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Élisabeth Remy, Paul Ruet, Denis Thieffry
Graphic requirements for multistability and
1 Positive or negative regulatory circuit inference from multilevel dynamics (2009)
Élisabeth Remy, Paul Ruet, Denis Thieffry, Marseille Cedex (france
Summary. In the course of his work on the analysis of genetic regulatory networks represented by signed directed graphs, R. Thomas has proposed that the occurrence of a positive regulatory circuit is...
Sahin, Özgür, Fröhlich, Holger, Löbke, Christian, Korf, Ulrike, Burmester, Sara, Majety, Meher, ...
Abstract Background In breast cancer, overexpression of the transmembrane tyrosine kinase ERBB2 is an adverse prognostic marker, and occurs in almost 30% of the patients. For therapeutic...
Analyzing various models of Circadian Clock and Cell Cycle coupling (2009)
Csikász-Nagy, Attila, Faure, Adrien, Larcher, Roberto, Lecca, Paola, Mura, Ivan, Jordan, Ferenc, ...
The daily rhythm can influence the proliferation rate of many cell types. In the mammalian system the transcription of the cell cycle regulatory protein Wee1 is controlled by the circadian clock....
CoCAS: a ChIP-on-chip analysis suite (2009)
Benoukraf, Touati, Cauchy, Pierre, Fenouil, Romain, Jeanniard, Adrien, Koch, Frederic, Jaeger, Sébastien, ...
Motivation: High-density tiling microarrays are increasingly used in combination with ChIP assays to study transcriptional regulation. To ease the analysis of the large amounts of data generated by...
Graphing genes, cells and embryos : cultures of seeing 3D and beyond (2009)
Brauckmann, Sabine, Brandt, Christina, Thieffry, Denis, Müller, Gerd B.
Metagenome Annotation Using a Distributed Grid of Undergraduate Students (2008)
Pascal Hingamp, Céline Brochier, Emmanuel Talla, Daniel Gautheret, Denis Thieffry, Carl Herrmann
Qualitative Petri Net Modelling of Genetic Networks (2008)
Claudine Chaouiya, Elisabeth Remy, Denis Thieffry
Abstract. The complexity of biological regulatory networks calls for the development of proper mathematical methods to model their structures and to give insight in their dynamical behaviours. One...
Denis Thieffry, Araceli M. Huerta, Ernesto Pérez-rueda, Julio Collado-vides
From specific gene regulation to genomic networks: a global analysis of transcriptional
Élisabeth Remy, Paul Ruet, Denis Thieffry
Graphic requirements for multistability and
Logical modelling and analysis of the budding yeast cell cycle (2007)
Fauré, Adrien, Chaouiya, Claudine, Ciliberto, Andrea, Thieffry, Denis
No abstract available.
GIN-db: a relational scheme for the integration of multi-species gene (2007)
Claude Sabatier, Azzeddine Kadi, Catherine Verheecke-mauzé, Karine Souquet, David Martin, Claudine Chaouiya, ...
interaction data.
Dynamical roles of biological regulatory circuits (2007)
Regulatory circuits are found at the basis of all non-trivial dynamical properties of biological networks. More specifically, positive circuits are involved in the generation of multiple...
Adrien Fauré, Claudine Chaouiya, Andrea Ciliberto, Denis Thieffry, Open Access
Biological background The budding yeast cell cycle core engine has been modelled in great detail, most notably by the groups of Béla Novak and John Tyson, using a differential formalism. Several...
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle (2006)
Fauré, Adrien, Naldi, Aurélien, Chaouiya, Claudine, Thieffry, Denis
Motivation: To understand the behaviour of complex biological regulatory networks, a proper integration of molecular data into a full-fledge formal dynamical model is ultimately required. As most...
Grange, Thierry, Imbert, Jean, Thieffry, Denis
No Abstract.
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...
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...
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...
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...
Claudine Chaouiya, Elisabeth Remy, Paul Ruet, Denis Thieffry
1 Introduction Regulatory networks are found at the core of all biological functions, from biochemical pathways, to gene regulation, and cell communication processes. Their complexity often defies...
David Martin, Christine Brun, Elisabeth Remy, Pierre Mouren, Denis Thieffry, Bernard Jacq
Software GOToolBox: functional analysis of gene datasets based on Gene
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...
Claudine Chaouiya, Aitor González González, Denis Thieffry
A flexible and rigorous logical formalism enabling the qualitative dynamical modelling of biological regulatory networks is described in [1]. This logical approach has been implemented in a Java...
Aitor Gonz Alez, Aitor González González, Claudine Chaouiya, Denis Thieffry, Lucas Sánchez, Ap Fng, ...
vate the NOTCH signalling pathway. However SER is not able to activate NOTCH in the dorsal cells due to FRINGE (FNG) presence. Therefore SER activates only NOTCH in ventral cells near the boundary...
Combining Logical Formalisation and Constraint Programming to Model (2003)
Wild-Type And Perturbed, Vincent Devloo, Denis Thieffry
Introduction Genetic regulatory networks play a crucial role in the control of most developmental and physiological processes. Extensive genetic sequencing now provides us with almost complete sets...
The genome in context: biologists and philosophers on epigenetics. (2002)
Van Speybroeck, Linda, JABLONKA, E, MATZKE, M, Thieffry, Denis
Prediction of transcriptional regulatory sites in the complete genome sequence of E.coli (1998)
Thieffry,Denis, Salgado,Heladia, Huerta,Araceli M., Collado-Vides,Julio
RegulonDB: A database on transcriptional regulation (1998)
Huerta,Araceli M., Salgado,Heladia, Thieffry,Denis, Collado-Vides,Julio
Prediction of transcriptional regulatory sites in the complete genome sequence of E.coli (1998)
Thieffry, Denis, Salgado, Heladia, Huerta, Araceli M., Collado-Vides, Julio
RegulonDB: A database on transcriptional regulation (1998)
Huerta, Araceli M., Salgado, Heladia, Thieffry, Denis, Collado-Vides, Julio
RegulonDB: a database on transcriptional regulation in Escherichia coli (1998)
Araceli M. Huerta, Heladia Salgado, Denis Thieffry, Julio Collado-vides
RegulonDB is a DataBase that integrates biological knowledge of the mechanisms that regulate the transcription initiation in Escherichia coli, as well as knowledge on the organization of the genes...
RegulonDB: a database on transcriptional regulation in Escherichia Coli (1998)
Araceli M. Huerta, Heladia Salgado, Denis Thieffry, Julio Collado-Vides
RegulonDB is a DataBase that integrates biological knowledge of the mechanisms that regulate the transcription initiation in Escherichia coli, as well as knowledge on the organization of the genes...
Syntactic recognition of regulatory regions in Escherichia coli (1996)
Rosenblueth, David A., Thieffry, Denis, Huerta, Araceli M., Salgado, Heladia, Collado-Vides, Julio
Motivation One of the most common methodologies identify cis-regulatory sites in regulatory regions in the DNA is that of weight matrices, as testified by several articles this issue. An alternative...
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.
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.
González, Aitor, Chaouiya, Claudine, Thieffry, Denis
The larval development of the Drosophila melanogaster wings is organized by the protein Wingless, which is secreted by cells adjacent to the dorsal–ventral (DV) boundary. Two signaling processes...
Dynamical modeling of syncytial mitotic cycles in Drosophila embryos
Calzone, Laurence, Thieffry, Denis, Tyson, John J, Novak, Bela
Immediately following fertilization, the fruit fly embryo undergoes 13 rapid, synchronous, syncytial nuclear division cycles driven by maternal genes and proteins. During these mitotic cycles, there...
Metagenome Annotation Using a Distributed Grid of Undergraduate Students
Hingamp, Pascal, Brochier, Céline, Talla, Emmanuel, Gautheret, Daniel, Thieffry, Denis, Herrmann, Carl
The Annotathon is a novel bioinformatics teaching environment, where undergraduate students join in a community annotation effort. Besides being a rewarding educational tool, it holds the added...
CoCAS: a ChIP-on-chip analysis suite
Benoukraf, Touati, Cauchy, Pierre, Fenouil, Romain, Jeanniard, Adrien, Koch, Frederic, Jaeger, Sébastien, ...
Motivation: High-density tiling microarrays are increasingly used in combination with ChIP assays to study transcriptional regulation. To ease the analysis of the large amounts of data generated by...
Functional organisation of Escherichia coli transcriptional regulatory network
Martínez-Antonio, Agustino, Janga, Sarath Chandra, Thieffry, Denis
Taking advantage of available functional data associated with 115 transcription and 7 sigma factors, we have performed a structural analysis of the regulatory network of Escherichia coli. While the...