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Mark A. Jensen, PhD

I received my PhD in Molecular Evolution from the University of Chicago in 2000, did post-docs in HIV at the University of Washington and in bacterial pathogens at Emory University. I was an assistant professor for a short time. My major professional interest is the epidemiological sequence analysis of pathogens, with particular emphasis on HIV and Staphylococcus aureus. I work regularly with colleauges in Canada, Europe, India, and the US. Currently, I am doing business as Fortinbras Research. My full CV is here.

I have been involved in BioPerl since October 2008, where I contributed modules to Release 1.6 that allow query-based access of annotated HIV sequence data via the Los Alamos HIV Sequence Database. See my user page for more detailed information about my BioPerl habit.

Beyond purely mercenary self-training interests, I hope to make some progress at the hackathon on a computable ontology for sequence and phylogenetic annotation of microbial pathogens, that can incorporate clinical and pathogenesis data associated with the sequenced pathogen samples. Please see this use case for a few ideas that I hope will stimulate discussion and code.

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