Research in the Computational RNA Biology group focuses on the development of computational methods to study the mechanisms of regulation of alternative pre-mRNA splicing and their role in disease, with a strong focus on cancer.
PhD Theses from the group (2010-2017)
- Large-scale study of RNA processing alterations in multiple cancers. Babita Singh, UPF, 11/May/2017
- Computational tools for the study of RNA processing and function. Amadís Pagès. UPF, 27/October/2016
- Assessing the relationship between chromatin and splicing factors in alternative splicing. Isaac J. Kremsky. UPF, 14/July/2015.
- Software development and analysis of High Throughput Sequencing data for genomic enhancer prediction. Juan González-Vallinas, UPF, 9/Sept/2013.
- Epigenetics in alternative splicing: links between chromatin structure, transcription and non-coding RNA mediated regulation. Eneritz Agirre, UPF, 21/June/2013.
- Elucidating Mechanisms of Gene Regulation – Integration of High-throughput Sequencing Data for Studying the Epigenome. Sonja Althammer. UPF, 27/April/2012.
- Comparative Analysis of Splicing in Eukaryotes. Mireya Plass. UPF, 12/July/2011.
- Computational Analyses on the Evolution and Regulation of Alternative Splicing in Metazoans. André Corvelo, 2010. GABBA student. UPF / University of Porto. 13/December/2010.
Master Theses from the group (2006-2017)
- Ribosome profiling at isoform level: a step towards unveiling the functional impact of alternative splicing. Marina Reixachs, June 2017.
- An extended catalogue of branchpoint sequences reveal new splicing-related mechanisms in cancer. Beatriz Ruz-Caracuel. UPF, June 2017.
- A tool for fast and accurate analysis of differential splicing across multiple conditions. J.C. Entizne, July 2016
- A new method for uncovering binding specificities of RBPs from alternative splicing regulation in cancer. Ezequiel Anokian. UPF, July 2015.
- Analysis of alternative splicing between knockdown of RBPs and control experiments to find new RNA binding motifs. Cristina Hernán. UPF, July 2015.
- Modulation of protein interactions by alternative splicing reveals new functional alterations in lung adenocarcinoma, Hector Climente. UPF June 2014.
- Study of the chromatin code for splicing regulation. Gael P. Alamancos. UPF, June 2013
- Machine Learning tools for the study of RNA regulation by chromatin. Amadis Pagés. UPF, June 2010.
- Computational analysis of the co-evolution between RNA motifs and proteins that bind to them. Isabella Bernardis. Universita di Bologna, Italy. June 2009.
- Large-scale analysis of splicing signals and factors. João Silva. Univerdade do Porto, Portugal. 2008
- Comparative Analysis of splicing regulation. Pablo Martinez. UPF 2007.
- Study of Intron Retention in Cryptococcus. Giovanni Dall’Olio. Universita di Bologna. 2007.
- Characterization of the coding properties in alternative exons. Mireya Plass. UPF 2006