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。Bioaerosols Play a Major Role in the Nasopharyngeal Microbiota Content in Agricultural Environment
Hamza Mbareche et al.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH (2019)
Quantifying and Understanding Well-to-Well Contamination in Microbiome Research
Jeremiah J. Minich et al.
MSYSTEMS (2019)
Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments
Lisa Karstens et al.
MSYSTEMS (2019)
A fungal mock community control for amplicon sequencing experiments
Matthew G. Bakker
MOLECULAR ECOLOGY RESOURCES (2018)
Current understanding of the human microbiome
Jack A. Gilbert et al.
NATURE MEDICINE (2018)
The Madness of Microbiome: Attempting To Find Consensus Best Practice for 16S Microbiome Studies
Jolinda Pollock et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2018)
Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis
Simon A. Hardwick et al.
NATURE COMMUNICATIONS (2018)
Systematic evaluation of error rates and causes in short samples in next-generation sequencing
Franziska Pfeiffer et al.
SCIENTIFIC REPORTS (2018)
Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data
Nicole M. Davis et al.
MICROBIOME (2018)
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
Benjamin J. Callahan et al.
ISME JOURNAL (2017)
Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium
Rashmi Sinha et al.
NATURE BIOTECHNOLOGY (2017)
Bioaerosol sampling and detection methods based on molecular approaches: No pain no gain
Hamza Mbareche et al.
SCIENCE OF THE TOTAL ENVIRONMENT (2017)
A next generation sequencing approach with a suitable bioinformatics workflow to study fungal diversity in bioaerosols released from two different types of composting plants
Hamza Mbareche et al.
SCIENCE OF THE TOTAL ENVIRONMENT (2017)
Bioaerosols concentrations in working areas in biomethanization facilities
Marie-Eve Dubuis et al.
JOURNAL OF THE AIR & WASTE MANAGEMENT ASSOCIATION (2017)
Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer
Alfonso Benitez-Paez et al.
GIGASCIENCE (2017)
Different Amplicon Targets for Sequencing-Based Studies of Fungal Diversity
Francesca De Filippis et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2017)
Central limit theorem: the cornerstone of modern statistics
Sang Gyu Kwak et al.
KOREAN JOURNAL OF ANESTHESIOLOGY (2017)
Occurrence of Fungal DNA Contamination in PCR Reagents: Approaches to Control and Decontamination
S. Czurda et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2016)
Decontamination of 16S rRNA gene amplicon sequence datasets based on bacterial load assessment by qPCR
Vladimir Lazarevic et al.
BMC MICROBIOLOGY (2016)
DADA2: High-resolution sample inference from Illumina amplicon data
Benjamin J. Callahan et al.
NATURE METHODS (2016)
Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples
Angela Glassing et al.
GUT PATHOGENS (2016)
VSEARCH: a versatile open source tool for metagenomics
Torbjorn Rognes et al.
PEERJ (2016)
Functional genomic and metagenomic approaches to understanding gut microbiota-animal mutualism
Sang Sun Yoon et al.
CURRENT OPINION IN MICROBIOLOGY (2015)
Microbial diversity in bioaerosol samples causing ODTS compared to reference bioaerosol samples as measured using Illumina sequencing and MALDI-TOF
Anne Mette Madsen et al.
ENVIRONMENTAL RESEARCH (2015)
Sources of PCR-induced distortions in high-throughput sequencing data sets
Justus M. Kebschull et al.
NUCLEIC ACIDS RESEARCH (2015)
Who qualifies to be a bioinformatician?
Antony T. Vincent et al.
FRONTIERS IN GENETICS (2015)
Broadening the definition bioinformation
David Roy Smith
FRONTIERS IN GENETICS (2015)
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
Susannah J. Salter et al.
BMC BIOLOGY (2014)
Conducting a Microbiome Study
Julia K. Goodrich et al.
CELL (2014)
Advancing the Microbiome Research Community
Curtis Huttenhower et al.
CELL (2014)
The Treatment-Naive Microbiome in New-Onset Crohn's Disease
Dirk Gevers et al.
CELL HOST & MICROBE (2014)
A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses
Pier Luigi Buttigieg et al.
FEMS MICROBIOLOGY ECOLOGY (2014)
Assessing the aerodynamic diameters of taxon-specific fungal bioaerosols by quantitative PCR and next-generation DNA sequencing
Naomichi Yamamoto et al.
JOURNAL OF AEROSOL SCIENCE (2014)
Sequencing depth and coverage: key considerations in genomic analyses
David Sims et al.
NATURE REVIEWS GENETICS (2014)
Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes
Martin Laurence et al.
PLOS ONE (2014)
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
Paul J. McMurdie et al.
PLOS COMPUTATIONAL BIOLOGY (2014)
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Michael I. Love et al.
GENOME BIOLOGY (2014)
Unravelling the bacterial diversity in the atmosphere
Isabella Gandolfi et al.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2013)
A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
Marie-Agnes Dillies et al.
BRIEFINGS IN BIOINFORMATICS (2013)
PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing?
Marti J. Anderson et al.
ECOLOGICAL MONOGRAPHS (2013)
Advances in computational analysis of metagenome sequences
Colin F. Davenport et al.
ENVIRONMENTAL MICROBIOLOGY (2013)
Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes
Jianjun Wang et al.
ISME JOURNAL (2013)
Differential abundance analysis for microbial marker-gene surveys
Joseph N. Paulson et al.
NATURE METHODS (2013)
UPARSE: highly accurate OTU sequences from microbial amplicon reads
Robert C. Edgar
NATURE METHODS (2013)
Going back to the roots: the microbial ecology of the rhizosphere
Laurent Philippot et al.
NATURE REVIEWS MICROBIOLOGY (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)
Beyond the Venn diagram: the hunt for a core microbiome
Ashley Shade et al.
ENVIRONMENTAL MICROBIOLOGY (2012)
Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification
R. Henrik Nilsson et al.
Evolutionary Bioinformatics (2012)
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
J. Gregory Caporaso et al.
ISME JOURNAL (2012)
A framework for human microbiome research
Barbara A. Methe et al.
NATURE (2012)
Unlocking the potential of metagenomics through replicated experimental design
Rob Knight et al.
NATURE BIOTECHNOLOGY (2012)
Quantifying Phylogenetic Beta Diversity: Distinguishing between 'True' Turnover of Lineages and Phylogenetic Diversity Gradients
Fabien Leprieur et al.
PLOS ONE (2012)
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
Conrad L. Schoch et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
The Human Gut Microbiome: Ecology and Recent Evolutionary Changes
Jens Walter et al.
ANNUAL REVIEW OF MICROBIOLOGY, VOL 65 (2011)
Accessing the Soil Metagenome for Studies of Microbial Diversity
Tom O. Delmont et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)
New Directions: A revolution in DNA sequencing now allows for the meaningful integration of biology with aerosol science
Jordan Peccia et al.
ATMOSPHERIC ENVIRONMENT (2011)
UCHIME improves sensitivity and speed of chimera detection
Robert C. Edgar et al.
BIOINFORMATICS (2011)
The evolution of Pyrosequencing® for microbiology: From genes to genomes
R. C. Novais et al.
JOURNAL OF MICROBIOLOGICAL METHODS (2011)
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
J. Gregory Caporaso et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
The Roots of Bioinformatics in Theoretical Biology
Paulien Hogeweg
PLOS COMPUTATIONAL BIOLOGY (2011)
Search and clustering orders of magnitude faster than BLAST
Robert C. Edgar
BIOINFORMATICS (2010)
A diversity of beta diversities: straightening up a concept gone awry. Part 1. Defining beta diversity as a function of alpha and gamma diversity
Hanna Tuomisto
ECOGRAPHY (2010)
Advanced nonparametric tests for multiple comparisons in the design of experiments in computational intelligence and data mining: Experimental analysis of power
Salvador Garcia et al.
INFORMATION SCIENCES (2010)
Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data
Pierre Legendre et al.
MOLECULAR ECOLOGY RESOURCES (2010)
Microbial community resemblance methods differ in their ability to detect biologically relevant patterns
Justin Kuczynski et al.
NATURE METHODS (2010)
QIIME allows analysis of high-throughput community sequencing data
J. Gregory Caporaso et al.
NATURE METHODS (2010)
Differential expression analysis for sequence count data
Simon Anders et al.
GENOME BIOLOGY (2010)
Culture-Independent Characterization of Archaeal Biodiversity in Swine Confinement Building Bioaerosols
Benjamin Nehme et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)
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)
Classification of breast tissues using Moran's index and Geary's coefficient as texture signatures and SVM
Geraldo Braz Junior et al.
COMPUTERS IN BIOLOGY AND MEDICINE (2009)
A core gut microbiome in obese and lean twins
Peter J. Turnbaugh et al.
NATURE (2009)
Next-Generation DNA Sequencing Methods
Elaine R. Mardis
Annual Review of Genomics and Human Genetics (2008)
Testing of null hypotheses in exploratory community analyses: similarity profiles and biota-environment linkage
K. Robert Clarke et al.
JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY (2008)
Modern Robust Statistical Methods An Easy Way to Maximize the Accuracy and Power of Your Research
David M. Erceg-Hurn et al.
AMERICAN PSYCHOLOGIST (2008)
Multivariate analyses in microbial ecology
Alban Ramette
FEMS MICROBIOLOGY ECOLOGY (2007)
Global patterns in bacterial diversity
Catherine A. Lozupone et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Homogenization of regional river dynamics by dams and global biodiversity implications
N. LeRoy Poff et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context
Catherine Lozupone et al.
BMC BIOINFORMATICS (2006)
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
T. Z. DeSantis et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2006)
UNITE:: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi
U Koljalg et al.
NEW PHYTOLOGIST (2005)
Environmental genome shotgun sequencing of the Sargasso Sea
JC Venter et al.
SCIENCE (2004)