Members

Principle

Dr. William Hsiao

Principal Investigator

Research Interest: microbial genomics, knowledge engineering, public health, data sharing

Dr. Hsiao joined BCCDC Public Health Laboratory in September 2011 as chief bioinformatician and subsequently became a senior scientist (bioinformatics) in January 2017. He is cross appointed at University of BC and at Simon Fraser University for research and teaching. He is dedicated to bioinformatics education and outreach – serving as an instructor for the Canadian Bioinformatics Workshops (www.bioinformatics.ca) and a faculty advisor for the Vancouver Bioinformatics Users Group (www.vanbug.org). Dr. Hsiao completed his PhD in the area of microbial genomics and horizontal gene transfer at SFU under Dr. Fiona Brinkman’s supervision, and a post-doctoral fellowship in the area of microbiome and clinical microbiology in Dr. Claire Fraser’s laboratory at the Institute for Genome Sciences in University of Maryland School of Medicine.

Staff

Dr. Lauren Tindale

Postdoctoral Researcher (co-supervised with Dr. Natalie Prystajecky)

 

Research Interest: genetics, disease surveillance, common-complex diseases, data analysis

Lauren completed her PhD at Canada’s Michael Smith Genome Sciences Centre where she researched the genetics of healthy aging and longevity in Super-Seniors. Her current research focuses on methods for avian influenza surveillance in the environment.

Dr. Pratima Shrivastava

Laboratory/Project Manager

Research Interest: Public Health, Immunology, Clinical Research

Pratima completed her PhD in Immunology at the Banaras Hindu University (India). She then worked as a post-doctoral researcher at the National University of Singapore and Singapore immunology network. Pratima has close to 5 years of experience in project management in academics and hospital settings. She is currently working as a Project Manager with the group.

Dr. Emma Griffiths

GenEpiO Project Coordinator, Curator and Research Associate

 

Research Interest: ontologies, public health genomics, and microbiology

Emma completed her PhD in Biochemistry at McMaster University (Ontario) studying bacterial phylogeny and evolutionary molecular markers. She also has postdoctoral experience in fungal and chemical genetics, as well as developing ontologies for infectious disease outbreak investigation and surveillance. Her current research focuses on applying ontology-based applications and One Health approaches to improving WGS contextual data sharing for combatting antimicrobial resistance.

Gurinder Gosal

NLP Researcher

 

Research Interest: Bio-ontologies, Bio-NLP, Semantic Technologies, Databases, Data Science and Machine Learning

Gurinder is a researcher, academician and computer professional with 18+ years of experience. Gurinder was a graduate research assistant at the University of Georgia, USA where he developed a system “Ontological Based Semantic Annotation System (OBSAS) for Protein Kinases in Cancer” that integrates and builds upon NLP, Ontologies and Semantic technologies. Gurinder formerly has been a faculty at the Department of Computer Science, Punjabi University, India. He is currently working on the development of LexMapr, a text mining tool that mines the short biomedical sample descriptions and maps the detected entities to the selected domain ontologies.

Dr. Jun Duan

Research Associate (genomics)

 

Research Interest: Bioinformatics, Genomics

Jun completed his Ph.D. at Southwest University of China, he was involved in the silkworm genome project focusing on genome sequencing, gene expression and gene function studies. He then worked at Chongqing University of China to carry on his genomics and bioinformatics research. He then did his postdoctoral study at the University of Guelph involving whole-genome sequencing of forest pests and screening for potential pest-control target genes by RNAi-mediated method. Jun currently works as a Research Associate at University of British Columbia and BC Centre for Disease Control, focusing on NGS data analysis and bioinformatics pipeline development (AIV Seeker, SeqUDAS) for avian and human influenza project. Outside of her academic studies, Jun enjoys fishing, tablet tennis, hiking, and soccer.

Dr. Cletus D’Souza

Research Coordinator

 

Research Interest: Biomedical Science, complementary approaches in prevention and treatment of chronic disease

Cletus has a Master of Science degree in Biochemistry and Nutrition, and a Ph.D. in Biochemistry and Molecular Biology. He has over 24 years’ experience in diverse research areas including microbial development and pathogenesis, bioinformatics and clinical research. In his current work, Cletus helps in research facilitation and manages the financial and administrative affairs of the lab.

Damion Dooley

Scientific Programmer

 

Research Interest: ontologies, public health genomics, infectious disease epidemiology, farm-to-fork food ontology

Damion is the platform architect and lead software developer for the Genomic Epidemiology Ontology Mart (GEEM) project which aims to support the quality curation and uptake of genomic epidemiology data, leading to timely and more precise health care analysis and research findings. For the last three years at the Hsiao Lab he has been the principle ontology developer for the consortium-driven IRIDA.ca project and the www.genepio.org and www.foodon.org ontology projects that it engendered. Decades of experience as a software developer, starting as CTO of one of Vancouver’s first web development service companies, Communicopia.ca, and later with start-ups Ecotagious.org and JitsuTech.com, have given him experience in understanding the usability challenges that software needs to solve in catering to various communities of user. Damion’s Honours BA in cognitive scientist has led naturally to specializing in ontology system delivery.

Students

Ginny Pichler

PhD Student (Co-supervised, Primary Supervisor: Dr. Jennifer Gardy)

Research Interest: Microbiology, Genomic Epidemiology, Infectious Diseases

Virginia completed her Master of Science in bioarcheology at the University of York in 2014. She is currently a PhD candidate in the Department of Microbiology and Immunology at the University of British Columbia and is part of the Tuberculosis Antimicrobial Resistance Project.

Dalia Alghamdi

PhD Student

Research Interest: Research Interest: Biobanking, Ontology, Data science

Dalia completed her Masters in Bioinformatics at the University of Leicester in 2014. She is currently a PhD candidate in the Bioinformatics graduate program at the University of British Columbia. Her project, Next generation Biobanking ontology (NGBO) focuses on the extensive integration of bio-banking data to allow data analysis and specimen sharing.

Dr. Michelle Coombe

PhD Student (Co-supervised, Primary supervisor: Dr. Chelsea Himsworth)

Research Interest: Zoonotic diseases, Epidemiology, Disease surveillance, One Health, Data science

Michelle completed her BSc in Ecology at the University of Calgary in 2005 and her DVM at the Western College of Veterinary Medicine through the University of Saskatchewan in 2011. She is currently a PhD candidate in the School of Population and Public Health at the University of British Columbia. Her project focuses on the utility of environmental sampling for the surveillance of avian influenza in wild waterfowl.

Master Students

Michael Gergely

Software developer (co-op student)

 

Research Interest: Bioinformatics, Systems design

Michael is in the process of completing his Joint major in Molecular Biology and Biochemistry and Computing Science from Simon Fraser University. His current work involves the development of the SeqUDAS bioinformatics pipeline.

Ali Mirza

Developer

Research Interest: semantic web, ontologies

Ivan completed his Bachelor of Computer Science at the University of British Columbia (UBC), where he gained co-op experience as a web developer and scientific programmer. He also completed a B.Sc. (Hons) in animal biology at UBC, where he studied metabolic rate depression in three-spined stickleback. His current work is focused on the development of GEEM, a web application designed to provide a user-friendly way of utilizing ontology-driven specifications for standardized data.

Kevin Kuchinski

Masters Student (Primary Supervisor: Dr. Natalie Prystajecky)

Research Interest: Zoonotic diseases, disease surveillance, clinical microbiology, microbial genomics and bioinformatics

Kevin completed his Bachelor of Microbiology and Immunology at the University of British Columbia in 2015. He is currently a Masters student in the Department of Pathology ad Laboratory Medicine at the University of British Columbia. His project focuses on developing laboratory and bioinformatics methods for enriching viral targets from clinical and environmental samples. These methods are primarily being applied to the recovery of avian influenza genomes from environmental samples collected in wild bird habitats.