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Staff at EMBL

Shinichi Sunagawa

Staff Scientist
Bork Group

EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

E-mail: send a mail

Publications

A fair comparison. Costea, P.I., Zeller, G., Sunagawa, S. & Bork, P. Nat Methods. 2014 Mar 28;11(4):359. doi: 10.1038/nmeth.2897. Europe PMC

Classification and quantification of bacteriophage taxa in human gut metagenomes. Waller, A.S., Yamada, T., Kristensen, D.M., Kultima, J.R., Sunagawa, S., Koonin, E.V. & Bork, P. ISME J. 2014 Mar 13. doi: 10.1038/ismej.2014.30. Europe PMC

Metagenomic insights into the human gut resistome and the forces that shape it. Forslund, K., Sunagawa, S., Coelho, L.P. & Bork, P. Bioessays. 2014 Jan 29. doi: 10.1002/bies.201300143. Europe PMC

Metagenomic species profiling using universal phylogenetic marker genes. Sunagawa, S., Mende, D.R., Zeller, G., Izquierdo-Carrasco, F., Berger, S.A., Kultima, J.R., Coelho, L.P., Arumugam, M., Tap, J., Nielsen, H.B., Rasmussen, S., Brunak, S., Pedersen, O., Guarner, F., de Vos, W.M., Wang, J., Li, J., Dore, J., Ehrlich, S.D., Stamatakis, A. & Bork, P. Nat Methods. 2013 Dec;10(12):1196-9. doi: 10.1038/nmeth.2693. Epub 2013 Oct 20. Europe PMC

Accurate and universal delineation of prokaryotic species. Mende, D.R., Sunagawa, S., Zeller, G. & Bork, P. Nat Methods. 2013 Sep;10(9):881-4. doi: 10.1038/nmeth.2575. Epub 2013 Jul 28. Europe PMC

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. Hingamp, P., Grimsley, N., Acinas, S.G., Clerissi, C., Subirana, L., Poulain, J., Ferrera, I., Sarmento, H., Villar, E., Lima-Mendez, G., Faust, K., Sunagawa, S., Claverie, J.M., Moreau, H., Desdevises, Y., Bork, P., Raes, J., de Vargas, C., Karsenti, E., Kandels-Lewis, S., Jaillon, O., Not, F., Pesant, S., Wincker, P. & Ogata, H. ISME J. 2013 Sep;7(9):1678-95. doi: 10.1038/ismej.2013.59. Epub 2013 Apr 11. Europe PMC

Richness of human gut microbiome correlates with metabolic markers. Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J.M., Kennedy, S., Leonard, P., Li, J., Burgdorf, K., Grarup, N., Jorgensen, T., Brandslund, I., Nielsen, H.B., Juncker, A.S., Bertalan, M., Levenez, F., Pons, N., Rasmussen, S., Sunagawa, S., Tap, J., Tims, S., Zoetendal, E.G., Brunak, S., Clement, K., Dore, J., Kleerebezem, M., Kristiansen, K., Renault, P., Sicheritz-Ponten, T., de Vos, W.M., Zucker, J.D., Raes, J., Hansen, T., Bork, P., Wang, J., Ehrlich, S.D., Pedersen, O., Guedon, E., Delorme, C., Layec, S., Khaci, G., van de Guchte, M., Vandemeulebrouck, G., Jamet, A., Dervyn, R., Sanchez, N., Maguin, E., Haimet, F., Winogradski, Y., Cultrone, A., Leclerc, M., Juste, C., Blottiere, H., Pelletier, E., LePaslier, D., Artiguenave, F., Bruls, T., Weissenbach, J., Turner, K., Parkhill, J., Antolin, M., Manichanh, C., Casellas, F., Boruel, N., Varela, E., Torrejon, A., Guarner, F., Denariaz, G., Derrien, M., van Hylckama Vlieg, J.E., Veiga, P., Oozeer, R., Knol, J., Rescigno, M., Brechot, C., M'Rini, C., Merieux, A. & Yamada, T. Nature. 2013 Aug 29;500(7464):541-6. doi: 10.1038/nature12506. Europe PMC

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, F.M., 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, S.G. Environ Microbiol. 2013 Aug 18. doi: 10.1111/1462-2920.12250. Europe PMC

Country-specific antibiotic use practices impact the human gut resistome. Forslund, K., Sunagawa, S., Kultima, J.R., Mende, D.R., Arumugam, M., Typas, A. & Bork, P. Genome Res. 2013 Jul;23(7):1163-9. doi: 10.1101/gr.155465.113. Epub 2013 Apr 8. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

Transcriptomic responses to darkness stress point to common coral bleaching mechanisms. DeSalvo, M.K., Estrada, E., Sunagawa, S. & Medina M. Coral Reefs 2012 31(1) 215-228

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

Threatened corals provide underexplored microbial habitats. Sunagawa, S., Woodley, C.M. & Medina, M. PLoS One. 2010 Mar 5;5(3):e9554. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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. Europe PMC

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.