Alterations of the human gut microbiome in liver cirrhosis, Nature, vol.513, pp.59-64, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-02639870
Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition, Genome Biol, vol.15, issue.6, pp.1-12, 2014. ,
Potential of fecal microbiota for early-stage detection of colorectal cancer, Mol Syst Biol, vol.10, p.766, 2014. ,
, Proc Natl Acad Sci U S A, vol.113, pp.5706-5717, 2016.
Bifidobacterium animalis subsp. lactis fermented milk product reduces inflammation by altering a niche for colitogenic microbes, Proc Natl Acad Sci, vol.107, issue.42, pp.18132-18139, 2010. ,
De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units, PeerJ, vol.3, p.1487, 2015. ,
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities, Appl Environ Microbiol, vol.75, pp.7537-7578, 2009. ,
UPARSE: highly accurate OTU sequences from microbial amplicon reads, Nat Methods, vol.10, pp.996-1004, 2013. ,
DADA2: high-resolution sample inference from Illumina amplicon data, Nat Methods, vol.13, pp.581-584, 2016. ,
VSEARCH: a versatile open source tool for metagenomics, PeerJ, vol.4, p.2584, 2016. ,
QIIME allows analysis of high-throughput community sequencing data, Nat Methods, vol.7, issue.5, pp.335-341, 2010. ,
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome, GigaScience, vol.1, issue.1, pp.2047-2064, 2012. ,
Metastats: an improved statistical method for analysis of metagenomic data, Genome Biol, vol.12, issue.1, pp.1-27, 2011. ,
Differential abundance analysis for microbial marker-gene surveys, Nat Methods, vol.10, pp.1200-1202, 2013. ,
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.550, 2014. ,
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.26, issue.1, pp.139-179, 2010. ,
Waste not, want not: why rarefying microbiome data is inadmissible, PLoS Comput Biol, vol.10, issue.4, p.1003531, 2014. ,
Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics, BMC Genomics, vol.17, issue.1, p.78, 2016. ,
FROGS: find, rapidly, OTUs with galaxy solution, Bioinformatics, vol.34, issue.8, pp.1287-94, 2017. ,
ASaiM: a Galaxy-based framework to analyze microbiota data. GigaScience, vol.7, p.57, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01990448
Qiita: rapid, web-enabled microbiome meta-analysis, Nat Methods, vol.15, pp.796-804, 2018. ,
MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data, vol.8, 2019. ,
Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking, Bioinformatics, vol.31, pp.282-285, 2015. ,
Metaviz: interactive statistical and visual analysis of metagenomic data, Nucleic Acids Res, vol.46, issue.6, pp.2777-87, 2018. ,
VAMPS: a website for visualization and analysis of microbial population structures, BMC Bioinformatics, vol.15, p.41, 2014. ,
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses, Nucleic Acids Res, vol.46, pp.537-581, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01360125
Carryover effects of larval exposure to different environmental bacteria drive adult trait variation in a mosquito vector, Sci Adv, vol.3, issue.8, p.1700585, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01580399
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol, vol.10, issue.3, p.25, 2009. ,
AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads, Genomics, vol.102, issue.5-6, pp.500-506, 2013. ,
PEAR: a fast and accurate Illumina Paired-End reAd mergeR, Bioinformatics, vol.30, issue.5, pp.614-634, 2014. ,
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin. Microbiome, vol.6, p.90, 2018. ,
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB, Nucleic Acids Res, vol.35, issue.21, pp.7188-96, 2007. ,
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB, Appl Environ Microbiol, vol.72, pp.5069-72, 2006. ,
Mycobiome: approaches to analysis of intestinal fungi, J Immunol Methods, vol.421, pp.112-133, 2015. ,
The UNITE database for molecular identification of fungi-recent updates and future perspectives, New Phytol, vol.186, pp.281-286, 2010. ,
Topographic diversity of fungal and bacterial communities in human skin, Nature, vol.498, pp.367-70, 2013. ,
Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences, Nat Rev Microbiol, vol.12, pp.635-680, 2014. ,
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl Environ Microbiol, vol.73, pp.5261-5268, 2007. ,
MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol Biol Evol, vol.30, issue.4, pp.772-80, 2013. ,
Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, BMC Evol Biol, vol.10, issue.1, p.210, 2010. ,
URL : https://hal.archives-ouvertes.fr/pasteur-02445904
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix, Mol Biol Evol, vol.26, issue.7, pp.1641-50, 2009. ,
UniFrac: a new phylogenetic method for comparing microbial communities, Appl Environ Microbiol, vol.71, pp.8228-8263, 2005. ,
Sequencing depth and coverage: key considerations in genomic analyses, Nat Rev Genet, vol.15, pp.121-153, 2014. ,
phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data, PloS ONE, vol.8, issue.4, p.61217, 2013. ,
Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions, Brief Bioinform, vol.19, issue.5, pp.776-92, 2017. ,
A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis, Brief Bioinform, vol.14, issue.6, pp.671-83, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00782486
Interactive metagenomic visualization in a Web browser, BMC Bioinformatics, vol.12, issue.1, p.385, 2011. ,
UpSetR: an R package for the visualization of intersecting sets and their properties, Bioinformatics, vol.33, issue.18, pp.2938-2978, 2017. ,
MEMHDX: an interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets, Bioinformatics, vol.32, issue.22, pp.3413-3422, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01377055
Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa, Proc Natl Acad Sci, vol.115, issue.36, pp.8489-98, 2018. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01925069
PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample, Appl Environ Microbiol, vol.71, issue.12, pp.8966-8975, 2005. ,
Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis, FEMS Microbiol Ecol, vol.60, pp.341-50, 2007. ,