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Research Bernoulli Institute Calendar

Colloquium Mathematics/ Prof. Dr. G. Lunter

When:Tu 22-05-2018 16:00
Where:5161.0293 (Zernike, Bernoulliborg)


Bayesian modeling in biological data analysis:  

applications to recombination and human demography


Next-generation sequencing (NGS) has transformed the biological sciences, giving access to genomes, but also to myriad phenotypes including gene expression and DNA-protein interactions.  The amount of data generated by NGS pose significant computational and modeling challenges.  Perhaps surprisingly, Bayesian approaches remain relevant: signals can be subtle despite the volume of data, and modern Deep Learning models have many free parameters, requiring regularization to prevent overfitting.

I will show applications of Bayesian inference in two modeling problems involving genome-wide data sets.  In the first we use particle filters and Variational Bayes to study human demography. Results indicate that the out-of-Africa event might be more complicated than thought, and suggest a new explanation for the relatively high ancient diversity in the African population.

In the second application we adapt a Variational Bayes techniques for Artificial Neural Networks to exploit a symmetry in DNA sequence models.  Using low-resolution empirical recombination maps, we infer the binding motifs of PRDM9, a key protein regulating recombination, and obtain a predictive model that matches that of direct experimental measurement of PRDM9 activity.  I will show first results of applying these techniques to broader phenotypic prediction from DNA.

Colloquium coordinators are Prof.dr. A.J. van der Schaft ( a.j.van.der.schaft ),

Dr. A.V. Kiselev (e-mail: a.v.kiselev )