Background and scope: Large networks, such as protein interaction networks, are extremely difficu... more Background and scope: Large networks, such as protein interaction networks, are extremely difficult to analyze as a whole. We developed Clust&See, a Cytoscape plugin dedicated to the identification, visualization and analysis of clusters extracted from such networks. Implementation and performance: Clust&See provides the ability to apply three different, recently developed graph clustering algorithms to networks and to visualize: (i) the obtained partition as a quotient graph in which nodes correspond to clusters and (ii) the obtained clusters as their corresponding subnetworks. Importantly, tools for investigating the relationships between clusters and vertices as well as their organization within the whole graph are supplied.
In this paper we propose a dynamic programming algorithm to evaluate local similarity between uno... more In this paper we propose a dynamic programming algorithm to evaluate local similarity between unordered trees using a constrained edit distance. The core of the method relies on an adaptation of an algorithm proposed by Zhang for comparing unordered rooted trees. The method is currently being used in plant architecture modeling to outline similar sub-parts on plant structure and in genomic analysis to evaluate variability between secondary structures of RNA.
In this paper, we define several quantitative measures that are useful when using ontologies to d... more In this paper, we define several quantitative measures that are useful when using ontologies to describe biological data. More precisely, we define the precision of a term inside an ontology, and use this concept to quantify the similarity between terms inside an ontology, or, by extension, between biological entities annotated to terms of the ontology. This similarity measure is used
We are interested in RNA secondary structure comparison, using an approach which consists to repr... more We are interested in RNA secondary structure comparison, using an approach which consists to represent these structures by labeled ordered trees. Following the problem considered, this tree representation can be rough (considering only the structural patterns), or reÿned until an exact coding of the structure is obtained. After some preliminary deÿnitions and the description of the Zhang-Shasha (SIAM J. Comput. 18 (6) (1989) 1245) tree edit algorithm, which is on the one hand the reference when dealing with ordered labeled trees comparison, and on the other hand the starting point of our work, this article will present an exact analysis of its complexity. The purpose of this work is also to lead us to a better comprehension of the parameters of this algorithm, in order to be able to modify it more easily without changing its time complexity to take into account biological constraints that occur when comparing RNA secondary structures.
RNA interference (RNAi), mediated by the introduction of a specific double-stranded RNA, is a pow... more RNA interference (RNAi), mediated by the introduction of a specific double-stranded RNA, is a powerful method to investigate gene function. It is widely used in the Caenorhabditis elegans research community. An expanding number of laboratories conduct genome-wide RNAi screens, using standard libraries of bacterial clones each designed to produce a specific double-stranded RNA. Proper interpretation of results from RNAi experiments requires a series of analytical steps, from the verification of the identity of bacterial clones, to the identification of the clones' potential targets. Despite the popularity of the technique, no user-friendly set of tools allowing these steps to be carried out accurately, automatically, and at a large scale, is currently available. We report here the design and production of Clone Mapper, an online suite of tools specifically adapted to the analysis pipeline typical for RNAi experiments with C. elegans. We show that Clone Mapper overcomes the limita...
An increasing number of laboratories are using the COPAS Biosort™ to implement high-throughput ap... more An increasing number of laboratories are using the COPAS Biosort™ to implement high-throughput approaches to tackle diverse biological problems. While providing a powerful tool for generating quantitative data, the utility of the Biosort is currently limited by the absence of resources for data management. We describe a simple electronic database designed to allow easy storage and retrieval of Biosort data for C. elegans, but that has a wide potential application for organizing electronic files and data sets. ICeE is an Open Source application. The code and accompanying documentation are freely available via the web at http://www.ciml.univ-mrs.fr/EWBANK_jonathan/software.html.
While Caenorhabditis elegans specifically responds to infection by the up-regulation of certain g... more While Caenorhabditis elegans specifically responds to infection by the up-regulation of certain genes, distinct pathogens trigger the expression of a common set of genes. We applied new methods to conduct a comprehensive and comparative study of the transcriptional response of C. elegans to bacterial and fungal infection. Using tiling arrays and/or RNAsequencing, we have characterized the genome-wide transcriptional changes that underlie the host's response to infection by three bacterial (Serratia marcescens, Enterococcus faecalis and otorhabdus luminescens) and two fungal pathogens (Drechmeria coniospora and Harposporium sp.). We developed a flexible tool, the WormBase Converter (available at http:// wormbasemanager.sourceforge.net/), to allow cross-study comparisons. The new data sets provided more extensive lists of differentially regulated genes than previous studies. Annotation analysis confirmed that genes commonly up-regulated by bacterial infections are related to stress responses. We found substantial overlaps between the genes regulated upon intestinal infection by the bacterial pathogens and Harposporium, and between those regulated by Harposporium and D. coniospora, which infects the epidermis. Among the fungus-regulated genes, there was a significant bias towards genes that are evolving rapidly and potentially encode small proteins. The results obtained using new methods reveal that the response to infection in C. elegans is determined by the nature of the pathogen, the site of infection and the physiological imbalance provoked by infection. They form the basis for future functional dissection of innate immune signaling. Finally, we also propose alternative methods to identify differentially regulated genes that take into account the greater variability in lowly expressed genes.
tiques. Abstract. Traditionally, lexical morphology has been diachronic and has established the n... more tiques. Abstract. Traditionally, lexical morphology has been diachronic and has established the notion of word families. This notion is reused in synchronic studies and implies strong seman- tic coherence within the words of a same family. In this paper, we propose an approach in synchrony which highlights phonological and semantic continuity. Our interests go on morpho- phonology and on the semantic dispersion of words in a family. A first study (Gala & Rey, 2008) showed that the semantic spaces of the families displayed either a strong semantic cohesion or a strong dispersion. In order to validate this observation, w e present here a corpus-based method that automatically weights the semantic units of a word and a family. An experience carried out with 30 native speakers validates our approach and allows us to foresee a thorough study of the lexicon based on phonological and semantic basis. Mots-clés : morpho-phonologie lexicale, traitement automatique des familles dériva- tionnel...
In this paper we propose a dynamic programming algorithm to evaluate local similarity between ord... more In this paper we propose a dynamic programming algorithm to evaluate local similarity between ordered quotiented trees using a constrained edit scoring scheme. A quotiented tree is a tree defined with an additional equivalent relation on vertices and such that the quotient graph is also a tree. The core of the method relies on two adaptations of an algorithm proposed by Zhang et al.
We present a web-based service, SimCT, which allows to graphically display the relationships betw... more We present a web-based service, SimCT, which allows to graphically display the relationships between biological objects (e.g. genes or proteins) based on their annotations to a biomedical ontology. The result is presented as a tree of these objects, which can be viewed and explored through a specific java applet designed to highlight relevant features. Unlike the numerous tools that search for overrepresented terms, SimCT draws a simplified representation of biological terms present in the set of objects, and can be applied to any ontology for which annotation data is available. Being webbased, it does not require prior installation, and provides an intuitive, easy-to-use service. Availability: http://tagc.univ-mrs.fr/SimCT
Background and scope: Large networks, such as protein interaction networks, are extremely difficu... more Background and scope: Large networks, such as protein interaction networks, are extremely difficult to analyze as a whole. We developed Clust&See, a Cytoscape plugin dedicated to the identification, visualization and analysis of clusters extracted from such networks. Implementation and performance: Clust&See provides the ability to apply three different, recently developed graph clustering algorithms to networks and to visualize: (i) the obtained partition as a quotient graph in which nodes correspond to clusters and (ii) the obtained clusters as their corresponding subnetworks. Importantly, tools for investigating the relationships between clusters and vertices as well as their organization within the whole graph are supplied.
In this paper we propose a dynamic programming algorithm to evaluate local similarity between uno... more In this paper we propose a dynamic programming algorithm to evaluate local similarity between unordered trees using a constrained edit distance. The core of the method relies on an adaptation of an algorithm proposed by Zhang for comparing unordered rooted trees. The method is currently being used in plant architecture modeling to outline similar sub-parts on plant structure and in genomic analysis to evaluate variability between secondary structures of RNA.
In this paper, we define several quantitative measures that are useful when using ontologies to d... more In this paper, we define several quantitative measures that are useful when using ontologies to describe biological data. More precisely, we define the precision of a term inside an ontology, and use this concept to quantify the similarity between terms inside an ontology, or, by extension, between biological entities annotated to terms of the ontology. This similarity measure is used
We are interested in RNA secondary structure comparison, using an approach which consists to repr... more We are interested in RNA secondary structure comparison, using an approach which consists to represent these structures by labeled ordered trees. Following the problem considered, this tree representation can be rough (considering only the structural patterns), or reÿned until an exact coding of the structure is obtained. After some preliminary deÿnitions and the description of the Zhang-Shasha (SIAM J. Comput. 18 (6) (1989) 1245) tree edit algorithm, which is on the one hand the reference when dealing with ordered labeled trees comparison, and on the other hand the starting point of our work, this article will present an exact analysis of its complexity. The purpose of this work is also to lead us to a better comprehension of the parameters of this algorithm, in order to be able to modify it more easily without changing its time complexity to take into account biological constraints that occur when comparing RNA secondary structures.
RNA interference (RNAi), mediated by the introduction of a specific double-stranded RNA, is a pow... more RNA interference (RNAi), mediated by the introduction of a specific double-stranded RNA, is a powerful method to investigate gene function. It is widely used in the Caenorhabditis elegans research community. An expanding number of laboratories conduct genome-wide RNAi screens, using standard libraries of bacterial clones each designed to produce a specific double-stranded RNA. Proper interpretation of results from RNAi experiments requires a series of analytical steps, from the verification of the identity of bacterial clones, to the identification of the clones' potential targets. Despite the popularity of the technique, no user-friendly set of tools allowing these steps to be carried out accurately, automatically, and at a large scale, is currently available. We report here the design and production of Clone Mapper, an online suite of tools specifically adapted to the analysis pipeline typical for RNAi experiments with C. elegans. We show that Clone Mapper overcomes the limita...
An increasing number of laboratories are using the COPAS Biosort™ to implement high-throughput ap... more An increasing number of laboratories are using the COPAS Biosort™ to implement high-throughput approaches to tackle diverse biological problems. While providing a powerful tool for generating quantitative data, the utility of the Biosort is currently limited by the absence of resources for data management. We describe a simple electronic database designed to allow easy storage and retrieval of Biosort data for C. elegans, but that has a wide potential application for organizing electronic files and data sets. ICeE is an Open Source application. The code and accompanying documentation are freely available via the web at http://www.ciml.univ-mrs.fr/EWBANK_jonathan/software.html.
While Caenorhabditis elegans specifically responds to infection by the up-regulation of certain g... more While Caenorhabditis elegans specifically responds to infection by the up-regulation of certain genes, distinct pathogens trigger the expression of a common set of genes. We applied new methods to conduct a comprehensive and comparative study of the transcriptional response of C. elegans to bacterial and fungal infection. Using tiling arrays and/or RNAsequencing, we have characterized the genome-wide transcriptional changes that underlie the host's response to infection by three bacterial (Serratia marcescens, Enterococcus faecalis and otorhabdus luminescens) and two fungal pathogens (Drechmeria coniospora and Harposporium sp.). We developed a flexible tool, the WormBase Converter (available at http:// wormbasemanager.sourceforge.net/), to allow cross-study comparisons. The new data sets provided more extensive lists of differentially regulated genes than previous studies. Annotation analysis confirmed that genes commonly up-regulated by bacterial infections are related to stress responses. We found substantial overlaps between the genes regulated upon intestinal infection by the bacterial pathogens and Harposporium, and between those regulated by Harposporium and D. coniospora, which infects the epidermis. Among the fungus-regulated genes, there was a significant bias towards genes that are evolving rapidly and potentially encode small proteins. The results obtained using new methods reveal that the response to infection in C. elegans is determined by the nature of the pathogen, the site of infection and the physiological imbalance provoked by infection. They form the basis for future functional dissection of innate immune signaling. Finally, we also propose alternative methods to identify differentially regulated genes that take into account the greater variability in lowly expressed genes.
tiques. Abstract. Traditionally, lexical morphology has been diachronic and has established the n... more tiques. Abstract. Traditionally, lexical morphology has been diachronic and has established the notion of word families. This notion is reused in synchronic studies and implies strong seman- tic coherence within the words of a same family. In this paper, we propose an approach in synchrony which highlights phonological and semantic continuity. Our interests go on morpho- phonology and on the semantic dispersion of words in a family. A first study (Gala & Rey, 2008) showed that the semantic spaces of the families displayed either a strong semantic cohesion or a strong dispersion. In order to validate this observation, w e present here a corpus-based method that automatically weights the semantic units of a word and a family. An experience carried out with 30 native speakers validates our approach and allows us to foresee a thorough study of the lexicon based on phonological and semantic basis. Mots-clés : morpho-phonologie lexicale, traitement automatique des familles dériva- tionnel...
In this paper we propose a dynamic programming algorithm to evaluate local similarity between ord... more In this paper we propose a dynamic programming algorithm to evaluate local similarity between ordered quotiented trees using a constrained edit scoring scheme. A quotiented tree is a tree defined with an additional equivalent relation on vertices and such that the quotient graph is also a tree. The core of the method relies on two adaptations of an algorithm proposed by Zhang et al.
We present a web-based service, SimCT, which allows to graphically display the relationships betw... more We present a web-based service, SimCT, which allows to graphically display the relationships between biological objects (e.g. genes or proteins) based on their annotations to a biomedical ontology. The result is presented as a tree of these objects, which can be viewed and explored through a specific java applet designed to highlight relevant features. Unlike the numerous tools that search for overrepresented terms, SimCT draws a simplified representation of biological terms present in the set of objects, and can be applied to any ontology for which annotation data is available. Being webbased, it does not require prior installation, and provides an intuitive, easy-to-use service. Availability: http://tagc.univ-mrs.fr/SimCT
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Papers by Laurent Tichit