Bioinformatician

The Department of Paediatric Laboratory Medicine (DPLM) at SickKids is a leading, world-class facility working towards reducing the impact of childhood illness by providing diagnostic information that allows for early selection of best treatment options. DPLM is a valuable and integral part of the SickKids team, generating original research and providing timely, specialized diagnostic services for health care providers in Canada and around the world. The department comprises of five divisions: Clinical Biochemistry, Genome Diagnostics, Haematopathology, Microbiology, and Pathology. All DPLM laboratories are accredited by Accreditation Canada Diagnostics. 

The Hospital for Sick Children in Toronto is looking for a talented and motivated Bioinformatician to work in the field of clinical molecular diagnostics. The successful candidate will join a multidisciplinary team employing state-of-the-art sequencing technologies and advanced analysis methods to better diagnose and treat genetic and infectious diseases.  

The group is situated in the Department of Paediatric Laboratory Medicine and works collaboratively between the Division of Genome Diagnostics and the Division of Microbiology 

The Division of Microbiology at SickKids has been engaged in clinical SARS-CoV-2 viral sequencing and fungal sequencing and continues to develop and deploy new tests into routine clinical practice to support epidemiology for hospital acquired infections, clinical outbreak response, and clinical metagenomic sequencing for rapid diagnosis.  

Genome Diagnostics is the largest CLIA certified laboratory in Canada and is working on a number of clinical initiatives, whose aims include translation of new sequencing technologies into diagnostic testing for human disease and building databases and data sharing capacity to better interpret genomic variation for clinical use.  

Here’s What You’ll Get to Do  

•        Develop and maintain custom pipelines as well as utilize commercial and open-source software to support ongoing clinical activities with a direct impact on patient care. 
•        Keep abreast of new and emerging technologies and develop novel ways of analyzing genomic data sets for both clinical care and research opportunities.  
•        Build, test, and maintain analysis pipelines using both onsite high performance computing clusters and cloud-based solutions 
•        With oversight from bioinformaticians and medical/scientific staff, ensure that analysis workflows meet accreditation standards for the accuracy and turnaround times required for clinical diagnostic and surveillance testing.
•        Develop standard operating procedures, validation documents and quality control metrics that conform to accreditation requirements 

Here’s What You’ll Need  

•        Minimum of a Bachelor degree (Master or equivalent experience preferred) in a relevant field such as bioinformatics, or computer science. 
•        Advanced understanding of computer science and bioinformatics including a basic knowledge of biological sciences associated with testing offered by the Hospital of Sick Children (e.g. human genetics, microbiology, biochemistry). 
•        Experience analyzing next-generation sequencing technologies (e.g. ONT Nanopore, Illumina, PacBio) 
•        Demonstrated programming abilities for pipeline development with a preference for Python but abilities in other languages (e.g. CWL, Nextflow, R statistical programming) as well as cloud-based computing knowledge (e.g. AWS/Kubernetes, GCP). 
•        Experience with creating and deploying containers (e.g. Dockers, Singularity) for local and cloud-based pipelines. 
•        Experience with Unix operating systems and high-performance computing and workload managers (e.g. Torque/Moab, Slurm). 
•        Familiarity with developing, testing and maintenance of local (e.g. MySQL, MongoDB) and cloud-based (e.g. Snowflake, BigQuery) databases. 
•        Excellent verbal and written communication skills with the ability to prepare and present scientific data in a clear and concise manner. 
•        Demonstrated interpersonal skills including the ability to work effectively with others in a team environment. 
•        Ability to work independently with demonstrated skills in troubleshooting and problem solving. 
•        Demonstrated commitment and actions in advancing equity, diversity, and inclusion objectives