Agent-Based Modelling Laboratory

Faculty of Science | York University



Seyed M. Moghadas, PhD

Director, ABM-Lab

 

My research broadly includes dynamical systems and their applications to the fields of mathematical biology and ecology. In particular, I am interested in the theoretical and computational aspects of mathematical models describing the underlying biological phenomena. I am currently involved in several projects related to the modelling of infectious diseases, with particular emphasis on establishing strong links between “Mathematical Epidemiology” and “Theoretical Immunology”. One important aspect of my research is to develop innovative knowledge translation methodologies through which strong links between theory, policy and practice are forged, and modeling outcomes are translated to improve health policy and support decision-making.




Marek Laskowski, PhD

ABM-Lab Manager (2013 - present), Postdoctoral (2010 - 2013)

 

Marek Laskowski received his PhD in Electrical and Computer Engineering from the University of Manitoba in 2011. His research interests include software architecture of agent based modeling and decision support systems, pervasive internet systems, natural language processing, computational game theory, and applied machine learning. He is actively involved in developing novel agent based models for public health decision support, directing the release of the next-generation open-source Simstitution framework for agent based modeling, and devising smart phone based public health surveillance technologies.



David Champredon, PhD

Postdoctoral (2016 - 2017)

 

David Champredon worked in the financial industry for 13 years and then decided to focus on academic research, more specifically on modelling the spread of infectious disease in populations. He received his Ph.D. from McMaster University in 2016. His research is aimed at developing mathematical and computational tools to support public health policies. Most of his academic work was centered on sexually transmitted infections and Ebola. David joined the ABM-lab in 2016 to investigate vaccination strategies for pandemic influenza.



Lin Chen, PhD

Postdoctoral (2014 - 2016)


Lin Chen received her PhD in Systems Biology from MD Anderson Cancer Center in Houston, in 2014. She uses computational biology to understand how cells undergo distinct growth modes to form complex multicellular structure, and uncover the relevant biological advantage. Her research involves a wide range of techniques, such as molecular cloning, microscopic imaging, quantitative analysis and mathematical modeling. She has joined the ABM-Lab to conduct research in genome annotation and disease risk prediction. She will apply tools and techniques in genetics and bioinformatics, graph theory and modelling to understand the causative factors, and assess personalized risk, of complex and inherited diseases.




Mehdi Najafi, PhD

Postdoctoral (2015 - 2016)


Mehdi Najafi received his PhD from Sharif University of Technology in 2014, and joined the ABM-Lab in 2015 as a postdoctoral fellow in the area of scientific computing and agent-based simulations. His research interests include applied mathematics, theoretical and numerical methods for interdisciplinary applications, computational biology and disease modeling, as well as scientific and parallel computing. He is currently involved in developing a model to evaluate the effect of influenza vaccination in a healthcare setting using movements data.




Affan Shoukat

PhD Student (2015 - present)


Affan Shoukat received his MSc in Applied Mathematics from York University in 2015. He started his PhD program in the ABM-Lab in September 2015. His research topics include bioinformatics and computational biology. In particular, he is interested in modelling and predicting transcription factor binding sites and mapping the dynamic epigenetic landscape of the mammalian genome using statistical techniques such as Hidden Markov Models. He is currently working on health economics of Haemophilus influenzae serotype 'a' vaccine.




Sara Maghdoori

PhD Student (2015 - present)


Sara Maghdoori received her MA in Applied Mathematics from York University simultaneously with Financial Engineering degree from Schulich School of Business in 2014. She commenced her PhD program in September 2015 in ABM-Lab, working in the area of disease modelling and epidemiology. Her research interests broadly involve modelling of complex and biological systems, mathematical disease modelling, data and statistical analysis, mathematical optimization, agent-based simulations, and risk analysis.




Rachael Milwid

Research Associate (PhD Student 2015)


Rachael Milwid received her MSc at York University in Applied Mathematics. Her thesis involved studying vaccination and screening strategies for HPV.  She is currently a PhD student at the University of Guelph, conducting research involving agent-based models of equine diseases. Rachael joined the ABM-Lab to lead an exciting new project which involves standardizing the lexicon of terminology used by epidemiologists, disease modellers, and public health personnel. She is a member of mod4PH group that is established using LinkedIn, with ongoing discussion on projects related to the use of models in public health and disease control.




Aquino Espindola, PhD

Research Affiliate (2013 - present)


Aquino Espindola received his PhD in Physics from the University Federal Fluminense (Brazil) in 2006. His research involves statistical physics, agent-based computational modeling, complex systems, migration patterns, computational modeling of infectious diseases and population dynamics. He is currently involved in developing a stochastic agent-based model framework for tuberculosis infection with drug-resistance.


Lab Alumni



Angjelina Konini

PhD Student (2016 - completed)

Angjelina Konini received her MSc in Applied Mathematics from York University in 2011. She started her PhD program in the ABM-Lab in September 2012, and completed successfully in May 2016. She was also nominated for the outstanding thesis award. Her research broadly involves the impact of pathogen-host dynamics on optimizing intervention strategies (e.g., vaccination) and developing novel methods for integrating micro-dynamics of pathogen-host interactions with stochastic models of disease epidemics, particularly for Heamophilus influenza serotype 'a'.



Diana Knipl, PhD

Postdoctoral (2014 - 2015)

Diana Knipl received her PhD in Applied Mathematics form the University of Szeged, Hungary in 2014. Her research interests include the modelling of infectious diseases, particularly influenza, using advanaced systems of differential equations. She has joined the ABM-Lab to participate in projects related to computational modelling of vaccination, and evaluate the effect of local herd immunity on the dynamics of disease spread. She is also involved in modelling dengue infection and evaluating control programs under the auspices of a Science Withour Borders' project in collaboration with Brazilian partners.


Mingsong Kang, PhD

Postdoctoral (2014 - 2015)

Mingsong Kang received his PhD in Medical Sciences, specialized in biochemistry, immunology and microbiology, from Texas A&M Health Science Center, Texas A&M University in 2014. His Ph.D thesis research focused on host-pathogen interactions and protein-protein interactions using detailed molecular biology, biochemical, biophysical and immunological approaches. He has joined the ABM-lab to conduct research on projects involving in-host dynamics of infectious diseases, and the effect of interventions, such as vaccination, at the individual level. His current research also involves the dynamics of T-cell dependent and T-cell independent humoral immune response development.


Luiz Guidolin, PhD

Past position: Postdoctoral (2010 - 2012)

Luiz Guidolin received his PhD in Physics Applied to Medicine and Biology form the University of São Paulo, Brazil in 2011. In the field of computational science, his research interests include the modelling of complex and biological systems, statistical analysis, mathematical and software optimization, complex networks, and multi-agent systems. He is currently involved in the development of agent-based modelling computational frameworks for simulating the spread of emerging infectious diseases in large-scales and interconnected populations, through which the assessment of public health intervention strategies can be performed and optimal scenarios identified.


Majid Jaberi, PhD

Past position: Postdoctoral (2011 - 2012) 

Majid Jaberi received his PhD in Applied Mathematics from Université Laval in 2009. His research broadly involves dynamical systems with applications to the real-world problems, primarily in ecology and infectious disease epidemiology. He works in areas which are centered around interdisciplinary subjects and have interface with several branches of Applied Mathematics, including Mathematical Biology and Modeling. His is currently conducting the analysis and simulations of epidemic models to address the issues of drug resistance and optimal treatment strategies using control theory.


Yanyu Xiao, PhD

Past position: Postdoctoral (2012 - 2014) 

Yanyu Xiao received her PhD in Applied Mathematics from the University of Western Ontario in 2011. Her research involves mathematical analyses of infectious disease dynamical models, with recent focus on malaria and influenza. She has performed extensive research on how disease latency and the spatial mobility of individuals together affect disease dynamics at the population level. In the ABM Lab, she will be involved in several projects on optimal vaccination strategies and the development of agent-based models for management of emerging infectious pathogens, linking pathogen-host dynamics with the spread of infection in the population.


Zsolt Vizi

Visiting PhD Student (2015)

Zsolt Vizi received his MSc in Applied Mathematics from the University of Szeged, Hungary in 2013 and now he is a second year PhD student there, under the supervision of Gergely Röst and János Karsai. His research interests include mathematical models in life sciences, particularly epidemiological models, using dynamical systems. His PhD research focuses on modeling of non-Markovian type epidemics on networks applying analytical and computational tools to study the model dynamics.



Pieter de Boer

Visiting PhD Student (2015)

Pieter de Boer received his MSc in Pharmacy in 2014. He is currently a PharmD/PhD student at the University of Groningen, conducting his research on the cost-effectiveness of interventions against infectious diseases, with particular focus on vaccination against varicella zoster virus and influenza virus. His work includes infectious disease modelling. During his stay at ABM-Lab, York University, he will work on the cost-effectiveness of a high-dose antigen Flu-Zone influenza vaccine on the geriatric population.



Karen Huynh Wong, BSc

Past position: Research Associate (2012) 

Karen Huynh received her BSc in Mathematics from York University in 2012. She started her research as a summer student in the ABM-Lab. Her research involves modelling Meningitis B to determine the most effective and cost-effective vaccination programs to reduce the burden of disease. This research, in collaboration with Public Health Ontario, will develop computational models for simulation incidence scenarios and estimating key disease-specific parameters using age-structured epidemic models.


Jiacheng Wu, BSc

Past position: Globalink Research Intern (Summer 2013) 

Jiacheng Wu received MITACS Globalink award to join the ABM-Lab. His research involves the use of statistical methods for analysis of large-scale databases and implementation of agent-based simulation models for disease spread. He performs sensitivity and uncertainty analyses to develop and test rigorous validation strategies.


Jingwei Li

Globalink Research Intern (Summer 2014)

Jingwei Li received MITACS Globalink award to join the ABM-Lab. Her research involves the use of statistical methods and regression analysis for epidemiological and clinical data to estimate key parameters involved in micro and macro modelling of infectious diseases. She conducts statistical analysis using linear and non-linear models and develops rigorous validation strategies for parameter estimation.