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THURSDAY Biostatistics Seminar (Joint Sven Furberg Seminar): Dr. Pekka Marttinen

Speaker: Dr. Pekka Marttinen, Assistant Professor, Helsinki Institute for Information Technology HIIT, Aalto University, Finland, will present his current research.

Location: Domus Medica, Nye Auditorium 13 At the end of the seminar simple food and refreshments will be served.

Title: A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation

Abstract: Bacterial populations that colonize a host can play important roles in host health, including serving as a reservoir that transmits to other hosts and from which invasive strains emerge, thus emphasizing the importance of understanding rates of acquisition and clearance of colonizing populations. Studies of colonization dynamics have been based on assessment of whether serial samples represent a single population or distinct colonization events. With the use of whole genome sequencing to determine genetic distance between isolates, a common solution to estimate acquisition and clearance rates has been to assume a fixed genetic distance threshold below which isolates are considered to represent the same strain. However, this approach is often inadequate to account for the diversity of the underlying within-host evolving population, the time intervals between consecutive measurements, and the uncertainty in the estimated acquisition and clearance rates. Here, we present a fully Bayesian model that provides probabilities of whether two strains should be considered the same, allowing us to determine bacterial clearance and acquisition from genomes sampled over time. Our method explicitly models the within-host variation using population genetic simulation, and the inference is done using a combination of Approximate Bayesian Computation (ABC) and Markov Chain Monte Carlo (MCMC). We validate the method with multiple carefully conducted simulations and demonstrate its use in practice by analyzing a collection of methicillin resistant Staphylococcus aureus (MRSA) isolates from a large recently completed longitudinal clinical study.

Meeting the speaker
Please send a quick email to if you would like to meet with Dr. Pekka Marttinen. Information at and

Looking forward to seeing you all at the seminar.

Manuela Zucknick, Jon Michael Gran, Anthony Mathelier

Organizer: Oslo Centre for Biostatistics and Epidemiology (OCBE), Research group in Statistics and Biostatistics, Dept. of Mathematics, UiO, Big Insight and the Sven Furberg Seminars in Bioinformatics and Statistical Genomics