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。Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing
Andrei Prodan et al.
PLOS ONE (2020)
Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe-microbe interaction networks in plant leaves
Julian Regalado et al.
ISME JOURNAL (2020)
Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions
Stien Beirinckx et al.
MICROBIOME (2020)
Microbial abundance, activity and population genomic profiling with mOTUs2
Alessio Milanese et al.
NATURE COMMUNICATIONS (2019)
Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass
Vincent Caruso et al.
MSYSTEMS (2019)
What is new and relevant for sequencing-based microbiome research? A mini-review
Alena M. Fricker et al.
JOURNAL OF ADVANCED RESEARCH (2019)
Improving eDNA-based protist diversity assessments using networks of amplicon sequence variants
Dominik Forster et al.
ENVIRONMENTAL MICROBIOLOGY (2019)
Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline
Charlie Pauvert et al.
FUNGAL ECOLOGY (2019)
Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome
Victor J. Carrion et al.
SCIENCE (2019)
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications
Rolf Henrik Nilsson et al.
NUCLEIC ACIDS RESEARCH (2019)
High-level classification of the Fungi and a tool for evolutionary ecological analyses
Leho Tedersoo et al.
FUNGAL DIVERSITY (2018)
Best practices for analysing microbiomes
Rob Knight et al.
NATURE REVIEWS MICROBIOLOGY (2018)
A global atlas of the dominant bacteria found in soil
Manuel Delgado-Baquerizo et al.
SCIENCE (2018)
Analysis of sequencing strategies and tools for taxonomic annotation: Defining standards for progressive metagenomics
Alejandra Escobar-Zepeda et al.
SCIENTIFIC REPORTS (2018)
Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches
Jacob T. Nearing et al.
PEERJ (2018)
Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding
Sten Anslan et al.
MYCOKEYS (2018)
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
Benjamin J. Callahan et al.
ISME JOURNAL (2017)
Quantitative microbiome profiling links gut community variation to microbial load
Doris Vandeputte et al.
NATURE (2017)
A communal catalogue reveals Earth's multiscale microbial diversity
Luke R. Thompson et al.
NATURE (2017)
Temporal Dynamics of Soil Microbial Communities below the Seedbed under Two Contrasting Tillage Regimes
Florine Degrune et al.
FRONTIERS IN MICROBIOLOGY (2017)
Accuracy of microbial community diversity estimated by closed- and open-reference OTUs
Robert C. Edgar
PEERJ (2017)
A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome
Imane Allali et al.
BMC MICROBIOLOGY (2017)
Farm compost amendment and non-inversion tillage improve soil quality without increasing the risk for N and P leaching
Tommy D'Hose et al.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT (2016)
DADA2: High-resolution sample inference from Illumina amplicon data
Benjamin J. Callahan et al.
NATURE METHODS (2016)
The healthy human microbiome
Jason Lloyd-Price et al.
GENOME MEDICINE (2016)
Dynamics in the Strawberry Rhizosphere Microbiome in Response to Biochar and Botrytis cinerea Leaf Infection
Caroline De Tender et al.
FRONTIERS IN MICROBIOLOGY (2016)
Back to the Future of Soil Metagenomics
Joseph Nesme et al.
FRONTIERS IN MICROBIOLOGY (2016)
The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies
J. Paul Brooks et al.
BMC MICROBIOLOGY (2015)
Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses
Marie Lisandra Zepeda Mendoza et al.
BRIEFINGS IN BIOINFORMATICS (2015)
Functional overlap of the Arabidopsis leaf and root microbiota
Yang Bai et al.
NATURE (2015)
Nanopore-based Fourth-generation DNA Sequencing Technology
Yanxiao Feng et al.
GENOMICS PROTEOMICS & BIOINFORMATICS (2015)
Emergence Shapes the Structure of the Seed Microbiota
Matthieu Barret et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2015)
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger et al.
BIOINFORMATICS (2014)
UPARSE: highly accurate OTU sequences from microbial amplicon reads
Robert C. Edgar
NATURE METHODS (2013)
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Christian Quast et al.
NUCLEIC ACIDS RESEARCH (2013)
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
Paul J. McMurdie et al.
PLOS ONE (2013)
Diversity and heritability of the maize rhizosphere microbiome under field conditions
Jason A. Peiffer et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities
Katarina Ihrmark et al.
FEMS MICROBIOLOGY ECOLOGY (2012)
Grinder: a versatile amplicon and shotgun sequence simulator
Florent E. Angly et al.
NUCLEIC ACIDS RESEARCH (2012)
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
Daniel McDonald et al.
GIGASCIENCE (2012)
UCHIME improves sensitivity and speed of chimera detection
Robert C. Edgar et al.
BIOINFORMATICS (2011)
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
Mark D. Robinson et al.
BIOINFORMATICS (2010)
Search and clustering orders of magnitude faster than BLAST
Robert C. Edgar
BIOINFORMATICS (2010)
QIIME allows analysis of high-throughput community sequencing data
J. Gregory Caporaso et al.
NATURE METHODS (2010)
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)
Defining operational taxonomic units using DNA barcode data
M Blaxter et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2005)
分享论文
