Phase Space Reconstruction of Multivariate Time Series from Molecular and Field Biology.

I will present the work done during my graduate studies in the biomathematics group of ITQB. We have been interested in uncovering biological systems and processes from the time series they generate, and therefore, we have proposed a more efficient method to reconstruct a phase space from a scalar time series of measurements on the system, and extended this new method to multivariate time series. We then applied these methods and ideas to the identification of key proteins in the development of the chicken embryo heart from 2-dimensional electrophoresis gels, and to the identification of data-driven predictive models for the Atlantic white shrimp using artificial neural networks.

Emergence of young genes after burst of retroposition in primates.

We conducted a systematic survey to gauge to what extent the high rate of retroposition in primates has generated young functional retrogenes in humans. We utilized an approach that combines comparative genomic sequencing, evolutionary analysis, and gene expression experiments to obtain an initial estimate of the number of recent human retrogenes. We estimate that at least 70 new retrogenes originated in the past 55 million years since the common ancestor of extant primates. Most of these new genes were progressively recruited during primate evolution to enhance male germline functions. Retrogenes obtained such new functions (after evolving testis-specific expression) either by the preservation of ancestral proteins (genes derived from the X chromosome) or by adaptive protein evolution driven by positive selection (other genes). Our study points to a significant role of retroposition in providing raw material for the evolution of new genes and phenotypes on the primate lineage leading to humans.

Gene regulatory networks: tools for an enhanced understanding.

In this talk I will present the work done during my PhD. It consisted in the development of data integration techniques, namely for the measurement of global and local agreement between two data sources about the same set of biological entities. The aim was to apply these methods to the integration of transcription factor binding data with gene expression and functional anotation data, uncovering relevant architectural features of gene regulatory networks. To be able to apply the developed tools, a definition of co-regulatory distance based in the network architecture was needed. In the search for a useful co-regulatory distance definition several probabilistic properties of gene regulatory networks were found and described.

Towards Comprehensive Biology. What happens when an immunologist looks around?

On the next EAO seminar I am going to outline the different research lines of my group, that range from basic questions on cell biology to questions on multicellular systems and organisms. The common thread is the process of individuation by which the undifferentiated develops individual characteristics in physical, molecular, or cognitive domains.

Chemical Tuning Changes in the Rat Gustatory Cortex.

The rodent primary gustatory cortex (GC) is the main cortical target of chemosensory, somatosensory and visceral information related to food consumption. I will present data showing that GC single-neuronal responses to liquid tastants present considerable variability in the time scale of 1.5 hours.