Publications (*=equal contribution; #=corresponding author; total citations: 17140; h-factor: 48)
81. Gut microbial beta-glucuronidase and glycerol/diol dehydratase activity contribute to dietary heterocyclic amine biotransformation.
Zhang J, Lacroix C, Wortmann E, Ruscheweyh HJ, Sunagawa S, Sturla SJ, Schwab C
BMC Microbiol: 19(1), 99, 2019.
[PMID: 31096909 - open access - View abstract].
80. Marine DNA Viral Macro- and Microdiversity from Pole to Pole.
Gregory AC*, Zayed AA*, Conceicao-Neto N, Temperton B, Bolduc B, Alberti A, Ardyna M, Arkhipova K, Carmichael M, Cruaud C, Dimier C, Dominguez-Huerta G, Ferland J, Kandels S, Liu Y, Marec C, Pesant S, Picheral M, Pisarev S, Poulain J, Tremblay JE, Vik D; Tara Oceans Coordinators, Babin M, Bowler C, Culley AI, de Vargas C, Dutilh BE, Iudicone D, Karp-Boss L, Roux S, Sunagawa S, Wincker P, Sullivan MB
Cell: 177(5), 1109-1123, 2019.
[PMID: 31031001 - doi - View abstract].
79. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.
Wirbel J*, Pyl PT*, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E9, Habermann N, Nimeus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G
Nat Med: 25(4), 679-689, 2019.
[PMID: 30936547 - doi - View abstract].
78. Microbial abundance, activity, and population genomic profiling with mOTUs2.
Milanese A*, Mende DR*, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves R, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, Bork P, Zeller G#, Sunagawa S#
Nat Commun: 10, 1014, 2019.
[PMID: 30833550 - open access - View abstract].
77. Community-Level Responses to Iron Availability in Open Ocean Planktonic Ecosystems.
Caputi L*, Carradec Q*, Eveillard D*, Kirilovsky A*, Pelletier E*, Karlusich JJP, Vieira FRJ, Villar E, Chaffron S, Malviya S, Scalco E, Acinas SG, Alberti A, Aury JM, Benoiston AS, Bertrand A, Biard T, Bittner L, Boccara M, Brum JR, Brunet C, Busseni G, Carratala A, Claustre H, Coelho LP, Colin S, D'Aniello S, Da Silva C, Del Core M, Dore H, Gasparini S, Kokoszka F, Jamet JL, Lejeusne C, Lepoivre C, Lescot M, Lima-Mendez G, Lombard F, Lukes J, Maillet N, Madoui MA, Martinez E, Mazzocchi MG, Neou MB, Paz-Yepes J, Poulain J, Ramondenc S, Romagnan JB, Roux S, Manta DS, Sanges R, Speich S, Sprovieri M, Sunagawa S, Taillandier V, Tanaka A, Tirichine L, Trottier C, Uitz J, Veluchamy A, Vesela J, Vincent F, Yau S, Kandels-Lewis S, Searson S, Dimier C, Picheral M, Bork P, Boss E, De Vargas C, Follows MJ, Grimsley N, Guidi L, Hingamp P, Karsenti E, Sordino P, Stemmann L, Sullivan MB, Tagliabue A, Zingone A, Garczarek L, d'Ortenzio F, Testor P, Not F, d'Alcala MR, Wincker P, Bowler C, Iudicone D, Gorsky G, Jaillon O, Karp-Boss L, Krzic U, Ogata H, Pesant S, Raes J, Reynaud EG, Sardet C, Sieracki M, Velayoudon D, Weissenbach J and Tara Oceans Coordinators
Global Biogeochem Cycles: 33(3), 391-419, 2019.
[doi - View abstract].
76. Extensive transmission of microbes along the gastrointestinal tract.
Schmidt TSB*, Hayward MR*, Coelho LP, Li SS, Costea PI, Voigt AY, Wirbel J, Maistrenko OM, Alves RJ, Bergsten E, de Beaufort C, Sobhani I, Heintz-Buschart A, Sunagawa S, Zeller G, Wilmes P, Bork P
eLIFE: 8, e42693, 2019.
[PMID: 30747106 - open access - View abstract].
75. Antibiotics-induced monodominance of a novel gut bacterial order.
Hildebrand F, Moitinho-Silva L, Blasche S, Jahn MTT, Gossmann TI, Heuerta Cepas J, Hercog R, Luetge M, Bahram M, Pryszlak A, Alves RJ, Waszak SM, Zhu A, Ye L, Costea PI, Aalvink S, Belzer C, Forslund SK, Sunagawa S, Hentschel U, Merten C, Patil KR, Benes V, Bork P
Gut: , in press, 2019.
[PMID: 30658995 - open access - View abstract].
74. Minimum Information about an Uncultivated Virus Genome (MIUViG).
Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA
Nat Biotechnol: 37, 29-37, 2019.
[PMID: 30556814 - open access - View abstract].
73. Microbiota stability in healthy individuals after single-dose lactulose challenge - a randomized controlled study.
Wotzka SY*, Kreuzer M*, Maier L*, Zünd M*, Schlumberger M, Nguyen B, Fox M, Pohl D, Heinrich H, Rogler G, Biedermann L, Scharl M, Sunagawa S#, Hardt WD#, Misselwitz B#
PLoS ONE: 3(10), e0206214, 2018.
[PMID: 30359438 - open access - View abstract].
72. Structure and function of the global topsoil microbiome.
Bahram M*, Hildebrand F*, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H, Huerta-Cepas J, Medema MH, Maltz MR, Mundra S, Olsson PA, Pent M, Põlme S, Sunagawa S, Ryberg M, Tedersoo L, Bork P
Nature: 560(7717), 233-237, 2018.
[PMID: 30069051 - doi - View abstract].
71. Metagenomic analysis of gut microbial communities from a Central Asian population.
Kushugulova A*, Forslund SK*, Costea PI, Kozhakhmetov S, Khassenbekova Z, Urazova M, Nurgozhin T, Zhumadilov Z, Benberin V, Driessen M, Hercog R, Voigt AY, Benes V, Kandels-Lewis S, Sunagawa S, Letunic I, Bork P
BMJ Open: 8(7), e021682, 2018.
[PMID: 30056386 - open access - View abstract].
70. The Ocean Gene Atlas: exploring the biogeography of plankton genes online.
Villar E, Vannier T, Vernette C, Lescot M, Cuenca M, Alexandre A, Bachelerie P, Rosnet T, Pelletier E, Sunagawa S, Hingamp P
Nucl Acids Res: 46(W1), W289-W295, 2018.
[PMID: 29788376 - doi - View abstract].
69. Natural noncanonical protein splicing yields products with diverse β-amino acid residues.
Morinaka BI, Lakis E, Verest M, Helf MJ, Scalvenzi T, Vagstad AL, Sims J, Sunagawa S, Gugger M, Piel J
Science: 359(6377), 779-782, 2018.
[PMID: 29449488 - doi - View abstract].
68. A global ocean atlas of eukaryotic genes.
Carradec Q*, Pelletier E*, Da Silva C, Alberti A, Seeleuthner Y, Blanc-Mathieu R, Lima-Mendez G, Rocha F, Tirichine L, Labadie K, Kirilovsky A, Bertrand A, Engelen S, Madoui MA, Meheust R, Poulain J, Romac S, Richter DJ, Yoshikawa G, Dimier C, Kandels-Lewis S, Picheral M, Searson S; Tara Oceans Coordinators, Jaillon O, Aury JM, Karsenti E, Sullivan MB, Sunagawa S, Bork P, Not F, Hingamp P, Raes J, Guidi L, Ogata H, de Vargas C, Iudicone D, Bowler C, Wincker P
Nat Commun: 9, 373, 2018.
[PMID: 29371626 - open access - View abstract].
67. Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans.
Seeleuthner Y*, Mondy S*, Lombard V, Carradec Q, Pelletier E, Wessner M, Leconte J, Mangot JF, Poulain J, Labadie K, Logares R, Sunagawa S, de Berardinis V, Salanoubat M, Dimier C, Kandels-Lewis S, Picheral M, Searson S; Tara Oceans Coordinators, Pesant S, Poulton N, Stepanauskas R, Bork P, Bowler C, Hingamp P, Sullivan MB, Iudicone D, Massana R, Aury JM, Henrissat B, Karsenti E, Jaillon O, Sieracki M, de Vargas C, Wincker P
Nat Commun: 9, 310, 2018.
[PMID: 29358710 - open access - View abstract].
66. Enterotypes in the landscape of gut microbial community composition.
Costea PI, Hildebrand F, Manimozhiyan A, Backhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P
Nat Microbiol: 3(1), 8-16, 2018.
[PMID: 29255284 - doi - View abstract].
65. Subspecies in the global human gut microbiome.
Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P
Mol Syst Biol: 13(12), 960, 2017. [ IF: 8.5 ]
[PMID: 29242367 - open access - View abstract].
64. Salt-responsive gut commensal modulates TH17 axis and disease.
Wilck N, Matus MG, Kearney SM, Olesen SW, Forslund K, Bartolomaeus H, Haase S, Mahler A, Balogh A, Marko L, Vvedenskaya O, Kleiner FH, Tsvetkov D, Klug L, Costea PI, Sunagawa S, Maier L, Rakova N, Schatz V, Neubert P, Fratzer C, Krannich A, Gollasch M, Grohme DA, Corte-Real BF, Gerlach RG, Basic M, Typas A, Wu C, Titze JM, Jantsch J, Boschmann M, Dechend R, Kleinewietfeld M, Kempa S, Bork P, Linker RA, Alm EJ, Muller DN
Nature: 551(7682), 585-589, 2017. [ IF: 41.6 ]
[PMID: 29143823 - doi - View abstract].
63. Towards standards for human fecal sample processing in metagenomic studies.
Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P
Nat Biotechnol: 35(11), 1069-1076, 2017. [ IF: 35.7 ]
[PMID: 28967887 - doi - View abstract].
62. Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes.
Colin S, Coelho LP, Sunagawa S, Bowler C, Karsenti E, Bork P, Pepperkok R, de Vargas C
eLIFE: 6, e26066, 2017. [ IF: 7.6 ]
[PMID: 29087936 - open access - View abstract].
61. RNase H As Gene Modifier, Driver of Evolution and Antiviral Defense.
Moelling K*, Broecker F*, Russo G, Sunagawa S
Front Microbiol: 8, 1745, 2017. [ IF: 4 ]
[PMID: 28959243 - open access - View abstract].
60. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.
Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M; Genoscope Technical Team, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernandez-Gomez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL; Tara Oceans Consortium Coordinators, Pesant S, Karsenti E, Wincker P
Sci Data: 4, 170093, 2017. [ IF: 5.3 ]
[PMID: 28763055 - open access - View abstract].
59. metaSNV: A tool for metagenomic strain level analysis.
Costea PI*, Munch R*, Coelho LP, Paoli L, Sunagawa S, Bork P
PLoS ONE: 12(7), e0182392, 2017. [ IF: 2.8 ]
[PMID: 28753663 - open access - View abstract].
58. Marine microbial diversity.
Salazar G, Sunagawa S#
Curr Biol: 27(11), R489-R494, 2017. [ IF: 9.3 ]
[PMID: 28586685 - doi - View abstract].
57. Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naive Parkinson's disease patients.
Bedarf JR*, Hildebrand F*, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wullner U
Genome Med: 9(1), 3952-3971, 2017. [ IF: 8.9 ]
[PMID: 28449715 - open access - View abstract].
56. Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition - a metagenomic analysis.
Knoll RL, Forslund K, Kultima JR, Meyer CU, Kullmer U, Sunagawa S, Bork P, Gehring S
Am J Physiol Gastrointest Liver Physiol: 312(4), G327-G339, 2017. [ IF: 3.3 ]
[PMID: 28039159 - doi - View abstract].
55. proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.
Mende DR, Letunic I, Huerta-Cepas J, Li SS, Forslund K, Sunagawa S, Bork P
Nucl Acids Res: 45(D1), D529-D534, 2016. [ IF: 10.1 ]
[PMID: 28053165 - open access - View abstract].
54. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.
Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, Pesant S, Kandels-Lewis S, Dimier C, Picheral M, Searson S, Cruaud C, Alberti A, Duarte CM, Gasol JM, Vaque D; Tara Oceans Coordinators, Bork P, Acinas SG, Wincker P, Sullivan MB
Nature: 537(7622), 689-693, 2016. [ IF: 40.1 ]
[PMID: 27654921 - doi - View abstract].
53. Human gut microbes impact host serum metabolome and insulin sensitivity.
Pedersen HK*, Gudmundsdottir V*, Nielsen HB*, Hyotylainen T*, Nielsen T*, Jensen BAH, Forslund K, Hildebrand F, Prifti E, Falony G, Le Chatelier E, Levenez F, Dore J, Mattila I, Plichta DR, Poho P, Hellgren LI, Arumugam M, Sunagawa S, Vieira-Silva S, Jorgensen T, Holm JB, Trost K, MetaHit consortium, Kristiansen K, Brix S, Raes J, Wang J, Hansen T, Bork P, Brunak S, Oresic M, Ehrlich SD, Pedersen O
Nature: 535(7612), 376-381, 2016. [ IF: 40.1 ]
[PMID: 27409811 - doi - View abstract].
52. Colorectal cancer and the human gut microbiome: Reproducibility with whole-genome shotgun sequencing.
Vogtmann E, Hua X, Zeller G, Sunagawa S, Voigt AY, Hercog R, Goedert JJ, Shi J, Bork P, Sinha R
PLoS ONE: 11(5), e0155362, 2016. [ IF: 2.8 ]
[PMID: 27171425 - open access - View abstract].
51. Global genetic capacity for mixotrophy in marine picocyanobacteria.
Yelton A, Acinas SG, Sunagawa S, Bork P, Pedros-Alio C, Chisholm S
ISME J: 10(12), 2946-2957, 2016. [ IF: 9.7 ]
[PMID: 27137127 - doi - View abstract].
50. Durable coexistence of donor and recipient strains after fecal microbiota transplantation.
Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Niewdorp M, Salojarvi J, Voigt AY, Zeller G, Sunagawa S#, de Vos WM#, Bork P#
Science: 352(6285), 586-589, 2016. [ IF: 37.2 ]
[PMID: 27126044 - doi - View abstract - View features].
49. MOCAT2: a metagenomics assembly, annotation and profiling framework.
Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P
Bioinformatics: 32(16), 2520-2523, 2016. [ IF: 7.3 ]
[PMID: 27153620 - doi - View abstract].
48. Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.
Cornejo-Castillo FM, Cabello AM, Salazar G, Sanchez-Baracaldo P, Lima-Mendez G, Hingamp P, Alberti A, Sunagawa S, Bork P, de Vargas C, Raes J, Bowler C, Wincker P, Zehr JP, Gasol JM, Massana R, Acinas SG
Nature Commun: 7, 11071, 2016. [ IF: 12.1 ]
[PMID: 27002549 - doi - View abstract].
47. Plankton networks driving carbon export in the oligotrophic ocean.
Guidi L*, Chaffron S*, Bittner L*, Eveillard D*, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum J, Coelho LP, Ignacio Espinoza JC, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S, Tara Oceans coordinators, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G
Nature: 532(7600), 465-470, 2016. [ IF: 40.1 ]
[PMID: 26863193 - doi - View abstract].
46. Disentangling disease- and drug signatures of the human gut microbiome: the case of type 2 diabetes mellitus.
Forslund K*, Hildebrand F*, Nielsen T*, Falony G*, Le Chatelier E*, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Pedersen HK, Arumugam M, Kristiansen L, Voigt AY, Vestergaard H, Hercog R, Costea PI, Kultima JR, Li J, Jorgensen T, Levenez F, Dore J, MetaHIT consort., Nielsen HB, Brunak A, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O
Nature: 528(7581), 262-266, 2015. [ IF: 38.1 ]
[PMID: 26633628 - doi - View abstract].
45. eggNOG 4.5: A hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
Huerta-Cepas, J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen L, von Mering C, Bork P
Nucl Acids Res: 44(D1), D286-D293, 2015. [ IF: 9.2 ]
[PMID: 26582926 - open access - View abstract].
44. Gonadal transcriptomics elucidate patterns of adaptive evolution within marine rockfishes (Sebastes).
Heras J, McClintock K, Sunagawa S, Aguilar A
BMC Genomics: 16, 656, 2015. [ IF: 3.9 ]
[PMID: 26329285 - open access - View abstract].
43. Open science resources for the discovery and analysis of Tara Oceans data.
Pesant S, Not F, Picheral M, Kandels-Lewis S, Le Bescot N, Gorsky G, Iudicone D, Karsenti E, Speich S, Trouble R, Dimier C, Searson S, Tara Oceans Consortium Coordinators
Sci Data: 2, 150023, 2015. [ IF: NA ]
[PMID: 26029378 - open access - View abstract].
42. Computational eco-systems biology in Tara Oceans: translating data into knowledge.
Sunagawa S, Karsenti E, Bowler C, Bork P
Mol Syst Biol: 11(5), 809, 2015. [ IF: 10.6 ]
[PMID: 25999085 - open access - View abstract].
41. Structure and function of the global ocean microbiome.
Sunagawa S*#, Coelho LP*, Chaffron S*, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans Coordinators , Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P
Science: 348(6237), 1261359, 2015. [ IF: 34.7 ]
[PMID: 25999513 - doi - View abstract - View features].
40. Eukaryotic plankton diversity in the sunlit ocean.
de Vargas C*, Audic S*, Henry N*, Decelle J*, Mahe F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, Bittner L, Chaffron S, Dunthorn M, Engelen S, Flegontova O, Guidi L, Horak A, Jaillon O, Lima-Mendez G, Lukes J, Malviya S, Morard R, Mulot M, Scalco E, Siano R, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans Coordinators , Acinas SG, Bork P, Bowler C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Raes J, Sieracki M, Speich S, Stemmann L, Sunagawa S, Weissenbach J, Wincker P, Karsenti E
Science: 348(6237), 1261605, 2015. [ IF: 34.7 ]
[PMID: 25999516 - doi - View abstract].
39. Patterns and ecological drivers of ocean viral communities.
Brum JR*, Ignacio-Espinoza C*, Roux S*, Doulcier G, Acinas S, Alberti A, Chaffron S, Cruaud C, de Vargas C, Gasol JM, Gorsky G, Gregory AC, Guidi L, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Poulos BT, Schwenck SM, Speich S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans Coordinators , Karsenti E, Bork P, Bowler C, Sunagawa S, Wincker P, Sullivan MB
Science: 348(6237), 1261498, 2015. [ IF: 34.7 ]
[PMID: 25999515 - doi - View abstract].
38. Environmental characteristics of Agulhas rings affect interocean plankton transport.
Villar E, Farrant GK, Follows M, Garczarek L, Speich S, Audic S, Bittner L, Blanke B, Brum JR, Brunet C, Casotti R, Chase A, Dolan JR, d'Ortenzio F, Gattuso JP, Grima N, Guidi L, Hill CN, Jahn O, Jamet JL, Le Goff H, Lepoivre C, Malviya S, Pelletier E, Romagnan JB, Roux S, Santini S, Scalco E, Schwenck SM, Tanaka A, Testor P, Vannier T, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans coordinators, Acinas SG, Bork P, Boss E, de Vargas C, Gorsky G, Ogata H, Pesant S, Sullivan MB, Sunagawa S, Wincker P, Karsenti E, Bowler C, Not F, Hingamp P, Iudicone D
Science: 348(6237), 1261447, 2015. [ IF: 34.7 ]
[PMID: 25999514 - doi - View abstract].
37. Determinants of community structure in the global plankton interactome.
Lima-Mendes G*, Faust K*, Henry N*, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Cabello AM, Coppola L, Cornejo-Castillo FM, d'Ovidio F, De Meester L, Ferrera I, Garet-Delmas MJ, Guidi L, Lara E, Pesant S, Royo-Lonch M, Salazar G, Sanchez P, Sebastian M, Souffreau C, Dimier C, Picheral P, Searson S, Kandels-Lewis S, Tara Oceans Coordinators, Gorsky G, Not F, Ogata H, Speich S, Weissenbach J, Wincker P, Bontempi G, Acinas SG, Sunagawa S, Bork P, Sullivan MB, Bowler C, Karsenti E, de Vargas C, Raes J
Science: 348(6237), 1262073, 2015. [ IF: 34.7 ]
[PMID: 25999517 - doi - View abstract].
36. Inter-individual differences in the gene content of human gut bacterial species.
Zhu A, Sunagawa S, Mende DR, Bork P
Genome Biol: 16(1), 82, 2015. [ IF: 11.3 ]
[PMID: 25896518 - open access - View abstract].
35. Temporal and technical variability of human gut metagenomes.
Voigt AY, Costea PI, Kultima JR, Li SS, Zeller G, Sunagawa S, Bork P
Genome Biol: 16(1), 73, 2015. [ IF: 11.3 ]
[PMID: 25888008 - open access - View abstract].
34. Potential of fecal microbiota for early stage detection of colorectal cancer.
Zeller G*, Tap J*, Voigt AY*, Sunagawa S, Kultima JR, Costea PI, Amiot A, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Bohm J, Tournigand C, Van Nhieu JT, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P
Mol Syst Biol: 10, 766, 2014. [ IF: 10.9 ]
[PMID: 25432777 - open access - View abstract].
33. Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata.
Closek CJ, Sunagawa S, DeSalvo MD, Piceno YM, DeSantis TZ, Brodie EL, Weber MX, Voolstra CR, Andersen GL, Medina M
ISME J: 8(12), 2411-2422, 2014. [ IF: 9.3 ]
[PMID: 24950107 - doi - View abstract].
32. An integrated catalog of reference genes in the human gut microbiome.
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 E, Yang H, Wang J, Hansen T, Nielsen HB, Brunak S, Kristiansen K, Guarner F, Pedersen O, Dore J, Ehrlich SD, MetaHIT Consortium, Bork P, Wang J
Nat Biotechnol: 32(8), 834-841, 2014. [ IF: 41.5 ]
[PMID: 24997786 - doi - View abstract].
31. 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, Dore J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Leonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sorensen S, Tap J, Tims S, Ussery DW, Yamada T, MetaHIT Consortium, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD
Nat Biotechnol: 32(8), 822-828, 2014. [ IF: 41.5 ]
[PMID: 24997787 - doi - View abstract].
30. 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, Ogata H, Hingamp P, de Vargas C, Raes J, Lima-Mendez G, Poulain J, Jaillon O, Wincker P, Kandels-Lewis S, Karsenti E, Bork P, Acinas SG
Environ Microbiol: 16(9), 2659-2671, 2014. [ IF: 6.2 ]
[PMID: 24102695 - doi - View abstract].
29. Classification and quantification of bacteriophage taxa in human gut metagenomes.
Waller A, Yamada T, Kristensen DM, Kultima JR, Sunagawa S, Koonin EV, Bork P
ISME J: 8(7), 1391-1402, 2014. [ IF: 9.3 ]
[PMID: 24621522 - doi - View abstract].
28. A fair comparison.
Costea PI, Zeller G, Sunagawa S, Bork P
Nat Methods: 11, 359, 2014. [ IF: 32 ]
[PMID: 24681719 - doi - View abstract].
27. Metagenomic insights into the human gut resistome and the forces that shape it.
Forslund K, Sunagawa S, Coelho LP, Bork P
Bioessays: 36, 316-329, 2014. [ IF: 4.7 ]
[PMID: 24474281 - doi - View abstract].
26. Metagenomic species profiling using universal phylogenetic marker genes.
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 OP, Guarner F, de Vos WM, Wang J, Li J, Dore J, Ehrlich SD, Stamatakis A, Bork P
Nat Methods: 10(12), 1196-1199, 2013. [ IF: 26 ]
[PMID: 24141494 - doi - View abstract].
25. 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 JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jorgensen T, Brandslund I, Nielsen B, Juncker A, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Cleement K, Dore J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T, MetaHIT consortium, Bork P, Jun W, Ehrlich SD, Pedersen O
Nature: 500(7464), 541-546, 2013. [ IF: 42.4 ]
[PMID: 23985870 - doi - View abstract].
24. Accurate and universal delineation of prokaryotic species.
Mende DR, Sunagawa S, Zeller G, Bork P
Nat Methods: 10(9), 881-884, 2013. [ IF: 26 ]
[PMID: 23892899 - doi - View abstract].
23. Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.
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, DeVargas C, Karsenti E, Kandels-Lewis S, Jaillon O, Not F, Pesant S, Wincker P, Ogata H
ISME J: 7(9), 1678-1695, 2013. [ IF: 9.3 ]
[PMID: 23575371 - open access - View abstract].
22. Country-specific antibiotic use practices impact the human gut resistome.
Forslund K, Sunagawa S, Kultima JR, Mende D, Arumugam M, Typas A, Bork P
Genome Res: 23(7), 1163-1169, 2013. [ IF: 13.9 ]
[PMID: 23568836 - doi - View abstract].
21. Genomic variation landscape of the human gut microbiome.
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
Nature: 493(7430), 45-50, 2013. [ IF: 42.4 ]
[PMID: 23222524 - doi - View abstract].
20. MOCAT: a metagenomics assembly and gene prediction toolkit.
Kultima JR*, Sunagawa S*, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J, Wang J, Bork P
PLoS ONE: 7(10), e47656, 2012. [ IF: 3.7 ]
[PMID: 23082188 - open access - View abstract].
19. Symbiodinium Transcriptomes: Genome Insights into the Dinoflagellate Symbionts of Reef-Building Corals.
Bayer T*, Aranda M*, Sunagawa S, Yum LK, DeSalvo MK, Lindquist E, Coffroth MA, Voolstra CR, Medina M
PLoS ONE: 7(4), e35269, 2012. [ IF: 3.7 ]
[PMID: 22529998 - open access - View abstract].
18. Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data.
Mende DR*, Waller AS*, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, Raes J, Bork P
PLoS ONE: 7(2), e31386, 2012. [ IF: 3.7 ]
[PMID: 22384016 - open access - View abstract].
17. Transcriptomic responses to darkness stress point to common coral bleaching mechanisms.
DeSalvo MK, Estrada E, Sunagawa S, Medina M
Coral Reefs: 31(1), 215-228, 2012. [ IF: 3.7 ]
[doi - View abstract].
16. A Holistic Approach to Marine Eco-Systems Biology.
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, Abergel C, Arslan D, Audic S, Aury JM, Babic N, Beaufort L, Bittner L, Boss E, Boutte C, Brum J, Carmichael M, Casotti R, Chambouvet A, Chang P, Chica C, Clerissi C, Colin S, Cornejo-Castillo FM, Da Silva C, De Monte S, Decelle J, Desdevises Y, Dimier C, Dolan J, Duhaime M, Durrieu de Madron X, d'Ortenzio F, d'Ovidio F, Ferrera I, Garczarek L, Garet-Delmas MJ, Gasmi S, Gasol JM, Grimsley N, Heilig R, Ignacio-Espinoza J, Jamet JL, Karp-Boss L, Katinka M, Khalili H, Kolber Z, Le Bescot N, Le Gofff H, Lima-Mendez G, Mahe F, Mazzocchi MG, Montresor M, Morin P, Noel B, Pedros-Alio C, Pelletier E, Perez Y, Picheral M, Piganeau G, Poirot O, Poulain J, Poulton N, Prejger F, Prihoda J, Probert I, Rampal J, Reverdin G, Romac S, Romagnan JB, Roullier F, Rouviere C, Samson G, Santini S, Sarmento H, Sciandra A, Solonenko S, Stemmann L, Subirana L, Sunagawa S, Tanaka A, Testor P, Thompson A, Tichanne-Seltzer V, Tirichine L, Toulza E, Tozzi S, Veluchamy A, Zingone A
PLoS Biol: 9(10), e1001177, 2011. [ IF: 11.5 ]
[PMID: 22028628 - open access - View abstract].
15. Rapid evolution of coral proteins responsible for interaction with the environment.
Voolstra CR*, Sunagawa S*, Matz MV, Bayer T, Aranda M, Buschiazzo E, DeSalvo MK, Lindquist E, Szmant AM, Coffroth MA, Medina M
PLoS ONE: 6(5), e20392, 2011. [ IF: 4.1 ]
[PMID: 21633702 - open access - View abstract].
14. 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, Dore J; MetaHIT Consortium, Antolin 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, 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 SD, Bork P
Nature: 473(7346), 174-180, 2011. [ IF: 36.3 ]
[PMID: 21508958 - doi - View abstract - View features].
13. 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. [ IF: 2.5 ]
[doi - View abstract].
12. Threatened Corals Provide Underexplored Microbial Habitats.
Sunagawa S, Woodley CM, Medina M
PLoS ONE: 5(3), e9554, 2010. [ IF: 4.4 ]
[PMID: 20221265 - open access - View abstract].
11. The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database.
Abderrahmane T, Wang M, Lindquist E, Tanaka Y, Teranishi KS, Sunagawa S, Wong M, Stillman JH
PLoS ONE: 5(2), e9327, 2010. [ IF: 4.4 ]
[PMID: 20174471 - open access - View abstract].
10. Coral host transcriptomic states are correlated with Symbiodinium genotypes.
DeSalvo MK*, Sunagawa S*, Fisher PL, Voolstra CR, Iglesias-Prieto R, Medina M
Mol Ecol: 19(6), 1174-1186, 2010. [ IF: 6.5 ]
[PMID: 20149089 - doi - View abstract].
9. Gene expression microarray analysis encompassing metamorphosis and the onset of calcification in the scleractinian coral Montastraea faveolata.
Reyes-Bermudez A, DeSalvo MK, Voolstra CR, Sunagawa S, Szmant AM, Iglesias-Prieto R, Medina M
Mar Genom: 2(3-4), 149-159, 2009. [ IF: 1.2 ]
[PMID: 21798184 - doi - View abstract].
8. 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 EC, Thaler M, Smith ML, Caruso C, Pringle JR, Weis VM, Medina M, Schwarz JA
BMC Genomics: 10, 258, 2009. [ IF: 3.8 ]
[PMID: 19500365 - open access - View abstract - View features].
7. Evolutionary analysis of orthologous cDNA sequences from cultured and symbiotic dinoflagellate symbionts of reef-building corals (Dinophyceae: Symbiodinium).
Voolstra CR, Sunagawa S, Schwarz JA, Coffroth MA, Yellowlees D, Leggat W, Medina M
Comp Biochem Physiol D Genomics Proteomics: 4(2), 67-74, 2009. [ IF: 1.8 ]
[PMID: 20403741 - doi - View abstract].
6. The host transcriptome remains unaltered during the establishment of coral-algal symbioses.
Voolstra CR, Schwarz JA, Schnetzer J, Sunagawa S, Desalvo MK, Szmant AM, Coffroth MA, Medina M
Mol Ecol: 18(9), 1823-1833, 2009. [ IF: 6 ]
[PMID: 19317843 - doi - View abstract - View features].
5. Identification and Gene Expression Analysis of a Taxonomically Restricted Cysteine-Rich Protein Family in Reef-Building Corals.
Sunagawa S, DeSalvo MK, Voolstra CR, Reyes-Bermudez A, Medina M
PLoS ONE: 4(3), e4865, 2009. [ IF: 4.4 ]
[PMID: 19283069 - open access - View abstract].
4. Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata.
Sunagawa S, DeSantis TZ, Piceno YM, Brodie EL, DeSalvo MK, Voolstra CR, Weil E, Andersen GL, Medina M
ISME J: 3(5), 512-521, 2009. [ IF: 6.4 ]
[PMID: 19129866 - doi - View abstract - View features].
3. Differential gene expression during thermal stress and bleaching in the Caribbean coral Montastraea faveolata.
DeSalvo MK, Voolstra CR, Sunagawa S, Schwarz JA, Stillman JH, Coffroth MA, Szmant AM, Medina M
Mol Ecol: 17(17), 3952-3971, 2008. [ IF: 5.3 ]
[PMID: 18662230 - doi - View abstract].
2. 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 HJ, Medina M
Comp Biochem Physiol B Biochem Mol Biol: 151(1), 133-138, 2008. [ IF: 1.5 ]
[PMID: 18602489 - doi - View abstract].
1. 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. [ IF: 1 ]
[ View abstract].
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Book Chapters

Metagenomics of the coral holobiont.
Medina M and Sunagawa S.
In Nelson K., (Ed.) Encyclopedia of Metagenomics: SpringerReference (www.springerreference.com). Springer-Verlag Berlin Heidelberg, 2013.
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Theses

Ph.D.: Microbial Diversity and Transcriptome Profiling in Coral Holobionts [pdf]

M.Sc.: Seasonal Variations in Symbiont Densities and Skeletal Phosphorus Concentrations in the Eastern Pacific (Costa Rica) Coral Pavona clavus [pdf]

Diploma: Analysis of Small Fusion Partners to Increase the Stability of Poorly-Soluble Proteins: a Perspective for the Structural Analysis by NMR Spectroscopy? [pdf]
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