Graduate Students

Oliver Fujiki: MSc (Coadvised by Sandy Rutherford)

Yexuan Song: PhD (Coadvised by Caroline Colijn)

Yexuan Song

I am interested in phylogenetics. In particular Ancestral State Reconstruction methods which are widely used in phylogenetics for identifying the character states of evolutionary ancestors. I am also interested in using mathematical models of infectious diseases to study how diseases spread.



Rebeccah Hall: MSc

Mahdi Salehzadeh: PhD (Coadvised by John Stockie)

Mahdi’s Homepage

Mahdi Salehzadeh


I have a wide range of research interests that are motivated by biological applications. My current work involves using epidemiology and evolutionary approaches to examine bark beetle infestations. I’m interested in exploring multi-scale questions that occur in a variety of fields, broadly speaking falling under the following categories:

  1. Investigating the dynamics within the host (tree) using computational fluid dynamics approaches.
  2. Creating a brand-new model to depict an outbreak of the bark beetle while refining the presumptions made in earlier literature studies. and evaluating the severity of many parameters to limit the outbreak.
  3. Examining issues brought up in the study of evolution, such as local adaptation.



Postdoctoral Fellows

Siavash Riazi: PDF (Cohosted by Caroline Colijn)

Siavash Riazi
``How much quantitative information is needed to predict a biological system? My research focuses on developing computational and mathematical tools to understand and predict biological systems. Currently I’m working on developing a new way to predict the spread of a viral disease over the course of an epidemic. I’m a computational biologist with a background in mathematical modeling of bacterial physiology/biochemistry. During my PhD I worked with Chris Marx and Chris Remien at University of Idaho. I developed a mathematical model to understand the physiological response of Methylobacterium extorquens to formaldehyde toxicity. This bacteria is a facultative Methylobacterium that lives naturally on plant leaves, and it is regularly exposed to formaldehyde. Further I used statistical methods to analyze global gene expression response of M. extorquens to formaldehyde toxicity and I investigated the role of EfgA, a newly found protein in tolerance to formaldehyde toxicity. In my current research I’m working on developing a new method to estimate epidemiological parameters from a given viral phylogenetic tree during the course of an epidemic. The research involves both stochastic and deterministic mathematical modeling, phylogenetic analysis and investigating parameter estimation methods.’’

Undergraduates

Ananaga Bajgai: (USRA 2023) Ananaga is analyzing data from IUCN Red List to assess the role that infectious diseases have on mediating threat status of their hosts.

Oliver Fujiki: (USRA 2022) Oliver developed likelihood methods for analyzing data from coevolutionary time-shift experiments between the nemotode C. elegans and its parasite B. thuringiensis.


## Alumni:

Amy Langdon: PDF (Cohosted by Caroline Colijn)