Using modular decomposition technique to solve the maximum clique problem

In this article we use the modular decomposition technique for exact solving the weighted maximum clique problem. Our algorithm takes the modular decomposition tree from the paper of Tedder et. al. and finds solution recursively. Also, we propose algorithms to construct graphs with modules. We show some interesting results, comparing our solution with Ostergard's algorithm on DIMACS benchmarks and on generated graph

Étude de l'impact des activités touristiques sur la qualité de l'eau et l'organisation des peuplements macrobenthiques au sein des cours d'eau de la Principauté d'Andorre

Le développement considérable de l'activité touristique hivernale et estivale entraîne des perturbations au niveau des principaux cours d'eau andorrans. Il est intéressant d'étudier l'impact de ces perturbations sur des réseaux hydrographiques de haute altitude caractérisés par des conditions du milieu particulières (basse température-forte pente). Les données disponibles concernant la physicochimie et la faune des eaux andorranes sont réduites (PUIG, 1979 ; PEÑA, 1983).Treize stations ont été étudiées dans le cadre de ces travaux.Au cours d'un cycle annuel (automne 1998 à automne 1999), huit prélèvements d'invertébrés benthiques ont été réalisés à chaque station à l'aide d'un filet Surber (vide de maille : 200 µm-surface échantillonnée : 1/ 20e m2).Neuf paramètres physicochimiques (température, pH, conductivité, DCO, DBO5, nitrates, nitrites, ammoniaque, phosphates) ont été mesurés de façon hebdomadaire à chaque station.Le traitement des données physicochimiques par analyses discriminantes révèle l'existence d'un gradient amont-aval de dégradation de la qualité de l'eau. Parallèlement, la qualité de l'eau suit un cycle saisonnier mis en évidence par l'opposition entre campagnes d'été et d'hiver-printemps 1999, d'une part, et campagnes d'automne 1998-1999, d'autre part.L'analyse de la répartition spatiotemporelle de la faune benthique, basée également sur des analyses discriminantes, met en évidence la disparition des taxons polluosensibles dans les stations intermédiaires et aval comme les filtreurs (Simuliidae), les prédateurs (Perlodae, Perlididae, Rhyacophilidae) et les fragmenteurs (Nemouridae, Leuctridae) et l'apparition de nouveaux taxons polluotolérants en aval (Chironomidae, Oligochètes). Ce genre de phénomène a déjà été observé dans d'autres cours d'eau de montagne soumis à des perturbations entraînant l'augmentation de la charge organique (DECAMPS et PUJOL, 1977).Ces taxons polluotolérants comme par exemple, les Oligochètes qui prolifèrent dans la zone aval du cours d'eau principal (Gran Valira) et en aval de l'unique station d'épuration située sur l'Ariège remplacent dans la structure trophique d'autres taxons polluosensibles. Ce phénomène s'observe également au sein d'un même groupe trophique, c'est le cas des prédateurs composés des Perlidae, des Perlodidae et des Rhyacophilidae présents dans les stations de haute altitude et qui disparaissent en aval où ils sont remplacés par les Achètes (Glossiphoniidae).Le calcul de plusieurs indices biologiques d'évaluation de la qualité des eaux (IBGN - BMWP), de richesse et de diversité spécifiques (indices de Shannon et de Margalef), de structure des peuplements (CUMMINS, 1979, 1985) met en évidence la diminution de la richesse et de la diversité spécifiques des stations amont vers les stations aval.L'impact du développement touristique se manifeste à partir des stations de moyenne altitude. Dans ces stations, la pollution est partiellement évacuée, chaque automne, par l'eau de bonne qualité en provenance des zones amont des cours d'eau. Ce phénomène se traduit par une grande variabilité des conditions physicochimiques et de la composition des communautés benthiques. Dans les stations aval, la pollution prend plutôt un caractère chronique suite à la concentration des pollutions en provenance des différentes zones perturbées. La variabilité des conditions du milieu et des assemblages faunistiques est donc moindre.Les résultats obtenus à partir du traitement des données physicochimiques et faunistiques mettent en évidence une dégradation de l'intégrité écologique des cours d'eau (modifications physicochimiques, modifications du peuplement, diminution de la diversité). L'impact des perturbations d'origine anthropique suit un cycle dépendant de la fréquentation touristique. Au cours de ce cycle, alternent deux périodes " critiques " caractérisées par des perturbations hivernales (ski) et estivales (tourisme, randonnées) et une période de " récupération " durant l'automne.Ces travaux ont permis de tester l'hypothèse des perturbations intermédiaires du milieu (CONNELL, 1978 ; RESH, 1988 ; TOWNSEND et al., 1997) et de rechercher les seuils d'intensité des perturbations et/ou l'amplitude de ces perturbations ainsi que leur impact négatif sur la composition faunistique (EDWARD et RYKIEL, 1985 ; PICKETT et al., 1989 ; REICE et al., 1990).The important development of tourism during winter and summer disturb the main Andorran streams. The impact of these disturbances were studied in high altitude streams characterised by particular environmental conditions (e.g. low temperature - steep slope) as little is known about water quality and associated benthic fauna in Andorran streams (PUIG, 1979; PEÑA, 1983).Thirteen sites were seasonally studied during one year, from autumn 1998 to autumn 1999, in each site, eight macroinverbrates samples were coffected using a Surber sampling net (mesh size 200 µm - sampling area : 1/20e m2). In addition, nine physicochemical parameters (temperature - pH - conductivity - DCO - DBO5 - nitrate- nitrite - ammonia - phosphate) were weekly measured in each site during the entire sampfing period.A discriminant analysis performed on the physicochemical data reaveled and upstreamdownstream gradient of the water quality, with highest disturbance in the downstream sites. From a temporal point of view, the water quality follows a seasonal cycle highlighted by the opposition between on the one hand winter-spring and summer 1999, and on the other hand autumn 1998-1999.The spatio-temporal distribution of the benthic fauna, based on the discriminant analysis, highlighted the disappearance of polluo-sensitive taxa in intermediate and downstream sites such as filtering collectors (Simuliidae), predators (Perfidae - Perlodidae - Rhyacophilidae) and shredders (Nemouridae - Leuctridae). In these areas, sensitive taxa were replaced by polluo-tolerant ones such as Chironomidae and Oligocheta. These patterns were already observed in other mountain streams subjected to high organic disturbances (DECANTS et PUJOL, 1977).As a consequence, polluo-tolerant taxa replace polluo-sensitives taxa with similar functionnal status. For example Oligocheta, proliferate in the downstream (Gran Valira), whereas upstream, they were only abundant on a point source pollution site located on the Ariege river. The same phenomenon was also observed for predators: high unpolluted altitude sites were characterised by stoneflies and caddisflies (Perlidae, Perlodidae, Rhyacophilidae) which were replaced downstream by leeches (Glossiphoniidae). As a consequence, the calculation of the several biological indices of water quality (I.B.G.N - B.M.W.Y'), and diversity descriptors (taxa richness - Shannon index - Margalef index), indicate a drastic reduction of the taxa diversity, evenness and water quality from. upstream to downstrearn sites.Disturbances associated with tourism developinent appeared in the medium altitude sites. In these sites, the water quality benefits from the good water quality from the upstream sites during high discharge periods (i.e. in autumn). This phenomena explained the observed temporal variabihty of both physicochemical conditions and benthic fauna structure. In the down-stream sites, the pollution can be considered as chronic and hence, low envirorimental variability was observed. These results show that Andorran stream ecological integrity is low fonn both physicochemical diversity and population assemblages point of views. Moreover, the impact of anthropic disturbances followed an annual cycle according to tourisin. activities with pollution peaks in winter and suminer corresponding respectively to ski resort and hiking tourisin. The only partial recovery period is represented by the autumn high drainage period.From a theoretical point of view, these results allowed to test the intermediate disturbance hypothesis (CONNELL, 1978; RESH, 1988; TOWNSFND et al., 1997) and to search the threshold of resistence/resilience characteristics of a stream ecosystern considering stream. benthic assemblages (EDWARD et RYKIEL, 1985; REICE et al., 1990; PICKETT et al., 1989)

Structural Kinetic Modeling of Metabolic Networks

To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit kinetic modeling based on differential equations is still often severely hampered by inadequate knowledge of the enzyme-kinetic rate laws and their associated parameter values. Here we propose a method that aims to give a detailed and quantitative account of the dynamical capabilities of metabolic systems, without requiring any explicit information about the particular functional form of the rate equations. Our approach is based on constructing a local linear model at each point in parameter space, such that each element of the model is either directly experimentally accessible, or amenable to a straightforward biochemical interpretation. This ensemble of local linear models, encompassing all possible explicit kinetic models, then allows for a systematic statistical exploration of the comprehensive parameter space. The method is applied to two paradigmatic examples: The glycolytic pathway of yeast and a realistic-scale representation of the photosynthetic Calvin cycle.Comment: 14 pages, 8 figures (color

Assessing Systems Properties of Yeast Mitochondria through an Interaction Map of the Organelle

Mitochondria carry out specialized functions; compartmentalized, yet integrated into the metabolic and signaling processes of the cell. Although many mitochondrial proteins have been identified, understanding their functional interrelationships has been a challenge. Here we construct a comprehensive network of the mitochondrial system. We integrated genome-wide datasets to generate an accurate and inclusive mitochondrial parts list. Together with benchmarked measures of protein interactions, a network of mitochondria was constructed in their cellular context, including extra-mitochondrial proteins. This network also integrates data from different organisms to expand the known mitochondrial biology beyond the information in the existing databases. Our network brings together annotated and predicted functions into a single framework. This enabled, for the entire system, a survey of mutant phenotypes, gene regulation, evolution, and disease susceptibility. Furthermore, we experimentally validated the localization of several candidate proteins and derived novel functional contexts for hundreds of uncharacterized proteins. Our network thus advances the understanding of the mitochondrial system in yeast and identifies properties of genes underlying human mitochondrial disorders

Genome-wide allele- and strand-specific expression profiling

Recent reports have shown that most of the genome is transcribed and that transcription frequently occurs concurrently on both DNA strands. In diploid genomes, the expression level of each allele conditions the degree to which sequence polymorphisms affect the phenotype. It is thus essential to quantify expression in an allele- and strand-specific manner. Using a custom-designed tiling array and a new computational approach, we piloted measuring allele- and strand-specific expression in yeast. Confident quantitative estimates of allele-specific expression were obtained for about half of the coding and non-coding transcripts of a heterozygous yeast strain, of which 371 transcripts (13%) showed significant allelic differential expression greater than 1.5-fold. The data revealed complex allelic differential expression on opposite strands. Furthermore, combining allele-specific expression with linkage mapping enabled identifying allelic variants that act in cis and in trans to regulate allelic expression in the heterozygous strain. Our results provide the first high-resolution analysis of differential expression on all four strands of an eukaryotic genome

Selective Phenotyping, Entropy Reduction, and the Mastermind game

<p>Abstract</p> <p>Background</p> <p>With the advance of genome sequencing technologies, phenotyping, rather than genotyping, is becoming the most expensive task when mapping genetic traits. The need for efficient selective phenotyping strategies, <it>i</it>.<it>e</it>. methods to select a subset of genotyped individuals for phenotyping, therefore increases. Current methods have focused either on improving the detection of causative genetic variants or their precise genomic location separately.</p> <p>Results</p> <p>Here we recognize selective phenotyping as a Bayesian model discrimination problem and introduce SPARE (Selective Phenotyping Approach by Reduction of Entropy). Unlike previous methods, SPARE can integrate the information of previously phenotyped individuals, thereby enabling an efficient incremental strategy. The effective performance of SPARE is demonstrated on simulated data as well as on an experimental yeast dataset.</p> <p>Conclusions</p> <p>Using entropy reduction as an objective criterion gives a natural way to tackle both issues of detection and localization simultaneously and to integrate intermediate phenotypic data. We foresee entropy-based strategies as a fruitful research direction for selective phenotyping.</p

Metabolic design of macroscopic bioreaction models: application to Chinese hamster ovary cells

The aim of this paper is to present a systematic methodology to design macroscopic bioreaction models for cell cultures based upon metabolic networks. The cell culture is seen as a succession of phases. During each phase, a metabolic network represents the set of reactions occurring in the cell. Then, through the use of the elementary flux modes, these metabolic networks are used to derive macroscopic bioreactions linking the extracellular substrates and products. On this basis, as many separate models are obtained as there are phases. Then, a complete model is obtained by smoothly switching from model to model. This is illustrated with batch cultures of Chinese hamster ovary cells

Computing the shortest elementary flux modes in genome-scale metabolic networks

This article is available open access through the publisher’s website through the link below. Copyright @ The Author 2009.Motivation: Elementary flux modes (EFMs) represent a key concept to analyze metabolic networks from a pathway-oriented perspective. In spite of considerable work in this field, the computation of the full set of elementary flux modes in large-scale metabolic networks still constitutes a challenging issue due to its underlying combinatorial complexity. Results: In this article, we illustrate that the full set of EFMs can be enumerated in increasing order of number of reactions via integer linear programming. In this light, we present a novel procedure to efficiently determine the K-shortest EFMs in large-scale metabolic networks. Our method was applied to find the K-shortest EFMs that produce lysine in the genome-scale metabolic networks of Escherichia coli and Corynebacterium glutamicum. A detailed analysis of the biological significance of the K-shortest EFMs was conducted, finding that glucose catabolism, ammonium assimilation, lysine anabolism and cofactor balancing were correctly predicted. The work presented here represents an important step forward in the analysis and computation of EFMs for large-scale metabolic networks, where traditional methods fail for networks of even moderate size. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online (http://bioinformatics.oxfordjournals.org/cgi/content/full/btp564/DC1).Fundação Calouste Gulbenkian, Fundação para a Ciência e a Tecnologia (FCT) and Siemens SA Portugal

4DXpress: a database for cross-species expression pattern comparisons

In the major animal model species like mouse, fish or fly, detailed spatial information on gene expression over time can be acquired through whole mount in situ hybridization experiments. In these species, expression patterns of many genes have been studied and data has been integrated into dedicated model organism databases like ZFIN for zebrafish, MEPD for medaka, BDGP for Drosophila or GXD for mouse. However, a central repository that allows users to query and compare gene expression patterns across different species has not yet been established. Therefore, we have integrated expression patterns for zebrafish, Drosophila, medaka and mouse into a central public repository called 4DXpress (expression database in four dimensions). Users can query anatomy ontology-based expression annotations across species and quickly jump from one gene to the orthologues in other species. Genes are linked to public microarray data in ArrayExpress. We have mapped developmental stages between the species to be able to compare developmental time phases. We store the largest collection of gene expression patterns available to date in an individual resource, reflecting 16 505 annotated genes. 4DXpress will be an invaluable tool for developmental as well as for computational biologists interested in gene regulation and evolution. 4DXpress is available at http://ani.embl.de/4DXpress

Complex networks theory for analyzing metabolic networks

One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of the organism, while networks are appropriate abstract description of all kinds of interactions. In the past few years, great achievement has been made in developing theory of complex networks for revealing the organizing principles that govern the formation and evolution of various complex biological, technological and social networks. This paper reviews the accomplishments in constructing genome-based metabolic networks and describes how the theory of complex networks is applied to analyze metabolic networks.Comment: 13 pages, 2 figure