GHTM

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Home / Archives for Alcantara LC

Genome Detective: an automated system for virus identification from high-throughput sequencing data

  • Authors: Vilsker M, Moosa Y, Nooij S, Fonseca V, Ghysens Y, Dumon K, Pauwels R, Alcantara LC, Vanden Eynden E, Vandamme AM, Deforche K, De Oliveira T
  • Publication Year: 2019
  • Journal: Bioinformatics
  • Link: https://www.ncbi.nlm.nih.gov/pubmed/30124794

Genome Detective is an easy to use web-based software application that assembles the genomes of viruses quickly and accurately. The application uses a novel alignment method that constructs genomes by reference-based linking of de novo contigs by combining amino-acids and nucleotide scores. The software was optimized using synthetic datasets to represent the great diversity of […]
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A public HTLV-1 molecular epidemiology database for sequence management and data mining.

  • Authors: Alcantara LC, Araújo TH, de Albuquerque-Junior AE, Edwards D, Galvão-Castro B, Souza-Brito LI, Deforche K, Libin P, Vandamme AM
  • Journal: PLoS One
  • Link: http://www.ncbi.nlm.nih.gov/pubmed/?term=A+Public+HTLV-1+Molecular+Epidemiology+Database+for+Sequence+Management+and+Data+Mining

BACKGROUND:
It is estimated that 15 to 20 million people are infected with the human T-cell lymphotropic virus type 1 (HTLV-1). At present, there are more than 2,000 unique HTLV-1 isolate sequences published. A central database to aggregate sequence information from a range of epidemiological aspects including HTLV-1 infections, pathogenesis, origins, and evolutionary dynamics would be useful to scientists and physicians worldwide.
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RegaDB: Community-driven data management and analysis for infectious diseases

  • Authors: Alcantara LC, Assel M, Ayouba A, Beheydt G, Boucher C, Camacho RJ, Carvalho AP, Cavaco-Silva J, De Bel A, De Munter P, De Oliveira T, Deforche K, Ferreira F, Grossman Z, Imbrechts S, Kaiser R, Lacor P, Lapadula G, Libin P, Otelea D, Paraschiv S, Peeters M, Ruelle J, Sloot P, Snoeck J, Theys K, Torti C, Van Laethem K, Van Wijngaerden E, Vandamme AM, Wesner S, Zazzi M
  • Journal: Bioinformatics
  • Link: http://www.ncbi.nlm.nih.gov/pubmed/23645815

RegaDB is a free and open source data management and analysis environment for infectious diseases. RegaDB allows clinicians to store, manage and analyse patient data, including viral genetic sequences. Moreover, RegaDB provides researchers with a mechanism to collect data in a uniform format and offers them a canvas to make newly developed bioinformatics tools available to clinicians and virologists through a user friendly interface.
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About GHTM

GHTM is a R&D Unit that brings together researchers with a track record in Tropical Medicine and International & Global Health. It aims at strengthening Portugal's role as a leading partner in the development and implementation of a global health research agenda. Our evidence-based interventions contribute to the promotion of equity in health and to improve the health of populations.

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