Thesis defence of Juan Ramón González-Vallinas "Software development and analysis of High Throughput Sequencing data for genomic enhancer prediction"

High Throughput Sequencing technologies (HTS) are becoming the standard in genomic regulation analysis. During my thesis I developed and published software for the analysis of HTS data. Through collaborations with other research groups, I specialized in the analysis of ChIP-Seq short mapped reads. Making use of expertise and the software developed during this time, I analyzed ENCODE datasets in order to detect active genomic enhancers. Genomic enhancers are regions in the genome known to regulate transcription levels of close by or distant genes. Mechanism of activation and silencing of enhancers is still poorly understood. Epigenomic elements, like histone modifications and transcription factors play a critical role in enhancer activity. Modeling epigenomic signals, I predicted active and silenced enhancers in two cell lines and studied their effect in splicing and transcription initiation.