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Publications

May 2013

  • Barbosa FC, Arrais J, Oliveira JL. Quantitative Characterization of Protein Networks of the Oral Cavity. PACBB 2013. Proceedings of the 8th International Conference on Practical Applications of Computational Biology & Bioinformatics. 2013

Feb 2013

  • Arrais JP, Rosa N, Melo J, Coelho ED, Amaral D, Correia MJ, Barros M, Oliveira JL. OralCard: A bioinformatic tool for the study of oral proteome. Arch Oral Biol. 2013 Feb 7. pii: S0003-9969(13)00003-4

Jan 2013

  • Gaspar P, Moura G, Santos MA, Oliveira JL. mRNA secondary structure optimization using a correlated stem-loop prediction. Nucleic Acids Res. 2013 Jan 15. [Epub ahead of print]
  • Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, et al. Ensembl 2013. Nucleic Acids Res 2013;41(Database issue):D48-55

Dec 2012

  • Lopes P, Oliveira JL. COEUS: "semantic web in a box" for biomedical applications. J Biomed Semantics. 2012 Dec 17;3(1):11

Oct 2012

  • Bioinformatics J (2012) (submitted). BioDAG Builder: An Ontology Graph Builder for Bioresearch and Healthcare. T.Beck, R.C.Free, J.Lusted, A.J.Brookes, J.Tedds.
  • Byrne et al. VarioML framework for comprehensive variation 3 data representation and exchange. BMC Bioinformatics 2012, 13:254
  • J. Biomed. Semantics (2012) (in press). Semantically enabling a genome-wide association study database. T.Beck, R.C.Free, G.A.Thorisson, A.J.Brookes
  • Gaspar P, Oliveira JL, Frommlet J, Santos MA, Moura G. EuGene: maximizing synthetic gene design for heterologous expression. Bioinformatics. 2012 Oct 15;28(20):2683-4

Jun 2012

  • Dalgleish, R., Molero, E., Kidd, R., Jansen, M., Past, D., Robl, A., Mons, B., Diaz, C., Mons, A. and Brookes, A. J. Solving bottlenecks in data sharing in the life sciences. Hum. Mutat., 2012, 33: 1494–1496

May 2012

  • Adamusiak T, Parkinson H, Muilu J, Roos E, van der Velde KJ, Thorisson GA, Byrne M, Pang C, Gollapudi S, Ferretti V, Hillege H, Brookes AJ,Swertz MA. Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information. Hum. Mutat., 2012, 33: 867–873
  • Beck T, Gollapudi S, Brunak S, Graf N, Lemke HU, Dash D, Buchan I, Díaz C, Sanz F, Brookes AJ. Knowledge engineering for health: a new discipline required to bridge the "ICT gap" between research and healthcare. Hum Mutat. 2012 May;33(5):797-802.

Apr 2012

Mar 2012

  • Murtagh, et al. Navigating the perfect [data] storm. Norsk Epidemiologi 2012; 21 (2): 203-209
  • Bower M et al.Update of PAX2 mutations in renal coloboma syndrome and establishment of a locus-specific database, Hum Mutat. 2012 Mar;33(3):457-66. Epub 2012 Jan 31.

Jan 2012

  • Wilson-Sayres et al. 'HGV2011: personalized genomic medicine meets the incidentalome'. Human Mutation 2012, 33, 582-585

Dec 2011

  • Beck T, Thorisson GT, Brookes AJ. Applying ontologies and exploring nanopublishing in a genome-wide association study database. SWAT4LS 11, Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences. 2012: 1-2.

Sep 2011

  • Dalgleish R, Oetting WS, Auerbach AD, Beckmann JS, Cambon-Thomsen A, Devereau A, Greenblatt MS, Patrinos GP, Taylor GR, Vihinen M, Brookes AJ. Clarity and Claims in Variation/Mutation Databasing. [A response to: "MutaDATABASE: a centralized and standardized DNA variation database" by Bale et al., 2011]. Nature Biotechnology, 2011, 29, 790–792

Oct 2009

  • Lopes P, Davide C, Oliveira J L. ARABELLA - A Directed Web Crawler. KDIR International Conference on Knowledge Discovery and Information Retieval. 2009 Apr 28; Madeira, Portugal.

Sep 2009

  • Potamias G. Grid-enabling G2P association studies: a knowledge discovery scenario. Engineering in Medicine and Biology Society (EMBC'09). 2009 Sep 2-6; Minesota, USA.

Apr 2009

  • Desmet FO, Hamroun D, Lalande M, Collod-Béroud G, Claustres M, Béroud C. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res. 2009;37(9):e67. Epub 2009 Apr 1.
  • Lopes P, Arrais J , Oliveira J L. LSDB INTEGRATOR - A Link-based Information Integration Architecture. KDIR International Conference on Knowledge Discovery and Information Retieval. 2009 Oct 6 - 8; Madeira, Portugal.

Jan 2009

  • Tuffery-Giraud S, Béroud C, Leturcq F, Yaou RB, Hamroun D, Michel-Calemard L, Moizard MP, Bernard R, Cossée M, Boisseau P, Blayau M, Creveaux I, Guiochon-Mantel A, de Martinville B, Philippe C, Monnier N, Bieth E, Van Kien PK, Desmet FO, Humbertclaude V, Kaplan JC, Chelly J, Claustres M. Genotype-phenotype analysis in 2,405 patients with a dystrophinopathy using the UMD-DMD database: a model of nationwide knowledgebase. Hum Mutat. 2009 Jun;30(6):934-45.
  • Brookes AJ, Lehvaslaiho H, Muilu J, Shigemoto Y, Oroguchi T, Tomiki T, Mukaiyama A, Konagaya A, Kojima T, Inoue I, Kuroda M, Mizushima H, Thorisson GA, D.Dash, Rajeevan H, Darlison MW, M.Woon, Fredman D, Smith AV, Senger M, Naito K and Sugawara H. The Phenotype and Genotype Experiment Object Model (PaGE-OM): A robust data structure for information related to DNA variation. Hum Mutat. 2009 Mar 18. 30(6): 968-977.
  • Thorisson GA, Lancaster O, R.C.Free, R.K.Hastings, P.Sarmah, D.Dash,S.Brahmachari and A.J.Brookes. HGVbaseG2P: a Central Genetic Association Database. Nucleic Acids Res. 37:D797-802.

Dec 2008

  • Michael H, Hogan J, Kel A, Kel-Margoulis O, Schacherer F, Voss N and Wingender E. Building a knowledge base for systems pathology. Brief Bioinform. 2008 Nov; 9(6):518-31. Epub 2008 Dec 10.
  • Kaput J, Cotton RGH, Hardman L, Al Aqeel AI, Al-Aama JY,Al-Mulla F, et al. Planning the Human Variome Project: The Spain Report. Hum Mutat. 30 (4): 496–510.

Apr 2008

  • Kauffmann F; Cambon-Thomsen A. Tracing biological collections: between books and clinical trials. JAMA. 2008; 299(19):2316-2318.

Mar 2008

  • Gudmundur T, Muilu J & Brookes AJ. Genotype–phenotype databases: challenges and solutions for the post-genomic era. Nature Rev. Gen. 2009:10, 9-18.
G2P Knowledge Centre is part of GEN2PHEN and funded by the Health Thematic Area of the Cooperation Programme of the European Commission within the VII Framework Programme for Research and Technological Development.

© GEN2PHEN 2011