Comparison of Bioinformatics Pipelines and Operating Systems for the Analyses of 16S rRNA Gene Amplicon Sequences in Human Fecal Samples

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing

(2020) Andrei Prodan et al.   PLoS One

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Quantitative appraisal of the Amyloid Imaging Taskforce appropriate use criteria for amyloid-PET

(2018) Daniele Altomare et al.   Alzheimers & Dementia

Gut microbiome and depression: what we know and what we need to know

(2018) Gal Winter et al.   REVIEWS IN THE NEUROSCIENCES

The role of the gut microbiota in schizophrenia: Current and future perspectives

(2018) Daniela Rodrigues-Amorim et al.   WORLD JOURNAL OF BIOLOGICAL PSYCHIATRY

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments

(2018) Alexandre Almeida et al.   GigaScience

Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction

(2018) Youlian Zhou et al.   mSystems

Gut microbiome analysis as a tool towards targeted non-invasive biomarkers for early hepatocellular carcinoma

(2018) Zhigang Ren et al.   GUT

Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences

(2018) Adrian López-García et al.   Frontiers in Microbiology

Metabolic and Microbiota Measures as Peripheral Biomarkers in Major Depressive Disorder

(2018) Rachael Horne et al.   Frontiers in Psychiatry

Association of brain amyloidosis with pro-inflammatory gut bacterial taxa and peripheral inflammation markers in cognitively impaired elderly

(2017) Annamaria Cattaneo et al.   NEUROBIOLOGY OF AGING

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine

(2016) Alejandra V. Contreras et al.   Frontiers in Physiology

The fecal microbiota as a biomarker for disease activity in Crohn’s disease

(2016) Danyta. I. Tedjo et al.   Scientific Reports

Sample storage conditions significantly influence faecal microbiome profiles

(2015) Jocelyn M Choo et al.   Scientific Reports

Reproducibility of neuroimaging analyses across operating systems

(2015) Tristan Glatard et al.   Frontiers in Neuroinformatics

Type 2 Diabetes Biomarkers of Human Gut Microbiota Selected via Iterative Sure Independent Screening Method

(2015) Lihua Cai et al.   PLoS One

jvenn: an interactive Venn diagram viewer

(2014) Philippe Bardou et al.   BMC BIOINFORMATICS

Gut microbiota are related to Parkinson's disease and clinical phenotype

(2014) Filip Scheperjans et al.   MOVEMENT DISORDERS

The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16S rRNA Gene Sequencing

(2014) Nicholas A. Kennedy et al.   PLoS One

Comparative Metagenomic Analysis of Human Gut Microbiome Composition Using Two Different Bioinformatic Pipelines

(2014) Valeria D’Argenio et al.   Biomed Research International

Gut microbiota-based translational biomarkers to prevent metabolic syndrome via nutritional modulation

(2013) Shuiming Xiao et al.   FEMS MICROBIOLOGY ECOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility

(2012) Anton Nekrutenko et al.   NATURE REVIEWS GENETICS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements

(2012) Ed H. B. M. Gronenschild et al.   PLoS One

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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