Thesis Defence!

written by Eric J. Ma on 2017-04-24 | tags: graduate school thesis defence

My thesis defence announcement has been made to the department!

  • Date: Thursday, April 27th, 2017
  • Time: 2:00 PM
  • Location: 56-614
Identification of Reassortant Influenza Viruses at Scale - Algorithm and Applications
Eric Ma


Reassortment is a reticulate evolutionary process that results in genome shuffling; the most prominent virus known to reassort is the influenza A virus. Methods to identify reassortant influenza viruses do not scale well beyond hundreds of isolates at a time, because they rely on phylogenetic reconstruction, a computationally expensive method. This thus hampers our ability to test systematically whether reassortment is associated with host switching events. In this thesis, I use phylogenetic heuristics to develop a new reassortment detection algorithm capable of finding reassortant viruses in tens of thousands viral isolates. Together with colleagues, we then use the algorithm to test whether reassortment events are over-represented in host switching events and whether reassortment is an alternative 'transmission strategy' for viral persistence.


  • Jonathan Runstadler, Assistant Professor of Biological Engineering and Comparative Medicine, MIT (Advisor)
  • Mark Bathe, Associate Professor of Biological Engineering, MIT (Committee Chair)
  • Jukka-Pekka Onnela, Assistant Professor of Biostatistics, Harvard School of Public Health