Staff at EMBL
Shinichi Sunagawa
Senior Technical Officer
Bork Group
EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
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Publications
Country-specific antibiotic use practices impact the human gut resistome. Forslund, K., Sunagawa, S., Roat Kultima, J., Mende, D., Arumugam, M., Typas, A. & Bork, P. Genome Res. 2013 Apr 8. PubMed
Genomic variation landscape of the human gut microbiome. Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D.R., Kultima, J.R., Martin, J., Kota, K., Sunyaev, S.R., Weinstock, G.M. & Bork, P. Nature. 2013 Jan 3;493(7430):45-50. doi: 10.1038/nature11711. Epub 2012 Dec 5. PubMed
MOCAT: a metagenomics assembly and gene prediction toolkit. Kultima, J.R., Sunagawa, S., Li, J., Chen, W., Chen, H., Mende, D.R., Arumugam, M., Pan, Q., Liu, B., Qin, J., Wang, J. & Bork, P. PLoS One. 2012;7(10):e47656. doi: 10.1371/journal.pone.0047656. Epub 2012 Oct 17. PubMed
Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals. Bayer, T., Aranda, M., Sunagawa, S., Yum, L.K., Desalvo, M.K., Lindquist, E., Coffroth, M.A., Voolstra, C.R. & Medina, M. PLoS One. 2012;7(4):e35269. doi: 10.1371/journal.pone.0035269. Epub 2012 Apr 18. PubMed
Assessment of metagenomic assembly using simulated next generation sequencing data. Mende, D.R., Waller, A.S., Sunagawa, S., Jarvelin, A.I., Chan, M.M., Arumugam, M., Raes, J. & Bork, P. PLoS One. 2012;7(2):e31386. Epub 2012 Feb 23. PubMed
A holistic approach to marine eco-systems biology. Karsenti, E., Acinas, S.G., Bork, P., Bowler, C., De Vargas, C., Raes, J., Sullivan, M., Arendt, D., Benzoni, F., Claverie, J.M., Follows, M., Gorsky, G., Hingamp, P., Iudicone, D., Jaillon, O., Kandels-Lewis, S., Krzic, U., Not, F., Ogata, H., Pesant, S., Reynaud, E.G., Sardet, C., Sieracki, M.E., Speich, S., Velayoudon, D., Weissenbach, J. & Wincker, P. PLoS Biol. 2011 Oct;9(10):e1001177. doi: 10.1371/journal.pbio.1001177. Epub 2011Oct 18. PubMed
Rapid evolution of coral proteins responsible for interaction with the environment. Voolstra, C.R., Sunagawa, S., Matz, M.V., Bayer, T., Aranda, M., Buschiazzo, E., Desalvo, M.K., Lindquist, E., Szmant, A.M., Coffroth, M.A. & Medina, M. PLoS One. 2011;6(5):e20392. Epub 2011 May 25. PubMed
Enterotypes of the human gut microbiome. Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D.R., Fernandes, G.R., Tap, J., Bruls, T., Batto, J.M., 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, H.B., Nielsen, T., Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E.G., Wang, J., Guarner, F., Pedersen, O., de Vos, W.M., Brunak, S., Dore, J., Antolin, M., Artiguenave, F., Blottiere, H.M., Almeida, M., Brechot, C., Cara, C., Chervaux, C., Cultrone, A., Delorme, C., Denariaz, G., Dervyn, R., Foerstner, K.U., 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., Merieux, 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, S.D. & Bork, P. Nature. 2011 May 12;473(7346):174-80. Epub 2011 Apr 20. PubMed
Transcriptomic responses to darkness stress point to common coral bleaching mechanisms. DeSalvo MK, Estrada E, Sunagawa S, Medina M Coral Reefs: , DOI: 10.1007/s00338-011-0833-4, 2011.
Coral host transcriptomic states are correlated with Symbiodinium genotypes. DeSalvo, M.K., Sunagawa, S., Fisher, P.L., Voolstra, C.R., Iglesias-Prieto, R. & Medina, M. Mol Ecol. 2010 Mar;19(6):1174-86. Epub 2010 Feb 8. PubMed
The porcelain crab transcriptome and PCAD, the porcelain crab microarray and sequence database. Tagmount, A., Wang, M., Lindquist, E., Tanaka, Y., Teranishi, K.S., Sunagawa, S., Wong, M. & Stillman, J.H. PLoS One. 2010 Feb 19;5(2):e9327. PubMed
Threatened corals provide underexplored microbial habitats. Sunagawa, S., Woodley, C.M. & Medina, M. PLoS One. 2010 Mar 5;5(3):e9554. PubMed
Transcriptomic responses to heat stress and bleaching in the Elkhorn coral Acropora palmata. DeSalvo MK, Sunagawa S, Voolstra CR, Medina M Mar Ecol Prog Ser: 402, 97-113, 2010.
Gene expression microarray analysis encompassing metamorphosis and the onset of calcification in the scleractinian coral Montastraea faveolata. Reyes-Bermudez, A., Desalvo, M.K., Voolstra, C.R., Sunagawa, S., Szmant, A.M., Iglesias-Prieto, R. & Medina, M. Mar Genomics. 2009 Sep-Dec;2(3-4):149-59. doi: 10.1016/j.margen.2009.07.002. Epub2009 Aug 31. PubMed
Evolutionary analysis of orthologous cDNA sequences from cultured and symbiotic dinoflagellate symbionts of reef-building corals (Dinophyceae: Symbiodinium). Voolstra, C.R., Sunagawa, S., Schwarz, J.A., Coffroth, M.A., Yellowlees, D., Leggat, W. & Medina, M. Comp Biochem Physiol Part D Genomics Proteomics. 2009 Jun;4(2):67-74. Epub2008 Dec 6. PubMed
The host transcriptome remains unaltered during the establishment of coral-algal symbioses. Voolstra, C.R., Schwarz, J.A., Schnetzer, J., Sunagawa, S., Desalvo, M.K., Szmant, A.M., Coffroth, M.A. & Medina, M. Mol Ecol. 2009 May;18(9):1823-33. Epub 2009 Mar 20. PubMed
Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata. Sunagawa, S., DeSantis, T.Z., Piceno, Y.M., Brodie, E.L., DeSalvo, M.K., Voolstra, C.R., Weil, E., Andersen, G.L. & Medina, M. ISME J. 2009 May;3(5):512-21. Epub 2009 Jan 8. PubMed
Generation and analysis of transcriptomic resources for a model system on the rise: the sea anemone Aiptasia pallida and its dinoflagellate endosymbiont. Sunagawa, S., Wilson, E.C., Thaler, M., Smith, M.L., Caruso, C., Pringle, J.R., Weis, V.M., Medina, M. & Schwarz, J.A. BMC Genomics. 2009 Jun 5;10:258. PubMed
Identification and gene expression analysis of a taxonomically restricted cysteine-rich protein family in reef-building corals. Sunagawa, S., DeSalvo, M.K., Voolstra, C.R., Reyes-Bermudez, A. & Medina, M. PLoS One. 2009;4(3):e4865. Epub 2009 Mar 13. PubMed
Hyperthermic stress-induced increase in the expression of glutamate-cysteine ligase and glutathione levels in the symbiotic sea anemone Aiptasia pallida. Sunagawa, S., Choi, J., Forman, H.J. & Medina, M. Comp Biochem Physiol B Biochem Mol Biol. 2008 Sep;151(1):133-8. Epub 2008Jun 17. PubMed
Differential gene expression during thermal stress and bleaching in the Caribbean coral Montastraea faveolata. DeSalvo, M.K., Voolstra, C.R., Sunagawa, S., Schwarz, J.A., Stillman, J.H., Coffroth, M.A., Szmant, A.M. & Medina, M. Mol Ecol. 2008 Sep;17(17):3952-71. Epub 2008 Jul 24. PubMed
Variation in cell densities and pigment concentrations of symbiotic dinoflagellates in the coral Pavona clavus in the eastern Pacific (Costa Rica). Sunagawa S, Cortés J, Jiménez C, Lara R Cienc Mar: 34(2), 113-123, 2008.