Funded Projects

  • DeST: Deep Semantic Tagger, suppported by FCT between 2018 and 2021
  • Classifying Relations via Long Short-Term Memory Networks along Biomedical Ontologies, supported as an Open Tender by OpenMinTeD in 2018
  • TV Recommendation Algorithms, suppported by NOS since 2015
  • BiobankCloud: Scalable, Secure Storage of Biobank Data, suppported by FP7 between 2012 and 2015
  • Lusica na Web 2.0, suppported by SAPO Labs between 2014 and 2015
  • SOMER: Semantic Ontology Matching using External Resources, suppported by FCT between 2012 and 2014
  • O Mundo em Pessoa, suppported by SAPO Labs between 2013 and 2014
  • SPNET: In silico reconstruction of Streptococcus pneumoniae cellular networks and their impact on virulence, suppported by FCT between 2011 and 2013
  • REACTION: Retrieval, Extraction, and Aggregation Computing Technology for Integrating and Organizing News, suppported by FCT between 2010 and 2013
  • EPIWORK: Developing the Framework for an Epidemic Forecast infrastructure, suppported by FP7 between 2009 and 2012
  • VPH: Virtual Physiological Human Network of Excellence, suppported by FP7 between 2010 and 2012
  • Methods for Carbohydrate Enzyme Family Coherency Assessment, suppported by CRUP between 2010 and 2011
  • GREASE-II: Geographic Reasoning for Search Engines, suppported by FCT between 2008 and 2010
  • ARN: Algorithms for the identification of Genetic Regulatory Networks, suppported by FCT between 2008 and 2010
  • REBIL: Relating Biological Information through Literature, suppported by CRUP between 2004 and 2005
  • GOAnnotator: Verification of Electronic Protein Annotations using GO Terms automatically extracted from Literature,
    supported by Marie Curie Training Site fellowship in 2004

Supervision of Doctoral Projects

  • Muhamed Asif, Systems Medicine approach to improve diagnosis and prognosis in Autism Spectrum Disorders (ASD), based on extensive genomic, biochemical and clinical data, supported by FCT (BioSys-PhD Programme), supervisor Astrid Vicente, 2018
  • João Ferreira, Semantic Similarity across Biomedical Ontologies, supported by FCT scholarship SFRH/BD/69345/2010, 2016
  • Hugo Bastos, Robustness Analysis Methods for Enzyme Functional Prediction, supported by FCT scholarship SFRH/BD/48035/2008, co-supervisor Luka Clarke, 2015
  • Miguel Costa, Information Search in Web Archives, supervisor Mário J. Silva, 2014
  • Catia Machado, Integration and Exploration of Clinical and Biological data about HCM disease, supported by FCT scholarship SFRH/BD/65257/2009, co-supervisor Ana Teresa Freitas, 2014
  • 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
  • Catia Pesquita, Automated Extension of Biomedical Ontologies, supported by FCT scholarship SFRH/BD/42481/2007, 2012
  • Márcia Barros, Big Data Visualization of Stars in our Galaxy, supported by GAIA Mission from ESA (European Space Agency) since 2016, co-supervisor André Moitinho de Almeida
  • Maria Fernandes, Privacy-preserving algorithms and workflows for next-generation genomics, since 2016, supervisor Paulo Verissimo
  • André Lamurias, Development of a Text Mining Approach to Disease Network Discovery, supported by FCT (BioSys-PhD Programme) between 2015 and 2019, co-supervisor Luka Clarke

Theses Supervised available at the ULisboa Repository

Invited Talks