Abstract Modelling complex biological systems is necessary for their study and understanding. Biomodels a repository of peer-reviewed models represented in the Systems Biology Markup Language (SBML). Most these are quantitative, but some cases, qualitative models—such as Boolean networks (BNs)—are better suited. This paper focuses on automatic transformation quantitative SBML to networks. We pr...

Predictive quantitative structure–activity relationship was performed on the novel 4-oxo-1,4-dihydroquinoline and 4-oxo-4H-pyrido[1,2-a]pyrimidine derivatives to explore relationship between the structure of synthesized compounds and their anti-HIV-1 activities. In this way, the suitable set of the molecular descriptors was calculated and the important descriptors using the variable selections ...

Expression quantitative trait loci (eQTL) studies are an integral tool to investigate the genetic component of gene expression variation. A major challenge in the analysis of such studies are hidden confounding factors, such as unobserved covariates or unknown subtle environmental perturbations. These factors can induce a pronounced artifactual correlation structure in the expression profiles, ...

Our goal is gene network inference in genetical genomics or systems genetics experiments. For species where sequence information is available, we first perform expression quantitative trait locus (eQTL) mapping by jointly utilizing cis-, cis-trans-, and trans-regulation. After using local structural models to identify regulator-target pairs for each eQTL, we construct an encompassing directed n...

With the advances in high-throughput genotyping technology, the study of quantitative trait loci (QTL) has emerged as a promising tool to understand the genetic basis of complex traits. Methodology development for the study of QTL recently has attracted significant research attention. Local phylogeny-based methods have been demonstrated to be powerful tools for uncovering significant associatio...

In this paper, we propose a regression framework for steganalysis of digital images that utilizes the recently proposed rich models – high-dimensional statistical image descriptors that have been shown to substantially improve classical (binary) steganalysis. Our proposed system is based on gradient boosting and utilizes a steganalysis-specific variant of regression trees as base learners. The ...

When developing a safety-critical system it is essential to obtain an assessment of different design alternatives. In particular, an early safety assessment of the architectural design of a system is desirable. In spite of the plethora of available formal quantitative analysis methods it is still difficult for software and system architects to integrate these techniques into their every day wor...