NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference.

BACKGROUND: In the last decade, a great number of methods for reconstructing gene regulatory networks from expression data have been proposed. However, very few tools and datasets allow to evaluate accurately and reproducibly those methods. Hence, we propose here a new tool, able to perform a systematic, yet fully reproducible, evaluation of transcriptional network inference methods. RESULTS: Our open-source and freely available Bioconductor package aggregates a large set of tools to assess the robustness of network inference algorithms against different simulators, topologies, sample sizes and noise intensities. CONCLUSIONS: The benchmarking framework that uses various datasets highlights the specialization of some methods toward network types and data. As a result, it is possible to identify the techniques that have broad overall performances.

Elevated basal hepcidin levels in the liver may inhibit the development of malaria infection: another piece towards solving the malaria puzzle?

BACKGROUND: Inflammatory cytokines play a crucial role in the human immune response to infection by malaria. During the initial sporozoite infection of the liver the presence of Interleukin-6 (IL-6) can be determinant. IL-6 controls systemic iron homeostasis through hepcidin, which is produced mainly by hepatocytes. An elevated basal hepcidin level in the liver can be induced by chronic inflammatory disease. Hepcidin is also a peptide with antimicrobial properties. PRESENTATION OF THE HYPOTHESIS: We hypothesize that elevated basal hepcidin levels in the liver inhibit the development of malaria infection. When hepcidin is abundant, hepatocytes sequester iron, and this inhibits sporozoite development in liver-stage malaria infection. TESTING THE HYPOTHESIS: The validity of our hypothesis can be proven by observing sporozoite growth in hepcidin-treated hepatocytes, or in hepatocytes, stimulated with IL-6 to increase hepcidin levels before incubation with malaria sporozoites and observing the effect the hepcidin knockout function has on the infection. IMPLICATIONS OF THE HYPOTHESIS: Confirmation of our hypothesis could help to understand the complexity of the malaria infection.

Hierarchical clustering combining numerical and biological similarities for gene expression data classification.

High throughput data analysis is a challenging problem due to the vast amount of available data. A major concern is to develop algorithms that provide accurate numerical predictions and biologically relevant results. A wide variety of tools exist in the literature using biological knowledge to evaluate analysis results. Only recently, some works have included biological knowledge inside the analysis process improving the prediction results.