Anna Cichonska

Anna Cichonska · Mon, 09.10.2017


Beginning August 21 and ending September 8, 2017, I visited the research group of Professor Manuel Rivas in the Department of Biomedical Data Science at Stanford University, USA. The group develops statistical models and computational tools for the analysis of populationscale genomic studies. In particular, the focus of the lab is on the 1) interpretation and translation of genome sequencing data from large population biobanks and precision medicine initiatives; 2) generation of effective therapeutic and preventive strategies for human diseases based on genetic, clinical outcome, imagining, wearable sensor, and
environmental data; 3) digitization of clinical notes and integration of resulting health information with genomic data towards learning healthcare systems.

Along the same lines, my research is focused on developing new computational approaches for identifying associations between genomes and health-related traits as well as predictive modeling of drug-target interactions. I am particularly interested in the use of computational methods to facilitate development of new therapeutic strategies, as well as pharmacogenomic models linking genetic information to drug indications. My recent work is focused on the use of multiple kernel learning in predictive modeling of binding affinities between chemical compounds and protein targets for drug discovery applications. At Stanford, we started the work on a new three-layer model that could integrate drug repositioning and drug-target interaction prediction into a unified framework. To do so, descriptors of diseases are needed in addition to descriptors of drug compounds and their targets, and the group of Prof. Rivas provided me with great genetics-based data on those. I am continuing this work back in Finland. During the visit, I also gained some experience in interactive data visualization and identified prominent research directions in the field of causal inference of effects of therapeutic interventions on both their proximal targets and actual clinical outcomes.

Overall, I found the visit to Stanford to be a remarkable experience. I had an opportunity to meet and interact with many great people in this encouraging and really dynamic research environment. Experiencing the life in Silicon Valley and seeing the immense number of opportunities that exist there both in the academia and industry was truly eye opening.