Search Results - "Lima‐Mendez, Gipsi"

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities by Logares, Ramiro, Sunagawa, Shinichi, Salazar, Guillem, Cornejo‐Castillo, Francisco M, Ferrera, Isabel, Sarmento, Hugo, Hingamp, Pascal, Ogata, Hiroyuki, Vargas, Colomban, Lima‐Mendez, Gipsi, Raes, Jeroen, Poulain, Julie, Jaillon, Olivier, Wincker, Patrick, Kandels‐Lewis, Stefanie, Karsenti, Eric, Bork, Peer, Acinas, Silvia G

“…Sequencing of 16S rDNA polymerase chain reaction (PCR) amplicons is the most common approach for investigating environmental prokaryotic diversity, despite the…”
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Cross-biome comparison of microbial association networks by Faust, Karoline, Lima-Mendez, Gipsi, Lerat, Jean-Sébastien, Sathirapongsasuti, Jarupon F, Knight, Rob, Huttenhower, Curtis, Lenaerts, Tom, Raes, Jeroen

“…Clinical and environmental meta-omics studies are accumulating an ever-growing amount of microbial abundance data over a wide range of ecosystems. With a…”
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first global analysis of plasmid encoded proteins in the ACLAME database by Leplae, Raphaël, Lima-Mendez, Gipsi, Toussaint, Ariane

“…Many plasmids are mobile genetic elements (MGEs) and, as other members of that group of DNA entities, their genomes display a mosaic and combinatorial…”
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ACLAME: a CLAssification of Mobile genetic Elements, update 2010 by Leplae, Raphaël, Lima-Mendez, Gipsi, Toussaint, Ariane

“…The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids)…”
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Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota by Tito, Raul Y, Chaffron, Samuel, Caenepeel, Clara, Lima-Mendez, Gipsi, Wang, Jun, Vieira-Silva, Sara, Falony, Gwen, Hildebrand, Falk, Darzi, Youssef, Rymenans, Leen, Verspecht, Chloë, Bork, Peer, Vermeire, Severine, Joossens, Marie, Raes, Jeroen

“…Human gut microbiome studies are mainly bacteria- and archaea-oriented, overlooking the presence of single-cell eukaryotes such as an enteric stramenopiles…”
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Rhizomania: Hide and Seek of Polymyxa betae and the Beet Necrotic Yellow Vein Virus with Beta vulgaris by Decroës, Alain, Mahillon, Mathieu, Genard, Margaux, Lienard, Charlotte, Lima-Mendez, Gipsi, Gilmer, David, Bragard, Claude, Legrève, Anne

“…The molecular interactions between Polymyxa betae, the protist vector of sugar beet viruses, beet necrotic yellow vein virus (BNYVV), the causal agent of…”
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The powerful law of the power law and other myths in network biology by Lima-Mendez, Gipsi, van Helden, Jacques

“…For almost 10 years, topological analysis of different large-scale biological networks (metabolic reactions, protein interactions, transcriptional regulation)…”
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Species–function relationships shape ecological properties of the human gut microbiome by Vieira-Silva, Sara, Falony, Gwen, Darzi, Youssef, Lima-Mendez, Gipsi, Garcia Yunta, Roberto, Okuda, Shujiro, Vandeputte, Doris, Valles-Colomer, Mireia, Hildebrand, Falk, Chaffron, Samuel, Raes, Jeroen

“…Despite recent progress, the organization and ecological properties of the intestinal microbial ecosystem remain under-investigated. Here, using a manually…”
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Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes by Hingamp, Pascal, Grimsley, Nigel, Acinas, Silvia G, Clerissi, Camille, Subirana, Lucie, Poulain, Julie, Ferrera, Isabel, Sarmento, Hugo, Villar, Emilie, Lima-Mendez, Gipsi, 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

“…Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the…”
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Prophinder: a computational tool for prophage prediction in prokaryotic genomes by Lima-Mendez, Gipsi, Van Helden, Jacques, Toussaint, Ariane, Leplae, Raphaël

“…Prophinder is a prophage prediction tool coupled with a prediction database, a web server and web service. Predicted prophages will help to fill the gaps in…”
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Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton by Cornejo-Castillo, Francisco M., Cabello, Ana M., Salazar, Guillem, Sánchez-Baracaldo, Patricia, Lima-Mendez, Gipsi, 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.

“…The unicellular cyanobacterium UCYN-A, one of the major contributors to nitrogen fixation in the open ocean, lives in symbiosis with single-celled…”
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Disentangling environmental effects in microbial association networks by Deutschmann, Ina Maria, Lima-Mendez, Gipsi, Krabberød, Anders K, Raes, Jeroen, Vallina, Sergio M, Faust, Karoline, Logares, Ramiro

“…Ecological interactions among microorganisms are fundamental for ecosystem function, yet they are mostly unknown or poorly understood. High-throughput-omics…”
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Meeting Report of the Second Symposium of the Belgian Society for Viruses of Microbes and Launch of the Phage Valley by Desmecht, Salomé, Latka, Agnieszka, Ceyssens, Pieter-Jan, Garcia-Pino, Abel, Gillis, Annika, Lavigne, Rob, Lima-Mendez, Gipsi, Matthijnssens, Jelle, Vázquez, Roberto, Venneman, Jolien, Wagemans, Jeroen, Briers, Yves, Thiry, Damien

“…The second symposium of the Belgian Society for Viruses of Microbes (BSVoM) took place on 8 September 2023 at the University of Liège with 141 participants…”
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HOXA1 Is an Antagonist of ERα in Breast Cancer by Belpaire, Magali, Ewbank, Bruno, Taminiau, Arnaud, Bridoux, Laure, Deneyer, Noémie, Marchese, Damien, Lima-Mendez, Gipsi, Baurain, Jean-François, Geerts, Dirk, Rezsohazy, René

“…Breast cancer is a heterogeneous disease and the leading cause of female cancer mortality worldwide. About 70% of breast cancers express ERα. HOX proteins are…”
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Foundation of the Belgian Society for Viruses of Microbes and Meeting Report of Its Inaugural Symposium by Latka, Agnieszka, Aertsen, Abram, Boeckaerts, Dimitri, Blasdel, Bob, Ceyssens, Pieter-Jan, Garcia-Pino, Abel, Gillis, Annika, Lavigne, Rob, Lima-Mendez, Gipsi, Matthijnssens, Jelle, Onsea, Jolien, Peeters, Eveline, Pirnay, Jean-Paul, Thiry, Damien, Vandenheuvel, Dieter, Van Mechelen, Els, Venneman, Jolien, Verbeken, Gilbert, Wagemans, Jeroen, Briers, Yves

“…The Belgian Society for Viruses of Microbes (BSVoM) was founded on 9 June 2022 to capture and enhance the collaborative spirit among the expanding community of…”
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At the Gate of Mutualism: Identification of Genomic Traits Predisposing to Insect-Bacterial Symbiosis in Pathogenic Strains of the Aphid Symbiont Serratia symbiotica by Renoz, François, Foray, Vincent, Ambroise, Jérôme, Baa-Puyoulet, Patrice, Bearzatto, Bertrand, Mendez, Gipsi Lima, Grigorescu, Alina S, Mahillon, Jacques, Mardulyn, Patrick, Gala, Jean-Luc, Calevro, Federica, Hance, Thierry

“…Mutualistic associations between insects and heritable bacterial symbionts are ubiquitous in nature. The aphid symbiont is a valuable candidate for studying…”
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Correction to: Disentangling environmental effects in microbial association networks by Deutschmann, Ina Maria, Lima-Mendez, Gipsi, Krabberød, Anders K, Raes, Jeroen, Vallina, Sergio M, Faust, Karoline, Logares, Ramiro

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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 by Bezuidt, Oliver, Pierneef, Rian, Mncube, Kingdom, Lima-Mendez, Gipsi, Reva, Oleg N

“…Escherichia coli O104:H4 caused a severe outbreak in Europe in 2011. The strain TY-2482 sequenced from this outbreak allowed the discovery of its closest…”
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Analysis of the phage sequence space: The benefit of structured information by Lima-Mendez, Gipsi, Toussaint, Ariane, Leplae, Raphaël

“…Abstract Phages are the most abundant biological entities on Earth and are central players in the evolution of their bacterial hosts and the emergence of new…”
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Comparative Analyses of Prophage-Like Elements Present in Bifidobacterial Genomes by Ventura, Marco, Turroni, Francesca, Lima-Mendez, Gipsi, Foroni, Elena, Zomer, Aldert, Duranti, Sabrina, Giubellini, Vanessa, Bottacini, Francesca, Horvath, Philippe, Barrangou, Rodolphe, Sela, David A, Mills, David A, van Sinderen, Douwe

“…So far, only scarce and rather diffuse information is available on bacteriophages infecting members of the genus BIFIDOBACTERIUM: In the current study, we…”
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