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1. Full Text STRING 8-a global view on proteins and their functional interactions in 630 organisms
by Jensen, Lars J and Kuhn, Michael and Stark, Manuel and Chaffron, Samuel and Creevey, Chris and Muller, Jean and Doerks, Tobias and Julien, Philippe and Roth, Alexander and Simonovic, Milan and Bork, Peer and von Mering, Christian
Nucleic Acids Research, ISSN 0305-1048, 1/2009, Volume 37, Issue suppl_1, pp. D412 - D416
Functional partnerships between proteins are at the core of complex cellular phenotypes, and the networks formed by interacting proteins provide researchers... 
INTERACTION DATABASE | GENOMIC DATA | ASSOCIATIONS | BIOLOGICAL NETWORKS | BIOCHEMISTRY & MOLECULAR BIOLOGY | ENVIRONMENT | INTERACTION NETWORKS | UPDATE | SOFTWARE | PREDICTION | RESOURCE | Life Sciences | Bioinformatics | Biochemistry, Molecular Biology | Genomics | Computer Science
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2. Full Text Community Proteogenomics Reveals Insights into the Physiology of Phyllosphere Bacteria
by Nathanaël Delmotte and Claudia Knief and Samuel Chaffron and Gerd Innerebner and Bernd Roschitzki and Ralph Schlapbach and Christian von Mering and Julia A. Vorholt and Steven E. Lindow
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 9/2009, Volume 106, Issue 38, pp. 16428 - 16433
Aerial plant surfaces represent the largest biological interface on Earth and provide essential services as sites of carbon dioxide fixation, molecular oxygen... 
Proteins | Metagenomics | Soybeans | Databases | Phyllosphere | Bacteria | Sphingomonas | Plants | Pseudomonas | Methylobacterium | Metaproteomics | Methylotrophy | Plant phyllosphere | POPULATION | metaproteomics | MULTIDISCIPLINARY SCIENCES | METHYLOBACTERIUM-EXTORQUENS AM1 | GENERAL STRESS-RESPONSE | PSEUDOMONAS-SYRINGAE | methylotrophy | MICROBIAL COMMUNITIES | METHYLOTROPHIC BACTERIA | plant phyllosphere | DIVERSITY | EPIPHYTIC FITNESS | LEAF SURFACES | PROTEOMICS | Bacteria - metabolism | Electrophoresis, Polyacrylamide Gel | Molecular Sequence Data | Bacterial Physiological Phenomena | Plants - microbiology | DNA, Bacterial - chemistry | Phylogeny | Bacterial Proteins - analysis | Bacteria - genetics | Sequence Analysis, DNA | DNA, Bacterial - genetics | Spectrometry, Mass, Electrospray Ionization | Ecosystem | Bacteria - classification | RNA, Ribosomal, 16S - genetics | Proteomics - methods | Genomics - methods | Adaptations | Carbohydrates | Oxygen | Plant communities | outer membrane proteins | Biomass | Coexistence | Carbon | Leaves | Carbon dioxide fixation | Microorganisms | Energy | Methanol | Life Sciences | Bioinformatics | Biochemistry, Molecular Biology | Genomics | Computer Science | Biological Sciences
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3. Full Text Structure and function of the global ocean microbiome
by Sunagawa, Shinichi and Coelho, Luis Pedro and Chaffron, Samuel and Kultima, Jens Roat and Labadie, Karine and Salazar, Guillem and Djahanschiri, Bardya and Zeller, Georg and Mende, Daniel R and Alberti, Adriana and Cornejo-Castillo, Francisco M and Costea, Paul I and Cruaud, Corinne and D'Ovidio, Francesco and Engelen, Stefan and Ferrera, Isabel and Gasol, Josep M and Guidi, Lionel and Hildebrand, Falk and Kokoszka, Florian and Lepoivre, Cyrille and Lima-Mendez, Gipsi and Poulain, Julie and Poulos, Bonnie T and Royo-Llonch, Marta and Sarmento, Hugo and Vieira-Silva, Sara and Dimier, Céline and Picheral, Marc and Searson, Sarah and Kandels-Lewis, Stefanie and Boss, Emmanuel and Follows, Michael and Karp-Boss, Lee and Krzic, Uros and Reynaud, Emmanuel G and Sardet, Christian and Sieracki, Mike and Velayoudon, Didier and Bowler, Chris and De Vargas, Colomban and Gorsky, Gabriel and Grimsley, Nigel and Hingamp, Pascal and Iudicone, Daniele and Jaillon, Olivier and Not, Fabrice and Ogata, Hiroyuki and Pesant, Stephane and Speich, Sabrina and Stemmann, Lars and Sullivan, Matthew B and Weissenbach, Jean and Wincker, Patrick and Karsenti, Eric and Raes, Jeroen and Acinas, Silvia G and Bork, Peer and Tara Oceans Coordinators and Tara Oceans coordinators
Science, ISSN 0036-8075, 05/2015, Volume 348, Issue 6237, pp. 1261359 - 1261359
Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their... 
BACTERIAL DIVERSITY | MULTIDISCIPLINARY SCIENCES | GENES | MARINE-BACTERIA | METAGENOMES | PATTERNS | SAMPLING EXPEDITION | COMMUNITIES | RIBOSOMAL-RNA | SEA | TOOL | Microbiology | Oceans | Ecosystems | Geography | Microorganisms | Communities | Genes | Viruses | Globes | Stratification | Physics | Geophysics
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4. Full Text Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice
by Knief, Claudia and Delmotte, Nathanaël and Chaffron, Samuel and Stark, Manuel and Innerebner, Gerd and Wassmann, Reiner and Von Mering, Christian and Vorholt, Julia A
ISME Journal, ISSN 1751-7362, 07/2012, Volume 6, Issue 7, pp. 1378 - 1390
The above- and below-ground parts of rice plants create specific habitats for various microorganisms. In this study, we characterized the phyllosphere and... 
Oryza sativa | microbial community | phyllosphere | rice | metaproteogenomics | rhizosphere | PLANTS ORYZA-SATIVA | METHANE-OXIDIZING BACTERIA | METHYLOBACTERIUM-EXTORQUENS AM1 | METHANOTROPHIC BACTERIA | MICROBIOLOGY | SP NOV | NITROGEN-FIXATION | FIELD SOIL | ENDOPHYTIC BACTERIA | ROOTS | ECOLOGY | DIVERSITY | Carbon - metabolism | Bacteria - metabolism | Oryza - metabolism | Methylobacterium - classification | Archaea - isolation & purification | Proteome - analysis | Archaea - classification | Bacteria - genetics | Methanol - metabolism | Rhizosphere | Archaea - metabolism | Bacteria - isolation & purification | Oryza - microbiology | Bacteria - classification | Archaea - genetics | Metagenome | Methylobacterium - metabolism | reductase | Microorganisms | Methanogenesis | Phyllosphere | NifH gene | Pyruvic acid | Habitat | Stress | Original
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5. Full Text Patterns and ecological drivers of ocean viral communities
by Brum, Jennifer R and Cesar Ignacio-Espinoza, J and Roux, Simon and Doulcier, Guilhem and Acinas, Silvia G and Alberti, Adriana and Chaffron, Samuel and Cruaud, Corinne and De Vargas, Colomban and Gasol, Josep M and Gorsky, Gabriel and Gregory, Ann C and Guidi, Lionel and Hingamp, Pascal and Iudicone, Daniele and Not, Fabrice and Ogata, Hiroyuki and Pesant, Stéphane and Poulos, Bonnie T and Schwenck, Sarah M and Speich, Sabrina and Dimier, Celine and Kandels-Lewis, Stefanie and Picheral, Marc and Searson, Sarah and Bork, Peer and Bowler, Chris and Sunagawa, Shinichi and Wincker, Patrick and Karsenti, Eric and Sullivan, Matthew B and Boss, Emmanuel and Follows, Michael and Grimsley, Nigel and Jaillon, Olivier and Karp-Boss, Lee and Krzic, Uros and Raes, Jeroen and Reynaud, Emmanuel G and Sardet, Christian and Sieracki, Mike and Stemmann, Lars and Velayoudon, Didier and Weissenbach, Jean and Tara Oceans Coordinators
Science, ISSN 0036-8075, 05/2015, Volume 348, Issue 6237, pp. 1261498 - 1261498
Viruses influence ecosystems by modulating microbial population size, diversity, metabolic outputs, and gene flow. Here, we use quantitative double-stranded... 
PACIFIC-OCEAN | METAGENOMICS | EPIFLUORESCENCE | DNA | MULTIDISCIPLINARY SCIENCES | FLOW-CYTOMETRIC DETECTION | COUNTING VIRUSES | SEQUENCE | MARINE VIRUSES | ENUMERATION | BACTERIAL | Proteins | Viruses | Oceans | Ecosystems | Deoxyribonucleic acid--DNA | Communities | Genes | Data sets | Clusters | Expeditions | Life Sciences | Environmental Sciences
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6. Full Text Population-level analysis of gut microbiome variation
by Falony, Gwen and Joossens, Marie and Vieira-Silva, Sara and Wang, Jun and Darzi, Youssef and Faust, Karoline and Kurilshchikov, Aleksan and Bonder, Marc Jan and Valles-Colomer, Mireia and Vandeputte, Doris and Tito, Raul Y and Chaffron, Samuel and Rymenans, Leen and Verspecht, Chlo and De Sutter, Lise and Lima-Mendez, Gipsi and D'hoe, Kevin and Jonckheere, Karl and Homola, Daniel and Garcia, Roberto and Tigchelaar, Ettje F and Eeckhaudt, Linda and Fu, Jingyuan and Henckaerts, Liesbet and Zhernakova, Alexana and Wijmenga, Cisca and Raes, Jeroen
Science, ISSN 0036-8075, 04/2016, Volume 352, Issue 6285, pp. 560 - 564
Fecal microbiome variation in the average, healthy population has remained under-investigated. Here, we analyzed two independent, extensively phenotyped... 
Feces - microbiology | Bacteria - isolation & purification | Drug Interactions | Belgium | Humans | Gastrointestinal Microbiome | Bacteria - classification | Bacteria - genetics | Cohort Studies | Microbiota (Symbiotic organisms) | Analysis | Genetic aspects | Observations | Genetic variation | Microbial colonies | Studies | Biomarkers | Microbiology | Life Sciences | Bioinformatics | Biochemistry, Molecular Biology | Genomics | Computer Science
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7. Full Text Plankton networks driving carbon export in the oligotrophic ocean
by Guidi, Lionel and Chaffron, Samuel and Bittner, Lucie and Eveillard, Damien and Larhlimi, Abdelhalim and Roux, Simon and Darzi, Youssef and Audic, Stephane and Berline, Léo and Brum, Jennifer R and Coelho, Luis Pedro and Espinoza, Julio Cesar Ignacio and Malviya, Shruti and Sunagawa, Shinichi and Dimier, Céline and Kandels-Lewis, Stefanie and Picheral, Marc and Poulain, Julie and Searson, Sarah and Stemmann, Lars and Not, Fabrice and Hingamp, Pascal and Speich, Sabrina and Follows, Mick and Karp-Boss, Lee and Boss, Emmanuel and Ogata, Hiroyuki and Pesant, Stephane and Weissenbach, Jean and Wincker, Patrick and Acinas, Silvia G and Bork, Peer and De Vargas, Colomban and Iudicone, Daniele and Sullivan, Matthew B and Raes, Jeroen and Karsenti, Eric and Bowler, Chris and Gorsky, Gabriel and Tara Oceans Consortium Coordinator and Tara Oceans coordinators and Tara Oceans Consortium Coordinators
Nature, ISSN 0028-0836, 04/2016, Volume 532, Issue 7600, pp. 465 - 470
The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally... 
COMMUNITY STRUCTURE | TARA OCEANS | PRINCIPAL COMPONENT | MULTIDISCIPLINARY SCIENCES | DEEP-SEA | ECOLOGY | ZOOPLANKTON | VARIABLE SELECTION | SIZE DISTRIBUTION | PHYTOPLANKTON | PARTICULATE ORGANIC-CARBON | Geography | Plankton - isolation & purification | Seawater - chemistry | Synechococcus - isolation & purification | Dinoflagellida - genetics | Synechococcus - genetics | Ecosystem | Dinoflagellida - isolation & purification | Dinoflagellida - metabolism | Genes, Viral | Plankton - genetics | Seawater - parasitology | Aquatic Organisms - metabolism | Aquatic Organisms - isolation & purification | Carbon - metabolism | Genes, Bacterial | Aquatic Organisms - genetics | Oceans and Seas | Seawater - microbiology | Chlorophyll - metabolism | Synechococcus - virology | Plankton - metabolism | Expeditions | Photosynthesis | Synechococcus - metabolism | Environmental aspects | Ocean | Marine plankton | Carbon cycle (Biogeochemistry) | Studies | Biogeochemistry | Plankton | Oceans | Ecosystems | Prokaryotes | Sediments | Carbon | Earth Sciences | Sciences of the Universe | Oceanography
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8. Full Text Determinants of community structure in the global plankton interactome
by Lima-Mendez, Gipsi and Faust, Karoline and Henry, Nicolas and Decelle, Johan and Colin, Sébastien and Carcillo, Fabrizio and Chaffron, Samuel and Ignacio-Espinosa, J. Cesar and Roux, Simon and Vincent, Flora and Bittner, Lucie and Darzi, Youssef and Wang, Jun and Audic, Stéphane and Berline, Léo and Bontempi, Gianluca and Cabello, Ana M and Coppola, Laurent and Cornejo-Castillo, Francisco M and D'Ovidio, Francesco and De Meester, Luc and Ferrera, Isabel and Garet-Delmas, Marie-José and Guidi, Lionel and Lara, Elena and Pesant, Stéphane and Royo-Llonch, Marta and Salazar, Guillem and Sánchez, Pablo and Sebastian, Marta and Souffreau, Caroline and Dimier, Céline and Picheral, Marc and Searson, Sarah and Kandels-Lewis, Stefanie and Gorsky, Gabriel and Not, Fabrice and Ogata, Hiroyuki and Speich, Sabrina and Stemmann, Lars and Weissenbach, Jean and Wincker, Patrick and Acinas, Silvia G and Sunagawa, Shinichi and Bork, Peer and Sullivan, Matthew B and Karsenti, Eric and Bowler, Chris and De Vargas, Colomban and Raes, Jeroen and Boss, Emmanuel and Follows, Michael and Grimsley, Nigel and Hingamp, Pascal and Iudicone, Daniele and Jaillon, Olivier and Karp-Boss, Lee and Krzic, Uros and Reynaud, Emmanuel G and Sardet, Christian and Sieracki, Mike and Velayoudon, Didier and Tara Oceans Coordinators and Tara Oceans coordinators
Science, ISSN 0036-8075, 05/2015, Volume 348, Issue 6237, pp. 1262073 - 1262073
Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using... 
BACTERIA | RIBOSOMAL-RNA SEQUENCES | TOP-DOWN | MULTIDISCIPLINARY SCIENCES | SPATIAL COMPONENT | NETWORKS | DIVERSITY | MARINE | PROTISTS | MORPHOLOGY | ECOLOGICAL VARIATION | Plankton | Oceans | Microscopy | Networks | Ocean models | Communities | Viruses | Mathematical models | Physics | Geophysics
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9. Full Text Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota
by Stecher, Bärbel and Robbiani, Riccardo and Walker, Alan W and Westendorf, Astrid M and Barthel, Manja and Kremer, Marcus and Chaffron, Samuel and Macpherson, Andrew J and Buer, Jan and Parkhill, Julian and Dougan, Gordon and Von Mering, Christian and Hardt, Wolf-Dietrich
PLoS Biology, ISSN 1544-9173, 10/2007, Volume 5, Issue 10, pp. 2177 - 2189
Most mucosal surfaces of the mammalian body are colonized by microbial communities ("microbiota''). A high density of commensal microbiota inhabits the... 
OLIGONUCLEOTIDE PROBES | PATHOGENICITY ISLAND-1 | CROHNS-DISEASE | BIOCHEMISTRY & MOLECULAR BIOLOGY | ULCERATIVE-COLITIS | MOUSE MODEL | GUT | BIOLOGY | STREPTOMYCIN-PRETREATED MICE | INFECTIOUS ENTEROCOLITIS | ANTIMICROBIAL PEPTIDES | BOWEL-DISEASE | Life Sciences | Bioinformatics | Biochemistry, Molecular Biology | Genomics | Computer Science | Mus (Mouse) | Infectious Diseases | Immunology | Microbiology | Gastroenterology and Hepatology | Inflammatory bowel disease | Competition | Salmonella | Bacteria | Infections | Immune system
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10. Full Text Like will to like: Abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria
by Stecher, Bärbel and Chaffron, Samuel and Käppeli, Rina and Hapfelmeier, Siegfried and Freedrich, Susanne and Weber, Thomas C and Kirundi, Jorum and Suar, Mrutyunjay and McCoy, Kathy D and Von Mering, Christian and Macpherson, Andrew J and Hardt, Wolf-Dietrich
PLoS Pathogens, ISSN 1553-7366, 01/2010, Volume 6, Issue 1, p. e1000711
The intestinal ecosystem is formed by a complex, yet highly characteristic microbial community. The parameters defining whether this community permits invasion... 
ALTERED SCHAEDLER FLORA | ESCHERICHIA-COLI | GASTROINTESTINAL-TRACT | MICROBIOLOGY | CLOSTRIDIUM-DIFFICILE | VIROLOGY | PROBIOTIC LACTOBACILLUS | MICROBIAL DIVERSITY | SEROVAR TYPHIMURIUM COLITIS