Evaluation of hazards associated with exposure to chemicals, understanding of relationships between dose and adverse effect, extrapolation of effects from high experimental doses to low doses associated with actual exposures, and extrapolation from effects observed in animals to effects expected...

The expanding availability of protein data enforces the application of empirical methods necessary to recognize protein structures. In this paper a sequence-structure alignment method is described and applied to various Ubiquitin-like folded Ras-binding domains. On the basis of two probability...

The correlated Weibull regression model for the analysis of correlated binary data is presented. This regression model is based on Bonney’s disposition model for the regression analysis of correlated binary outcomes. Parameter estimation was done through the maximum likelihood method. The...

Microarrays are part of a new class of biotechnologies which allow the monitoring of expression levels of thousands of genes simultaneously. In microarray data analysis, the comparison of gene-expression profiles with respect to different conditions and the selection of biologically interesting...

The protein family of septins is analyzed with the SOM methodology of Andrade et al. (1997) to determine the family relationships and the key residues responsible for the obtained classification. These key residues are candidates for determining functional sites of the proteins. The advantages...

The structural analysis of proteins is fundamental to the analysis of protein functions. In this context, sequence-structure alignment methods are important among the different empirical methods. In order to assess the quality of sequence-structure alignments, a statistical method using a...

Microarrays are part of a new class of biotechnologies which allow the monitoring of expression levels of thousands of genes simultaneously. In microarray data analysis, the comparison of gene-expression profiles with respect to different conditions and the selection of biologically interesting...

The determination of toxicokinetic parameters is an essential component in the risk assessment of potential harmful chemicals. It is a key step to analyse the processes involved in the formation of DNA adducts which are connected with the development of chemical-induced cancer. A general problem...

In this paper, hidden Markov models (HMMs) are discussed in the context of molecular biological sequence analysis. The statistics relevant in the HMM approach are described in detail. An HMM based method is used to analyze two proteins that contain short protein repeats (SPRs). As a benchmark, a...

These report presents two methods for the identification of signal peptides and their cleavage sites. The first method is based on based neural networks and the second on hidden Markov models. The transmembrane protein topology can also be identified by a method based on hidden Markov models,...