William Hsiao

Associate Professor MSHRBC Scholar

Health Sciences

William Hsiao

Associate Professor, MSHRBC Scholar

Health Sciences

Areas of interest

Bioinformatics, health informatics and public health infectious disease genomics.


  • BSc (Hon), Microbiology and Immunology, McGill University
  • PhD, Molecular Biology and Biochemistry, Simon Fraser University
  • Postdoctoral Fellow, Institute for Genome Sciences, University of Maryland School of Medicine


Dr. William Hsiao joined the Faculty of Health Sciences at Simon Fraser University as an associate professor in September 2020. He is also an affiliated scientist at the BC Centre for Disease Control Public Health Laboratory (BCCDC PHL) and at Canada’s Michael Smith Genome Sciences Centre, and a genomic consultant with the BC Ministry of Agriculture Animal Health Centre. Prior to joining FHS, Dr. Hsiao was the chief bioinformatician and a senior scientist at the BCCDC PHL for 8 years and a clinical associate professor at the University of British Columbia. Dr. Hsiao obtained his PhD in the Department of Molecular Biology and Biochemistry at Simon Fraser University followed by a postdoctoral fellowship at the Institute for Genome Sciences at University of Maryland School of Medicine. During his formal training, his research focused on microbial genomics and metagenomics. During his time at the BCCDC PHL, he incorporated data science and knowledge engineering into his research and developed expertise in public health data sharing, integration, and harmonization. With experience conducting and applying genomics and data science research both in academia and in government laboratories (public health and animal health), Dr. Hsiao brings to FHS a special perspective on integrating basic and applied research to improve our public health system.

Dr. Hsiao also teaches short-term, intensive workshops through the Canadian Bioinformatics Workshops (www.bioinformatics.ca/)

Research interests

Dr. Hsiao directs the Public Health Bioinformatics Group, an interdisciplinary group of researchers interested in solving practical public health and animal health problems through a One Health lens. The team combines knowledge engineering techniques and bioinformatics tool development to improve data sharing and integrated analysis in public health. Dr. Hsiao’s team developed several ontologies used to consistently describe health knowledge and data. These include the Genomic Epidemiology Ontology (GenEpiO) to describe genomics-based infectious disease surveillance data and the Food Ontology (FoodOn), a comprehensive set of vocabularies to describe various aspects of “food” ranging from food processing, food products, food consumers, to diet, linking together agricultural and nutritional data. FoodOn is currently being adopted by the USDA FoodData Central. His team is also developing ontology-driven text-mining tools to improve the extraction and re-use of biological data following FAIR principles.

Dr. Hsiao is a co-lead of the IRIDA Consortium (www.irida.ca), a group of bioinformatics researchers building a high-quality, user-friendly genomic epidemiology analysis platform. His team also develops several workflows to automate pathogen genomic data analysis. He strongly believes in Open Science and actively promotes open source software and open access to his team’s work. His team also develops data standards to promote the interoperability of systems and datasets. Examples include an international (ISO) standard for the use of whole genome sequencing for food microbiology, and a standard for SARS-CoV-2 data sharing which will enable researchers around the world to better use sequence data to fight the virus during the global pandemic. Recognizing the One Health (interconnected) nature of many infectious diseases, Dr. Hsiao’s team collaborates extensively with researchers and practitioners from a wide range of disciplines in quantitative sciences, social sciences and medical and veterinary sciences with the aim of understanding the microbial world better and to improve the health and well-being of humans and animals.  

Dr. Hsiao is also the Principal Investigator for The Centre for Infectious Disease Genomics and One Health (https://cidgoh.ca/our-team/). They are a multi-disciplinary team of researchers interested in solving infectious disease challenges through a One Health Lens using advanced computational approaches and innovative knowledge engineering, and stakeholder engagement.

Publications and activities

View Dr. Hsiao’s publications at here