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1. • Journal article

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   Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton

   Cornejo-Castillo, Francisco M. Cabello, Ana M. Salazar, Guillem Sánchez-Baracaldo, Patricia Lima Mendez, Gipsi[UCL] Hingamp, Pascal Alberti, Adriana Sunagawa, Shinichi Bork, Peer de Vargas, Colomban Raes, Jeroen Bowler, Chris Wincker, Patrick Zehr, Jonathan P. Gasol, Josep M. Massana, Ramon Acinas, Silvia G. (2016) Nature Communications — Vol. 7, no.1, p. 1 (2016)
2. • Journal article

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   Network Analysis Tools: from biological networks to clusters and pathways

   Brohée, Sylvain Faust, Karoline Lima Mendez, Gipsi[UCL] Vanderstocken, Gilles van Helden, Jacques (2008) Nature Protocols — Vol. 3, no.10, p. 1616-1629 (2008)
3. • Journal article

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   Toxin-Antitoxin Gene Pairs Found in Tn3 Family Transposons Appear To Be an Integral Part of the Transposition Module

   Lima Mendez, Gipsi[UCL] Oliveira Alvarenga, Danillo Ross, Karen Hallet, Bernard[UCL] Van Melderen, Laurence Varani, Alessandro M. Chandler, Michael Buchrieser, Carmen (2020) mBio — Vol. 11, no.2, p. 2 (2020)
4. • Journal article

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   Cross-biome comparison of microbial association networks

   Faust, Karoline Lima Mendez, Gipsi[UCL] Lerat, Jean-Sébastien[UCL] Sathirapongsasuti, Jarupon F. Knight, Rob Huttenhower, Curtis Lenaerts, Tom Raes, Jeroen (2015) Frontiers in Microbiology — Vol. 6, no.1, p. 1200 (2015)
5. • Journal article

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   A Holistic Approach to Marine Eco-Systems Biology

   Karsenti, Eric Acinas, Silvia G. Bork, Peer Bowler, Chris De Vargas, Colomban Raes, Jeroen Sullivan, Matthew Arendt, Detlev Benzoni, Francesca Claverie, Jean-Michel Follows, Mick Gorsky, Gaby Hingamp, Pascal Iudicone, Daniele Jaillon, Olivier Kandels-Lewis, Stefanie Krzic, Uros Not, Fabrice Ogata, Hiroyuki Pesant, Stéphane Reynaud, Emmanuel Georges Sardet, Christian Sieracki, Michael E. Speich, Sabrina Velayoudon, Didier Weissenbach, Jean Wincker, Patrick Lima Mendez, Gipsi[UCL] (2011) PLoS Biology — Vol. 9, no.10, p. e1001177 (2011)
6. • Journal article

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   Determinants of community structure in the global plankton interactome

   Lima Mendez, Gipsi[UCL] Faust, K. Henry, N. Decelle, J. Colin, S. Carcillo, F. Chaffron, S. Ignacio-Espinosa, 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. d'Ovidio, F. De Meester, L. Ferrera, I. Garet-Delmas, M.-J. Guidi, L. Lara, E. Pesant, S. Royo-Llonch, M. Salazar, G. Sanchez, 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) Science — Vol. 348, no.6237, p. 1262073-1262073 (2015)
7. • Journal article

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   Prophinder: a computational tool for prophage prediction in prokaryotic genomes

   Lima Mendez, Gipsi[UCL] Van Helden, Jacques Toussaint, Ariane Leplae, Raphaël (2008) Bioinformatics — Vol. 24, no.6, p. 863-865 (2008)
8. • Journal article

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   Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota

   Tito, Raul Y. Chaffron, Samuel Caenepeel, Clara Lima Mendez, Gipsi[UCL] Wang, Jun Vieira-Silva, Sara Falony, Gwen Hildebrand, Falk Darzi, Youssef Rymenans, Leen Verspecht, Chloë Bork, Peer Vermeire, Severine Joossens, Marie Raes, Jeroen (2018) Gut — Vol. 68, no.7, p. 1180-1189 (2018)
9. • Journal article

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   Comparative Analyses of Prophage-Like Elements Present in Bifidobacterial Genomes

   Ventura, Marco Turroni, Francesca Lima Mendez, Gipsi[UCL] Foroni, Elena Zomer, Aldert Duranti, Sabrina Giubellini, Vanessa Bottacini, Francesca Horvath, Philippe Barrangou, Rodolphe Sela, David A. Mills, David A. van Sinderen, Douwe (2009) Applied and Environmental Microbiology — Vol. 75, no.21, p. 6929-6936 (2009)
10. • Journal article

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    A modular view of the bacteriophage genomic space: identification of host and lifestyle marker modules

    Lima Mendez, Gipsi[UCL] Toussaint, Ariane Leplae, Raphael (2011) Research in Microbiology — Vol. 162, no.8, p. 737-746 (2011)
11. • Journal article

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    Structure and function of the global ocean microbiome

    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, Gipsi[UCL] 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. Sullivan, M. B. Weissenbach, J. Wincker, P. Karsenti, E. Raes, J. Acinas, S. G. Bork, P. Boss, E. Bowler, C. Follows, M. Karp-Boss, L. Krzic, U. Reynaud, E. G. Sardet, C. Sieracki, M. Velayoudon, D. (2015) Science — Vol. 348, no.6237, p. 1261359-1261359 (2015)
12. • Journal article

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    The powerful law of the power law and other myths in network biology

    Lima Mendez, Gipsi[UCL] van Helden, Jacques (2009) Molecular BioSystems — Vol. 5, no.12, p. 1482 (2009)
13. • Journal article

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    A first global analysis of plasmid encoded proteins in the ACLAME database

    Leplae, Raphaël Lima Mendez, Gipsi[UCL] Toussaint, Ariane (2006) FEMS Microbiology Reviews — Vol. 30, no.6, p. 980-994 (2006)
14. • Journal article

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    Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

    Hingamp, Pascal Grimsley, Nigel Acinas, Silvia G Clerissi, Camille Subirana, Lucie Poulain, Julie Ferrera, Isabel Sarmento, Hugo Villar, Emilie Lima Mendez, Gipsi[UCL] Faust, Karoline Sunagawa, Shinichi Claverie, Jean-Michel Moreau, Hervé Desdevises, Yves Bork, Peer Raes, Jeroen de Vargas, Colomban Karsenti, Eric Kandels-Lewis, Stefanie Jaillon, Olivier Not, Fabrice Pesant, Stéphane Wincker, Patrick Ogata, Hiroyuki (2013) The ISME Journal — Vol. 7, no.9, p. 1678-1695 (2013)
15. • Journal article

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    Analysis of the phage sequence space: The benefit of structured information

    Lima Mendez, Gipsi[UCL] Toussaint, Ariane Leplae, Raphaël (2007) Virology — Vol. 365, no.2, p. 241-249 (2007)
16. • Journal article

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    Species–function relationships shape ecological properties of the human gut microbiome

    Vieira-Silva, Sara Falony, Gwen Darzi, Youssef Lima Mendez, Gipsi[UCL] Garcia Yunta, Roberto Okuda, Shujiro Vandeputte, Doris Valles-Colomer, Mireia Hildebrand, Falk Chaffron, Samuel Raes, Jeroen (2016) Nature Microbiology — Vol. 1, no.8, p. 1 (2016)
17. • Journal article

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    Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes

    Van Houdt, Rob Leplae, Raphael Lima Mendez, Gipsi[UCL] Mergeay, Max Toussaint, Ariane (2012) Mobile DNA — Vol. 3, no.1, p. 6 (2012)
18. • Journal article

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    Population-level analysis of gut microbiome variation

    Falony, Gwen Joossens, Marie Vieira-Silva, Sara Wang, Jun Darzi, Youssef Faust, Karoline Kurilshikov, Alexander Bonder, Marc Jan Valles-Colomer, Mireia Vandeputte, Doris Tito, Raul Y. Chaffron, Samuel Rymenans, Leen Verspecht, Chloë De Sutter, Lise Lima Mendez, Gipsi[UCL] D’hoe, Kevin Jonckheere, Karl Homola, Daniel Garcia, Roberto Tigchelaar, Ettje F. Eeckhaudt, Linda Fu, Jingyuan Henckaerts, Liesbet Zhernakova, Alexandra Wijmenga, Cisca Raes, Jeroen (2016) Science — Vol. 352, no.6285, p. 560-564 (2016)
19. • Journal article

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    Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

    Lima Mendez, Gipsi[UCL] Van Helden, J. Toussaint, A. Leplae, R. (2008) Molecular Biology and Evolution — Vol. 25, no.4, p. 762-777 (2008)
20. • Journal article

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    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, J.-M. Bittner, L. Chaffron, S. Dunthorn, M. Engelen, S. Flegontova, O. Guidi, L. Horak, A. Jaillon, O. Lima Mendez, Gipsi[UCL] Luke , 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. Boss, E. Follows, M. Karp-Boss, L. Krzic, U. Reynaud, E. G. Sardet, C. Sullivan, M. B. Velayoudon, D. (2015) Science — Vol. 348, no.6237, p. 1261605-1261605 (2015)
21. • Journal article

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    ACLAME: A CLAssification of Mobile genetic Elements, update 2010

    Leplae, Raphaël Lima Mendez, Gipsi[UCL] Toussaint, Ariane (2009) Nucleic Acids Research — Vol. 38, no.suppl_1, p. D57-D61 (2009)
22. • Journal article

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    A global ocean atlas of eukaryotic genes

    Carradec, Quentin Pelletier, Eric Da Silva, Corinne Alberti, Adriana Seeleuthner, Yoann Blanc-Mathieu, Romain Lima Mendez, Gipsi[UCL] Rocha, Fabio Tirichine, Leila Labadie, Karine Kirilovsky, Amos Bertrand, Alexis Engelen, Stefan Madoui, Mohammed-Amin Méheust, Raphaël Poulain, Julie Romac, Sarah Richter, Daniel J. Yoshikawa, Genki Dimier, Céline Kandels-Lewis, Stefanie Picheral, Marc Searson, Sarah Jaillon, Olivier Aury, Jean-Marc Karsenti, Eric Sullivan, Matthew B. Sunagawa, Shinichi Bork, Peer Not, Fabrice Hingamp, Pascal Raes, Jeroen Guidi, Lionel Ogata, Hiroyuki de Vargas, Colomban Iudicone, Daniele Bowler, Chris Wincker, Patrick (2018) Nature Communications — Vol. 9, no.1, p. 1 (2018)
23. • Journal article

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    Mainstreams of Horizontal Gene Exchange in Enterobacteria: Consideration of the Outbreak of Enterohemorrhagic E. coli O104:H4 in Germany in 2011

    Bezuidt, Oliver Pierneef, Rian Mncube, Kingdom Lima Mendez, Gipsi[UCL] Reva, Oleg N. Hartskeerl, Rudy A. (2011) PLoS ONE — Vol. 6, no.10, p. e25702 (2011)
24. • Journal article

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    Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities : Usingmitags to explore microbial communities

    Logares, Ramiro Sunagawa, Shinichi Salazar, Guillem Cornejo-Castillo, Francisco M. Ferrera, Isabel Sarmento, Hugo Hingamp, Pascal Ogata, Hiroyuki de Vargas, Colomban Lima Mendez, Gipsi[UCL] Raes, Jeroen Poulain, Julie Jaillon, Olivier Wincker, Patrick Kandels-Lewis, Stefanie Karsenti, Eric Bork, Peer Acinas, Silvia G. (2013) Environmental Microbiology — Vol. 16, no.9, p. 2659-2671 (2013)
25. • Book

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    Reticulate Classification of Mosaic Microbial Genomes Using NeAT Website

    Lima Mendez, Gipsi[UCL] (2011)

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