Research
Projects
DISNET
“Drug repositioning and disease understanding through complex networks creation and analysis”, http://disnet.ctb.upm.es/, RTI2018-094576-A-I00, Spanish Ministry of Science, Innovation and Universities.
- Human disease complex networks to gain a better disease understanding and drug repurposing. Extraction and integration of biomedical data structured in 3 levels: the phenotypical, the biological and pharmacological.
- Intensive analysis of the information and generation of drug repurposing hypotheses. Employment of machine learning techniques both supervised and unsupervised.
- Management tasks. Scientific writing and communication, as well as dissemination to the general public.
CUREX
“Secure and private health data exchange”, https://curex-project.eu/, European Commission, Horizon 2020, G.A. n 826404
- Creation of a basic NLP module for texts related to computer network topologies.
- Development of an ontology for the semantic representation of data regarding asset discovery in distributed networks for healthcare environments.
P4-LUCAT
“Personalized medicine for lung cancer treatment”, https://p4-lucat.eu/, ERA PerMed of Joint Transnational Call 2019 No. 163.
- Design and implementation of a relational database for the storage of lung cancer patient information.
- Drafting of deliverables and assistance in the project management tasks in its initial stages.
MAVIS
Study of sentiments expressed in social media during the period 2015-2018 in post related to vaccines, funded by MSD, Spain, VEAP ID: 7789.
- Analysis, visualization and understanding of data collected from Twitter posts and their polarity.
- Scientific writing and dissemination in the form of journal papers.
3DR-GNN
“Data-driven drug repositioning applying graph neural networks”, PID2021-122659OB-I00 from the Spanish Ministry of Science, Innovation and Universities.
- Writing of the project proposal. Project planification and management.
- Implementation and supervision of the technical tasks to predict repurposing disease-drug links in a biomedical heterogeneous graph.
- Scientific writing and dissemination in the form of journal and conference papers
GRENADA
“Drug repurposing hypotheses through a data-driven approach”, PDC2022-133173-I00 from the Spanish Ministry of Science, Innovation and Universities
- Writing of the project proposal. Project planification and management.
- Implementation of a relational database to store drug repurposing predictions generated by different data-driven methodologies.
LUCIA
“Understanding Lung Cancer related risk factors and their Impact”,
https://luciaeuproject.technion.ac.il/, European Commission – Horizon Europe, ref 101096473.
- Technical tasks related to mapping lung cancer terminologies and creating a lung cancer risk factors ontology.
- Assistance on the prediction of risk factors by means of Artificial Intelligence applied to knowledge graphs.
Publications
JCR-indexed journals
[2024]
- A. Collin, A. Ayuso-Muñoz, P. Tejera-Nevado, L. Prieto-Santamaría, A. Verdejo-García, C. Díaz-Batanero, F. Fernández-Calderón, N. Albein-Urios, O.M. Lozano, and Alejandro Rodríguez-González, «Analyzing Dropout in Alcohol Recovery Programs: A Machine Learning Approach», Journal of Clinical Medicine, vol. 13, no. 16, Art. no. 16, Aug. 2024, doi: 10.3390/jcm13164825.
- N. García Sánchez, E. Ugarte Carro, L. Prieto-Santamaría, and A. Rodríguez-González, «Protein sequence analysis in the context of drug repurposing», BMC Med Inform Decis Mak, vol. 24, no. 1, p. 122, May 2024, doi: 10.1186/s12911-024-02531-1. [DISNET]
- B. Otero-Carrasco, E. Ugarte Carro, L. Prieto-Santamaría, M. Diaz Uzquiano, J. P. Caraça-Valente Hernández, and A. Rodríguez-González, «Identifying patterns to uncover the importance of biological pathways on known drug repurposing scenarios», BMC Genomics, vol. 25, no. 1, p. 43, Jan. 2024, doi: 10.1186/s12864-023-09913-1. [DISNET]
[2023]
- A. Ayuso-Muñoz, L. Prieto-Santamaría, E. Ugarte Carro, E. Serrano, and A. Rodríguez-González, «Uncovering hidden therapeutic indications through drug repurposing with graph neural networks and heterogeneous data», Artificial Intelligence in Medicine, p. 102687, Oct. 2023, doi: 10.1016/j.artmed.2023.102687. [3DR-GNN]
[2022]
- A.J. Diaz-Honrubia, A. Blázquez Herranz, L. Prieto Santamaría, E. Menasalvas Ruiz, A. Rodríguez-González, G. Gonzalez-Granadillo, R.Diaz, E. Panaousis, and C. Xenakis, «A Trusted Platform Module-based, Pre-emptive and Dynamic Asset Discovery Tool», J. Inf. Secur. Appl., vol. 71, p. 103350, Dec. 2022, doi: 10.1016/j.jisa.2022.103350. [CUREX]
- L. Prieto Santamaría*, M. Díaz Uzquiano*, E. Ugarte Carro, N. Ortiz-Roldán, Y. Pérez Gallardo, and A. Rodríguez-González, «Integrating heterogeneous data to facilitate COVID-19 drug repurposing», Drug Discov. Today, vol. 27, no. 2, pp. 558–566, Feb. 2022, doi: 10.1016/j.drudis.2021.10.002. [DISNET]
- B. Otero-Carrasco, L. Prieto Santamaría, E. Ugarte Carro, J. P. Caraça-Valente Hernández, and A. Rodríguez-González, «Repositioning Drugs for Rare Diseases Based on Biological Features and Computational Approaches», Healthcare, vol. 10, no. 9, Art. no. 9, Sep. 2022, doi: 10.3390/healthcare10091784. [DISNET]
[2021]
- L. Prieto Santamaría, E. P. García del Valle, M. Zanin, G. S. Hernández Chan, Y. Pérez Gallardo, and A. Rodríguez-González, «Classifying diseases by using biological features to identify potential nosological models», Sci. Rep., vol. 11, no. 1, p. 21096, Oct. 2021, doi: 10.1038/s41598-021-00554-6. [DISNET]
- L. Prieto Santamaría*, E. Ugarte Carro*, M. Díaz Uzquiano, E. Menasalvas Ruiz, Y. Pérez Gallardo, and A. Rodríguez-González, «A data-driven methodology towards evaluating the potential of drug repurposing hypotheses», Comput. Struct. Biotechnol. J., vol. 19, pp. 4559–4573, 2021, doi: 10.1016/j.csbj.2021.08.003. [DISNET]
- L. Prieto Santamaría, J. M. Tuñas, D. Fernández Peces-Barba, A. Jaramillo, M. Cotarelo, E. Menasalvas Ruiz, A. J. Conejo Fernández, A. Arce, A. Gil de Miguel, and A. Rodríguez-González, «Influenza and Measles-MMR: two case study of the trend and impact of vaccine-related Twitter posts in Spanish during 2015-2018», Hum. Vaccines Immunother., pp. 1-15, Mar. 2021, doi: 10.1080/21645515.2021.1877597. [MAVIS]
- L. Prieto Santamaría, D. Fernández Lobón, A. J. Díaz-Honrubia, E. Menasalvas Ruiz, S. Nifakos, and A. Rodríguez-González, «Towards the representation of network assets in health care environments using ontologies», Methods Inf. Med., vol. 60, no. S 02, pp. e89–e102, Dec. 2021, doi: 10.1055/s-0041-1735621. [CUREX]
- E. P. García del Valle, G. Lagunes García, L. Prieto Santamaría, M. Zanin, E. Menasalvas Ruiz, and A. Rodríguez-González, «DisMaNET: A network-based tool to cross map disease vocabularies», Comput. Methods Programs Biomed., p. 106233, Jun. 2021, doi: 10.1016/j.cmpb.2021.106233. [DISNET]
- E. P. García del Valle, G. Lagunes García, L. Prieto Santamaría, M. Zanin, E. Menasalvas Ruiz, and A. Rodríguez-González, «Leveraging network analysis to evaluate biomedical named entity recognition tools», Sci. Rep., vol. 11, no. 1, Jun. 2021, doi: 10.1038/s41598-021-93018-w. [DISNET]
[2020]
- A. Rodríguez-González, J. M. Tuñas, L. Prieto Santamaría, D. Fernández Peces-Barba, E. Menasalvas Ruiz, A. Jaramillo, M. Cotarelo, A. J. Conejo Fernández, A. Arce, and A. Gil de Miguel, «Identifying Polarity in Tweets from an Imbalanced Dataset about Diseases and Vaccines Using a Meta-Model Based on Machine Learning Techniques», Appl. Sci., vol. 10, no. 24, p. 9019, Dec. 2020, doi: 10.3390/app10249019. [MAVIS]
- G. Lagunes García, A. Rodríguez-González, L. Prieto Santamaría, E. P. García del Valle, M. Zanin, and E. Menasalvas Ruiz, «How does Wikipedia disease information evolve over time? An analysis of disease-based articles changes», Inf. Process. Manag., vol. 57, no. 3, p. 102225, May 2020, doi: 10.1016/j.ipm.2020.102225. [DISNET]
- G. Lagunes García, A. Rodríguez González, L. Prieto Santamaría, E. P. García del Valle, M. Zanin, and E. Menasalvas Ruiz, «DISNET: a framework for extracting phenotypic disease information from public sources», PeerJ, vol. 8, p. e8580, Feb. 2020, doi: 10.7717/peerj.8580. [DISNET]
[2019]
- E. P. García del Valle, G. Lagunes García, L. Prieto Santamaría, M. Zanin, E. Menasalvas Ruiz, and A. Rodríguez-González, «Disease networks and their contribution to disease understanding: A review of their evolution, techniques and data sources», J. Biomed. Inform., vol. 94, p. 103206, Jun. 2019, doi: 10.1016/j.jbi.2019.103206. [DISNET]
Other journals
[2024]
- E. Anokian, J. Bernett, A. Freeman, M. List, L. Prieto-Santamaría, Z. Tanoli, and S. Bonnin, «Machine Learning and Artificial Intelligence in Drug Repurposing – Challenges and Perspectives», Drug Repurposing, vol. 1, p. 20240004, Jul. 2024, doi: 10.58647/DRUGREPO.24.1.0004. [3DR-GNN]
Conference Proceedings
[2024]
- B. Otero Carrasco, L. Prieto-Santamaría, and A. Rodríguez-González, ‘Exploring Innovative Approaches to Drug Repurposing: Emphasizing the Relevance of Biological Pathways’, in RExPO24 Conference, REPO4EU, Jul. 2024. doi: 10.58647/REXPO.24000039.v1. [DISNET]
- M. Marín Tercero, L. Prieto-Santamaría, and A. Rodríguez-González, ‘Exploring Drug Repurposing Opportunities for Schizophrenia: A Network Medicine Approach’, in 2024 IEEE 37th International Symposium on Computer-Based Medical Systems (CBMS), Jun. 2024, pp. 106–111. doi: 10.1109/CBMS61543.2024.00026. [3DR-GNN] [Best paper award]
- R. Artiñano-Muñoz, L. Prieto-Santamaría, A. Pérez-Pérez, and A. Rodríguez-González, ‘DRAGON: Drug Repurposing via Graph Neural Networks with Drug and Protein Embeddings as Features’, in 2024 IEEE 37th International Symposium on Computer-Based Medical Systems (CBMS), Jun. 2024, pp. 170–175. doi: 10.1109/CBMS61543.2024.00036. [3DR-GNN]
- Á. García-Barragán, A. González Calatayud, L. Prieto-Santamaría, V. Robles, E. Menasalvas, and A. Rodríguez-González, “Step-forward structuring disease phenotypic entities with LLMs for disease understanding,” in 2024 IEEE 37th International Symposium on Computer-Based Medical Systems (CBMS), Jun. 2024, pp. 213–218. doi: 10.1109/CBMS61543.2024.00043.
[2023]
- L. Prieto Santamaría, A. Ayuso-Muñoz, and A. Rodríguez-González, ‘Enhancing drug repurposing through graph neural networks and link prediction’, in RExPO23 Conference, REPO4EU, Oct. 2023. doi: 10.58647/REXPO.23000022.v1. [3DR-GNN]
- A. Ayuso-Muñoz, L. Prieto-Santamaría, A. Álverez-Pérez, B. Otero-Carrasco, E. Serrano, and A. Rodríguez-González, “Enhancing Drug Repurposing on Graphs by Integrating Drug Molecular Structure as Feature,” in 2023 IEEE 36th International Symposium on Computer-Based Medical Systems (CBMS), Jun. 2023, pp. 192–197. doi: 10.1109/CBMS58004.2023.00215. [3DR-GNN]
- B. Otero-Carrasco, S. Romero-Brufau, A. Álvarez-Pérez, A. Ayuso-Muñoz, L. Prieto-Santamaría, J. P. Caraça-Valente Hernández, A. Rodríguez-González, “Orphan Drugs and Rare Diseases: Unveiling Biological Patterns through Drug Repurposing,” in 2023 IEEE 36th International Symposium on Computer-Based Medical Systems (CBMS), Jun. 2023, pp. 185–191. doi: 10.1109/CBMS58004.2023.00214. [DISNET]
- A. Álvarez-Pérez, L. Prieto-Santamaría, E. Ugarte Carro, B. Otero-Carrasco, A. Ayuso-Muñoz, and A. Rodríguez-González, “Exploring disease-drug pairs in Clinical Trials information for personalized drug repurposing,” in 2023 IEEE 36th International Symposium on Computer-Based Medical Systems (CBMS), Jun. 2023, pp. 179–184. doi: 10.1109/CBMS58004.2023.00213 [DISNET]
- A. J. Díaz-Honrubia, L. Prieto-Santamaría, A. Rodríguez-González, E. Menasalvas-Ruiz, L. Mengual-Galán, and C. Fernández-Baizán, “THE GREAT QUIZ OF DATABASES”, INTED2023 Proceedings, pp. 1395–1403, 2023, doi: 10.21125/inted.2023.0408.
[2022]
- L. Prieto Santamaría and A. Rodríguez-González, ‘DISNET: Drug repositioning and disease understanding through complex networks creation and analysis’, presented at the RExPO22 – 1st International Conference on Drug Repurposing, ScienceOpen, Sep. 2022. doi: 10.14293/S2199-1006.1.SOR-.PPPGCKMC.v1.[DISNET]
- A. Álvarez Pérez, A. Iglesias-Molina, L. Prieto Santamaría, M. Poveda-Villalón, C. Badenes-Olmedo, and A. Rodríguez-González, ‘EBOCA: Evidences for BiOmedical Concepts Association Ontology’, in Knowledge Engineering and Knowledge Management, Cham, 2022, pp. 152–166. doi: 10.1007/978-3-031-17105-5_11. [DISNET] & [Drugs4COVID]
- A. Ayuso Muñoz, E. Ugarte Carro, L. Prieto Santamaría, B. Otero-Carrasco, E. Menasalvas Ruiz, Y. Pérez Gallardo, and A. Rodríguez-González, “REDIRECTION: Generating drug repurposing hypotheses using link prediction with DISNET data”, in 2022 IEEE 35th International Symposium on Computer-Based Medical Systems (CBMS), Jul. 2022, pp. 7-12, doi: 10.1109/CBMS55023.2022.00009. [DISNET]
- B. Otero-Carrasco, A. Pérez Pérez, E. Mensalvas Ruiz, J. P. Caraça-Valente Hernández, L. Prieto Santamaría, and A. Rodríguez-González, “Drug repositioning with gender perspective focused on Adverse Drug Reactions” in 2022 IEEE 35th International Symposium on Computer-Based Medical Systems (CBMS), Jul. 2022, pp. 435-440, doi: 10.1109/CBMS55023.2022.00084. [DISNET]
- B. Otero-Carrasco, L. Prieto Santamaría, E. Ugarte Carro, J.P. Caraça-Valente Hernández, A. Rodríguez González, ‘A computational drug repositioning method for rare diseases’, in Bio-inspired Systems and Applications: from Robotics to Ambient Intelligence. IWINAC 2022. Lecture Notes in Computer Science, vol 13259, pp. 551-561. Springer, Cham. doi: 10.1007/978-3-031-06527-9_55. [DISNET]
[2021]
- E. P. García Del Valle, L. Prieto Santamaría, G. Lagunes García, M. Zanin, E. Menasalvas Ruiz, and A. Rodríguez-Gonzalez, ‘A meta-path-based prediction method for disease comorbidities’, in 2021 IEEE 34th International Symposium on Computer-Based Medical Systems (CBMS), Jun. 2021, pp. 219–224. doi: 10.1109/CBMS52027.2021.00022. [DISNET]
[2020]
- L. Prieto Santamaría, E. P. García Del Valle, G. Lagunes Garcia, M. Zanin, A. Rodríguez-Gonzalez, E. Menasalvas Ruiz, Y. Pérez Gallardo, G. S. Hernández Chan. ‘Analysis of new nosological models from disease similarities using clustering’, in 2020 IEEE 33rd International Symposium on Computer-Based Medical Systems (CBMS), Jul. 2020, pp. 183–188. doi: 10.1109/CBMS49503.2020.00042. [DISNET]
[2019]
- E. P. García del Valle, G. Lagunes García, E. Menasalvas Ruiz, L. Prieto Santamaría, M. Zanin, and A. Rodríguez-González, ‘Completing missing MeSH code mappings in UMLS through alternative expert-curated sources’, in 2019 IEEE 32nd International Symposium on Computer-Based Medical Systems (CBMS), Jun. 2019, pp. 174–179. doi: 10.1109/CBMS.2019.00044. [DISNET]
- G. Lagunes García, L. Prieto Santamaría, E. P. García del Valle, M. Zanin, E. Menasalvas Ruiz, and A. Rodríguez González, ‘Wikipedia disease articles: an analysis of their content and evolution’, in 2019 IEEE 32nd International Symposium on Computer-Based Medical Systems (CBMS), Jun. 2019, pp. 664–671. doi: 10.1109/CBMS.2019.00136. [DISNET]
[2018]
- E. P. Garcia del Valle, G. Lagunes García, L. Prieto Santamaría, M. Zanin, E. Menasalvas Ruiz, and A. Rodríguez González, ‘Evaluating wikipedia as a source of information for disease understanding’, in 2018 IEEE 31st International Symposium on Computer-Based Medical Systems (CBMS), Jun. 2018, pp. 399–404. doi: 10.1109/CBMS.2018.00076. [DISNET]
PhD
Creation, integration, and analysis of disease networks towards a better disease understanding and drug repurposing
July 14, 2023
The supervisors of this thesis have been Alejandro Rodríguez González and Yuliana Pérez Gallardo. The doctoral program in which the thesis has been carried out is the PhD. in Software, Systems and Computing, which takes place at the Escuela Técnica Superior de Ingenieros Informáticos (ETSIInf) of the Universidad Politécnica de Madrid (UPM), Spain.
The thesis has been developed under the scope of the DISNET project, executed at the Medical Data Analytics Laboratory (MEDAL) of the Center for Biomedical Technology (CTB). The thesis is a result of an industrial doctorate in conjunction with Ezeris Networks Global Services, S.L.
The thesis is presented as a compendium of 3 publications:
- Publication I: Classifying diseases by using biological features to identify potential nosological models.
- Publication II: A data-driven methodology towards evaluating the potential of drug repurposing hypotheses.
- Publication III: Integrating heterogeneous data to facilitate COVID-19 drug repurposing.
Visiting PhD research stay
January 2023 – June 2023
Barabasi’s Lab
Center for Complex Networks Research (CCNR)
Network Science Institute (NetSI)
Northeastern University (NEU), Boston, MA
Supervised by Albert-László Barabási, researched on network medicine to generate new drug repurposing hypotheses, focusing on different complex human diseases.
5-month research stay funded by UPM.
Awards
Premio Francisco del Pozo 2023. Awarded to the best doctoral thesis defended at the Center for Biomedical Technology in UPM 2023.
