The validation of clusters discovered in bio-molecular data is a central issue in bioinformatics. Recently, stability-based methods have been successfully applied to the analysis of the reliability of clusterings characterized by a relatively low number of examples and clusters. Nevertheless, several problems in functional genomics are characterized by a very large number of examples and cluste...

MOTIVATION Automatic procedures to obtain pharmacophore models from experimentally determined macromolecular complexes can help in the drug discovery process, especially when protein-protein recognition plays an important biological role. RESULTS The GRID-based pharmacophore model (GBPM) is a fully objective method for defining most relevant interaction areas in complexes deriving pharmacopho...

Flow cytometry is a technique that is used to count cells and to characterize property of the cells. In spite of enormous information content on the cells provided by flow cytometry, cytometry data is still analyzed based on stepby-step gating, either manually or automatically via bioinformatics. This paper presents a new strategy of interpreting cytometry data in a different manner. The propos...

Fast evolution of Internet technologies has led to an explosive growth of video data available in the public domain and created unprecedented challenges in the analysis, organization, management, and control of such content. The problems encountered in video analysis such as identifying a video in a large database (e.g. detecting pirated content in YouTube), putting together video fragments, fi...

The Galois Lattice of a binary relation formalizes it as a concept system, dually ordered in "extension" / "intension". All implications between conjunctions of properties holding in it are summarized by a (recursive) canonical basis -all basis having the same cardinality (see [MR #87k:08009]). We report here how these tools structure phenotypes / genotypes in behavior genetics. On a generic vi...

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In this paper, we present work in progress towards a methodology for the analysis of domain-specific sentiment. In our case, we consider highly specialized scientific disciplines at the boundaries of computer science and selected other disciplines (e.g., computational linguistics, bioinformatics). Our approach is corpus-based and comprises the detection, extraction and annotation of features re...

The assessment of the reliability of clusters discovered in bio-molecular data is a central issue in several bioinformatics problems. Several methods based on the concept of stability have been proposed to estimate the reliability of each individual cluster as well as the ”optimal” number of clusters. In this conceptual framework a clustering ensemble is obtained through bootstrapping technique...

This issue of the In Silico Biology journal covers the materials reported at the Fifth International Conference on Bioinformatics of Genome Regulation and Structure-BGRS’2006 (Akademgorodok, Novosibirsk, Russia, July 16–22, 2006; http://www.bionet.nsc.ru/meeting/bgrs2006/index.html). At the Conference, a wide range of basic issues of bioinformatics resolved by in silico methods, in conjunction ...

This chapter aims to describe concepts and methods required to understand the development of this investigation. An introduction to cancer research and bioinformatics is provided, considering a description, brief historical review, current status and important challenges for the future. The chapter also considers techniques in statistics and data analysis that provide the basis for the search o...