Defining a Modular Signalling Network from the Fly Interactome (2008)
Baudot, Anaïs, Angelelli, Jean-Baptiste, Guénoche, Alain, Jacq, Bernard, Brun, Christine
Abstract Background Signalling pathways relay information by transmitting signals from cell surface receptors to intracellular effectors that eventually activate the transcription of target genes....
TreeDyn: towards dynamic graphics and annotations for analyses of trees (2006)
Chevenet, François, Brun, Christine, Bañuls, Anne-Laure, Jacq, Bernard, Christen, Richard
Abstract Background Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but...
GOToolBox: functional analysis of gene datasets based on Gene Ontology. (2006)
Martin, David, Brun, Christine, Remy, Elisabeth, Mouren, Pierre, Thieffry, Denis, Jacq, Bernard
We have developed methods and tools based on the Gene Ontology (GO) resource allowing the identification of statistically over- or under-represented terms in a gene dataset; the clustering of...
GOToolBox: functional analysis of gene datasets based on Gene Ontology. (2006)
Martin, David, Brun, Christine, Remy, Elisabeth, Mouren, Pierre, Thieffry, Denis, Jacq, Bernard
We have developed methods and tools based on the Gene Ontology (GO) resource allowing the identification of statistically over- or under-represented terms in a gene dataset; the clustering of...
GOToolBox: functional analysis of gene datasets based on Gene Ontology (2004)
Martin, David, Brun, Christine, Remy, Elisabeth, Mouren, Pierre, Thieffry, Denis, Jacq, Bernard
Abstract We have developed methods and tools based on the Gene Ontology (GO) resource allowing the identification of statistically over- or under-represented terms in a gene dataset; the clustering...
Baudot, Anaïs, Jacq, Bernard, Brun, Christine
Abstract Background Studying the evolution of the function of duplicated genes usually implies an estimation of the extent of functional conservation/divergence between duplicates from comparison of...
Clustering proteins from interaction networks for the prediction of cellular functions (2004)
Brun, Christine, Herrmann, Carl, Guénoche, Alain
Abstract Background Developing reliable and efficient strategies allowing to infer a function to yet uncharacterized proteins based on interaction networks is of crucial interest in the current...
GOToolBox: functional analysis of gene datasets based on Gene Ontology. (2004)
Martin, David, Brun, Christine, Remy, Elisabeth, Mouren, Pierre, Thieffry, Denis, Jacq, Bernard
We have developed methods and tools based on the Gene Ontology (GO) resource allowing the identification of statistically over- or under-represented terms in a gene dataset; the clustering of...
Brun, Christine, Chevenet, François, Martin, David, Wojcik, Jérôme, Guénoche, Alain, Jacq, Bernard
Abstract We here describe PRODISTIN, a new computational method allowing the functional clustering of proteins on the basis of protein-protein interaction data. This method, assessed biologically and...
GIN-db: a relational scheme for the integration of multi-species (2003)
Claude Sabatier, Azzeddine Kadi, Catherine Verheecke-mauz, Karine Souquet, David Martin, Magali Lescot, ...
Introduction Massive genome sequencing provides us with complete sequence data, which in turn lead to derivation of close to complete gene sets for model organisms. In addition, a complete genome...
Evolution of the Function of Duplicated Genes (2003)
Anas Baudot, Alain Gunoche, Bernard Jacq, Christine Brun
Introduction Gene duplications are considered as a source of evolutionary novelties, leading to the emergence of new gene functions. The extent of functional conservation or divergence between pairs...
Mapping and identification of essential gene functions on the X chromosome of Drosophila (2002)
Peter, Annette, Schoettler, Petra, Werner, Meike, Beinert, Nicole, Dowe, Gordon, Burkert, Peter, ...
The Drosophila melanogaster genome consists of four chromosomes that contain 165 Mb of DNA, 120 Mb of which are euchromatic. The two Drosophila Genome Projects, in collaboration with Celera Genomics...
Benos, Panayiotis V., Gatt, Melanie K., Murphy, Lee, Harris, David, Barrell, Bart, Ferraz, Concepcion, ...
We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94...
Ancelin, Katia, Brunori, Michele, Bauwens, Serge, Koering, Catherine-Elaine, Brun, Christine, Ricoul, Michelle, ...
We investigated the control of telomere length by the human telomeric proteins TRF1 and TRF2. To this end, we established telomerase-positive cell lines in which the targeting of these telomeric...
Chimeric RNA transposition intermediates of the I factor produce precise retrotransposed copies
Chambeyron, Séverine, Brun, Christine, Robin, Stéphanie, Bucheton, Alain, Busseau, Isabelle
I elements in Drosophila melanogaster are non-long terminal repeat (LTR) retrotransposons of particular interest because high levels of transposition can be induced by appropriate crosses. They use a...
Benos, Panayiotis V., Gatt, Melanie K., Murphy, Lee, Harris, David, Barrell, Bart, Ferraz, Concepcion, ...
We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94...
Brun, Christine, Chevenet, François, Martin, David, Wojcik, Jérôme, Guénoche, Alain, Jacq, Bernard
PRODISTIN, a new computational method allowing the functional clustering of proteins on the basis of protein-protein interaction data. This method was used to classify 11% of the Saccharomyces...
Baudot, Anaïs, Jacq, Bernard, Brun, Christine
Protein-protein interaction networks were used to analyze the functional evolution of duplicated genes in yeast. Pairs of paralogs can be grouped into 3 classes, which likely form part of a...
GOToolBox: functional analysis of gene datasets based on Gene Ontology
Martin, David, Brun, Christine, Remy, Elisabeth, Mouren, Pierre, Thieffry, Denis, Jacq, Bernard
Tools are presented to identify Gene Ontology terms that are over- or under-represented in a dataset, to cluster genes by function and to find genes with similar annotations.
Del Carmen Seleme, Maria, Disson, Olivier, Robin, Stéphanie, Brun, Christine, Teninges, Danielle, Bucheton, Alain
According to the current model of non-LTR retrotransposon (NLR) mobilization, co-expression of the RNA transposition intermediate, and the proteins it encodes (ORF1p and ORF2p), is a requisite for...
Mapping and identification of essential gene functions on the X chromosome of Drosophila
Peter, Annette, Schöttler, Petra, Werner, Meike, Beinert, Nicole, Dowe, Gordon, Burkert, Peter, ...
The Drosophila melanogaster genome consists of four chromosomes that contain 165 Mb of DNA, 120 Mb of which are euchromatic. The two Drosophila Genome Projects, in collaboration with Celera Genomics...
Koering, Catherine Elaine, Pollice, Alessandra, Zibella, Maria Pia, Bauwens, Serge, Puisieux, Alain, Brunori, Michele, ...
We investigated the influence of telomere proximity and composition on the expression of an EGFP reporter gene in human cells. In transient transfection assays, telomeric DNA does not repress EGFP...
Protein interaction mapping: A Drosophila case study
Formstecher, Etienne, Aresta, Sandra, Collura, Vincent, Hamburger, Alexandre, Meil, Alain, Trehin, Alexandra, ...
The Drosophila (fruit fly) model system has been instrumental in our current understanding of human biology, development, and diseases. Here, we used a high-throughput yeast two-hybrid (Y2H)-based...
TreeDyn: towards dynamic graphics and annotations for analyses of trees
Chevenet, François, Brun, Christine, Bañuls, Anne-Laure, Jacq, Bernard, Christen, Richard
Ancelin, Katia, Brunori, Michele, Bauwens, Serge, Koering, Catherine-Elaine, Brun, Christine, Ricoul, Michelle, ...
We investigated the control of telomere length by the human telomeric proteins TRF1 and TRF2. To this end, we established telomerase-positive cell lines in which the targeting of these telomeric...
Chimeric RNA transposition intermediates of the I factor produce precise retrotransposed copies
Chambeyron, Séverine, Brun, Christine, Robin, Stéphanie, Bucheton, Alain, Busseau, Isabelle
I elements in Drosophila melanogaster are non-long terminal repeat (LTR) retrotransposons of particular interest because high levels of transposition can be induced by appropriate crosses. They use a...
Benos, Panayiotis V., Gatt, Melanie K., Murphy, Lee, Harris, David, Barrell, Bart, Ferraz, Concepcion, ...
We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94...
Brun, Christine, Chevenet, François, Martin, David, Wojcik, Jérôme, Guénoche, Alain, Jacq, Bernard
PRODISTIN, a new computational method allowing the functional clustering of proteins on the basis of protein-protein interaction data. This method was used to classify 11% of the Saccharomyces...
Baudot, Anaïs, Jacq, Bernard, Brun, Christine
Protein-protein interaction networks were used to analyze the functional evolution of duplicated genes in yeast. Pairs of paralogs can be grouped into 3 classes, which likely form part of a...
GOToolBox: functional analysis of gene datasets based on Gene Ontology
Martin, David, Brun, Christine, Remy, Elisabeth, Mouren, Pierre, Thieffry, Denis, Jacq, Bernard
Tools are presented to identify Gene Ontology terms that are over- or under-represented in a dataset, to cluster genes by function and to find genes with similar annotations.
Del Carmen Seleme, Maria, Disson, Olivier, Robin, Stéphanie, Brun, Christine, Teninges, Danielle, Bucheton, Alain
According to the current model of non-LTR retrotransposon (NLR) mobilization, co-expression of the RNA transposition intermediate, and the proteins it encodes (ORF1p and ORF2p), is a requisite for...
Protein interaction mapping: A Drosophila case study
Formstecher, Etienne, Aresta, Sandra, Collura, Vincent, Hamburger, Alexandre, Meil, Alain, Trehin, Alexandra, ...
The Drosophila (fruit fly) model system has been instrumental in our current understanding of human biology, development, and diseases. Here, we used a high-throughput yeast two-hybrid (Y2H)-based...
Mapping and identification of essential gene functions on the X chromosome of Drosophila
Peter, Annette, Schöttler, Petra, Werner, Meike, Beinert, Nicole, Dowe, Gordon, Burkert, Peter, ...
The Drosophila melanogaster genome consists of four chromosomes that contain 165 Mb of DNA, 120 Mb of which are euchromatic. The two Drosophila Genome Projects, in collaboration with Celera Genomics...
Koering, Catherine Elaine, Pollice, Alessandra, Zibella, Maria Pia, Bauwens, Serge, Puisieux, Alain, Brunori, Michele, ...
We investigated the influence of telomere proximity and composition on the expression of an EGFP reporter gene in human cells. In transient transfection assays, telomeric DNA does not repress EGFP...