Search Results - "Rouzé, Pierre"

ORCAE: online resource for community annotation of eukaryotes by Sterck, Lieven, Billiau, Kenny, Abeel, Thomas, Rouzé, Pierre, Van de Peer, Yves

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Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences by Bonnet, Eric, Wuyts, Jan, Rouzé, Pierre, Van de Peer, Yves

“…Motivation: Most non-coding RNAs are characterized by a specific secondary and tertiary structure that determines their function. Here, we investigate the…”
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Generic eukaryotic core promoter prediction using structural features of DNA by Abeel, Thomas, Saeys, Yvan, Bonnet, Eric, Rouzé, Pierre, Van de Peer, Yves

“…Despite many recent efforts, in silico identification of promoter regions is still in its infancy. However, the accurate identification and delineation of…”
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Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression by De Bodt, Stefanie, Proost, Sebastian, Vandepoele, Klaas, Rouzé, Pierre, Van de Peer, Yves

“…Large-scale identification of the interrelationships between different components of the cell, such as the interactions between proteins, has recently gained…”
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Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features by Derelle, E, Ferraz, C, Rombauts, S, Rouze, P, Worden, A.Z, Robbens, S, Partensky, F, Degroeve, S, Echeynie, S, Cooke, R

“…The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. In…”
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small RNA world of plants by Bonnet, Eric, Van de Peer, Yves, Rouzé, Pierre

“…RNA has many functions in addition to being a simple messenger between the genome and the proteome. Over two decades, several classes of small noncoding RNAs…”
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Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp by Farhat, Sarah, Le, Phuong, Kayal, Ehsan, Noel, Benjamin, Bigeard, Estelle, Corre, Erwan, Maumus, Florian, Florent, Isabelle, Alberti, Adriana, Aury, Jean-Marc, Barbeyron, Tristan, Cai, Ruibo, Da Silva, Corinne, Istace, Benjamin, Labadie, Karine, Marie, Dominique, Mercier, Jonathan, Rukwavu, Tsinda, Szymczak, Jeremy, Tonon, Thierry, Alves-de-Souza, Catharina, Rouzé, Pierre, Van de Peer, Yves, Wincker, Patrick, Rombauts, Stephane, Porcel, Betina M, Guillou, Laure

“…Dinoflagellates are aquatic protists particularly widespread in the oceans worldwide. Some are responsible for toxic blooms while others live in symbiotic…”
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A Comprehensive Analysis of Genes Encoding Small Secreted Proteins Identifies Candidate Effectors in Melampsora larici-populina (Poplar Leaf Rust) by HACQUARD, Stéphane, JOLY, David L, FREY, Pascal, DE PEER, Yves Van, ROUZE, Pierre, MARTIN, Francis, HAMELIN, Richard C, DUPLESSIS, Sébastien, LIN, Yao-Cheng, TISSERANT, Emilie, FEAU, Nicolas, DELARUELLE, Christine, LEGUE, Valérie, KOHLER, Annegret, TANGUAY, Philippe, PETRE, Benjamin

“…The obligate biotrophic rust fungus Melampsora larici-populina is the most devastating and widespread pathogen of poplars. Studies over recent years have…”
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ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles by Abeel, Thomas, Saeys, Yvan, Rouzé, Pierre, Van de Peer, Yves

“…Motivation: More and more genomes are being sequenced, and to keep up with the pace of sequencing projects, automated annotation techniques are required. One…”
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Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress by Dittami, Simon M, Scornet, Delphine, Petit, Jean-Louis, Ségurens, Béatrice, Da Silva, Corinne, Corre, Erwan, Dondrup, Michael, Glatting, Karl-Heinz, König, Rainer, Sterck, Lieven, Rouzé, Pierre, Van de Peer, Yves, Cock, J Mark, Boyen, Catherine, Tonon, Thierry

“…Brown algae (Phaeophyceae) are phylogenetically distant from red and green algae and an important component of the coastal ecosystem. They have developed…”
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PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences by Lescot, Magali, Déhais, Patrice, Thijs, Gert, Marchal, Kathleen, Moreau, Yves, Van de Peer, Yves, Rouzé, Pierre, Rombauts, Stephane

“…PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices,…”
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Current methods of gene prediction, their strengths and weaknesses by Mathé, Catherine, Sagot, Marie‐France, Schiex, Thomas, Rouzé, Pierre

“…While the genomes of many organisms have been sequenced over the last few years, transforming such raw sequence data into knowledge remains a hard task. A…”
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The complex intron landscape and massive intron invasion in a picoeukaryote provides insights into intron evolution by Verhelst, Bram, Van de Peer, Yves, Rouzé, Pierre

“…Genes in pieces and spliceosomal introns are a landmark of eukaryotes, with intron invasion usually assumed to have happened early on in evolution. Here, we…”
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A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling by Thijs, Gert, Lescot, Magali, Marchal, Kathleen, Rombauts, Stephane, De Moor, Bart, Rouzé, Pierre, Moreau, Yves

“…Motivation: Transcriptome analysis allows detection and clustering of genes that are coexpressed under various biological circumstances. Under the assumption…”
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In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists by Saeys, Yvan, Rouzé, Pierre, Van de Peer, Yves

“…Motivation: Prediction of the coding potential for stretches of DNA is crucial in gene calling and genome annotation, where it is used to identify potential…”
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Higher Intron Loss Rate in Arabidopsis thaliana Than A. lyrata Is Consistent with Stronger Selection for a Smaller Genome by Fawcett, Jeffrey A., Rouzé, Pierre, Van de Peer, Yves

“…The number of introns varies considerably among different organisms. This can be explained by the differences in the rates of intron gain and loss. Two factors…”
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Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine by Chancerel, Emilie, Lepoittevin, Camille, Le Provost, Grégoire, Lin, Yao-Cheng, Jaramillo-Correa, Juan Pablo, Eckert, Andrew J, Wegrzyn, Jill L, Zelenika, Diana, Boland, Anne, Frigerio, Jean-Marc, Chaumeil, Philippe, Garnier-Géré, Pauline, Boury, Christophe, Grivet, Delphine, González-Martínez, Santiago C, Rouzé, Pierre, Van de Peer, Yves, Neale, David B, Cervera, Maria T, Kremer, Antoine, Plomion, Christophe

“…Single nucleotide polymorphisms (SNPs) are the most abundant source of genetic variation among individuals of a species. New genotyping technologies allow…”
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Large-scale structural analysis of the core promoter in mammalian and plant genomes by Florquin, Kobe, Saeys, Yvan, Degroeve, Sven, Rouzé, Pierre, Van de Peer, Yves

“…DNA encodes at least two independent levels of functional information. The first level is for encoding proteins and sequence targets for DNA-binding factors,…”
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Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage by Moreau, Hervé, Verhelst, Bram, Couloux, Arnaud, Derelle, Evelyne, Rombauts, Stephane, Grimsley, Nigel, Van Bel, Michiel, Poulain, Julie, Katinka, Michaël, Hohmann-Marriott, Martin F, Piganeau, Gwenael, Rouzé, Pierre, Da Silva, Corinne, Wincker, Patrick, Van de Peer, Yves, Vandepoele, Klaas

“…BACKGROUND: Bathycoccus prasinos is an extremely small cosmopolitan marine green alga whose cells are covered with intricate spider's web patterned scales that…”
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SpliceMachine: predicting splice sites from high-dimensional local context representations by Degroeve, Sven, Saeys, Yvan, De Baets, Bernard, Rouzé, Pierre, Van de Peer, Yves

“…Motivation: In this age of complete genome sequencing, finding the location and structure of genes is crucial for further molecular research. The accurate…”
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