Research

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)

  1. Large-scale study of RNA processing alterations in multiple cancers. Babita Singh, UPF, 11/May/2017
  2. Computational tools for the study of RNA processing and function. Amadís Pagès. UPF, 27/October/2016
  3. Assessing the relationship between chromatin and splicing factors in alternative splicing. Isaac J. Kremsky. UPF, 14/July/2015.
  4. Software development and analysis of High Throughput Sequencing data for genomic enhancer prediction. Juan González-Vallinas, UPF, 9/Sept/2013.
  5. Epigenetics in alternative splicing: links between chromatin structure, transcription and non-coding RNA mediated regulation. Eneritz Agirre, UPF, 21/June/2013.
  6. Elucidating Mechanisms of Gene Regulation – Integration of High-throughput Sequencing Data for Studying the Epigenome. Sonja Althammer. UPF, 27/April/2012.
  7. Comparative Analysis of Splicing in Eukaryotes. Mireya Plass. UPF, 12/July/2011.
  8. 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)

  1. Ribosome profiling at isoform level: a step towards unveiling the functional impact of alternative splicing. Marina Reixachs, June 2017.
  2. An extended catalogue of branchpoint sequences reveal new splicing-related mechanisms in cancer. Beatriz Ruz-Caracuel. UPF, June 2017.
  3. A tool for fast and accurate analysis of differential splicing across multiple conditions. J.C. Entizne, July 2016
  4. A new method for uncovering binding specificities of RBPs from alternative splicing regulation in cancer. Ezequiel Anokian. UPF, July 2015.
  5. Analysis of alternative splicing between knockdown of RBPs and control experiments to find new RNA binding motifs. Cristina Hernán. UPF, July 2015.
  6. Modulation of protein interactions by alternative splicing reveals new functional alterations in lung adenocarcinoma, Hector Climente. UPF June 2014.
  7. Study of the chromatin code for splicing regulation. Gael P. Alamancos. UPF, June 2013
  8. Machine Learning tools for the study of RNA regulation by chromatin. Amadis Pagés. UPF, June 2010.
  9. Computational analysis of the co-evolution between RNA motifs and proteins that bind to them. Isabella Bernardis. Universita di Bologna, Italy. June 2009.
  10. Large-scale analysis of splicing signals and factors. João Silva. Univerdade do Porto, Portugal. 2008
  11. Comparative Analysis of splicing regulation. Pablo Martinez. UPF 2007.
  12. Study of Intron Retention in Cryptococcus. Giovanni Dall’Olio. Universita di Bologna. 2007.
  13. Characterization of the coding properties in alternative exons. Mireya Plass. UPF 2006