Publications
Oct 2011
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Celli J, Dalgleish R, Vihinen M, Taschner PE, den Dunnen JT. Curating gene variant databases (LSDBs): toward a universal standard. Hum Mutat 2011 (in press).
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Vihinen M, den Dunnen JT, Dalgleish R, Cotton RGH. Guidelines for establishing locus specific databases. Hum. Mut. 2011 [Online]
Jul 2011
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Laros JFJ, Blavier A, den Dunnen JT, Taschner PEM. A formalized description of the standard human variant nomenclature to improve sequence variant recognition in databases and the literature. BMC Bioinformatics 2011, 12(4):5.
Jun 2011
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Cambon-Thomsen et al. The role of a bioresource research impact factor as an incentive to share human bioresources. Nat Genet. 2011, 43(6):503-504.
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Kurbatova N, Adamusiak T, Kurnosov P, Swertz MA, and Kapushesky M. ontoCAT: an R package for ontology traversal and search Bioinformatics 2011 Jun: btr375v1-btr375.
May 2011
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Khatsanovskyy V, Litton J-E, Fomkin R. Improving security by using a database management system for integrated statistical data analysis. Proceedings of the 4th International Workshop on Privacy and Anonymity in the Information Society. Uppsala, Sweden: ACM; 2011. p. 9:1 - 9:4
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Adamusiak et al. OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript. BMC Bioinformatics. 2011, 12:218.
Apr 2011
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Lopes P, Dalgleish R and Oliveira JL. WAVe: web analysis of the variome. Hum Mutat. 2011. 32:1–6.
Mar 2011
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Webb AJ, Thorisson GA, Brookes AJ, on behalf of the GEN2PHEN Consortium. An Informatics Project and Online ‘‘Knowledge Centre’’ Supporting Modern Genotype-to-Phenotype Research. Hum. Mutat. 2011 Jan. 32(0):1–8.
Feb 2011
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Fokkema IFAC, Taschner PEM, Schaafsma Gerard CP, Celli J, Laros JFJ, den Dunnen JT. LOVD v.2.0: the next generation in gene variant databases. Hum. Mut. 2011 May; 32 (5): 557–563.
Jan 2011
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Ducournau P, Gourraud PA, Rial-Sebbag E, Bulle A and Cambon-Thomsen A. Tests génétiques en accès libre sur Internet. Med Sci (Paris) 2011 ; 27 : 95–102.
Dec 2010
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Taschner PE, den Dunnen JT. Describing structural changes by extending HGVS sequence variation nomenclature. Hum Mutat. 2011 Jan 25.
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Moustakis V., Laine ML., Koumakis L., Loos BG., and and Potamias G. Modeling and validating genotype knowledge. CIBEC 2010, December 16-18 2010, Cairo, Egypt.
Nov 2010
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Lopes, P. An Extensible Platform for Variome Data Integration. 10th IEEE International Conference on Information Technology and Applications in Biomedicine. 2010 Nov; Corfu, Greece.
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Lopes, P. A Tagging System for Bioinformatics Resources. 10th IEEE International Conference on Information Technology and Applications in Biomedicine. 2010 Nov; Corfu, Greece.
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Lopes P, Dalgleish R, Oliveira JL. WAVe: web analysis of the variome. Hum Mutat. 2011 Mar 10. [Epub ahead of print] PubMed PMID: 21394829.
Oct 2010
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Mitropoulou, C; Webb, AJ; Mitropoulos, K; Brookes, AJ; Patrinos, GP. Humu-2010-0187: Locus-specific database domain and data content analysis: Evolution and content maturation towards clinical use. Hum. Mutat.2010 Oct. 31 (10): 1109–1116.
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Lopes, P. A Holistic Approach for Integrating Genomic Variation Information. 10th IEEE International Conference on Information Technology and Applications in Biomedicine. 2010 Nov; Corfu, Greece.
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Potamias G., Kanterakis A. Revealing Disease Molecular Regulatory Mechanisms: Coupling Microarrays and Gene Regulatory Networks. Hellenic Society for Computational Biology and Bioinformatics, HSCBB. 2010; 3-4.
Sep 2010
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Kanterakis A, Potamias G, et al. Scientific discovery workflows in bioinformatics: A scenario for the coupling of molecular regulatory pathways and gene-expression profiles. Stud Health Technol Inform. 2010;160(Pt 2):1304-1308.
Jun 2010
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Arrais J, Pereira J, Lopes P, Matos S, Oliveira JL. Improving cross mapping in biomedical databases. 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2010). 2010 June, 16-18; Guimarães, Portugal. Springer.
May 2010
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Forzano F, Borry P, Cambon-Thomsen A, Hodgson SV, Tibben A, Vries P, van El C and Cornel M. Italian appeal court: a genetic predisposition to commit murder? European Journal of Human Genetics. 2010. 18, 519–521.
Apr 2010
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Dalgleish R, Flicek P, Cunningham F, Astashyn A, Tully RE, Proctor G, Chen Y, McLaren WM, Larsson P, Vaughan BW, Beroud C, Dobson G, Lehvaslaiho H, Taschner PEM, den Dunnen JT, Devereau A, Birney E, Brookes AJ and Maglott DR. Locus Reference Genomic sequences: an improved basis for describing human DNA variants. Genome Medicine 2010, 2:24.
Mar 2010
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Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A and Parkinson H. Modeling sample variables with an Experimental Factor Ontology. Bioinformatics 2010 26(8):1112-1118.
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Swertz MA, van der Velde KJ, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R, Dijkstra M, Schofield P, Schughart K, Hancock JM, Smedley D, Wolstencroft K, Goble C, de Brock EO, Jones AR, Parkinson HE, members of the Coordination of Mouse Informatics Resources (CASIMIR), Genotype-To-Phenotype (GEN2PHEN) Consortiums, Jansen RC. XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments. Genome Biology. 2010 11:R27.
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Mottaz A, David FPA, Veuthey AL and Yip YL. Easy retrieval of single amino-acid polymorphisms and phenotype information using SwissVar. Bioinformatics. 2010. 26 (6): 851–2.
Dec 2009
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Cambon-Thomsen, A. Synthesis of 6 Toulouse workshops. L’information genetique humaine est-elle particuliere? 2009
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Povey S, Al Aqueel AI, Cambon-Thomsen A, Dalgleish R, Den Dunnen JT, Firth HV, Greenblatt M, Isaacson Barash C, Parker M, Patrinos GP, Savige J, Sobrido MJ, Winship I, Cotton RGH. Practical guidelines addressing ethical issues pertaining to the curation of human locus specific variation databases (LSDBs). Hum Mutat. 1098-1004.
Oct 2009
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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
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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
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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.
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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
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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.
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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.
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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
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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.
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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
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Kauffmann F; Cambon-Thomsen A. Tracing biological collections: between books and clinical trials. JAMA. 2008; 299(19):2316-2318.
Mar 2008
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Gudmundur T, Muilu J & Brookes AJ. Genotype–phenotype databases: challenges and solutions for the post-genomic era. Nature Rev. Gen. 2009:10, 9-18.