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"I see my thesis as a contribution to the scientific community that helps to better understand different diseases".
Alumnus Juan Pablo Romero develops an algorithm that improves the accuracy of treatment for diseases such as cancer.
Juan Pablo Romero, a native of Mexico, has won this year's Extraordinary Doctoral Prize offered by the Spanish Ministry of Science and Technology. Tecnunfor developing an algorithm that improves the accuracy of treatment for diseases such as cancer. He proudly says that "it is available in Bioconductor, one of the most important databases of bioinformatics algorithms, and that since it was uploaded to this database, it has been downloaded more than 4,000 times". Juan Pablo Romero successfully completed his thesis two years ago, as he acknowledges, thanks also to the support of his directors Dr. Ángel Rubio and Dr. Francis Planes. Since then, he has been doing research in the Oncohematology department at CIMA.
1. What was the aim of your thesis?
The overall aim of the project was to develop an algorithm (EventPointer) to find alternative splicing events and analyse them statistically. altered due to the disease.
There are several scientific articles that talk about the cause-effect relationship of some genomic alterations in the development of various pathologies. One of these articles talks about the "Hallmarks of Cancer" and its authors define six characteristics common to all types of cancer that are used to explain the transformation of a normal cell into a malignant or tumour cell. Later, evidence of the relationship of some alterations with these Hallmarks appeared and another article appeared that makes a direct link between alternative splicing and the Hallmarks. With this information, we thought it would be interesting to develop tools to analyse these types of alterations and thus gain a better understanding of the development of these pathologies.
2. What is the main advance?
The main advance is mainly in the methodology. Some existing algorithms do these analyses, but they do not use all the available information. With EventPointer, we use mathematical and statistical tools to combine all this information and generate a much more robust and complete analysis. We not only give values for statistical significance, but also means to visualise these alterations.
The research group is currently further developing the algorithm and has included another tool to help experimentally validate all the splicing events detected by the algorithm.
3. Will it have practical application?
The algorithm is available in one of the most important databases of bioinformatics algorithms: Bioconductor. Since we uploaded it to this database, it has been downloaded more than 4 thousand times. We have also been cited in several scientific articles, demonstrating that the scientific community is using these tools in different research projects. Although it is true that, as it is a research algorithm, for the moment it is difficult for it to have a direct application in clinical cases.
On the other hand, the algorithm is also part of the software of Affymetrix (the world's number 1 microarray company). During a collaboration, we told them about the algorithm and they agreed to include it in their own software.
4. Why do you think you won the Extraordinary Doctorate Award offered by Tecnun?
Maybe because what was done in the PhD became a real tool available to everyone. I see my thesis as a contribution to the scientific community to better understand different diseases. On the other hand, I believe that, if I have had the opportunity to win this prize, it is also thanks to the support of my thesis supervisors Dr. Ángel Rubio and Dr. Francis Planes. They helped me a lot on a day-to-day basis to better understand all the steps of the doctorate and above all to prepare me for a future in the field of research. I see it more as an award for the whole bioinformatics team at Tecnun.