Dedicated exclusively to children and their families, The Hospital for Sick Children (SickKids) is one of the largest and most respected paediatric healthcare centres in the world. As innovators in child health, we lead and partner to improve the health of children through the integration of healthcare, leading-edge research and education. Our reputation would not have been built – nor could it be maintained – without the skills, knowledge and experience of the extraordinary people who come to work here every day. SickKids is committed to ongoing learning and development, and features a caring and supportive work environment that combines exceptionally high standards of practice.

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Funded by Genome Alberta, we have an opening for a postdoctoral fellow interested in furthering their skills in computational biology. Research in the Parkinson lab focuses on dissecting pathways in the gut microbiome that contribute to health and disease. Over the past seven years, we have been using the chicken gut microbiome as an excellent model system to examine microbial interactions through a combination of genomics, systems biology and computer modeling. In recent work we developed a metabolic model of communities in the chicken gut to reveal the contributions of keystone taxa (https://www.biorxiv.org/content/10.1101/2024.10.14.618310v1). In the current project we are building on this work to systematically identify stable gut communities that can be used to seed the developing gut microbiome of chicks to support poultry health and wellbeing. Based at SickKids in Toronto, the fellow will work with colleagues located in Alberta, as well as members of the Parkinson lab (http://www.compsysbio.org), to analyse and model poultry gut communities. In brief, the work will involve processing and analysis of metagenomic datasets generated from poultry samples, generating metabolic reconstructions for taxa identified from these samples and performing in silico modeling of these communities using established modeling tools on the University of Toronto's high performance compute platform. The fellow will be encouraged to use their creativity to develop the modeling platform to incorporate additional (non-metabolic) features that better reflect the gut environment, as well as perform rigorous benchmarking of the various tools used in the analyses. The fellow will be expected to contribute to writing of draft manuscripts, submission of sequencing datasets to public repositories and contribute code to the project GitHub.

The ideal candidate will be a talented and creative computational biologist with expertise in R and Python, interested in developing and applying modeling tools to study complex microbial communities. The candidate will be expected to bring expertise in some of the following areas: linear algebra, constraints based modeling (e.g. flux balance analysis), metagenomics, metabolic reconstruction and high performance computing. The position is available for 1 year in the first instance but subject to renewal for at least one additional year. Here's What You'll Get To Do

• Participate in a dynamic team developing cutting edge approaches to translate microbiome research to improve gut health
• Develop and apply new methods to identify microbial communities that can be used in commercial settings
• Disseminate research findings through publications, presentations, and seminars

Here's What You'll Need

• PhD degree in bioinformatics, computational biology or related field (candidates who have obtained their PhD within the last two years are preferred)
• Excellent computational/programing skills
• Creativity in development of new methods
• Motivation and the ability to work independently as well as part of a team
• Strong communications skills

Employment Type: Full-time temporary 1 year contract, 1.0 FTE

The children and families we care for are from a variety of communities, and so are our employees. We welcome and encourage everyone to join our organization and be part of our team.

When requested, SickKids will provide access and inclusion supports to eligible candidates to support their full engagement during the interview and assessment process. Information received related to access or inclusion will be addressed confidentially.

Thank you for your interest in joining SickKids. Only those applicants selected for an interview will be contacted. In accordance with our Hospital policy, employment at SickKids is conditional upon the Hospital's receipt of all necessary documentation.

How To Apply Tip: Combine your cover letter and resume into ONE document of 20 pages or less as you cannot upload multiple documents as part of your application.

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