Completed PhD Theses (Reverse Chronological Order)

  1. Pedro Ruas, Deep semantic entity linking, supported by FCT scholarship 2020.05393.BD, 2025
  2. Diana Sousa, Deep Learning System for Biomedical Relation Extraction Combining External Sources of Knowledge, supported by FCT scholarship SFRH/BD/145221/2019, 2023
  3. Márcia Barros, Recommender system to support comprehensive exploration of large scale scientific datasets, supported by FCT scholarship SFRH/BD/128840/2017, co-supervisor André Moitinho de Almeida, 2022
  4. Maria Fernandes, Reconciling data privacy with sharing in next-generation genomic workflows, supported by FNR, supervisor Paulo Verissimo, 2020
  5. André Lamurias, Development of a Text Mining Approach to Disease Network Discovery, supported by FCT (BioSys-PhD Programme), co-supervisor Luka Clarke, 2019
  6. Muhamed Asif, A systems medicine approach to study autism spectrum disorder based on genomic and clinical data, supported by FCT (BioSys-PhD Programme), supervisor Astrid Vicente, 2018
  7. João Ferreira, Semantic Similarity across Biomedical Ontologies, supported by FCT scholarship SFRH/BD/69345/2010, 2016
  8. Hugo Bastos, Functional coherence and annotation agreement metrics for enzyme families, supported by FCT scholarship SFRH/BD/48035/2008, co-supervisor Luka Clarke, 2015
  9. Miguel Costa, Information Search in Web Archives, supervisor Mário J. Silva, 2014
  10. Catia Machado, Knowledge representation for data integration and exploration in translational medicine, supported by FCT scholarship SFRH/BD/65257/2009, co-supervisor Ana Teresa Freitas, 2014
  11. Tiago Grego, Identifying Chemical Entities on Literature: a Machine Learning Approach using Dictionaries as Domain Knowledge, supported by FCT scholarship SFRH/BD/36015/2007, 2013
  12. Catia Pesquita, Automated Extension of Biomedical Ontologies, supported by FCT scholarship SFRH/BD/42481/2007, 2012

Completed Master Theses (Reverse Chronological Order)

  1. João Fernandes, Extracting n-ary Relations from Biomedical Literature using Deep-Learning Techniques, 2025.
  2. Christopher Anaya, LLM fine-tuning with biomedical open-source data, 2025.
  3. Maria Canelhas, MiCRA : a minimal pipeline for functional microbiome information retrieval using Natural Language Processing and Biomedical Ontologies, 2025.
  4. Rodrigo Cassanheira, Relation extraction for gene and chemical compounds, 2024
  5. Pedro Silvestre, Identifying negative results using biomedical relation extraction systems, 2024
  6. David Correia, Predicting non-coding RNA function using Artificial Intelligence, 2024.
  7. José Matos, Development of machine learning tool for filtering artifacts in the identification of CNVs, 2023
  8. Ana Monteiro, Unveiling co-transcriptional splicing kinetics using novel nascent transcriptomic techniques, 2023
  9. Ana Ilhéu, A computational pipeline to identify phenotypic manifestations related to genes, 2022
  10. Margarida Campos, Biomedical Question Answering with Deep Learning, 2021
  11. Vítor Andrade, Named Entity Recognition and Linking in a Multilingual Biomedical Setting, 2021
  12. Ana Rodrigues, Prostate MRI radiomics for prediction of gleason score, 2021
  13. Leonor Torcato, Extracting Negative Biomedical Relations from Literature, 2021
  14. Miguel Vieira, Development of a Corpus for User­based Scientific Question Answering, 2021
  15. Fábio Colaço, Recommender Systems Based on Deep Learning Techniques, 2020
  16. André Neves, Applying deep learning extreme multi-label classification to the biomedical and multilingual panoramas, 2020
  17. Pedro Santos, Validation of automatic similarity measures, 2020
  18. Diana Sousa, Extracting phenotype-gene relations from biomedical literature using distant supervision and deep learning, 2019
  19. Pedro Ruas, Exploring biomedical ontologies, personalized pagerank and semantic similarity in the entity linking task, 2019
  20. Sofia Jesus, Information retrieval using machine learning for database curation, 2019
  21. Rui Luís, The role of antisense transcription on regulation of gene expression, 2018
  22. Tânia Maldonado, Extracting biomedical relations from biomedical literature, 2018
  23. Manuel Lobo, Identifying human phenotype terms in text using a machine learning approach, 2017
  24. Luís Campos, Semantic annotation of electronic health records in a multilingual environment, 2017
  25. Miguel Rodrigues, Biomedical semantic question and answering system, 2017
  26. António Barata, Anthropometric data analytics: a portuguese case study, 2017
  27. Pedro Martins, Previsão da localização subcelular de proteínas humanas com base em aprendizagem automática, 2017
  28. Bruno Inácio, Quanto valem os metadados?, 2016
  29. Mónica Abreu, Impacto das obras musicais lusófonas nas redes sociais, 2016
  30. Rita Florêncio, Radiation monitoring system in clinical imaging, 2016
  31. Rodolfo Silva, Desenvolvimento de uma rede social desportiva, 2016
  32. Luís Oliveira, Desenvolvimento de aplicação web de pesquisa, gestão e partilha de eventos, 2015
  33. Maria Fernandes, Anti and pro-longevity genes differentiation and overlap with age-related diseases, 2015
  34. Natacha Leitão, Development of a scalable, precise, and high-coverage genomics mapping tool for NGS, 2015
  35. Miguel Gomes, 3D Visualization of very large databases - integrating and expanding the state of the art in bioinformatics and astroinformatics, 2015
  36. João Oliveira, Análise de corpora jornalístico através das ocorrências de N-gramas, 2015
  37. Vítor Martins, Towards an engaging social TV on a second screen, 2015
  38. Luís Simões, Assessing pseudogene expression during neural differentiation by RNA-Seq, 2015
  39. Tiago Aparício, Aplicações na web para validação e classificação de notícias pela crowd, 2015
  40. André Leal, Recognition and normalization of biomedical entities within clinical notes, 2015
  41. Diogo Gonçalves, Recommendation system for modern television, 2015
  42. Carlos Barata, Impacto de obras literárias nas redes sociais, 2014
  43. André Lamúrias, Identifying interactions between chemical entities in text, 2014
  44. José Carilho, Towards an intelligent biographical cognitive prosthesis, 2014
  45. Mickael Silva, NGSOnto: proposta de uma ontologia para descrever o processo de sequenciação de alto desempenho, 2014
  46. André Lopes, A tool for ontology instance matching, 2013
  47. Vera Carvalho, Metagenomic analysis of Mariana Trench sediment samples, 2013
  48. Tiago Santos, Implementação de uma base de dados geográficos para a gestão das matérias-primas do grupo Cimpor, 2013
  49. Tiago Sousa, Citation impact discerning self-citation: improving user interaction, 2012
  50. Bruno Tavares, Aplicações com base em ontologias biomédicas: uma abordagem web semântica, 2011
  51. João Ferreira, Structural and semantic similarity metrics for chemical compound classification, 2010
  52. Daniel Amoedo, Medidas de semelhança semántica aplicadas às ontologias geográficas, 2010
  53. Cátia Machado, GREAT: gene regulation evaluation tool, 2009
  54. Ana Teixeira, ThermInfo: sistema de informação para coligir e apresentar propriedades termoquímicas, 2009
  55. Pedro Nunes, Extensão de catalogação de informação para o SQL developer - ECIS, 2008
  56. José Santos, Gestão e análise de dados biomédicos, 2008
  57. Pedro Prats, Migração tecnologia SIEBEL no Banco BEST, 2008
  58. Sara Estrela, BWS: um sistema integrado de gestão empressarial, 2007
  59. Moisés Xavier, Bioinformatic studies on structural elements for the regulation of alternative oxidase (AOX) gene activities, 2007
  60. Cátia Pesquita, Improving semantic similarity for proteins based on the gene ontology, 2007
  61. Lídia Raimundo, Metadata: reporting de gestão, 2007