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Staff at EMBL

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Publications

Total: 12 publication(s)

2014

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 JJ, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Dore J, Weissenbach J, Ehrlich SD, Bork P. (2014)
Enterotypes of the human gut microbiome (vol 473, pg 174, 2011)
NATURE 506(7489) doi:10.1038/nature13075
doi


2013

Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P. (2013)
Metagenomic species profiling using universal phylogenetic marker genes
Nat. Methods 10(12):1196-1199. doi:10.1038/nmeth.2693
Europe PMC | doi

Mende DR, Sunagawa S, Zeller G, Bork P. (2013)
Accurate and universal delineation of prokaryotic species
Nat. Methods 10(9):881-884. doi:10.1038/nmeth.2575
Europe PMC | doi

Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, Typas A, Bork P. (2013)
Country-specific antibiotic use practices impact the human gut resistome
Genome Res. 23(7):1163-1169. doi:10.1101/gr.155465.113
Europe PMC | doi

van Noort V, Bradatsch B, Arumugam M, Amlacher S, Bange G, Creevey C, Falk S, Mende DR, Sinning I, Hurt E, Bork P. (2013)
Consistent mutational paths predict eukaryotic thermostability
BMC Evol. Biol. 13:7. doi:10.1186/1471-2148-13-7
Europe PMC | doi

Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P. (2013)
Genomic variation landscape of the human gut microbiome
Nature 493(7430):45-50. doi:10.1038/nature11711
Europe PMC | doi


2012

Alonso-Sáez L, Waller AS, Mende DR, Bakker K, Farnelid H, Yager PL, Lovejoy C, Tremblay JÉ, Potvin M, Heinrich F, Estrada M, Riemann L, Bork P, Pedrós-Alió C, Bertilsson S. (2012)
Role for urea in nitrification by polar marine Archaea
Proc. Natl. Acad. Sci. U.S.A. 109(44):17989-17994. doi:10.1073/pnas.1201914109
Europe PMC | doi

Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, Raes J, Bork P. (2012)
Assessment of metagenomic assembly using simulated next generation sequencing data
PLoS ONE 7(2):e31386. doi:10.1371/journal.pone.0031386
Europe PMC | doi

Minguez P, Parca L, Diella F, Mende DR, Kumar R, Helmer-Citterich M, Gavin AC, van Noort V, Bork P. (2012)
Deciphering a global network of functionally associated post-translational modifications
Mol. Syst. Biol. 8:599. doi:10.1038/msb.2012.31
Europe PMC | doi

Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J, Wang J, Bork P. (2012)
MOCAT: a metagenomics assembly and gene prediction toolkit
PLoS ONE 7(10):e47656. doi:10.1371/journal.pone.0047656
Europe PMC | doi


2011

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. (2011)
Enterotypes of the human gut microbiome
Nature 473(7346):174-180. doi:10.1038/nature09944
Europe PMC | doi


2010

Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, MetaHIT Consortium, Bork P, Ehrlich SD, Wang J. (2010)
A human gut microbial gene catalogue established by metagenomic sequencing
Nature 464(7285):59-65. doi:10.1038/nature08821
Europe PMC | doi