Department of Physics - University of Évora

The Chaotic Oscillations of Infantile Congenital Nystagmus

Congenital nystagmus (CN) is an incurable pathological spontaneous oscillation of the eyes with an onset in the first few months of life. The pathophysiology of CN is mysterious. There is no consistent neurological abnormality, but the majority of patients have a wide range of unrelated congenital visual abnormalities affecting the cornea, lens, retina, or optic nerve. In this seminar it is argued that these eye oscillations could develop as an adaptive response to maximise visual contrast with poor foveal function in the infant visuomotor system, at a time of peak neural plasticity. This can explain why CN does not emerge later in life and why CN is so refractory to treatment. It also implies that any therapeutic intervention would need to be very early in life.

Constructing Transcriptional Regulatory Networks Through Gene Functional Similarity.

The methods used nowadays to build transcriptional regulatory networks (differential cloning, microarray analysis, promoter analysis...etc) are expensive and time consuming. We devise a method that uses Gene Ontology to augment our training set of human transcriptional regulatory network.

Local Renyi entropic profiles of DNA sequences.

In a recent report the authors presented a new measure of continuous entropy for DNA sequences, which allows the estimation of their randomness level. The definition therein explored was based on the Rényi entropy of probability density estimation (pdf) using the Parzen's window method and applied to Chaos Game Representation/Universal Sequence Maps (CGR/USM).

The present work extends the concepts of continuous entropy by defining DNA sequence entropic profiles using the pdf estimations obtained previously. These profiles are applied to the study of the same dataset and a new, fractal, kernel function more adjusted to the estimation is explored, instead of normal distributions.

This work achieves two results. On the one hand it shows that the entropic profiles are directly related with the statistical significance of motifs, allowing the study of under and over-representation of segments. On the other hand, by spanning the parameters of the kernel function it is possible to extract important information about the scale of each DNA conserved region, which can have future applications on the recognition of foreign genomic material and inference of motif structures. This ability to detect local conservation is particularly relevant for biological applications of motif/pattern recognition.

Building ontologies for universal data reposition, integration, and systematic analysis. The S3DB Framework.

Knowledge discovery in the life sciences is at the critical turnover from techniques for acquiring, accessing and maintaining knowledge within an organizational structure to the integration of that data into comprehensive models. The emergence of the semantic web has revolutionized the way knowledge can be exchanged, thus creating a momentum for scientific discovery. The S3DB application is geared towards improving dataset use within the scientific community. This implementation is accomplished by creating a user-friendly and intuitive interface that empowers domain experts with the possibility of deciding on the architecture of the data schema to accommodate experimental data and weave its relationships. S3DB uses a semantic infused approach based on the RDF (Resource Description Framework) general-purpose language, which constitutes its main feature to make it independent of the underlying relational database in which it is set.

Chemoinformatics.

Not Supplied.

Modelling of intercellular communication in microbial communities.

Not Supplied.