Objective To develop a modular approach to infectious disease genomic analysis that can easily integrate with public health analytics systems. Using dynamic approaches to genomic sequence analysis, relevant whole genome data can be quickly and accurately visualized and correlated, using a minimum of computational resources. We propose to develop visualization modules that integrate disparate da...

MOTIVATION This paper reports on a survey of bioinformatics tasks currently undertaken by working biologists. The aim was to find the range of tasks that need to be supported and the components needed to do this in a general query system. This enabled a set of evaluation criteria to be used to assess both the biology and mechanical nature of general query systems. RESULTS A classification of ...

Assessing variations in DNA copy number is crucial for understanding constitutional or somatic diseases, particularly cancers. The recently developed array-CGH (comparative genomic hybridization) technology allows this to be investigated at the genomic level. We report the availability of a web tool for analysing array-CGH data. CAPweb (CGH array Analysis Platform on the Web) is intended as a u...

Association analysis is one of the most popular analysis paradigms in data mining. Despite the solid foundation of association analysis and its potential applications, this group of techniques is not as widely used as classification and clustering, especially in the domain of bioinformatics and computational biology. In this paper, we present different types of association patterns and discuss ...

In the wake of the numerous now-fruitful genome projects, we are entering an era rich in biological data. The field of bioinformatics is poised to exploit this information in increasingly powerful ways, but the abundance and growing complexity both of the data and of the tools and resources required to analyse them are threatening to overwhelm us. Databases and their search tools are now an ess...

This talk will review a little over a decade’s research on applying certain stochastic models to biological sequence analysis. The models themselves have a longer history, going back over 30 years, although many novel variants have arisen since that time. The function of the models in biological sequence analysis is to summarize the information concerning what is known as a motif or a domain in...

Co-clustering, that is, partitioning a numerical matrix into “homogeneous” submatrices, has many applications ranging from bioinformatics to election analysis. Many interesting variants of co-clustering are NP-hard. We focus on the basic variant of co-clustering where the homogeneity of a submatrix is defined in terms of minimizing the maximum distance between two entries. In this context, we s...

There are numerous applications that need to deal with a large graph, including bioinformatics, social science, link analysis, citation analysis, and collaborative networks. A fundamental query is to query whether a node is reachable from another node in a large graph, which is called a reachability query. In this survey, we discuss several existing approaches to process reachability queries. I...

Following the completion of the Human Genome Project in 2003, we were able to clarify the comprehensive profile of the whole human genome on DNA microarray. KeyMolnet is a bioinformatics tool for analyzing molecular interactions on the curated knowledge database. It promotes genome-based drug discovery research aimed at mining the most relevant molecular target to personalized medicine. Multipl...

2DE and 2D-DIGE based proteomics analysis of serum from women with endometriosis revealed several proteins to be dysregulated. A complete list of these proteins along with their mass spectrometry data and subsequent bioinformatics analysis are presented here. The data is related to "Investigation of serum proteome alterations in human endometriosis" by Dutta et al. [1].