Daniel Faria is a Post-Doc researcher working on the
and a member of LASIGE.
He has a Ph.D. in Bioinformatics from
and a degree in Biological Engineering from
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.
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
I am the lead developer of the
Ontology Matching tool, which obtained very good results in the
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.
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.