Tuesday, October 25, 2016

Lecture 12: Andrei Kucharavy (Rong Li Lab)

Cellular Adaptation Under Stress
Diagram for a cell population adaptation.
Whether the products of human activity, or naturally occurring social, economic or biological, complex systems share the same properties. Composed of a large number of individual components, their components do not have a straightforward relation to their properties and often interact one with another in unexpected ways. Because of that, different instances of the same complex systems are built from slightly different components. Such differences give rise to heterogeneity within a population, which in turn raises significant difficulties for their study. From the biological perspective, such events have been formalized as Fisher’s geometric model, that has been formalized in the thirties of the last century and has been independently re-discovered in unrelated domains as algorithms for ergodic explorations of multi-dimensional spaces for an optimal value function point. 

Andrei Kucharavy and Dr. Rong Li from Johns Hopkins Medicine propose an enhancement of Fisher’s geometric model, allowing to explain a range of previously unexplained observations in biology. Mathematical analysis of their enhancement provides a set of rules applicable to the optimization of a large class of ergodic exploration algorithms.

Related Journal Articles:
1. H. A. Orr, The genetic theory of adaptation: a brief history. Nat. Rev. Genet. 6, 119–127 (2005) 
2. H. A. Orr, R. L. Unckless, The Population Genetics of Evolutionary Rescue. PLoS Genet. 10, e1004551 (2014). 
3. P. S. Pennings, Standing genetic variation and the evolution of drug resistance in HIV. PLoS Comput. Biol. 8 (2012).
Andrei Kucharavy received his Engineer’s Degree in Physics, Mathematics, Programming and Bioinformatics from Ecole Polytechnique, France in 2011. After graduation, he did masters in computational biology at Ecole Polytechnique Fédérale de Lausanne, Switzerland. Currently, Andrei is a Ph.D. student under the joint direction of Dr. Rong Li from Johns Hopkins and Dr. Gilles Fischer, exploring molecular mechanisms of aneuploidy-enabled stress adaptation and drug resistance it enables in yeast and cancer. He works on developing computational methods enabling systematic analysis of molecular mechanisms underlying complex traits. The interface of biological network analysis and evolution theory is his particular interest.

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