Agent-Based Modelling Laboratory

Faculty of Science

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.

Congjie Shi

PhD Student (2021 - present)

Congjie Shi received her BS degree in mathematics from Harvey Mudd College in 2015, and her MEM and MF degrees in environmental management and forestry from Duke University in 2018. Her research interests include disease modeling, data analysis, and applied differential equations. She joined the ABM-Lab to focus on mathematical modeling and simulation of infectious diseases.

Jingjing Xu

Postdoctoral (2021 - present)

Jingjing Xu got her PhD degree in Applied Mathematics from the University of Western Ontario, studying the ecology and evolution of dispersal in metapopulations. Jingjing worked on predicting cyanobacterial blooms in Alberta lakes and modeling the chronic wasting disease spread in wild deer populations during her postdoc at the University of Alberta. At the ABM-Lab, she aims to study the mechanisms of emerging infectious diseases and intervention strategies using multi-variant models.

Thomas Vilches

Postdoctoral (2021 - present)

Thomas Vilches is a Medical Physicist who received his PhD in Biometry from the Universidade Estadual Paulista (UNESP), Brazil, in 2019. He has been working with mathematical and computational modelling of infectious diseases and collaborating with the ABM-Lab since his visit in 2017. After a 2-years postdoctoral position at the Universidade Estadual de Campinas (UNICAMP), in Brazil, Thomas returns to the ABM-Lab, as a post-doctoral fellow, to work on diseases dynamics, specially the COVID-19 pandemic.

Ao Li

Postdoctoral (2021 - present)

Ao Li earned her PhD in Applied Mathematics from the University of Western Ontario in 2021, and then she joined the ABM-Lab. She is interested in the use of mathematical models to understand ecological and epidemiological phenomena. As a member of the ABM-Lab, she is working on modelling the effect of control strategies during the COVID-19 pandemic as well as studying anti-microbial resistance.

Geneva Liwag

MSc Student (2020 - present)

Geneva Liwag obtained her Honours BSc degree in mathematics and chemistry from the University of Toronto Mississauga (UTM) in 2019, graduating with high distinction. As part of her undergraduate studies, she wrote an essay on different applications of mathematics in medicine, for which she was awarded the UTM Dean's Excellence Award in Writing in 2018. Her research interests mainly lie within mathematical modelling in life sciences and medicine, particularly population dynamics and disease modelling, with applications to public health. She is also currently involved in a project to develop a proof skills inventory for the introductory mathematical proofs course at UTM.

Ellie Abdollahi

PhD Student (2019 - present)

Ellie Abdollahi received her MSc in Statistics from Shiraz University. She commenced her PhD program in January 2019 in the ABM-Lab, working in the area of disease modelling and epidemiology with particular focus on TB infection and control. Her research interests broadly involve modelling of complex and biological systems, mathematical disease modelling, data and statistical analysis.

Cassandra Lisitza

MSc Student (2021 - present)

Cassandra graduated from the Honours Bachelor of Science program at MacEwan University in 2021, with a Mathematics major and Statistics minor. Her research experience has primarily been on the topic of meteorology. Further to her applied mathematics research, she has a background in statistics, with two awards granted for ASA Datafest 2019 and CANSSI National Case Study 2019. With her experience in applied mathematics and statistics, she sought a career in mathematical epidemiology where she can best combine these skills. Her current research is focused onmathmetical modelling of disease spread and the effect of interventions based on the characteristics of the invading pathogens. 

Affan Shoukat

Research Affiliate (2019 - present)

Past position: PhD Student (Completed 2019)

Affan Shoukat received his PhD in Applied Mathematics from York University in 2019. He started his PhD program in the ABM-Lab in September 2015. His research topics included biomathematics and computational epidemiology. In particular, he developed agent-based models for evaluating effectiveness and cost-effectiveness of disease intervention strategies. He is currently a postdoctoral fellow at Yale University School of Public Health. 

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.

Special Member

Sara Maghdoori

PhD Student (2015 - 2019; Passed away on February 1, 2020)

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 the ABM-Lab, working in the area of disease modelling and epidemiology. Her research interests broadly involved modelling of complex and biological systems, mathematical disease modelling, data and statistical analysis. She published the first paper of her PhD research program before taking the leave of absence. Her article was published in BMC Infectious Diseases and can be found here: 

Lab Alumni

Brendon Phillips

Postdoctoral (2021 - present)

Brendon Phillips obtained his PhD in Applied Mathematics at the University of Waterloo, where he modelled the spread of infectious disease and anti-vaccine sentiment through densely connected populations. Brendon has joined the ABM-Lab to continue work on modelling transmission dynamics and evaluating the effectiveness of vaccination with social and behavioural responses, among projects in other areas.

Di Shan

Research Assistant (2021 - present)

Di Shan is a Master of Biostatistics student at the Dalla Lana School of Public Health, University of Toronto. He obtained his Honours BSc degree in Statistics from the University of Toronto. His research interests lie within operation research in the field of health care and health economics. Di joined ABM-lab in summer 2021 as a research associate to work on the projects about COVID-19 patients in nursing homes and vaccination rates.

Shokoofeh Nourbakhsh, PhD

Postdoctoral (2019 - 2021)

Shokoofeh is a theoretical/computational biophysicist with a strong passion for quantitative modelling in a multidisciplinary approach. She obtained her PhD in physics from University of Waterloo in 2019, where she developed coarse-grained models of naturally-occurring antimicrobial peptides interactions with phospholipids and lipopolysaccharide membranes. Shokoofeh joined ABM-lab as a postdoctoral fellow to work on disease dynamics and health economics of respiratory syncytial virus (RSV) preventive strategies, using agent-based modelling, simulation tools, and statistical analysis.

Lyndon Juden-Kelly, PhD

Postdoctoral (2020 - 2021)

Lyndon Juden-Kelly is a quantitative Indigenous scholar from Eabematoong First Nation. He is an interdisciplinary neuroscientist who obtained his PhD in Human Studies at Laurentian University. His thesis concerned the biometeorological environmental influences on human behavior specifically relating to traumatic brain injury acquisition in professional sports. In joining the ABM-Lab as a postdoctoral fellow under Rapid Response Research, he will be involved in research projects related to the dynamics of disease characteristics in order to reduce and prevent the further spread of COVID-19. He is currently working on several projects in association with the National Collaborating Centre for Infectious Disease (NCCID).

Mehreen Tariq

MSc Student (2019 - 2021)

Mehreen Tariq received her Hons. BSc from McMaster University, graduating Summa Cum Laude in 2019. She completed her major in Mathematics and Statistics, with a minor in Biology. During her undergraduate studies, she worked in multiple professional settings and received a nomination for the 2017 Science Co-op Student of the Year Award. Her research interests lie within applied mathematics, mathematical biology, and mathematics education. In particular, she is interested in studying cellular processes with mathematical models to better understand the underlying kinetics.

Kevin Zhang

Research Associate (2020 - 2021)

Kevin is a medical student at the University of Toronto. Prior to his studies in the MD Program, he completed a Bachelor of Health Sciences degree at McMaster University. He has presented his research at national infectious disease meetings and published on the long-term prevention, spread, and treatment of Clostridium difficile infection. As part of a larger longitudinal health study, Kevin was involved in population health research related to smoking cessation in Germany. He joined the ABM-Lab as part of Rapid Reponse Research and is currently involved in several projects related to COVID-19.

David Champredon, PhD

Postdoctoral (2016 - 2019)


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 PhD 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. He is also developing agent-baed computational platforms for the evluation of health interventions by incorporating movement and epideimiological data into disease transmission models.

Zhen Wang, PhD

Postdoctoral (2018)


Zhen Wang received her PhD in Applied Mathematics from University of Waterloo in 2017. Her research interests broadly include building and analyzing mathematical models for a variety of biological systems. She is currently studying neural networks and infectious disease dynamical models. She joined the ABM-Lab to conduct research on projects involving the effect of disease latency, and optimal vaccination strategies using systems of delay differential equations.

Thomas Vilches

Visiting PhD Student (2017 - 2018)

Thomas Vilches received his MSc degree in Biometry from the Universidade Estadual Paulista, Brazil. He started his PhD in 2015 with research in mathematical epidemiology, applied computational models, complex networks and agent-based simulation systems. He is currently visiting ABM-Lab as part of his PhD program, and is involved in a research project for cost-effectiveness of vaccination against vector-borne diseases, with a case study for Zika. 

Mohammed Parvez

Summer "Research @ York" Intern (RAY, Summer 2018) 

Mohammed Parvez is currently pursuing a degree in Biotechnology (BSc) at York University. He is interested in combining applied mathematics and biology, and looking to gain experience over his first summer in York University. Beyond his undergraduate program, he plans on pursuing a career based in healthcare and medical research. Starting as a research assistant at the ABM-Lab, his target area of study is in developing an agent-based model on the use of acetaminophen and its effect on hepatocyte damage.

Andrea Gatica

Past position: Globalink Research Intern (Summer 2018) 

Andrea Gatica received MITACS Globalink award to join the ABM-Lab. Her research involves developing a summary of existing work on mathematical modelling related to vaccination, parsing and understanding of data. The modelling structures in this project will be informed by the nature of disease and the characteristics of vaccine candidates. The aim is to quantify factors affecting vaccine acceptance, so that researchers and infectious disease modellers can take initiatives on evaluating vaccination dynamics. The objectives will be achieved through a thorough search of literature, databases of the World Health Organization, and other sources available to the ABM-Lab.

Notice Ringa, PhD

Past position: Postdoctoral (2018)


Notice Ringa received his PhD in mathematics from the University of Guelph in 2014. Before joining the ABM-Lab as a postdoctoral fellow, he worked as a mathematics lecturer at Botswana International University of Science and Technology. He has carried out extensive research on the development, analysis, and application of pair approximation models to the dynamics and control of foot and mouth disease and human infections in general. He has joined the ABM-Lab to conduct research in modelling of vaccination to evaluate the effect of local herd immunity and optimal strategies in meta-population structures.

Dasaev Muñoz

Past position: Undergraduate Student Visitor (Summer 2018)

Dasaev Muñoz is completing his last year of bachelor degree in Industrial Relations at the University of Guanajuato, Mexico. He is participating in a research project on “Knowledge Management and Innovation in Healthcare Institutions”, where he aims to define and quantify relevant key performance indicators for chronic care models, and propose strategies that can improve hospital epidemiology and chrinic disease management. He will participate in data-driven modelling, with survey-based data collected for factors affecting diabetes.

Dean Vaksman, BSc

Past position: NSERC Research Associate (2017)

Dean Vaksman completed his Spec. Hons B.Sc. in Kinesiology & Health Science at York University. He is a recipient of an NSERC USRA, working at the ABM-Lab for summer 2017. His project is to systematically analyze the WHO's list of top emerging pathogens through computational and mathematical modelling tools. To further extend his understanding of the immune system and infectious diseases, he was recently accepted to a program facilitated through Harvard Medical School that provides students an opportunity to learn the fundamentals of immunology.

Lin Chen, PhD

Past position: 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 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.

Marek Laskowski, PhD

Past position: ABM-Lab Manager (2013 - 2016), 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 was 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.

Kim Rooprai, BSc

Past position: Research Associate (Undergrad Student 2016)

Kim Rooprai received her Honors Specialization in Health Sciences with Biology from Western University (2015). Since then, she has developed a strong interest for research in areas such as epidemiology, public and global health, and infectious diseases. She plans on pursuing a career as a health care professional where she is able to address public health challenges and by developing and implanting sustainable plans. She joined the ABM-Lab in 2016 to undertake a project related to exploring the epidemiology of pertussis based on available databases at the global scale.

Mehdi Najafi, PhD

Past position: 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.

Angjelina Konini, PhD

Past position: PhD Student (Completed 2016)

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'.

Rachael Milwid, MSc

Past position: 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.

Diana Knipl, PhD

Past position: 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

Past position: 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

Past position: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, BSc

Past position: 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.