P. Rouzé

发表

Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information.

Peter G. Korning, S. Brunak, S. M. Hebsgaard, 1996, Nucleic acids research.

Cleaning the GenBank Arabidopsis thaliana data set.

S. Brunak, S. M. Hebsgaard, P. Korning, 1996, Nucleic acids research.

Current methods of gene prediction, their strengths and weaknesses.

P. Rouzé, T. Schiex, C. Mathé, 2002, Nucleic acids research.

The Ectocarpus genome and the independent evolution of multicellularity in brown algae

Corinne Da Silva, Susana M. Coelho, J. Poulain, 2010, Nature.

The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)

M. Gribskov, E. Uberbacher, S. Wessler, 2006, Science.

The genome of the domesticated apple (Malus × domestica Borkh.)

Roger E Bumgarner, S. Masiero, M. Skolnick, 2010, Nature Genetics.

The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation

Nicholas H. Putnam, A. Salamov, P. Rouzé, 2007, Proceedings of the National Academy of Sciences.

Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

A. Salamov, P. Rouzé, I. Dubchak, 2009, Science.

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

Y. Van de Peer, A. Brun, I. V. Grigoriev, 2008, Nature.

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

Christina A. Cuomo, M. Grabherr, E. Mauceli, 2011, Proceedings of the National Academy of Sciences.

Obligate Biotrophy Features Unraveled by the Genomic Analysis of the Rust Fungi, Melampsora larici-populina and Puccinia graminis f. sp. tritici

Christina A. Cuomo, M. Grabherr, E. Mauceli, 2011 .

The genome of Tetranychus urticae reveals herbivorous pest adaptations

Stefan R. Henz, Richard M. Clark, Stephen D. Hudson, 2011, Nature.

Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features.

B. De Baets, S. Degroeve, Y. Saeys, 2006, Proceedings of the National Academy of Sciences of the United States of America.

EST data suggest that poplar is an ancient polyploid.

P. Rouzé, Y. van de Peer, F. Sterky, 2005, The New phytologist.

Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes.

P. Rouzé, Y. van de Peer, E. Bonnet, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Genome Annotation in Plants and Fungi: EuGene as a Model Platform

Thomas Schiex, Sylvain Foissac, Stephane Rombauts, 2008 .

Generic eukaryotic core promoter prediction using structural features of DNA.

Yvan Saeys, Eric Bonnet, Thomas Abeel, 2008, Genome research.

Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

Sebastian Proost, Klaas Vandepoele, Pierre Rouzé, 2009, BMC Genomics.

Genome-Wide Analysis of Core Cell Cycle Genes in Arabidopsis Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010445.

Stephane Rombauts, Dirk Inzé, Jeroen Raes, 2002, The Plant Cell Online.

Genome annotation

P. Rouzé, S. Aubourg, 2022 .

Large-scale structural analysis of the core promoter in mammalian and plant genomes

Yvan Saeys, Sven Degroeve, Pierre Rouzé, 2005, Nucleic acids research.

Computational Approaches to Identify Promoters and cis-Regulatory Elements in Plant Genomes1

Kathleen Marchal, Stephane Rombauts, Magali Lescot, 2003, Plant Physiology.

The small RNA world of plants.

P. Rouzé, Y. van de Peer, E. Bonnet, 2006, The New phytologist.

Genomewide Structural Annotation and Evolutionary Analysis of the Type I MADS-Box Genes in Plants

J. Raes, P. Rouzé, Y. van de Peer, 2003, Journal of Molecular Evolution.

PPMdb: a plant plasma membrane database.

M. Van Montagu, P. Rouzé, P. Déhais, 2000, Journal of biotechnology.

Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

P. Rouzé, P. Wincker, Y. van de Peer, 2021, BMC biology.

Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage

J. Poulain, P. Rouzé, P. Wincker, 2012, Genome Biology.

Annotation of a 95-kb Populus deltoides genomic sequence reveals a disease resistance gene cluster and novel class I and class II transposable elements

P. Rouzé, S. Aubourg, S. Rombauts, 2004, Theoretical and Applied Genetics.

Use of a proteome strategy for tagging proteins present at the plasma membrane.

P Dupree, P. Rouzé, D. Rouquié, 1998, The Plant journal : for cell and molecular biology.

Recognition of gene regulatory sequencesby bagging of neural

B. Moor, P. Rouzé, Y. Moreau, 2007 .

Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress

P. Rouzé, Y. van de Peer, R. König, 2009, Genome Biology.

Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen.

A. Salamov, P. Rouzé, J. Grimwood, 2012, The New phytologist.

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

Erich Bornberg-Bauer, Yves Van de Peer, Yao-Cheng Lin, 2016, Nature.

Author Correction to: Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

P. Rouzé, P. Wincker, Y. van de Peer, 2021, BMC biology.

Common evolutionary origin of the central portions of the Ri TL-DNA of Agrobacterium rhizogenes and the Ti T-DNAs of Agrobacterium tumefaciens

P. Rouzé, J. Slightom, P. Delepelaire, 1988, Plant Molecular Biology.

Heat sensitivity of porcine IgG.

P. Rouzé, C. Bourdieu, M. Houdayer, 1975, Journal of immunological methods.

Molecular cloning and characterisation of the two homeologous genes coding for nitrate reductase in tobacco

P. Rouzé, M. Vincentz, H. Vaucheret, 1989, Molecular and General Genetics MGG.

Isolation and molecular characterization of dTnp1, a mobile and defective transposable element of Nicotiana plumbaginifolia

P. Rouzé, M. Caboche, C. Meyer, 2004, Molecular and General Genetics MGG.

The transcriptome of the moss Physcomitrella patens : comparative analysis reveals a rich source of new genes

P. Rouzé, Y. Peer, S. Rensing, 2002 .

Cloning and analysis of the tomato nitrate reductase-encoding gene: protein domain structure and amino acid homologies in higher plants.

P. Rouzé, F. Daniel-Vedele, M. Caboche, 1989, Gene.

Antibody against octopine dehydrogenase from crown gall tumor tissue, a tool in studies of plant cell transformation

P. Rouzé, A. Goldmann, T. Moureaux, 1981 .

Expression of Antigenic Determinants and Virus Synthesis in Mammalian Cells

P. Rouzé, M. A. Moyne, L. Lelièvre, 1971 .

Immunological comparative studies of octopine dehydrogenase and other “pyruvate reductases” from different species

P. Rouzé, A. Olomucki, L. Fort, 1982 .

Classification of Arabidopsis thaliana gene sequences: clustering of coding sequences into two groups according to codon usage improves gene prediction.

M. Van Montagu, P. Rouzé, C. Mathé, 1999, Journal of molecular biology.

Selecting Relevant Features for Splice Site Prediction by Estimation of Distribution Algorithms.

Yvan Saeys, Yves Van de Peer, Pierre Rouzé, 2002 .

Detection of cis-acting regulatory elements in plants: a Gibbs sampling approach

Kathleen Marchal, Bart De Moor, Stephane Rombauts, 2000 .

Recognition of gene regulatory sequences by bagging of neural networks

Stephane Rombauts, Pierre Rouzé, Yves Moreau, 1999 .

PlantCARE, a plant cis-acting regulatory element database

Stephane Rombauts, Pierre Rouzé, Marc Van Montagu, 1999, Nucleic Acids Res..

PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences

Kathleen Marchal, Stephane Rombauts, Yves Van de Peer, 2002, Nucleic Acids Res..

Identification by mutational analysis of four critical residues in the molybdenum cofactor domain of eukaryotic nitrate reductase

P. Rouzé, M. Caboche, C. Meyer, 1995, FEBS letters.

Nitrate reductase: a target for molecular and cellular studies in higher plants.

P. Rouzé, M. Caboche, P. Rouzé, 1990, Trends in genetics : TIG.

Characterization and classification of plant cyclin sequences related to A- and B-type cyclins

D. Inzé, M. Montagu, P. Rouzé, 1998 .

Sequence comparisons betweenAgrobacterium tumefaciens T-DNA-encoded octopine and nopaline dehydrogenases and other nucleotide-requiring enzymes: Structural and evolutionary implications

P. Rouzé, M. Monneuse, 1987, Journal of Molecular Evolution.

Complex Evolutionary Dynamics of Massively Expanded Chemosensory Receptor Families in an Extreme Generalist Chelicerate Herbivore

Richard M. Clark, P. Rouzé, Y. van de Peer, 2016, Genome biology and evolution.

Genome sequence of the recombinant protein production host Pichia pastoris

Yves Van de Peer, Yao-Cheng Lin, Pierre Rouzé, 2009, Nature Biotechnology.

Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences

Yves Van de Peer, Pierre Rouzé, Eric Bonnet, 2004, Bioinform..

Characterization of seven monoclonal antibodies directed against Nicotiana plumbaginifolia ribulose 1,5-biphosphate carboxylase/oxygenase

P. Rouzé, J. Grosclaude, C. Meyer, 1991 .

Sequence analysis of a 40-kb Arabidopsis thaliana genomic region located at the top of chromosome 1.

M. Van Montagu, P. Rouzé, N. Terryn, 1998, Gene.

Title Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine

P. Rouzé, Y. Peer, Y. van de Peer, 2011 .

ORCAE: online resource for community annotation of eukaryotes

Yves Van de Peer, Pierre Rouzé, Thomas Abeel, 2012, Nature Methods.

Higher intron loss rate in Arabidopsis thaliana than A. lyrata is consistent with stronger selection for a smaller genome.

P. Rouzé, Y. van de Peer, Jeffrey A. Fawcett, 2012, Molecular biology and evolution.

with stronger selection for a smaller genome

P. Rouzé, Y. Peer, Jeffrey A. Fawcett, 2011 .

A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling

Kathleen Marchal, Bart De Moor, Stephane Rombauts, 2001, Bioinform..

Exon prediction in eucaryotic genomes.

F. Lisacek, P. Rouzé, J. Quinqueton, 1996, Biochimie.

Non–canonical introns are at least 109 years old

M. Montagu, P. Rouzé, M. Delseny, 1996, Nature Genetics.

The sense of naturally transcribed antisense RNAs in plants.

P. Rouzé, N. Terryn, 2000, Trends in plant science.

Orphan gene finding - an exon assembly approach

Pierre Rouzé, Marie-France Sagot, Philippe Blayo, 2003, Theor. Comput. Sci..

The Ectocarpus genome and brown algal genomics: the Ectocarpus Genome Consortium

Corinne Da Silva, Gildas Le Corguillé, Susana M. Coelho, 2012 .

ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles

Yvan Saeys, Yves Van de Peer, Pierre Rouzé, 2008, ISMB.

Open access to sequence: Browsing the Pichia pastoris genome

P. Rouzé, N. Callewaert, Brigitte Gasser, 2009, Microbial cell factories.

Plant cyclins: a unified nomenclature for plant A-, B- and D-type cyclins based on sequence organization

Donna J. Freeman, D. Inzé, P. Rouzé, 1996, Plant Molecular Biology.

Orthology Guided Assembly in highly heterozygous crops: creating a reference transcriptome to uncover genetic diversity in Lolium perenne.

P. Rouzé, Y. van de Peer, L. Sterck, 2013, Plant biotechnology journal.

Analysis of T-DNA-mediated translational β-glucuronidase gene fusions

P. Rouzé, H. De Greve, J. Macas, 2004, Plant Molecular Biology.

Immunological comparisons of nitrate reductase of different plant species using monoclonal antibodies.

P. Rouzé, A. Marion-Poll, C. Meyer, 1986, Plant physiology.

Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications.

Thomas Altmann, Yves Moreau, Hans Lehrach, 2004, Genome research.

Phosphorylcholine antigens from Nippostrongylus brasiliensis. I.--Anti-phosphorylcholine antibodies in infected rats and location of phosphorylcholine antigens.

P. Rouzé, P. Péry, G. Luffau, 1979, Annales d'immunologie.

Phosphorylcholine antigens from Nippostrongylus brasiliensis. II.--Isolation and partial characterization of phosphorylcholine antigens from adult worm.

P. Rouzé, P. Péry, G. Luffau, 1979, Annales d'immunologie.

Cytidine-5'-diphospho-choline conjugates. I.--Synthesis and fixation to phosphorylcholine-binding proteins.

P. Rouzé, P. Péry, G. Luffau, 1979, Annales d'immunologie.

A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes

Kathleen Marchal, Bart De Moor, Stephane Rombauts, 2001, RECOMB.

Evaluation of gene prediction software using a genomic data set: application to <$O_SSF>Arabidopsis thaliana<$C_SSF>sequences

Ramana V. Davuluri, Stephane Rombauts, Pierre Rouzé, 1999, Bioinform..

Characterization of Mobile Endogenous Copia-Like Transposable Elements in the Genome of Solanaceae

P. Rouzé, M. Caboche, C. Meyer, 1991 .

An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNAs from Arabidopsis thaliana.

P. Rouzé, M. Caboche, C. Gigot, 1993, The Plant journal : for cell and molecular biology.

In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists

Yvan Saeys, Yves Van de Peer, Pierre Rouzé, 2007, Bioinform..

GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

Arnaud Couloux, Michel Schneider, Stephane Rombauts, 2004, Nucleic Acids Res..

The FTO Gene, Implicated in Human Obesity, Is Found Only in Vertebrates and Marine Algae

P. Rouzé, J. Spring, Y. Peer, 2007, Journal of Molecular Evolution.

INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Sampling

Kathleen Marchal, Bart De Moor, Stephane Rombauts, 2002, Bioinform..

Cloning of DNA fragments complementary to tobacco nitrate reductase mRNA and encoding epitopes common to the nitrate reductases from higher plants

P. Rouzé, M. Vincentz, H. Vaucheret, 1987, Molecular and General Genetics MGG.

SpliceMachine: predicting splice sites from high-dimensional local context representations

Yvan Saeys, Bernard De Baets, Yves Van de Peer, 2005, Bioinform..

The Complex Intron Landscape and Massive Intron Invasion in a Picoeukaryote Provides Insights into Intron Evolution

P. Rouzé, Y. van de Peer, B. Verhelst, 2013, Genome biology and evolution.

Unique Regulation of the Calvin Cycle in the Ultrasmall Green Alga Ostreococcus

P. Rouzé, Y. Peer, H. Brinkmann, 2007, Journal of Molecular Evolution.

[Neutralization of the infective power of the foot-and-mouth disease virus in cell culture by using serums from pigs immunized with a purified viral protein].

P. Rouzé, J. Grosclaude, J. Laporte, 1973, Comptes rendus hebdomadaires des seances de l'Academie des sciences. Serie D: Sciences naturelles.

Genome annotation: which tools do we have for it?

P. Rouzé, S. Rombauts, N. Pavy, 1999, Current opinion in plant biology.

EuGène : an eu aryoti gene nder that ombinesseveral sour es of eviden eThomas

P. Rouzé, S. hiex, Anni k Moisan, 2000 .

EUGÈNE: An Eukaryotic Gene Finder That Combines Several Sources of Evidence

Thomas Schiex, Annick Moisan, Pierre Rouzé, 2000, JOBIM.

A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites.

S Brunak, S. Brunak, N. Tolstrup, 1997, Nucleic acids research.

How many genes are there in plants (... and why are they there)?

Stephane Rombauts, Lieven Sterck, Klaas Vandepoele, 2007, Current opinion in plant biology.

Complete nucleotide sequence of the two homeologous tobacco nitrate reductase genes

P. Rouzé, H. Vaucheret, M. Caboche, 1989, Plant Molecular Biology.

Use of liposomes for the transfer of nucleic acids: Optimization of the method for tobacco mesophyll protoplasts with tobacco mosaic virus RNA

P. Rouzé, M. Caboche, A. Deshayes, 1983 .

Monoclonal antibodies identify multiple epitopes on maize leaf nitrate reductase

P. Rouzé, J. Grosclaude, Isabelle Cherel, 1985, Biochemical and Biophysical Research Communications.

Automatic design of gene-specific sequence tags for genome-wide functional studies

Pierre Rouzé, Pierre Hilson, Sébastien Aubourg, 2003, Bioinform..

Amino Acids and their Derivatives in Higher Plants: Biosynthesis of cyanogenic glucosides. Elucidation of the pathway and characterization of the cytochromes P-450 involved

P. Rouzé, B. Halkier, B. Møller, 1995 .

Feature selection for splice site prediction: A new method using EDA-based feature ranking

Yvan Saeys, Yves Van de Peer, Pierre Rouzé, 2004, BMC Bioinformatics.

CATMA: a complete Arabidopsis GST database

Pierre Rouzé, Philippe Reymond, Pierre Hilson, 2003, Nucleic Acids Res..

A comprehensive analysis of genes encoding small secreted proteins identifies candidate effectors in Melampsora larici-populina (poplar leaf rust).

P. Rouzé, Y. van de Peer, S. Hacquard, 2012, Molecular plant-microbe interactions : MPMI.

Sequence analysis of a 24‐kb contiguous genomic region at the Arabidopsis thaliana PFL locus on chromosome 1 1

M. Van Montagu, P. Rouzé, P. Déhais, 1997, FEBS letters.

Evidence for an ancient chromosomal duplication in Arabidopsis thaliana by sequencing and analyzing a 400‐kb contig at the APETALA2 locus on chromosome 4 1

K Mayer, N Terryn, M. Van Montagu, 1999, FEBS letters.

AFLPinSilico, simulating AFLP fingerprints

Stephane Rombauts, Yves Van de Peer, Pierre Rouzé, 2003, Bioinform..

Cyclin-dependent kinases in plants

D. Inzé, M. Montagu, P. Rouzé, 1998 .

Differentiation of mouse plasmocytomas in vitro: two phenotypically stabilized variants of the same cell.

P. Rouzé, J. Duplan, M. A. Moyne, 1970, Proceedings of the National Academy of Sciences of the United States of America.

Feature subset selection for splice site prediction

Bernard De Baets, Yves Van de Peer, Pierre Rouzé, 2002, ECCB.

Gene prediction and gene classes in Arabidopsis thaliana.

P. Rouzé, C. Mathé, P. Déhais, 2000, Journal of biotechnology.

Deciphering cis-acting regulatory elements in plant and drosophila promoter sequences

P. Rouzé, Y. Moreau, G. Thijs, 2002 .

Integrating quality-based clustering of microarray data with Gibbs sampling for the discovery of regulatory motifs

Kathleen Marchal, Bart De Moor, Stephane Rombauts, 2002 .

Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

P. Rouzé, K. Vandepoele, S. Proost, 2009, BMC Genomics.

Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen.

A. Salamov, P. Rouzé, J. Grimwood, 2012, New Phytologist.

Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine

P. Rouzé, D. Zélénika, C. Plomion, 2011, BMC Genomics.

Specific-GST design and database structure for the Complete Arabidopsis Transcriptome MicroArray (CATMA) project

P. Rouzé, M. Crowe, T. Schiex, 2003 .

Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

P. Rouzé, I. Dubchak, J. Badger, 2009, Science.

In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists

Y. Saeys, P. Rouzé, Y. Peer, 2007, Bioinform..

Fast feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction

Yvan Saeys, Yves Van de Peer, Pierre Rouzé, 2003, ECCB.