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Items: 24

1.

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, Méheust 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. 2018 Jan 25;9(1):373. doi: 10.1038/s41467-017-02342-1.

2.

Species-function relationships shape ecological properties of the human gut microbiome.

Vieira-Silva S, Falony G, Darzi Y, Lima-Mendez G, Garcia Yunta R, Okuda S, Vandeputte D, Valles-Colomer M, Hildebrand F, Chaffron S, Raes J.

Nat Microbiol. 2016 Jun 13;1(8):16088. doi: 10.1038/nmicrobiol.2016.88.

PMID:
27573110
3.

Population-level analysis of gut microbiome variation.

Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D'hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J.

Science. 2016 Apr 29;352(6285):560-4. doi: 10.1126/science.aad3503. Epub 2016 Apr 28.

4.

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

Cornejo-Castillo FM, Cabello AM, 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 JP, Gasol JM, Massana R, Acinas SG.

Nat Commun. 2016 Mar 22;7:11071. doi: 10.1038/ncomms11071.

5.

Cross-biome comparison of microbial association networks.

Faust K, Lima-Mendez G, Lerat JS, Sathirapongsasuti JF, Knight R, Huttenhower C, Lenaerts T, Raes J.

Front Microbiol. 2015 Oct 27;6:1200. doi: 10.3389/fmicb.2015.01200. eCollection 2015.

6.

Ocean plankton. Determinants of community structure in the global plankton interactome.

Lima-Mendez 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, Bontempi G, 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-Llonch M, Salazar G, Sánchez P, Sebastian M, Souffreau C, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans coordinators, Gorsky G, Not F, Ogata H, Speich S, Stemmann L, Weissenbach J, Wincker P, Acinas SG, Sunagawa S, Bork P, Sullivan MB, Karsenti E, Bowler C, de Vargas C, Raes J.

Science. 2015 May 22;348(6237):1262073. doi: 10.1126/science.1262073.

7.

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean.

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 JM, 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; 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 ME, Speich S, Stemmann L, Sunagawa S, Weissenbach J, Wincker P, Karsenti E.

Science. 2015 May 22;348(6237):1261605. doi: 10.1126/science.1261605.

8.

Ocean plankton. 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. 2015 May 22;348(6237):1261359. doi: 10.1126/science.1261359.

9.

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, 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.

Environ Microbiol. 2014 Sep;16(9):2659-71. doi: 10.1111/1462-2920.12250. Epub 2013 Sep 18.

PMID:
24102695
10.

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, 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.

11.

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

Van Houdt R, Leplae R, Lima-Mendez G, Mergeay M, Toussaint A.

Mob DNA. 2012 Apr 13;3(1):6. doi: 10.1186/1759-8753-3-6.

12.

Reticulate classification of mosaic microbial genomes using NeAT website.

Lima-Mendez G.

Methods Mol Biol. 2012;804:81-91. doi: 10.1007/978-1-61779-361-5_5.

PMID:
22144149
13.

Mainstreams of horizontal gene exchange in enterobacteria: consideration of the outbreak of enterohemorrhagic E. coli O104:H4 in Germany in 2011.

Bezuidt O, Pierneef R, Mncube K, Lima-Mendez G, Reva ON.

PLoS One. 2011;6(10):e25702. doi: 10.1371/journal.pone.0025702. Epub 2011 Oct 14.

14.

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

Lima-Mendez G, Toussaint A, Leplae R.

Res Microbiol. 2011 Oct;162(8):737-46. doi: 10.1016/j.resmic.2011.06.006. Epub 2011 Jun 28.

PMID:
21767638
15.

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

Lima-Mendez G, van Helden J.

Mol Biosyst. 2009 Dec;5(12):1482-93. doi: 10.1039/b908681a. Epub 2009 Oct 2. Review.

PMID:
20023717
16.

ACLAME: a CLAssification of Mobile genetic Elements, update 2010.

Leplae R, Lima-Mendez G, Toussaint A.

Nucleic Acids Res. 2010 Jan;38(Database issue):D57-61. doi: 10.1093/nar/gkp938. Epub 2009 Nov 23.

17.

Comparative analyses of prophage-like elements present in bifidobacterial genomes.

Ventura M, Turroni F, Lima-Mendez G, Foroni E, Zomer A, Duranti S, Giubellini V, Bottacini F, Horvath P, Barrangou R, Sela DA, Mills DA, van Sinderen D.

Appl Environ Microbiol. 2009 Nov;75(21):6929-36. doi: 10.1128/AEM.01112-09. Epub 2009 Sep 4.

18.

Network Analysis Tools: from biological networks to clusters and pathways.

Brohée S, Faust K, Lima-Mendez G, Vanderstocken G, van Helden J.

Nat Protoc. 2008;3(10):1616-29. doi: 10.1038/nprot.2008.100.

PMID:
18802442
19.

NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways.

Brohée S, Faust K, Lima-Mendez G, Sand O, Janky R, Vanderstocken G, Deville Y, van Helden J.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W444-51. doi: 10.1093/nar/gkn336. Epub 2008 Jun 4.

20.

Prophinder: a computational tool for prophage prediction in prokaryotic genomes.

Lima-Mendez G, Van Helden J, Toussaint A, Leplae R.

Bioinformatics. 2008 Mar 15;24(6):863-5. doi: 10.1093/bioinformatics/btn043. Epub 2008 Jan 30.

PMID:
18238785
21.

Reticulate representation of evolutionary and functional relationships between phage genomes.

Lima-Mendez G, Van Helden J, Toussaint A, Leplae R.

Mol Biol Evol. 2008 Apr;25(4):762-77. doi: 10.1093/molbev/msn023. Epub 2008 Jan 29.

PMID:
18234706
22.

PhiGO, a phage ontology associated with the ACLAME database.

Toussaint A, Lima-Mendez G, Leplae R.

Res Microbiol. 2007 Sep;158(7):567-71. Epub 2007 May 21.

PMID:
17614261
23.

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

Lima-Mendez G, Toussaint A, Leplae R.

Virology. 2007 Sep 1;365(2):241-9. Epub 2007 May 7. Review.

24.

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

Leplae R, Lima-Mendez G, Toussaint A.

FEMS Microbiol Rev. 2006 Nov;30(6):980-94. Review.

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