BIOINFORMATICS
- Human-Associated Microbial Signatures: Examining Their Predictive Value
- (2011) Dan Knights et al. Cell Host & Microbe
- An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
- (2011) Daniel McDonald et al. ISME Journal
- Field guide to next-generation DNA sequencers
- (2011) TRAVIS C. GLENN Molecular Ecology Resources
- Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
- (2011) Pelin Yilmaz et al. NATURE BIOTECHNOLOGY
- Bayesian community-wide culture-independent microbial source tracking
- (2011) Dan Knights et al. NATURE METHODS
- IMG: the integrated microbial genomes database and comparative analysis system
- (2011) V. M. Markowitz et al. NUCLEIC ACIDS RESEARCH
- antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
- (2011) Marnix H. Medema et al. NUCLEIC ACIDS RESEARCH
- Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes
- (2011) G. D. Wu et al. SCIENCE
- A human gut microbial gene catalogue established by metagenomic sequencing
- (2010) Junjie Qin et al. NATURE
- Microbial community resemblance methods differ in their ability to detect biologically relevant patterns
- (2010) Justin Kuczynski et al. NATURE METHODS
- QIIME allows analysis of high-throughput community sequencing data
- (2010) J Gregory Caporaso et al. NATURE METHODS
- Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives
- (2010) Jesse R. Zaneveld et al. NUCLEIC ACIDS RESEARCH
- Site and Strain-Specific Variation in Gut Microbiota Profiles and Metabolism in Experimental Mice
- (2010) Melissa K. Friswell et al. PLoS One
- Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation
- (2010) L. Dethlefsen et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Differential expression analysis for sequence count data
- (2010) Simon Anders et al. GENOME BIOLOGY
- Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
- (2009) P. D. Schloss et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- integrOmics: an R package to unravel relationships between two omics datasets
- (2009) Kim-Anh Lê Cao et al. BIOINFORMATICS
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
- (2009) M. D. Robinson et al. BIOINFORMATICS
- Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
- (2009) Victor Kunin et al. ENVIRONMENTAL MICROBIOLOGY
- Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
- (2009) Micah Hamady et al. ISME Journal
- The 'rare biosphere': a reality check
- (2009) Jens Reeder et al. NATURE METHODS
- Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites
- (2009) W. R. Wikoff et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Bacterial Community Variation in Human Body Habitats Across Space and Time
- (2009) E. K. Costello et al. SCIENCE
- Extensions of Sparse Canonical Correlation Analysis with Applications to Genomic Data
- (2009) Daniela M Witten et al. Statistical Applications in Genetics and Molecular Biology
- Systems biology: Metabonomics
- (2008) Jeremy K. Nicholson et al. NATURE
- The influence of sex, handedness, and washing on the diversity of hand surface bacteria
- (2008) N. Fierer et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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