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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

Caroline Colijn

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.

Paul Tupper

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.

Lloyd Elliott

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.

Cedric Chauve

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 MacPherson

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.

Postdoctoral Researchers

Ben Sobkowiak

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.

Pengyu (Peter) Liu

Pengyu is a post doc whose research interests lie in the fields of topology, combinatorics and their applications in biology, physics and other sciences. Current projects include tree metrics and topology and their applications in phylogenetics and infectious diseases, knots and links and their invariants and the topology of the kinetoplast DNA networks.

Website

Elisha Are

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.

Vijay Naidu

Vijay is a post doc with interests in sequence alignment, protein modelling and phylogenetic analysis and in the field of genomics, cybersecurity and image processing. Before moving to SFU in June 2019, he completed his PhD at the Auckland University of Technology, New Zealand, working on identifying polymorphic malware variants using biosequence analysis techniques, under the supervision of Prof. Ajit Narayanan. His current research with Prof. Caroline Colijn focuses on the epidemiological analysis of tuberculosis transmission using bioinformatics pipeline.

Website

Jessica Stockdale

Jessica is a post doc 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.

PhD Candidates

Aniket Mane

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 Abhari

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 Susvitasari

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 Geysar

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 Mulberry

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.

MSC Students

Madi Yerlanov

Madi is a MSc student in the Mathematics program at SFU. His main research interest lies in advancing algebra and applying it to biology, ecology and similar sciences, in particular, epidemiology. He is also interested in other unrepresented parts of (pure) mathematics that can be used to address real-life problems. He is currently searching for his future research topic in above mentioned fields.

Jessica Sithebe

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 Moshfegh

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.

Yexuan Song

Yexuan is a MSc student in the Mathematics program at SFU. He is interested in disease modelling as well as applying theoretical mathematics to real-life questions. Right now he is trying to explore the field of biomathematics for his future research.

Undergraduates

Jaskaran Oberoi

As Lab Manager, Jaskaran has a number of administrative roles within the MAGPIE Research Group. Jaskaran is a final year BSc student in the Faculty of Health Sciences, in the Life Sciences concentration, and his passion for combining statistics with life sciences led him to this role. He hopes to gain an understanding of statistical tools used in epidemiological research and expand his interdisciplinary research skillset during his time at MAGPIE.

Golrokh Nouri

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.