Thesis of Sonja Althamer, member of the Regulatory Genomics Group of GRIB (IMIM-UPF): "Elucidating Mechanisms of Gene Regulation. Integration of High-Throughput Sequencing Data for Studying the Epigenome"

This Friday, 27th of April, Sonja Althamer will defence her thesis at 15:00 at Xipre Seminar Room.


The recent advent of high-throughput sequencing (HTS) methods has triggered a revolution in gene regulation studies. Demand has never been higher to process the immense amount of emerging data to gain insight into the regulatory mechanisms of the cell.
We address this issue by describing methods to analyze, integrate and interpret HTS data from different sources. In particular, we developed and benchmarked Pyicos, a powerful toolkit that offers flexibility, versatility and efficient memory usage. We applied it to data from ChIP-Seq on progesterone receptor in breast cancer cells to gain insight into regulatory mechanisms of hormones. Moreover, we embedded Pyicos into a pipeline to integrate HTS data from different sources. In order to do so, we used data sets from ENCODE to systematically calculate signal changes between two cell lines. We thus created a model that accurately predicts the regulatory outcome of gene expression, based on epigenetic changes in a gene locus. Finally, we provide the processed data in a Biomart database to the scientific community.

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