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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

Total: 34 publication(s)

2014

Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, Wang J, Xu X, Xiao L, Liang S, Zhang D, Zhang Z, Chen W, Zhao H, Al-Aama JY, Edris S, Yang H, Wang J, Hansen T, Nielsen HB, Brunak S, Kristiansen K, Guarner F, Pedersen O, Doré J, Ehrlich SD, Bork P, Wang J. (2014)
An integrated catalog of reference genes in the human gut microbiome
Nat. Biotechnol. doi:10.1038/nbt.2942
Europe PMC | doi

Waller AS, Yamada T, Kristensen DM, Kultima JR, Sunagawa S, Koonin EV, Bork P. (2014)
Classification and quantification of bacteriophage taxa in human gut metagenomes
ISME J 8(7):1551-1552. doi:10.1038/ismej.2014.66
Europe PMC | doi

Waller AS, Yamada T, Kristensen DM, Kultima JR, Sunagawa S, Koonin EV, Bork P. (2014)
Classification and quantification of bacteriophage taxa in human gut metagenomes
ISME J 8(7):1391-1402. doi:10.1038/ismej.2014.30
Europe PMC | doi

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, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD. (2014)
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
Nat. Biotechnol. doi:10.1038/nbt.2939
Europe PMC | doi

Closek CJ, Sunagawa S, DeSalvo MK, Piceno YM, DeSantis TZ, Brodie EL, Weber MX, Voolstra CR, Andersen GL, Medina M. (2014)
Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata
ISME J doi:10.1038/ismej.2014.85
Europe PMC | doi

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

Forslund K, Sunagawa S, Coelho LP, Bork P. (2014)
Metagenomic insights into the human gut resistome and the forces that shape it
Bioessays doi:10.1002/bies.201300143
Europe PMC | 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

Hingamp P, Grimsley N, Acinas SG, Clerissi C, Subirana L, Poulain J, Ferrera I, Sarmento H, Villar E, Lima-Mendez G, Faust K, Sunagawa S, Claverie JM, 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. (2013)
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes
ISME J 7(9):1678-1695. doi:10.1038/ismej.2013.59
Europe PMC | doi

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. (2013)
Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities
Environ. Microbiol. doi:10.1111/1462-2920.12250
Europe PMC | doi

Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T, MetaHIT consortium, Bork P, Wang J, Ehrlich SD, Pedersen O. (2013)
Richness of human gut microbiome correlates with metabolic markers
Nature 500(7464):541-546. doi:10.1038/nature12506
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

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

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

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

Bayer T, Aranda M, Sunagawa S, Yum LK, Desalvo MK, Lindquist E, Coffroth MA, Voolstra CR, Medina M. (2012)
Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals
PLoS ONE 7(4):e35269. doi:10.1371/journal.pone.0035269
Europe PMC | doi

DeSalvo MK, Estrada A, Sunagawa S, Medina M. (2012)
Transcriptomic responses to darkness stress point to common coral bleaching mechanisms
Coral Reefs 31(1):215-228. doi:10.1007/s00338-011-0833-4
Europe PMC | doi


2011

Karsenti E, Acinas SG, Bork P, Bowler C, De Vargas C, Raes J, Sullivan M, Arendt D, Benzoni F, Claverie JM, Follows M, Gorsky G, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Krzic U, Not F, Ogata H, Pesant S, Reynaud EG, Sardet C, Sieracki ME, Speich S, Velayoudon D, Weissenbach J, Wincker P, Tara Oceans Consortium. (2011)
A holistic approach to marine eco-systems biology
PLoS Biol. 9(10):e1001177. doi:10.1371/journal.pbio.1001177
Europe PMC | doi

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

Voolstra CR, Sunagawa S, Matz MV, Bayer T, Aranda M, Buschiazzo E, Desalvo MK, Lindquist E, Szmant AM, Coffroth MA, Medina M. (2011)
Rapid evolution of coral proteins responsible for interaction with the environment
PLoS ONE 6(5):e20392. doi:10.1371/journal.pone.0020392
Europe PMC | doi


2010

DeSalvo MK, Sunagawa S, Fisher PL, Voolstra CR, Iglesias-Prieto R, Medina M. (2010)
Coral host transcriptomic states are correlated with Symbiodinium genotypes
Mol. Ecol. 19(6):1174-1186. doi:10.1111/j.1365-294x.2010.04534.x
Europe PMC | doi

Tagmount A, Wang M, Lindquist E, Tanaka Y, Teranishi KS, Sunagawa S, Wong M, Stillman JH. (2010)
The porcelain crab transcriptome and PCAD, the porcelain crab microarray and sequence database
PLoS ONE 5(2):e9327. doi:10.1371/journal.pone.0009327
Europe PMC | doi

Sunagawa S, Woodley CM, Medina M. (2010)
Threatened corals provide underexplored microbial habitats
PLoS ONE 5(3):e9554. doi:10.1371/journal.pone.0009554
Europe PMC | doi

DeSalvo MK, Sunagawa S, Voolstra CR, Medina M. (2010)
Transcriptomic responses to heat stress and bleaching in the elkhorn coral Acropora palmata
Mar. Ecol. Prog. Ser. 402:97-113. doi:10.3354/meps08372
Europe PMC | doi


2009

Voolstra CR, Sunagawa S, Schwarz JA, Coffroth MA, Yellowlees D, Leggat W, Medina M. (2009)
Evolutionary analysis of orthologous cDNA sequences from cultured and symbiotic dinoflagellate symbionts of reef-building corals (Dinophyceae: Symbiodinium)
Comp. Biochem. Physiol. Part D Genomics Proteomics 4(2):67-74. doi:10.1016/j.cbd.2008.11.001
Europe PMC | doi

Sunagawa S, DeSantis TZ, Piceno YM, Brodie EL, DeSalvo MK, Voolstra CR, Weil E, Andersen GL, Medina M. (2009)
Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata
ISME J 3(5):512-521. doi:10.1038/ismej.2008.131
Europe PMC | doi

Voolstra CR, Schwarz JA, Schnetzer J, Sunagawa S, Desalvo MK, Szmant AM, Coffroth MA, Medina M. (2009)
The host transcriptome remains unaltered during the establishment of coral-algal symbioses
Mol. Ecol. 18(9):1823-1833. doi:10.1111/j.1365-294x.2009.04167.x
Europe PMC | doi

Reyes-Bermudez A, Desalvo MK, Voolstra CR, Sunagawa S, Szmant AM, Iglesias-Prieto R, Medina M. (2009)
Gene expression microarray analysis encompassing metamorphosis and the onset of calcification in the scleractinian coral Montastraea faveolata
Mar Genomics 2(3-4):149-159. doi:10.1016/j.margen.2009.07.002
Europe PMC | doi

Sunagawa S, Wilson EC, Thaler M, Smith ML, Caruso C, Pringle JR, Weis VM, Medina M, Schwarz JA. (2009)
Generation and analysis of transcriptomic resources for a model system on the rise: the sea anemone Aiptasia pallida and its dinoflagellate endosymbiont
BMC Genomics 10:258. doi:10.1186/1471-2164-10-258
Europe PMC | doi

Sunagawa S, DeSalvo MK, Voolstra CR, Reyes-Bermudez A, Medina M. (2009)
Identification and gene expression analysis of a taxonomically restricted cysteine-rich protein family in reef-building corals
PLoS ONE 4(3):e4865. doi:10.1371/journal.pone.0004865
Europe PMC | doi


2008

DeSalvo MK, Voolstra CR, Sunagawa S, Schwarz JA, Stillman JH, Coffroth MA, Szmant AM, Medina M. (2008)
Differential gene expression during thermal stress and bleaching in the Caribbean coral Montastraea faveolata
Mol. Ecol. 17(17):3952-3971. doi:10.1111/j.1365-294x.2008.03879.x
Europe PMC | doi

Sunagawa S, Choi J, Forman HJ, Medina M. (2008)
Hyperthermic stress-induced increase in the expression of glutamate-cysteine ligase and glutathione levels in the symbiotic sea anemone Aiptasia pallida
Comp. Biochem. Physiol. B, Biochem. Mol. Biol. 151(1):133-138. doi:10.1016/j.cbpb.2008.06.007
Europe PMC | doi

Sunagawa S, Cortes J, Jimenez C, Lara R. (2008)
Variation in cell densities and pigment concentrations of symbiotic dinoflagellates in the coral Pavona clavus in the eastern Pacific (Costa Rica)
Cienc Mar 34(2):113-123.
Europe PMC