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Microbial interactions: from networks to models.
Faust K, Raes J. Faust K, et al. Among authors: raes j. Nat Rev Microbiol. 2012 Jul 16;10(8):538-50. doi: 10.1038/nrmicro2832. Nat Rev Microbiol. 2012. PMID: 22796884 Review.
Enterotypes of the human gut microbiome.
Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J; MetaHIT Consortium, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P. Arumugam M, et al. Among authors: raes j. Nature. 2011 May 12;473(7346):174-80. doi: 10.1038/nature09944. Epub 2011 Apr 20. Nature. 2011. PMID: 21508958 Free PMC article.
Microbial co-occurrence relationships in the human microbiome.
Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, Huttenhower C. Faust K, et al. Among authors: raes j. PLoS Comput Biol. 2012;8(7):e1002606. doi: 10.1371/journal.pcbi.1002606. Epub 2012 Jul 12. PLoS Comput Biol. 2012. PMID: 22807668 Free PMC article.
Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities.
Logares R, Sunagawa S, Salazar G, Cornejo-Castillo FM, Ferrera I, Sarmento H, Hingamp P, Ogata H, de Vargas C, Lima-Mendez G, Raes J, Poulain J, Jaillon O, Wincker P, Kandels-Lewis S, Karsenti E, Bork P, Acinas SG. Logares R, et al. Among authors: raes j. Environ Microbiol. 2014 Sep;16(9):2659-71. doi: 10.1111/1462-2920.12250. Epub 2013 Sep 18. Environ Microbiol. 2014. PMID: 24102695
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T; MetaHIT Consortium, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD; MetaHIT Consortium. Nielsen HB, et al. Among authors: raes j. Nat Biotechnol. 2014 Aug;32(8):822-8. doi: 10.1038/nbt.2939. Epub 2014 Jul 6. Nat Biotechnol. 2014. PMID: 24997787
A20 controls intestinal homeostasis through cell-specific activities.
Vereecke L, Vieira-Silva S, Billiet T, van Es JH, Mc Guire C, Slowicka K, Sze M, van den Born M, De Hertogh G, Clevers H, Raes J, Rutgeerts P, Vermeire S, Beyaert R, van Loo G. Vereecke L, et al. Among authors: raes j. Nat Commun. 2014 Sep 30;5:5103. doi: 10.1038/ncomms6103. Nat Commun. 2014. PMID: 25267258
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