455 days ago

Shared Hospital Laboratory Inc.



, Ontario


Job Type:


Degree Level Required:

Bachelor's, Masters

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Company Biography: Shared Hospital Laboratory Inc. (SHL) is an independent corporation owned and operated by Scarborough Health Network, North York General Hospital, Michael Garron Hospital and Sunnybrook Health Sciences Centre. SHL provides high quality, efficient, advanced microbiology services. SHL has proven to be one of the most successful and sustainable models of laboratory collaboration in Ontario. SHL has a Board approved strategic plan focused on growth through optimizing/expanding clinical scope, fostering new partnerships, and advancing technology/infrastructure to ensure long-term sustainability.

Position Overview: Reporting to the Medical Director at Shared Hospital Laboratory, this person will assist and provide support for the bioinformatics analysis of bacterial and viral pathogens that are of relevance to SHL and develop a research program relevant to the strategic plan of SHL.


The following are some tasks of the role:

a. Conducting the analysis of large microbial genomic and metagenomic datasets

b. Advising on the design and deployment of state-of-the-art computational tools

c. Validation of computational tools and analytical pipelines and contribute to accreditation processes for genomic data.

d. Verification of reproducibility and accuracy of findings.

d. Generating genomic epidemiological analyses (lineage identification, variant calling, outbreak phylogeny within a reasonable timeframe (<7 days) of microbial organisms of relevance to SHL).

e. Creation of procedures and guidelines for increasing in-house analytical capacity

f. Formalization of genomic epidemiology reporting templates for clinical and public health use

g. Drafting and co-authorship of research publications and reports within a timely fashion.

h. Advise on research projects and assist as needed.

i. Other related duties as assigned




• Completion of an advanced degree (e.g., PhD or Masters) in microbiology, virology, bioinformatics or another relevant related discipline

• Minimum of 2 years experience in bioinformatics related to microbiology

• Demonstrated proficiency in UNIX-based systems and fluency in one or more programming languages (eg. R or Python) and experience using bioinformatics workflows (e.g., snakemake, nextflow)

• Willingness to teach and train others in basics of bioinformatics

• Has published in peer-reviewed scientific journals on related areas (e.g. microbiology)

• Demonstrated problem recognition and problem solving-skills

• Demonstrated good organizational skills, ability to organize work and set priorities

• Ability work independently or as a team member in a fast-paced environment

• Excellent interpersonal and communication skills both verbal and written

• Demonstrates values consistent with hospital Code of Conduct and is committed to fostering a healthy and positive work environment in accordance with Health & Safety policy and legislation

• Utilize protective equipment provided and identify and reports hazards

• Engages in ethical conduct and strives to understand and appreciate the diversity of our patient/staff population and community

• Excellent work performance and attendance

Additional Information:

Applicants are requested to provide a link to their public github or gitlab profile if they have one on their CV.

CV and cover letter should be sent to:

Dr. Kevin Katz


Accommodation Statement: Scarborough Health Network (SHN) embraces and celebrates our community’s unique multicultural heritage and diversity. SHN is an equal opportunity employer, dedicated to a culture of inclusiveness and diversity reflecting our diverse patients, staff and community alike. We are committed to providing barrier-free and accessible employment practices in compliance with the Accessibility for Ontarians with Disabilities Act (AODA). Should you require accommodation through any stage of the recruitment process, please make them known when contacted and we will work with you to meet your needs. Learn more about our exciting opportunities by following us on Twitter at: SHNCareers





clinical microbiology

medical microbiology

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