Mathematics, Genomics and Prediction in Infection and Evolution
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Mathematics, Genomics and Prediction in Infection and Evolution

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The MAGPIE Group

Our team is led by Dr. Caroline Colijn and includes researchers who are applying mathematical and statistical tools to answer important questions in the areas of genomics, epidemiology, biology and other interdisciplinary fields.

Faculty

Dr. Caroline Colijn works at the interface of mathematics, evolution, infection and public health, and leads the MAGPIE research group. She joined SFU's Mathematics Department in 2018 as a Canada 150 Research Chair in Mathematics for Infection, Evolution and Public Health. She has broad interests in applications of mathematics to questions in evolution and public health, and was a founding member of Imperial College London's Centre for the Mathematics of Precision Healthcare. Contact ccolijn@sfu.ca.
Website: carolinecolijn.ca

Paul Tupper is a Professor of Mathematics at SFU. His work spans applications of mathematics to problems in linguistics, cognitive psychology, and phylogenetics. Recently he has been focusing on mathematical modelling for the COVID-19 pandemic, in collaboration with members of the MAGPIE research group.

Jessica is a faculty member with interests in mathematical and statistical modelling of infectious disease outbreaks, particularly using genomic data. Before moving to SFU in October 2018, she completed her PhD at the University of Nottingham, UK, working on Bayesian computational methods for stochastic epidemics. Her current projects focus on modelling of pathogen genomic data to better understand transmission and evolution, and predict future infection.

Cedric Chauve holds a PhD and Habilitation in Theoretical Computer Science from Bordeaux University and is a Professor of Mathematics at SFU. His research interest include the development of algorithms and software tool for analyzing genomic data, in comparative genomics, cancer genomics and pathogens genomics.

Ailene uses mathematical and statistical tools to address questions at the intersection of evolution, ecology, and epidemiology. Ailene develops phylodynamic (phylogenies+ epidemiological dynamics) methods to understand and control ongoing epidemics. In particular, Ailene's research focuses on quantifying how both host and pathogen genetics shape disease spread and severity. Additionally, Ailene strives to understand how these complex coevolutionary interactions shape the biological diversity of the natural world by studying the genetics and evolutionary dynamics of long-term associations between hosts and their infectious pathogens.

I am a mathematical biologist interested in the ecology and evolution of hosts and parasites. I use mathematical models to study how parasites spread through populations and how traits such as infectivity and virulence evolve, and in turn how this affects the evolution of host traits such as resistance or mating strategies. My research covers a broad range of topics in biology, including infectious diseases, the evolution and maintenance of diversity across space and time, sexual selection and reproductive strategies, and niche evolution.

Dr. Lloyd T. Elliott is an Assistant Professor of Big Data in the Department of Statistics and Actuarial Science at Simon Fraser University, and an Honorary Academic Visitor at the Nuffield Department of Clinical Neuroscience at the University of Oxford. His research interests include machine learning, brain imaging genetics, phylogenetics and Bayesian nonparametrics. Dr. Elliott collaborates with the MAGPIE group on COVID-19 epidemiological modelling. He also serves with CGEn's HostSeq project for SARS-CoV-2 host genetics.

Postdoctoral Researchers

Ben is a postdoc with a primary interest in investigating pathogen transmission using genomics, as well as developing methodological tools for genomic sequence analysis. After receiving a BSc in Biology from University of Bristol and an MRes in Biosystematics from Imperial College London, Ben received his PhD in Computational Biology from University College London under the supervision of Professor Francois Balloux, studying the genomics and epidemiology of Shigella spp. in Vietnam. He then took up a post doc position with Professor Taane Clark at the London School of Hygiene and Tropical Medicine working on TB transmission in Malawi. He moved to Canada for a position at UBC and the BCCDC to work with Dr. James Johnston on TB transmission in BC. He joined the MAGPIE group to work on various projects, mainly focusing on genomic analyses in M. tuberculosis and COVID-19.

Elisha is a postdoctoral researcher in the MAGPIE group. His research spans key areas of Mathematical modelling, including epidemiological modelling and analysis, rapid response modelling of emerging infectious diseases such as COVID-19. Before joining SFU, he completed his PhD in Mathematical biology in Stellenbosch University. His PhD thesis focused on using mathematical models to quantify and predict the impact of climate change on tsetse and trypanosomiasis in Africa. He has five years undergraduate teaching experience as a faculty member in the mathematics department, Federal University Oye-Ekiti.

Siavash is a computational biologist with a background in mathematical modeling and bacterial physiology/ biochemistry. Currently, he is working on developing a new method to estimate epidemiological parameters from a given viral phylogenetic tree during the course of an epidemic. His research focuses on developing computational and mathematical tools to understand and predict biological systems. During his PhD, he worked with Chris Marx and Chris Remien at University of Idaho working on : "Mathematical Modeling and Analysis of Gene Expression to Understand Phenotypic Heterogeneity and the Response of Methylobacterium extorquens to Formaldehyde Toxicity".

Amy joined the MAPGIE group in Dec 2021 as a postdoctoral fellow to work on transmission modeling for ongoing pandemics. She holds a PhD in Molecular Genetics and Genomics as well as a Masters of Population Health Science from Washington University in St. Louis. Her graduate research focused on predicting the effects of medical interventions on communities of human-associated microbes in global health settings.

Researchgate

PhD Candidates

Aniket is a PhD student in the Operations Research program at SFU. His interests primarily lie in the fields of discrete mathematics, combinatorial optimization. He works on designing optimization-based techniques to address questions posed in bioinformatics. His current project involves the assembly of plasmids using mixed integer linear programming.

Niloufar is a Ph.D. student in the Mathematics Department and a member of INS (Individualized Interdisciplinary Studies) Program at SFU. She holds a bachelor’s degree in Applied Mathematics and a master’s degree in Computer Science. During her master’s, she was a member of Bioinformatics and Computational Biology Lab at University of Tehran, Iran, working on imputation methods on sparse single-cell data and constructing Phylogenetic Trees on tumor data. Currently she is interested in Constructing and Inferring Phylogenetic Networks from binary trees and ordination in reduced space (or dimension reduction techniques) for biodiversity measures.

Kurnia is a PhD student in the Department of Mathematics, currently enrolled in the Applied Mathematics program. Her research interest is in statistical methods to understand infectious disease outbreaks using genomic data. She is currently working to understand cluster outbreaks using logistic regression.

Omid is a Ph.D. student in the Mathematics Department. He holds a bachelor’s degree in Applied Mathematics and a master’s degree in Operation Research from the University of Tabriz. Experienced in interdisciplinary works, his research interest lies in linking molecular studies of the pathogen genome to epidemiological information. Currently, he is designing an app for Covid-19 simulation.

Nicola is a PhD student in the Applied Mathematics program at SFU. Her interests are in mathematical modelling and computing with applications to public health. She is currently interested in the evolution of co-circulating pathogens. Nicola is also involved in an ongoing project to develop and promote open educational resources for undergraduate math students.

Pouya is a Graduate Visiting Research Student in the SFU Mathematics Department. He is currently a PhD candidate in Mathematical Analysis at KNTU, Tehran, Iran, mostly working on a recently introduced generalization of Metric Spaces called Diversities. He and his host supervisor Paul Tupper are currently working on software tools to simulate, visualize and cluster outbreak datasets. He holds a bachelor’s degree in Pure Mathematics at KNTU and a master’s degree in Mathematical Analysis at Amirkabir University of Technology.

Yexuan is a Ph.D. student in the Mathematics program at SFU. His interest lies in Ancestral State Reconstruction methods which are widely used in phylogenetics for identifying the character states of evolutionary ancestors. He is also interested in using mathematical models of infectious diseases to study how diseases spread and coalescent theory.

MSC Students

Jessica is an MSc Student in Applied Mathematics working under the supervision of Paul Tupper. They are interested in using their skills and modelling techniques to explore a variety of interesting questions.

Saba is second year master student of Applied Mathematics at Simon Fraser University. Currently, she and her supervisor Paul Tupper are working on a model that explains and simulates spread of Covid-19 infection in indoor spaces like on a plane, a bus, or in a restaurant. Their goal is to find a suitable model and model parameters looking at existing data for the outbreak. Saba’s undergraduate degree was in Electrical Engineering, sub-major in Control Systems. She volunteered in the Cognitive Science Lab, University of Tehran for two years through which she also got interested in human behaviour and cognitive science. Her bachelor’s project was about designing a cognitive game for data collection and investigating how people share their information in different economic situations.

Piyush is as MSc student in applied mathematics working under Dr. Cedric Chauve and Dr. Caroline Colijn. He intends to use his skills in mathematics and computer programming to extract insights from biological data, at the same time widening his knowledge regarding the different domains of bio-math.

Hannah is an MSc student in the INS (Individualised Interdisciplinary Studies) program at SFU, and is a member of both the Mathematics and Statistics Departments. Her senior supervisor is Caroline Coiljn, and her co-supervisor is Lloyd Elliott. She holds an honors BSc in Applied Mathematics from SFU, where she completed her undergraduate thesis with Nilima Nigam on the topic of eigenvalue PDEs. Her graduate thesis is focused on improving the interpretability of random forests by quantifying their structure through comparison functions on decision trees.

Undergraduates

Inayat is a fourth-year Data Science undergraduate student at Simon Fraser University. She has a number of administrative roles as the Lab Manager for the MAGPIE Research Group.

Golrokh is an undergraduate student in the Mathematics and Computing Science program at SFU. She is interested in the mathematical applications in neuroscience and pharmacology. She is currently working under the supervision of Paul Tupper on a USRA project modelling drug tolerance and finding optimal treatment plans.

Cody Zhang is a Computer Science student at BCIT. He has broad interests in using algorithms to solve relevant real-world problems. Currently, Cody is working as a Junior Software Developer at SFU on a co-op term. His project with the Magpie team revolves around modelling and creating a Covid Outbreak Simulation, in collaboration with Caroline Colijn and Jessica Stockdale. Cody previously completed a B.Sc in Chemistry from UBC and briefly worked in the fuel cells and renewable energy industry.

Vibhuti is a Data Science major at SFU. He is working under Dr. Caroline Colin and Dr. Jessica Stockdale as a research assistant on COVID-19 wave modelling. He is interested in exploring how programming and statistical methods can be utilized in the fields of biology and epidemiology.