Daniel Faria

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Name: Daniel Pedro de Jesus Faria
E-mail: dfaria@xldb.di.fc.ul.pt
Webpage: http://xldb.fc.ul.pt/~dfaria
Projects: SOMER, Peptides
Research interests: Bioinformatics, Machine Learning, Information Retrieval, Protein Function Prediction, Ontologies, Ontology Matching


Publications

BibTeX source
Daniel Faria, Catia Pesquita, Emanuel Santos, Matteo Palmonari, Isabel F Cruz, Francisco M Couto, The agreementmakerlight ontology matching system.On the Move to Meaningful Internet Systems: OTM 2013 Conferences p. 527--541, 2013. Springer.

BibTeX source
Catia Pesquita, Daniel Faria, Emanuel Santos, Francisco M Couto, To repair or not to repair: reconciling correctness and coherence in ontology reference alignments.Ontology Matching Workshop at ISWC 2013 p. 13, 2013.

BibTeX source
Catia Pesquita, Daniel Faria, Cosmin Stroe, Emanuel Santos, Isabel F Cruz, Francisco M Couto, What's in a 'nym'? Synonyms in Biomedical Ontology Matching.International Semantic Web Conference p. 526-541, 2013. Springer Berlin Heidelberg.

| BibTeX source
Daniel Faria, Andreas Schlicker, Catia Pesquita, Hugo Bastos, Antonio E N Ferreira, Mario Albrecht, Andre Falcao 2012: Mining GO Annotations for Improving Annotation Consistency. PLoS ONE 7(7), e40519.

| BibTeX source
T. Simões, N. Charro, J. Blonder, Daniel Faria, Francisco Couto, K.C. Chan, T. Waybright, H.J. Isaaq, T.D. Veenstra, D. Penque 2011: Molecular profiling of the human nasal epithelium: A proteomics approach. Journal of Proteomics 75(1), 56-69.

Document | BibTeX source
Bruno Tavares, Hugo Bastos, Daniel Faria, Joao D. Ferreira, Tiago Grego, Catia Pesquita, Francisco Couto, The Biomedical Ontology Applications (BOA) framework.Proceedings of ICBO 2011.

Document | BibTeX source
Hugo Bastos, Bruno Tavares, Catia Pesquita, Daniel Faria, Francisco Couto: Application of Gene Ontology to Gene Identification. In Silico Tools for Gene Discovery: Methods in Molecular Biology. Springer, 2011.

| Presentation | BibTeX source
Andre O Falcao, Daniel Faria, Antonio Ferreira, Peptide programs: applying fragment programs to protein classification.Proceedings of the CIKM 2008 - DTMBio 2008 Workshop November, 2008.

BibTeX source
N. Charro, B.L. Hood, Daniel Faria, P. Pacheco, P. Azevedo, C. Lopes, A. Almeida, Francisco Couto, T.P. 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.

Document | BibTeX source
Daniel Faria, Catia Pesquita, Francisco Couto, Andre O Falcao, GOclasses: molecular function as viewed by proteins.BioOntologies SIG at ISMB/ECCB - 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) July, 2009.

Poster | BibTeX source
Catia Pesquita, Delphine Pessoa, Daniel Faria, Francisco Couto, Collaborative Evaluation of GO-based Similarity Measures.The 12th Annual Bio-Ontologies Meeting at ISMB/ECCB 2009 2009.

Document | BibTeX source
Catia Pesquita, Delphine Pessoa, Daniel Faria, Francisco Couto, CESSM : Collaborative Evaluation of Semantic Similarity Measures.JB2009: Challenges in Bioinformatics November, 2009.

DOI | | BibTeX source
Daniel Faria, António EN Ferreira, Andre O Falcao 2009: Enzyme classification with peptide programs: a comparative study. BMC Bioinformatics (10), 231.

DOI | | BibTeX source
Catia Pesquita, Daniel Faria, Andre O Falcao, Philip Lord, Francisco Couto 2009: Semantic Similarity in Biomedical Ontologies. PLoS Computational Biology.

BibTeX source
I.W. Taylor, R. Linding, D. Warde-Farley, Y. Liu, Catia Pesquita, Daniel Faria, S. Bull, T. Pawson, Q. Morris, J.L. Wrana 2009: Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nature Biotechnology 27(), 199-204.

Document | BibTeX source
Catia Pesquita, Daniel Faria, Rui Lopes, Francisco Couto, Measuring coherence between electronic and manual annotations in biological databases.SAC '09: Proceedings of the 2009 ACM Symposium on Applied Computing 2009. ACM.

BibTeX source
Andre O Falcao, Daniel Faria, Antonio Ferreira, Peptide Programs: Applying Fragment Programs to Protein Classification.DTMBIO'08 : Proceedings of the 2008 ACM 2nd CIKM workshop on Data and Text Mining Methods in Bioinformatics New York, NY, USA, October, in press. ACM.

DOI | | BibTeX source
Catia Pesquita, Daniel Faria, Hugo Bastos, António Ferreira, Andre O Falcao, Francisco Couto 2008: Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinformatics Suppl 5(9), S4.

DOI | | BibTeX source
Hugo Bastos, Daniel Faria, Catia Pesquita, Andre O. Falcao, BOLOS: BLAST Ontology-Linked hOmologue Stars.SAC '08: Proceedings of the 2008 ACM symposium on Applied computing New York, NY, USA, March, 2008. ACM.

| Document | BibTeX source
Catia Pesquita, Daniel Faria, Tiago Grego, Francisco Couto, Mário J. Silva: Untangling BioOntologies for Mining Biomedical Information. in: Handbook of Research on Text and Web Mining Technologies. Idea Group Inc. 2008.

BibTeX source
Hugo Bastos, Daniel Faria, Catia Pesquita, Andre O. Falcao, Using GO terms to evaluate protein clustering.BioOntologies SIG at ISMB/ECCB - 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) July, 2007.

Document | BibTeX source
Catia Pesquita, Daniel Faria, Hugo Bastos, Andre O. Falcao, Francisco Couto, Evaluating GO-based Semantic Similarity Measures.BioOntologies SIG at ISMB/ECCB - 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) July, 2007.

Poster | BibTeX source
Daniel Faria, Catia Pesquita, Francisco Couto, Andre O. Falcao, ProteinOn: Web Tool for Protein Semantic Similarity.Poster at ISMB/ECCB 2007 July, 2007.

| Document | BibTeX source
Daniel Faria, Catia Pesquita, Francisco Couto, Andre O. Falcao, ProteInOn: A Web Tool for Protein Semantic Similarity Technical Report. TR 07-6. DI FCUL, March 2007.


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