Open access to sequence: Browsing the Pichia pastorisgenome (2009)
Mattanovich, Diethard, Callewaert, Nico, Rouzé, Pierre, Lin, Yao-Cheng, Graf, Alexandra, Redl, Andreas, ...
Abstract The first genome sequences of the important yeast protein production host Pichia pastoris have been released into the public domain this spring. In order to provide the scientific community...
De Bodt, Stefanie, Proost, Sebastian, Vandepoele, Klaas, Rouzé, Pierre, Van De Peer, Yves
Abstract Background Large-scale identification of the interrelationships between different components of the cell, such as the interactions between proteins, has recently gained great interest....
Dittami, Simon M, Scornet, Delphine, Petit, Jean-Louis, Ségurens, Béatrice, Da Silva, Corinne, Corre, Erwan, ...
Abstract Background Brown algae (Phaeophyceae) are phylogenetically distant from red and green algae and an important component of the coastal ecosystem. They have developed unique mechanisms that...
Worden, Alexandra Z., Lee, Jea-Hyeok, Mock, Thomas, Rouzé, Pierre, Simmons, Melinda P., Aerts, Andrea L., ...
Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from...
Genome sequence of the recombinant protein production host Pichia pastoris (2009)
De Schutter, Kristof, Lin, Yao-Cheng, Tiels, Petra, Van Hecke, Annelies, Glinka, S, Weber-Lehmann, J, ...
The methylotrophic yeast Pichia pastoris is widely used for the production of proteins and as a model organism for studying peroxisomal biogenesis and methanol assimilation. P. pastoris strains...
Dittami, Simon, Scornet, Delphine, Petit, Jean-Louis, Ségurens, Béatrice, Da Silva, Corinne, Corre, Erwan, ...
Background: Brown algae (Phaeophyceae) are phylogenetically distant from red and green algae and an important component of the coastal ecosystem. They have developed unique mechanisms that allow them...
De Bodt, Stefanie, Proost, Sebastian, Vandepoele, Klaas, Rouzé, Pierre, Van De Peer, Yves
Background: Large-scale identification of the interrelationships between different components of the cell, such as the interactions between proteins, has recently gained great interest. However,...
DOI: 10.1093/nar/gkg071 CATMA: a complete Arabidopsis GST database (2008)
Mark L. Crowe, Carine Serizet, Vincent Thareau, Sébastien Aubourg, Pierre Rouzé, Pierre Hilson, ...
The Complete Arabidopsis Transcriptome Micro Array (CATMA) database contains gene sequence tag (GST) and gene model sequences for over 70% of the predicted genes in the Arabidopsis thaliana genome as...
Yvan Saeys, Pierre Rouzé, Alfonso Valencia
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 exons and to position their boundaries in...
Sébastien Aubourg, Véronique Brunaud, Clémence Bruyère, Mark Cock, Pierre Rouzé, Michel Schneider, ...
GeneFarm, structural and functional annotation of
The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis (2008)
MARTIN, F, AERTS, A, AHREN, D, BRUN, A, DANCHIN, EGJ, DUCHAUSSOY, F, ...
The FTO gene, implicated in human obesity, is found only in vertebrates and marine algae (2008)
Robbens, Steven, Rouzé, Pierre, COCK, JM, SPRING, J, WORDEN, AZ, Van De Peer, Yves
Generic eukaryotic core promoter prediction using structural features of DNA (2008)
Abeel, Thomas, Saeys, Yvan, Bonnet, Eric, Rouzé, Pierre, Van De Peer, Yves
Genome annotation in plants and fungi: EuGene as a model platform. (2008)
FOISSAC, S, GOUZY, J, Rombauts, Stephane, Mathe, Catherine, AMSELEM, J, Sterck, Lieven, ...
ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles (2008)
Abeel, Thomas, Saeys, Yvan, Rouzé, Pierre, Van De Peer, Yves
Generic eukaryotic core promoter prediction using structural features of DNA (2008)
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 promoter regions is important for several...
ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles (2008)
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 of the most challenging problems in...
combines several sources of evidence (2007)
Thomas Schiex, Annick Moisan, Pierre Rouzé
EuGène: an eukaryotic gene finder that
Gene finding integrating external evidence (2007)
Thomas Schiex, Catherine Mathé, Annick Moisan, Pierre Rouzé
EuGène, a gene finder for Arabidopsis thaliana, combines the output of several information sources, including output of other software or user information. To achieve this, a weighted DAG is built...
How many genes are there in plants (. . . and why are they there)? (2007)
Sterck, Lieven, Rombauts, Stephane, Vandepoele, Klaas, Rouzé, Pierre, Van De Peer, Yves
Unique regulation of the Calvin cycle in the ultrasmall green alga Ostreococcus (2007)
Robbens, Steven, PETERSEN, J, BRINKMANN, H, Rouzé, Pierre, Van De Peer, Yves
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 exons and to position their boundaries in...
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 exons and to position their boundaries in...
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray) (2006)
TUSKAN, GA, DIFAZIO, S, JANSSON, S, BOHLMANN, J, GRIGORIEV, I, HELLSTEN, U, ...
SpliceMachine: predicting splice sites from high-dimensional local context representations (2005)
Degroeve, Sven, Saeys, Yvan, De Baets, Bernard, Rouzé, Pierre, Van De Peer, Yves
Large-scale structural analysis of the core promoter in mammalian and plant genomes. (2005)
Florquin, Kobe, Saeys, Yvan, Degroeve, Sven, Rouzé, Pierre, Van De Peer, Yves
EST data suggest that poplar is an ancient polyploid (2005)
Sterck, Lieven, Rombauts, Stephane, JANSSON, S, STERKY, F, Rouzé, Pierre, Van De Peer, Yves
Kobe Florquin, Yvan Saeys, Sven Degroeve, Pierre Rouzé
Large-scale structural analysis of the core promoter
Aubourg, Sébastien, Brunaud, Véronique, Bruyère, Clémence, Cock, Mark, Cooke, Richard, Cottet, Annick, ...
Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation...
Large-scale structural analysis of the core promoter in mammalian and plant genomes (2005)
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, while the second one is contained in the...
SpliceMachine: predicting splice sites from high-dimensional local context representations (2005)
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 prediction of intron boundaries largely...
Feature selection for splice site prediction: A new method using EDA-based feature ranking (2004)
Saeys, Yvan, Degroeve, Sven, Aeyels, Dirk, Rouzé, Pierre, Van De Peer, Yves
Abstract Background The identification of relevant biological features in large and complex datasets is an important step towards gaining insight in the processes underlying the data. Other...
Feature selection for splice site prediction: A new method using EDA-based feature ranking (2004)
Saeys, Yvan, Degroeve, Sven, Aeyels, Dirk, Rouzé, Pierre, Van De Peer, Yves
Selecting relevant features for gene structure prediction (2004)
Saeys, Yvan, Degroeve, Sven, Aeyels, Dirk, Rouzé, Pierre, Van De Peer, Yves
Lescot, Magali, Rombauts, Stephane, Zhang, Jiong, Aubourg, Sébastien, Mathé, Catherine, JANSSON, S, ...
Splice site prediction in eukaryote genome sequences: the algorithmic issues. (2004)
Degroeve, Sven, Saeys, Yvan, De Baets, Bernard, Van De Peer, Yves, Rouzé, Pierre
Yvan Saeys, Sven Degroeve, Dirk Aeyels, Pierre Rouzé, Yves Van De, Biomed Central
Background: The identification of relevant biological features in large and complex datasets is an important step towards gaining insight in the processes underlying the data. Other advantages of...
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 folding energy of the secondary structure of...
SpliceMachine: predicting splice sites from high-dimensional local context representations (2004)
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 prediction of intron boundaries largely...
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 folding energy of the secondary structure of...
Hilson, Pierre, Allemeersch, Joke, Altmann, Thomas, Aubourg, Sébastien, Avon, Alexandra, Beynon, Jim, ...
Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization...
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 folding energy of the secondary structure of...
SpliceMachine: predicting splice sites from high-dimensional local context representations (2004)
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 prediction of intron boundaries largely...
Automatic design of gene-specific sequence tags for genome-wide functional studies (2003)
Thareau, Vincent, Dehais, Patrice, Serizet, Carine, Hilson, Pierre, Rouzé, Pierre, Aubourg, Stephane
Computational approaches to identify promoters and cis-regulatory elements in plant genomes (2003)
Rombauts, Stephane, Florquin, Kobe, Lescot, Magali, MARCHAL, K, Rouzé, Pierre, Van De Peer, Yves
De Bodt, Stefanie, Raes, Jeroen, Florquin, Kobe, Rombauts, Stephane, Rouzé, Pierre, THEISSEN, G, ...
CATMA: a complete Arabidopsis GST database (2003)
CROWE, ML, Serizet, Carine, Thareau, Vincent, AUBOURG, B, Rouzé, Pierre, Hilson, Pierre, ...
DOI: 10.1093/bioinformatics/btg1076 (2003)
Yvan Saeys, Sven Degroeve, Dirk Aeyels, Pierre Rouzé
Vol. 19 Suppl. 2 2003, pages ii179–ii188
CATMA: a complete Arabidopsis GST database (2003)
Crowe, Mark L., Serizet, Carine, Thareau, Vincent, Aubourg, Sébastien, Rouzé, Pierre, Hilson, Pierre, ...
The Complete Arabidopsis Transcriptome Micro Array (CATMA) database contains gene sequence tag (GST) and gene model sequences for over 70% of the predicted genes in the Arabidopsis thaliana...
Saeys, Yvan, Degroeve, Sven, Aeyels, Dirk, Van De Peer, Yves, Rouzé, Pierre
Motivation: Feature subset selection is an important preprocessing step for classification. In biology, where structures or processes are described by a large number of features, the elimination of...
Automatic design of gene-specific sequence tags for genome-wide functional studies (2003)
Thareau, Vincent, Déhais, Patrice, Serizet, Carine, Hilson, Pierre, Rouzé, Pierre, Aubourg, Sébastien
Motivation: The availability of complete genome sequences allows the identification of short DNA segments that are specific to each annotated gene. Such unique gene sequence tags (GSTs) replace...
CATMA: a complete Arabidopsis GST database (2002)
Crowe,Mark L., Serizet,Carine, Thareau,Vincent, Aubourg,Sébastien, Rouzé,Pierre, Hilson,Pierre, ...
The Complete Arabidopsis Transcriptome Micro Array (CATMA) database contains gene sequence tag (GST) and gene model sequences for over 70% of the predicted genes in the Arabidopsis thaliana genome as...
CATMA: a complete Arabidopsis GST database (2002)
Crowe, Mark L., Serizet, Carine, Thareau, Vincent, Aubourg, Sébastien, Rouzé, Pierre, Hilson, Pierre, ...
The Complete Arabidopsis Transcriptome Micro Array (CATMA) database contains gene sequence tag (GST) and gene model sequences for over 70% of the predicted genes in the Arabidopsis thaliana genome as...
INCLUSive: INtegrated clustering, upstream of sequence retrieval and motif sampling. (2002)
THIJS, G, MOREAU, Y, De Smet, Fabienne, MATHYS, J, Lescot, Magali, Rombauts, Stephane, ...
Feature subset selection for splice site prediction. (2002)
Degroeve, Sven, De Baets, Bernard, Van De Peer, Yves, Rouzé, Pierre
Feature subset selection for splice site prediction by estimation of distribution algorithms. (2002)
Saeys, Yvan, Degroeve, Sven, Aeyels, Dirk, Van De Peer, Yves, Rouzé, Pierre
Genome-wide analysis of core cell cycle genes in Arabidopsis (2002)
Vandepoele, Klaas, Raes, Jeroen, De Veylder, Lieven, Rouzé, Pierre, Rombauts, Stephane, Inzé, Dirk
Gert Thijs, Kathleen Marchal, Magali Lescot, Stephane Rombauts, Bart De Moor, Pierre Rouzé, ...
Microarray experiments can reveal important information about transcriptional regulation. In our case, we look for potential promoter regulatory elements in the upstream region of coexpressed genes....
Pages S75–S83 Feature subset selection for splice site prediction (2002)
Sven Degroeve, Bernard De Baets, Pierre Rouzé
Motivation: The large amount of available annotated Arabidopsis thaliana sequences allows the induction of splice site prediction models with supervised learning algorithms (see Haussler (1998) for a...
Lescot, Magali, Déhais, Patrice, Thijs, Gert, Marchal, Kathleen, Moreau, Yves, Van De Peer, Yves, ...
PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on...
Feature subset selection for splice site prediction (2002)
Degroeve, Sven, De Baets, Bernard, Van De Peer, Yves, Rouzé, Pierre
Motivation: The large amount of available annotated Arabidopsis thaliana sequences allows the induction of splice site prediction models with supervised learning algorithms (see Haussler (1998) for a...
Current methods of gene prediction, their strengths and weaknesses (2002)
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 great number of prediction programs have...
In silico search of plant cis-acting regulatory elements. (2001)
Lescot, Magali, Rombauts, Stephane, THIJS, G, MARCHAL, K, DE MOOR, B, MOREAU, Y, ...
Automatic design of gene specific tags for transcriptome studies. (2001)
Thareau, Vincent, Dehais, Patrice, Rouzé, Pierre, Aubourg, Sébastien
Thijs, Gert, Lescot, Magali, Marchal, Kathleen, Rombauts, Stephane, De Moor, Bart, Rouzé, Pierre, ...
Motivation: Transcriptome analysis allows detection and clustering of genes that are coexpressed under various biological circumstances. Under the assumption that coregulated genes share cis-acting...
Gene prediction and gene classes in Arabidopsis thaliana. (2000)
Mathe, Catherine, Dehais, Patrice, PAVY, N, Rombauts, Stephane, Van Montagu, Marc, Rouzé, Pierre
PPMdb: a plant plasma membrane database. (2000)
SAHNOUN, I, Dehais, Patrice, Van Montagu, Marc, ROSSIGNOL, M, Rouzé, Pierre
PlantCARE, a plant cis-acting regulatory element database. (1999)
Rombauts, Stephane, Dehais, Patrice, Van Montagu, Marc, Rouzé, Pierre
Terryn, Nancy, HEIJNEN, L, De Keyser, Annick, VAN ASSELDONCK, M, De Clercq, Rebecca, VERBAKEL, H, ...
Recognition of gene regulatory sequences by bagging of neural networks. (1999)
THIJS, G, MOREAU, Y, Rombauts, Stephane, DE MOOR, B, Rouzé, Pierre
Pavy, Nathalie, Rombauts, Stephane, Déhais, Patrice, Mathé, Catherine, V. V.Ramana, Davuluri, Leroy, Philippe, ...
Motivation: The annotation of the Arabidopsis thalianagenome remains a problem in terms of time and quality. To improve the annotation process, we want to choose the most appropriate tools to use...
Use of a proteome strategy for tagging proteins present at the plasma membrane. (1998)
SANTONI, V, ROUQUIE, D, DOUMAS, P, MANSION, M, BOUTRY, M, DEGAND, H, ...
Analysis of T-DNA-mediated translational beta-glucuronidase gene fusions. (1998)
KERTBUNDIT, S, LINACERO, R, Rouzé, Pierre, GALIS, I, MACAS, J, DEBOECK, F, ...
Terryn, Nancy, Gielen, Jan, De Keyser, Annick, Van Den Daele, Hilde, Ardiles Diaz, Wilson, Neyt, Pia, ...
Classification des séquences codantes d'Arabidopsis thaliana. (1998)
Mathe, Catherine, PERESETSKY, A, Dehais, Patrice, Van Montagu, Marc, Rouzé, Pierre
Terryn, Nancy, Neyt, Pia, De Clercq, Rebecca, De Keyser, Annick, Van Den Daele, Hilde, Ardiles Diaz, Wilson, ...
Gene prediction in Arabidopsis thaliana: Genomic sequences. (1996)
Rouzé, Pierre, Rombauts, Stephane, VANLAERE, G, Van Wiemeersch, Luc, Van Montagu, Marc
Exon prediction in eucaryotic genomes. (1996)
VIGNAL, L, DAUBENTONCARAFA, Y, LISACEK, F, NGUIFO, EM, Rouzé, Pierre, QUINQUETON, J, ...
Non-canonical introns are at least 10(9) years old. (1996)
WU, HJ, GAUBIERCOMELLA, P, DELSENY, M, GRELLET, F, Van Montagu, Marc, Rouzé, Pierre
Terryn, Nancy, Villarroel-Mandiola, Raimundo, Neyt, Pia, De Clercq, Rebecca, Ardiles Diaz, Wilson, De Keyser, Annick, ...
Stefan M. Hebsgaard, Peter G. Korning, Niels Tolstrup, Jacob Engelbrecht, Pierre Rouzé, Søren Brunak
Artificial neural networks have been combined with a rule based system to predict intron splice sites in the dicot plant Arabidopsis thaliana. A two step prediction scheme, where a global prediction...
Lescot, Magali, Déhais, Patrice, Thijs, Gert, Marchal, Kathleen, Moreau, Yves, Van De Peer, Yves, ...
PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on...
SURVEY AND SUMMARY: Current methods of gene prediction, their strengths and weaknesses
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 great number of prediction programs have...
Genome-Wide Analysis of Core Cell Cycle Genes in Arabidopsis
Vandepoele, Klaas, Raes, Jeroen, De Veylder, Lieven, Rouzé, Pierre, Rombauts, Stephane, Inzé, Dirk
Cyclin-dependent kinases and cyclins regulate with the help of different interacting proteins the progression through the eukaryotic cell cycle. A high-quality, homology-based annotation protocol was...
CATMA: a complete Arabidopsis GST database
Crowe, Mark L., Serizet, Carine, Thareau, Vincent, Aubourg, Sébastien, Rouzé, Pierre, Hilson, Pierre, ...
The Complete Arabidopsis Transcriptome Micro Array (CATMA) database contains gene sequence tag (GST) and gene model sequences for over 70% of the predicted genes in the Arabidopsis thaliana genome as...
Computational Approaches to Identify Promoters and cis-Regulatory Elements in Plant Genomes1
Rombauts, Stephane, Florquin, Kobe, Lescot, Magali, Marchal, Kathleen, Rouzé, Pierre, Van De Peer, Yves
The identification of promoters and their regulatory elements is one of the major challenges in bioinformatics and integrates comparative, structural, and functional genomics. Many different...
Feature selection for splice site prediction: A new method using EDA-based feature ranking
Saeys, Yvan, Degroeve, Sven, Aeyels, Dirk, Rouzé, Pierre, Van De Peer, Yves
Bonnet, Eric, Wuyts, Jan, Rouzé, Pierre, Van De Peer, Yves
MicroRNAs (miRNAs) are an extensive class of tiny RNA molecules that regulate the expression of target genes by means of complementary base pair interactions. Although the first miRNAs were...
Hilson, Pierre, Allemeersch, Joke, Altmann, Thomas, Aubourg, Sébastien, Avon, Alexandra, Beynon, Jim, ...
Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization...
Aubourg, Sébastien, Brunaud, Véronique, Bruyère, Clémence, Cock, Mark, Cooke, Richard, Cottet, Annick, ...
Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation...
Large-scale structural analysis of the core promoter in mammalian and plant genomes
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, while the second one is contained in the...
Lescot, Magali, Déhais, Patrice, Thijs, Gert, Marchal, Kathleen, Moreau, Yves, Van De Peer, Yves, ...
PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on...
SURVEY AND SUMMARY: Current methods of gene prediction, their strengths and weaknesses
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 great number of prediction programs have...
Genome-Wide Analysis of Core Cell Cycle Genes in Arabidopsis
Vandepoele, Klaas, Raes, Jeroen, De Veylder, Lieven, Rouzé, Pierre, Rombauts, Stephane, Inzé, Dirk
Cyclin-dependent kinases and cyclins regulate with the help of different interacting proteins the progression through the eukaryotic cell cycle. A high-quality, homology-based annotation protocol was...
CATMA: a complete Arabidopsis GST database
Crowe, Mark L., Serizet, Carine, Thareau, Vincent, Aubourg, Sébastien, Rouzé, Pierre, Hilson, Pierre, ...
The Complete Arabidopsis Transcriptome Micro Array (CATMA) database contains gene sequence tag (GST) and gene model sequences for over 70% of the predicted genes in the Arabidopsis thaliana genome as...
Computational Approaches to Identify Promoters and cis-Regulatory Elements in Plant Genomes1
Rombauts, Stephane, Florquin, Kobe, Lescot, Magali, Marchal, Kathleen, Rouzé, Pierre, Van De Peer, Yves
The identification of promoters and their regulatory elements is one of the major challenges in bioinformatics and integrates comparative, structural, and functional genomics. Many different...
Feature selection for splice site prediction: A new method using EDA-based feature ranking
Saeys, Yvan, Degroeve, Sven, Aeyels, Dirk, Rouzé, Pierre, Van De Peer, Yves
Bonnet, Eric, Wuyts, Jan, Rouzé, Pierre, Van De Peer, Yves
MicroRNAs (miRNAs) are an extensive class of tiny RNA molecules that regulate the expression of target genes by means of complementary base pair interactions. Although the first miRNAs were...
Hilson, Pierre, Allemeersch, Joke, Altmann, Thomas, Aubourg, Sébastien, Avon, Alexandra, Beynon, Jim, ...
Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization...
Aubourg, Sébastien, Brunaud, Véronique, Bruyère, Clémence, Cock, Mark, Cooke, Richard, Cottet, Annick, ...
Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation...
Large-scale structural analysis of the core promoter in mammalian and plant genomes
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, while the second one is contained in the...
Derelle, Evelyne, Ferraz, Conchita, Rombauts, Stephane, Rouzé, Pierre, Worden, Alexandra Z., Robbens, Steven, ...
The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. In this study, we unveil the complete genome...
The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation
Palenik, Brian, Grimwood, Jane, Aerts, Andrea, Rouzé, Pierre, Salamov, Asaf, Putnam, Nicholas, ...
The smallest known eukaryotes, at ≈1-μm diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with...
Generic eukaryotic core promoter prediction using structural features of DNA
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 promoter regions is important for several...
Dittami, Simon M, Scornet, Delphine, Petit, Jean-Louis, Ségurens, Béatrice, Da Silva, Corinne, Corre, Erwan, ...
The brown alga Ectocarpus siliculosus, unlike terrestrial plants, undergoes extensive reprogramming of its transcriptome during the acclimation to mild abiotic stress.
ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles
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 of the most challenging problems in...
Open access to sequence: Browsing the Pichia pastoris genome
Mattanovich, Diethard, Callewaert, Nico, Rouzé, Pierre, Lin, Yao-Cheng, Graf, Alexandra, Redl, Andreas, ...
The first genome sequences of the important yeast protein production host Pichia pastoris have been released into the public domain this spring. In order to provide the scientific community easy and...