Combining optimization and machine learning techniques for genome-wide prediction of human cell cycle-regulated genes.

MOTIVATION: The identification of cell cycle-regulated genes through the cyclicity of messenger RNAs in genome-wide studies is a difficult task due to the presence of internal and external noise in microarray data. Moreover, the analysis is also complicated by the loss of synchrony occurring in cell cycle experiments, which often results in additional background noise. RESULTS: To overcome these problems, here we propose the LEON (LEarning and OptimizatioN) algorithm, able to characterize the 'cyclicity degree' of a gene expression time profile using a two-step cascade procedure. The first step identifies a potentially cyclic behavior by means of a Support Vector Machine trained with a reliable set of positive and negative examples. The second step selects those genes having peak timing consistency along two cell cycles by means of a non-linear optimization technique using radial basis functions. To prove the effectiveness of our combined approach, we use recently published human fibroblasts cell cycle data and, performing in vivo experiments, we demonstrate that our computational strategy is able not only to confirm well-known cell cycle-regulated genes, but also to predict not yet identified ones. AVAILABILITY AND IMPLEMENTATION: All scripts for implementation can be obtained on request.

Machine Learning-Based Classification to Disentangle EEG Responses to TMS and Auditory Input.

The combination of transcranial magnetic stimulation (TMS) and electroencephalography (EEG) offers an unparalleled opportunity to study cortical physiology by characterizing brain electrical responses to external perturbation, called transcranial-evoked potentials (TEPs). Although these reflect cortical post-synaptic potentials, they can be contaminated by auditory evoked potentials (AEPs) due to the TMS click, which partly show a similar spatial and temporal scalp distribution. Therefore, TEPs and AEPs can be difficult to disentangle by common statistical methods, especially in conditions of suboptimal AEP suppression. In this work, we explored the ability of machine learning algorithms to distinguish TEPs recorded with masking of the TMS click, AEPs and non-masked TEPs in a sample of healthy subjects. Overall, our classifier provided reliable results at the single-subject level, even for signals where differences were not shown in previous works. Classification accuracy (CA) was lower at the group level, when different subjects were used for training and test phases, and when three stimulation conditions instead of two were compared. Lastly, CA was higher when average, rather than single-trial TEPs, were used. In conclusion, this proof-of-concept study proposes machine learning as a promising tool to separate pure TEPs from those contaminated by sensory input.

MOSES: A New Approach to Integrate Interactome Topology and Functional Features for Disease Gene Prediction.

Disease gene prediction is to date one of the main computational challenges of precision medicine. It is still uncertain if disease genes have unique functional properties that distinguish them from other non-disease genes or, from a network perspective, if they are located randomly in the interactome or show specific patterns in the network topology. In this study, we propose a new method for disease gene prediction based on the use of biological knowledge-bases (gene-disease associations, genes functional annotations, etc.) and interactome network topology. The proposed algorithm called MOSES is based on the definition of two somewhat opposing sets of genes both disease-specific from different perspectives: warm seeds (i.e., disease genes obtained from databases) and cold seeds (genes far from the disease genes on the interactome and not involved in their biological functions). The application of MOSES to a set of 40 diseases showed that the suggested putative disease genes are significantly enriched in their reference disease. Reassuringly, known and predicted disease genes together, tend to form a connected network module on the human interactome, mitigating the scattered distribution of disease genes which is probably due to both the paucity of disease-gene associations and the incompleteness of the interactome.