RNA genes

Promoters identification and analysis

-

B1 L2 R2202

Promoter is a key region that is involved in differential transcription regulation of protein-coding and RNA genes. The gene-specific architecture of promoter sequences makes it extremely difficult to devise the general strategy for their computational identification.

Computational Analysis of Transcriptional Regulation after Single and Multiple Drug Administration.

-

B3 L5 R5209

With the advances in transcriptomic analysis, the monitoring of genome-wide gene expression provides a powerful approach for determining the action of drugs. In this thesis, we analyzed the transcriptional responses of cells treated with drugs either alone or in combinations to explore their effects in two different applications: breast cancer therapy and cell conversion.

Novel computational methods for promoter identification and analysis

-

B2 L5 R5209

In this dissertation, I present the methods I have developed for prediction of promoters for different organisms. Instead of focusing on the classification accuracy of the discrimination between promoter and non-promoter sequences, I predict the exact positions of the TSS inside the genomic sequences, testing every possible location. The developed methods significantly outperform the previous promoter prediction programs by considerably reducing the number of false positive predictions. Specifically, to reduce the false positive rate, the models are adaptively and iteratively trained by changing the distribution of samples in the training set based on the false positive errors made in the previous iteration. The new methods are used to gain insights into the design principles of the core promoters. Using model analysis, I have identified the most important core promoter elements and their effect on the promoter activity. I have developed a novel general approach to detect long range interactions in the input of a deep learning model, which was used to find related positions inside the promoter region. The final model was applied to the genomes of different species without a significant drop in the performance, demonstrating a high generality of the developed method.