Integrating molecular interaction data with existing knowledge of molecular function reveals mechanisms that underly cellular organization. We present NARADA, a software tool that implements a comprehensive analysis suite for functional annotation of pathways. NARADA takes as input a species-specific molecular interaction network and annotation of biomolecules in the network and provides the us...

Integrating molecular interaction data with existing knowledge of molecular function reveals mechanisms that underly cellular organization. We present NARADA, a software tool that implements a comprehensive analysis suite for functional annotation of pathways. NARADA takes as input a species-specific molecular interaction network and annotation of biomolecules in the network and provides the us...

Discovering motifs in protein–protein interaction networks is becoming a current major challenge in computational biology, since the distribution of the number of network motifs can reveal significant systemic differences among species. However, this task can be computationally expensive because of the involvement of graph isomorphic detection. In this paper, we present a new algorithm (CombiMo...

Many processes in the cell involve interaction among the proteins and determination of the networks of such interactions is of immense importance towards the complete understanding of cellular functions. As the experimental techniques for this purpose are expensive and potentially erroneous, there are many computational methods being put forward for prediction of protein-protein interactions. T...

This paper describes a new method of analysis of fluorescence images containing a mixture of fluorophores. Parametric maps showing the relative quantity and distribution of each individual fluorophore are generated using a predictive model of image formation. Error analysis applied to the model supplies objective criteria for choosing the optimal filters for image acquisition in the regions in ...

Motivations Protein interaction databases archive proteinprotein interaction (PPI) information from published articles. However, no database alone has sufficient literature coverage to offer a complete resource to investigate “the interactome”. We have developed mentha, a new resource that addresses this problem. mentha archives evidence about PPI in the human proteome evidence collected from d...

In biomedical texts, contradictions about proteinprotein interactions (PPIs) occur when an author reports observing a given PPI whereas another author argues that very same interaction does not take place: e.g., when author X argues that “protein A interacts with protein B” whereas author Y claims that “protein A does not interact with B”. Of course, merely discovering a potential contradiction...

We present a network model in which words over a specific alphabet, called structures, are associated to each node and undirected edges are added depending on some distance measure between different structures. It is shown that this model can generate, without the use of preferential attachment or any other heuristic, networks with topological features similar to biological networks: power law ...

The Human papillomavirus (HPV) E6 protein is one of the oncoproteins encoded by the virus. Inorder to understand the mechanism by which E6 interacts with the host cellular proteins to trigger the cascade of cancer cell transformation. STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) is a biological database has been used to model the pathway of the proteinprotein interaction...

In this paper we introduce BioPubMiner, a machine learning component-based platform for biomedical information analysis. BioPubMiner employs natural language processing techniques and machine learning based data mining techniques for mining useful biological information such as proteinprotein interaction from the massive literature. The system recognizes biological terms such as gene, protein, ...