The gut flora as a forgotten organ, EMBO reports, vol.13, issue.7, pp.688-693, 2006. ,
DOI : 10.1097/00001574-200411000-00011
Commensal Host-Bacterial Relationships in the Gut, Science, vol.292, issue.5519, pp.1115-1118, 2001. ,
DOI : 10.1126/science.1058709
High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota, Gut, vol.57, issue.11, pp.1605-1615, 2008. ,
DOI : 10.1136/gut.2007.133603
Who controls the crowd? New findings and old questions about the intestinal microflora, Immunology Letters, vol.99, issue.1, pp.12-16, 2005. ,
DOI : 10.1016/j.imlet.2004.12.013
Gut flora in health and disease. The Lancet, pp.512-519, 2003. ,
A dynamic partnership: Celebrating our gut flora, Anaerobe, vol.11, issue.5, pp.247-251, 2005. ,
DOI : 10.1016/j.anaerobe.2005.05.001
A human gut microbial gene catalogue established by metagenomic sequencing, Nature, vol.13, issue.7285, pp.59-65, 2010. ,
DOI : 10.1038/nature08821
URL : https://hal.archives-ouvertes.fr/cea-00908974
Mass spectrometry-based proteomics, Nature, vol.1, issue.6928, pp.198-207, 2003. ,
DOI : 10.1016/S0960-9822(01)00632-7
Proteogenomics: needs and roles to be filled by proteomics in genome annotation, Briefings in Functional Genomics and Proteomics, vol.7, issue.1, pp.50-62, 2008. ,
DOI : 10.1093/bfgp/eln010
Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology, Briefings in Functional Genomics and Proteomics, vol.8, issue.1, pp.75-87, 2009. ,
DOI : 10.1093/bfgp/elp005
How do shotgun proteomics algorithms identify proteins? Nat Biotech, pp.755-757, 2007. ,
DOI : 10.1038/nbt0707-755
The host-microbe interface within the gut. Best Practice & Research Clinical Gastroenterology, pp.915-931, 2002. ,
The Power and the Limitations of Cross-Species Protein Identification by Mass Spectrometry-driven Sequence Similarity Searches, Molecular & Cellular Proteomics, vol.3, issue.3, pp.238-249, 2004. ,
DOI : 10.1074/mcp.M300073-MCP200
Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium Bioremediation, Applied and Environmental Microbiology, vol.75, issue.20, pp.6591-6599, 2009. ,
DOI : 10.1128/AEM.01064-09
Systems Biology: Functional analysis of natural microbial consortia using community proteomics, Nature Reviews Microbiology, vol.42, issue.3, pp.196-205, 2009. ,
DOI : 10.1038/nrmicro2080
Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles, Environmental Science & Technology, vol.44, issue.23, 2010. ,
DOI : 10.1021/es101029f
Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults, Environmental Microbiology, vol.57, issue.7, pp.1736-1751, 2009. ,
DOI : 10.1111/j.1462-2920.2009.01900.x
The Mucin Degrader Akkermansia muciniphila Is an Abundant Resident of the Human Intestinal Tract, Applied and Environmental Microbiology, vol.74, issue.5, pp.1646-1648, 2008. ,
DOI : 10.1128/AEM.01226-07
Metagenomic Sequencing of an In Vitro-Simulated Microbial Community, PLoS ONE, vol.5, issue.4, p.10209, 2010. ,
DOI : 10.1371/journal.pone.0010209.t003
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry, Nature Methods, vol.4, issue.3, pp.207-214, 2007. ,
DOI : 10.1038/nmeth1019
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods, Nature Methods, vol.22, issue.6, pp.495-500, 2007. ,
DOI : 10.1038/nmeth1043
The effect of sequencing errors on metagenomic gene prediction, BMC Genomics, vol.10, issue.1, pp.520-520, 2009. ,
DOI : 10.1186/1471-2164-10-520
Mastering seeds for genomic size nucleotide BLAST searches, Nucleic Acids Research, vol.31, issue.23, pp.6935-6941, 2003. ,
DOI : 10.1093/nar/gkg886
URL : http://doi.org/10.1093/nar/gkg886
The COG database: new developments in phylogenetic classification of proteins from complete genomes, Nucleic Acids Research, vol.29, issue.1, pp.22-28, 2001. ,
DOI : 10.1093/nar/29.1.22
The SU.VI.MAX Study, Archives of Internal Medicine, vol.164, issue.21, pp.2335-2342, 2004. ,
DOI : 10.1001/archinte.164.21.2335
URL : https://hal.archives-ouvertes.fr/hal-01346671
One-step subcellular fractionation of rat liver tissue using a Nycodenz density gradient prepared by freezing-thawing and two-dimensional sodium dodecyl sulfate electrophoresis profiles of the main fraction of organelles, ELECTROPHORESIS, vol.22, pp.2872-2880, 2001. ,
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997. ,
DOI : 10.1093/nar/25.17.3389
Open Mass Spectrometry Search Algorithm, Journal of Proteome Research, vol.3, issue.5, pp.958-964, 2004. ,
DOI : 10.1021/pr0499491
URL : http://arxiv.org/abs/q-bio/0406002
PatternHunter: faster and more sensitive homology search, Bioinformatics, vol.18, issue.3, pp.440-445, 2002. ,
DOI : 10.1093/bioinformatics/18.3.440
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.147.8001