Algorithms and Optimization / Knowledge Discovery and Bioinformatics group (ALGOS/KDBIO) - Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento http://algos.inesc-id.pt/kdbio

From microbial molecular typing to population genetics: fBURST

Microbial typing methods are extensively used in a clinical microbiology setting to characterize and determine relationships between bacterial isolates. Some of these methods are also adequate to infer the phylogeny of those isolates as population analysis studies. One of those methods is Multi Locus Sequence Typing, which is based upon sequencing internal fragments of 7 housekeeping genes of a given strain. Based on the resulting allelic sequence and using an algorithm called eBURST (Based Upon Related Strain Types), one can produce an hypothesis of how the strains derived from one another. But this algorithm assumes only the number of differences between allelic sequences, not taking into consideration that new alleles are created by mutation or recombination. Recent studies show that eBURST results are less reliable for species with high levels of recombination. Here we propose the use of an information-theoretic similarity metric that takes into account the relative frequency of alleles of each gene in the sample of the population present in the MLST database and also a new way to create and display groups that could represent a more suitable evolutionary hypothesis for strains with high recombination rates: fBURST.

Unidade de Microbiologia Molecular e Infecção, Instituto de Medicina Molecular, FML

Pathogen diversity: what, when, how and why?

In this talk I will tell you about the life of a Bioinformatician /Computational Biologist in a clinical microbiology lab, the questions that we try to answer, what we have done so far to answer them and what we plan to do to complete these answers. The main questions are: What makes pathogens from the same species different? When in time did the several diversifying events occur? How did they occur (or through which mechanisms the changes where introduced and maintained in the population)? Why do these changes take place (or what is the evolutionary advantage associated with the changes)?

Instituto Gulbenkian de Ciência (Theoretical Epidemiology)

Infectious diseases: my life as a host

(not supplied)

Instituto Gulbenkian de Ciência (Population Genetics)

Selfish and spiteful behavior through parasites and pathogens - Hosts can increase their fitness via parasites and pathogens

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