Cancer computational genomics
Department of Biochemistry, Genetics and Immunology,
School of Biology, University of Vigo, Vigo 36310, Spain
My current work focuses on incorporating population genomics strategies to explore cancer evolution and progression, as well as to understand the underlying causes of somatic variation within tumours (i.e., intratumour heterogeneity). Overall, I am mainly interested in using high-throughput genomic data to quantify the relative contribution of neutral and selective forces underlying germline and somatic heterogeneity. In addition, I have been increasingly interested in applying model-based approaches together with solid inferential methods to reconstruct the evolutionary history of populations (individuals/cells).
- 2015 to present – Postdoctoral Fellow @ Evolutionary Genomics and Cancer lab, University of Vigo (Vigo, Spain).
- 2014 – EMBO Short-term Visiting Scientist, Institut de Biologia Evolutiva - Universitat Pompeu Fabra (Barcelona, Spain)
- 2010 to 2014 – PhD, GABBA PhD Program (University of Porto, Portugal)
- 2008 to 2009 – Research Fellow @ PCG Group, Instituto Gulbenkian de Ciência (Oeiras, Portugal)
- 2007 – Research trainee @ Limnology lab, Federal University of Rio de Janeiro (Rio de Janeiro, Brazil)
- 2003 to 2008 – Graduation in Applied Biology, University of Minho (Braga, Portugal)
Alves JM, Prieto T, Posada D. 2017. Multiregional tumor trees are not phylogenies. Trends in Cancer, doi: http://dx.doi.org/10.1016/j.trecan.2017.06.004
Alves JM, Prieto T, Posada D (Preprint: 2015). Biased evolutionary inferences from bulk tumor samples. bioRxiv, doi: https://doi.org/10.1101/089680.
Alves JM, Lima AC, Pais IA, Amir N, Celestino R, Piras G, Monne M, Comas D, Heutink P, Chiki L, Amorim A, Lopes AM (2015). Reassessing the evolutionary history of the 17q21 inversion polymorphism. Genome Biology and Evolution, doi: 10.1093/gbe/evv214.
Alves JM, Chiki L, Amorim A, Lopes AM (2014). The 8p23 inversion polymorphism determines local recombination heterogeneity across human populations. Genome Biology and Evolution, doi: 10.1093/gbe/evu064.
Alves JM, Lopes AM, Chikhi L, Amorim A (2012). On the structural plasticity of the human genome: chromosomal inversions revisited. Current Genomics,13:623-632.
Alves JM, Caliman A, Guariento RD, Figueiredo-Barros MP, Carneiro LS, Farjalla VF, Bozelli RL & Esteves FA (2010). Stoichiometry of benthic invertebrate nutrient recycling: interspecific variation and the role of body mass. Aquatic Ecology, 44, 421–430.
Prieto T, Alves JM, Posada D. ”NGS analysis of somatic mutations in cancer genomes” In Big Data Analytics in Genomics. Ed Wonk KC. (Springer, 2016)
Alves JM, Lopes A. “Population Genomics: Macro- vs. Microevolution”. Encyclopaedia of Genetics, 2nd Edition (Elsevier, 2012)