I completed my PhD at the University of Manchester, UK, in 2008 (supervised by Prof. David Robertson). My thesis focused on the evolutionary dynamics of HIV-1 and largely involved: analysis of next generation sequence data, software development, varying associated statistics, algorithm development, recombination detection and phylogeny. All chapters have been published.
My postdoctoral research has been driven by national and international collaborations. In 2008 I received funding from Pfizer, UK, to investigate the emergence of drug resistance mutations within HIV-1 populations. In 2009 I received funding from Case Western Reserve University Hospital, Cleveland, to develop a viral genotyping tool. Also in 2009 I wrote a successful Biotechnology and Biological Sciences Research Council (BBSRC) three year postdoc project with my PhD supervisor (as well as Prof. Andrew Rambaut). The project involved the development of an environment for the handling of NGS data derived from viral populations.
Since December 2014 I have been a bioinformatician at the Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-INBIO), University of Porto. This position has allowed me to collaborate on a range of FCT projects as well as to write my own involving chimerism within de novo assembly software and its effects (title: De Novo based sequence assembly of next generation sequence data without chimeras: improved annotation, gene expression profiles and haplotype reconstruction.).
My Latest Software include:
1. CStone: https://sourceforge.net/projects/cstone/
2. CSReadGen: https://sourceforge.net/projects/csreadgen/
3. CView: https://sourceforge.net/projects/cview/
4. ChimSim: https://sourceforge.net/projects/chimsim/
5. TVScript: https://sourceforge.net/projects/tvscript/