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KU Leuven; Rega-instituut; Department of Microbiology and Immunology; Bioinformatics and (eco-)systems biology lab, more
Function: Group Leader
Direct contact at institute:
Tel.: +32-(0)16-37 22 22
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| Publications (20) |
Top | Institute | Publications |
| A1 Publications (19) [show] |
 Acinas, S.G.; Sánchez, P.; Salazar, G.; Cornejo-Castillo, F.M.; Sebastian, M.; Logares, R.; Royo-Llonch, M.; Paoli, L.; Sunagawa, S.; Hingamp, P.; Ogata, H.; Lima-Mendez, G.; Roux, S.; González, J.M.; Arrieta, J.M.; Alam, I.S.; Kamau, A.; Bowler, C.; Raes, J.; Pesant, S.; Bork, P.; Agusti, S.; Gojobori, T.; Vaqué, D.; Sullivan, M.B.; Pedrós-Alió, C.; Massana, R.; Duarte, C.M.; Gasol, J.M. (2021). Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Communications Biology 4(1): 604. https://dx.doi.org/10.1038/s42003-021-02112-2, more- Deutschmann, I.M.; Lima-Mendez, G.; Krabberod, A.K.; Raes, J.; Vallina, S.M.; Faust, K.; Logares, R. (2021). Disentangling environmental effects in microbial association networks. Microbiome 9(1): 232. https://dx.doi.org/10.1186/s40168-021-01141-7, more
- Deutschmann, I.M.; Lima-Mendez, G.; Krabberod, A.K.; Raes, J.; Vallina, S.M.; Faust, K.; Logares, R. (2021). Correction to: Disentangling environmental effects in microbial association networks. Microbiome 9(1): 245. https://dx.doi.org/10.1186/s40168-021-01209-4, more
- Royo-Llonch, M.; Sánchez, P.; Ruiz-González, C.; Salazar, G.; Pedrós-Alió, C.; Sebastian, M.; Labadie, K.; Paoli, L.; Ibarbalz, F.M.; Zinger, L.; Churcheward, B.; Chaffron, S.; Eveillard, D.; Karsenti, E.; Sunagawa, S.; Wincker, P.; Karp-Boss, L.; Bowler, C.; Acinas, S.G.; Tara Oceans Coordinators* (2021). Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean. Nature Microbiology 6(12): 1561-1574. https://dx.doi.org/10.1038/s41564-021-00979-9, more
- 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, M.-A.; Méheust, R.; Poulain, J.; Romac, S.; Richter, D.J.; Yoshikawa, G.; Dimier, C.; Kandels-Lewis, S.; Picheral, M.; Searson, S.; Tara Oceans Coordinators; Jaillon, O.; Aury, J.-M.; Karsenti, E.; Sullivan, M.B.; Sunagawa, S.; Bork, P.; Not, F.; Hingamp, P.; Raes, J.; Guidi, L.; Ogata, H.; de Vargas, C.; Iudicone, D.; Bowler, C.; Wincker, P. (2018). A global ocean atlas of eukaryotic genes. Nature Comm. 9(1): 13 pp. https://dx.doi.org/10.1038/s41467-017-02342-1, more
- Alberti, A.; Poulain, J.; Engelen, S.; Labadie, K.; Romac, S.; Ferrera, I.; Albini, G.; Aury, J.-M.; 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.; Acinas, S.G.; Royo-Llonch, M.; Cornejo-Castillo, F.M.; Logares, R.; Fernandez-Gomez, B.; Bowler, C.; Cochrane, G.; Amid, C.; ten Hoopen, P.; de Vargas, C.; Grimsley, N.; Desgranges, E.; Kandels-Lewis, S.; Ogata, H.; Poulton, N.; Sieracki, M.E.; Stepanauskas, R.; Sullivan, M.B.; Brum, J.R.; Duhaime, M.B.; Poulos, B.T.; Hurwitz, B.L.; Pesant, S.; Karsenti, E.; Wincker, P.; Bork, P.; Boss, E.; Follows, M.; Gorsky, G.; Hingamp, P.; Iudicone, D.; Karp-Boss, L.; Not, F.; Raes, J.; Sardet, C.; Speich, S.; Stemmann, L.; Sunagawa, S.; Bazire, P.; Beluche, O.; Besnard-Gonnet, M.; Bordelais, I.; Boutard, M.; Dubois, M.; Dumont, C.; Ettedgui, E.; Fernández, P.; Garcia, E.; Aiach, N.G.; Guerin, T.; Hamon, C.; Brun, E.; Lebled, S.; Lenoble, P.; Louesse, C.; Mahieu, E.; Mairey, B.; Martins, N.; Megret, C.; Milani, C.; Muanga, J.; Orvain, C.; Payen, E.; Perroud, P.; Petit, E.; Robert, D.; Ronsin, M.; Vacherie, B. (2017). Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Scientific Data 4: 20. https://dx.doi.org/10.1038/sdata.2017.93, more
- Cornejo-Castillo, F.M.; Cabello, A.M.; Salazar, G.; Sánchez-Baracaldo, P.; Lima-Mendez, G.; Hingamp, P.; Alberti, A.; Sunagawa, S.; Bork, P.; de Vargas, C.; Raes, J.; Bowler, C.; Wincker, P.; Zehr, J.P.; Gasol, J.M.; Massana, R.; Acinas, S.G. (2016). Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton. Nature Comm. 7(11071). http://dx.doi.org/10.1038/ncomms11071, more
- Edwards, R.A.; McNair, K.; Faust, K.; Raes, J.; Dutilh, B.E. (2016). Computational approaches to predict bacteriophage-host relationships. FEMS Microbiol. Rev. 40(2): 258-272. https://dx.doi.org/10.1093/femsre/fuv048, more
- Guidi, L.; Chaffron, S.; Bittner, L.; Eveillard, D.; Larhlimi, A.; Roux, S.; Darzi, Y.; Audic, S.; Berline, L.; Brum, J.R.; Coelho, L.P.; Ignacio-Espinoza, J.C.; Malviya, S.; Sunagawa, S.; Dimier, C.; Kandels-Lewis, S.; Picheral, M.; Poulain, J.; Searson, S.; Tara Oceans Consortium Coordinators; Stemmann, L.; Not, F.; Hingamp, P.; Speich, S.; Follows, M.; Karp-Boss, L.; Boss, E.S.; Ogata, H.; Pesant, S.; Weissenbach, J.; Wincker, P.; Acinas, S.G.; Bork, P.; de Vargas, C.; Iudicone, D.; Sullivan, M.B.; Raes, J.; Karsenti, E.; Bowler, C.; Gorsky, G. (2016). Plankton networks driving carbon export in the oligotrophic ocean. Nature (Lond.) 532(7600): 465-470. https://hdl.handle.net/10.1038/nature16942, more
- de Vargas, C.; Audic, S.; Henry, N.; Decelle, J.; Mahé, F.; Logares, R.; Lara, E.; Berney, C.; Le Bescot, N.; Probert, I.; Carmichael, M.; Poulain, J.; Romac, S.; Colin, S.; Aury, J.-M.; Bittner, L.; Chaffron, S.; Dunthorn, M.; Engelen, S.; Flegontova, O.; Guidi, L.; Horák, A.; Jaillon, O.; Lima-Mendez, G.; Lukeš, J.; Malviya, S.; Morard, R.; Mulot, M.; Scalco, E.; Siano, R.; Vincent, F.; Zingone, A.; Dimier, C.; Picheral, M.; Searson, S.; Kandels-Lewis, S.; Acinas, S.G.; Bork, P.; Bowler, C.; Gorsky, G.; Grimsley, N.; Hingamp, P.; Iudicone, D.; Not, F.; Ogata, H.; Pesant, S.; Raes, J.; Sieracki, M.E.; Speich, S.; Stemmann, L.; Sunagawa, S.; Weissenbach, J.; Wincker, P.; Karsenti, E. (2015). Eukaryotic plankton diversity in the sunlit ocean. Science (Wash.) 348(6237): 11 pp. http://dx.doi.org/10.1126/science.1261605, more
- Faust, K.; Lahti, L.; Gonze, D.; de Vos, W.M.; Raes, J. (2015). Metagenomics meets time series analysis: unraveling microbial community dynamics. Curr. Opin. Microbiol. 25: 56-66. https://dx.doi.org/10.1016/j.mib.2015.04.004, more
- Lima-Mendez, G.; Faust, K.; Henry, N.; Decelle, J.; Colin, S.; Carcillo, F.; Chaffron, S.; Ignacio-Espinoza, J.C.; Roux, S.; Vincent, F.; Bittner, L.; Darzi, Y.; Wang, J.; Audic, S.; Berline, L.; Bontempi, G.; Cabello, A.M.; Coppola, L.; Cornejo-Castillo, F.M.; De Meester, L.; Ferrera, I.; Garet-Delmas, M.-J.; Guidi, L.; Lara, E.; Pesant, S.; Royo-Llonch, M.; Salazar, G.; Sánchez, P.; Sebastian, M.; Souffreau, C.; Dimier, C.; Picheral, M.; Searson, S.; Kandels-Lewis, S.; Gorsky, G.; Not, F.; Ogata, H.; Speich, S.; Stemmann, L.; Weissenbach, J.; Wincker, P.; Acinas, S.G.; Sunagawa, S.; Bork, P.; Sullivan, M.B.; Karsenti, E.; Bowler, C.; de Vargas, C.; Raes, J. (2015). Determinants of community structure in the global plankton interactome. Science (Wash.) 348(6237): 9 pp. http://dx.doi.org/10.1126/science.1262073, more
- Sunagawa, S.; Coelho, L.P.; Chaffron, S.; Kultima, J.R.; Labadie, K.; Salazar, G.; Djahanschiri, B.; Zeller, G.; Mende, D.R.; Alberti, A.; Cornejo-Castillo, F.M.; Costea, P.I.; Cruaud, C.; d'Ovidio, F.; Engelen, S.; Ferrera, I.; Gasol, J.M.; Guidi, L.; Hildebrand, F.; Kokoszka, F.; Lepoivre, C.; Lima-Mendez, G.; Poulain, J.; Poulos, B.T.; Royo-Llonch, M.; Sarmento, H.; Vieira-Silva, S.; Dimier, C.; Picheral, M.; Searson, S.; Kandels-Lewis, S.; 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.; Suillivan, M.B.; Weissenbach, J.; Wincker, P.; Karsenti, E.; Raes, J.; Acinas, S.G.; Bork, P. (2015). Structure and function of the global ocean microbiome. Science (Wash.) 348(6237): 9 pp. http://dx.doi.org/10.1126/science.1261359, more
- Hildebrand, F.; Tadeo, R.; Voigt, A.Y.; Bork, P.; Raes, J. (2014). LotuS: an efficient and user-friendly OTU processing pipeline. Microbiome 2: 7. https://dx.doi.org/10.1186/2049-2618-2-30, more
- Hildebrand, F.; Tito, R.Y.; Voigt, A.Y.; Bork, P.; Raes, J. (2014). Correction: LotuS: an efficient and user-friendly OTU processing pipeline. Microbiome 2(1): 37. https://dx.doi.org/10.1186/2049-2618-2-37, more
- Logares, R.; Sunagawa, S.; Salazar, G.; Cornejo-Castillo, F.; 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. (2014). Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. Environ. Microbiol. 16(9): 2659-2671. https://dx.doi.org/10.1111/1462-2920.12250, more
- 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. (2013). Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. ISME J. 7(9): 1678-1695. https://dx.doi.org/10.1038/ismej.2013.59, more
- 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.; Tara Oceans Consortium (2011). A holistic approach to marine eco-systems biology. PLoS Biology 9(10): e1001177. http://dx.doi.org/10.1371/journal.pbio.1001177, more
- Raes, J.; Letunic, I.; Yamada, T.; Jensen, L.; Bork, P. (2011). Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Mol. Syst. Biol. 7(473): 9 pp. dx.doi.org/10.1038/msb.2011.6, more
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| Abstract [show] |
- Raes, J. (2012). Metagenomics: from parts lists to ecology, in: Sabbe, K. et al. (Ed.) Twenty-second International Diatom Symposium, Aula Academica, Ghent, 26-31 August 2012. Abstracts. VLIZ Special Publication, 58: pp. 14, more
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