Short Bio

Daniel Faria is a Post-Doc researcher working on the SOMER project and a member of LASIGE.
He has a Ph.D. in Bioinformatics from FCUL (2012) and a degree in Biological Engineering from IST (2004).
His research interests include mining biomedical data (e.g. protein function prediction) and representing and integrating biomedical knowledge (e.g. ontologies and ontology matching).
He is curious about several other topics, and plans to work on some of them in the not-so-near future. These include game theory, game design, and the theory and mechanisms of evolution.
On his free time, he enjoys such diverse activities as cooking, playing Magic: the Gathering and strategy board games, reading fantasy and sci-fi novels, playing the guitar, writting, and outdoors activities. He finds it amusing to write about himself in the third person.


dfaria [at]

(+351) 21 750 05 32

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Since I joined the SOMER project in October 2012, my research has focused on Ontology Matching, with emphasis on the use of external knowledge and on matching large ontologies efficiently.
I am the lead developer of the AgreementMakerLight Ontology Matching tool, which obtained very good results in the OAEI 2013 competition.
Before the SOMER project, I worked on the CIDS project in benchmarking portuguese R&D institutions.
During my Ph.D. studies, my research focused on automated protein function prediction, on the quality of protein annotations, and on measuring the functional similarity between proteins via semantic similarity.

Selected Publications

  • D Faria, A Schlicker, C Pesquita, H Bastos, AEN Ferreira, M Albrecht, AO Falcao 2012: Mining GO Annotations for Improving Annotation Consistency. PLoS ONE 7(7): e40519.
  • T Simões, N Charro, J Blonder, D Faria, FM Couto, KC Chan, T Waybright, HJ Isaaq, TD Veenstra, D Penque 2011: Molecular profiling of the human nasal epithelium: A proteomics approach. Journal of Proteomics 75(1): 56-69.
  • N Charro, BL Hood, D Faria, P Pacheco, P Azevedo, C Lopes, A Almeida, FM Couto, TP Conrads, D Penque 2011: Serum proteomics signature of Cystic Fibrosis patients: A complementary 2-DE and LC--MS/MS approach. Journal of Proteomics 74(1): 110-126.
  • C Pesquita, D Faria, AO Falcao, P Lord, FM Couto 2009: Semantic Similarity in Biomedical Ontologies. PLoS Computational Biology, 5(7): e1000443.
  • D Faria, AEN Ferreira, AO Falcao 2009: Enzyme classification with peptide programs: a comparative study. BMC Bioinformatics 10: 231.
  • IW Taylor, R Linding, D Warde-Farley, Y Liu, C Pesquita, D Faria, S Bull, T Pawson, Q Morris, JL Wrana 2009: Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nature Biotechnology 27: 199-204.
  • C Pesquita, D Faria, H Bastos, AEN Ferreira, AO Falcao, FM Couto 2008: Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinformatics Suppl 5(9): S4.