John Archer

Following an undergraduate degree at the University of Liverpool (in microbiology), a certificate and masters at the same (in software technology and software engineering respectively), and a PhD (in bioinformatics) from the University of Manchester (supervised by prof. David Robertson), my main areas of research interest have become software development, largely in relation to sequence analysis, transcriptomics, in relation to short-read data, evolutionary biology and data visualization. These are combined in my current research position as group leader in bioinformatics at CIBIO-InBIO where I have been active numerous genomic, transcriptomic and metagenomic projects.

To date I have been involved in bioinformatics projects ranging from the characterization of virus diversity (mainly HIV-1 and Influenza), implementing read mapping, assembly and visualization tools, characterizing low frequency polymorphisms obscured by read error, recombination breakpoint detection, phylogenetic analysis, database development, as well as varying transcriptomic experiments covering a range of organisms including: dogs, foxes, wolfs, birds, fish, snakes, rabbits, frogs and scorpions. I have also worked as a software developer prior to initiating my research career. 

Presently my main interest is in the de novo assembly of short-read RNA-Seq data, and in characterizing the extent of chimerism introduced during such assembly. The latter has a relatively poorly characterized effect on downstream data analysis. Some of my recent software tools associated with the latter (and funded by FCT) 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/