Job Description

Position Description

Area: Microbiology and Bioinformatics
Duration: One-year position
Start Date: As soon as possible
Salary: $55,000-$60,000

The Cumming School of Medicine at the University of Calgary is accepting applications for a Postdoctoral Scholar with expertise in bacterial genomics to study infection transmission amongst individuals with cystic fibrosis.

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The post doc will be part of an interdisciplinary research project that seeks to use genomic analysis of bacterial pathogens to study airways infections amongst individuals with cystic fibrosis. The post doc will work directly with aligned researchers in the Cumming School of Medicine, Department of Microbiology, Immunology and Infectious Diseases as well as clinical collaborators in the Adult CF Clinic and Bronchiectasis clinic. The project will leverage the Calgary Adult Cystic Fibrosis (CF) Clinic Biobank - the largest, most comprehensive collection of CF derived isolates in the world. This collection of
60,000 isolates includes bacterial pathogens recovered from each and every clinical encounter of every single patient attending the clinic over the last thirty years linked with detailed clinical information. Furthermore, an associated biobank of sputum includes ~23,000 individual whole sputum samples available for subsequent analysis. The successful applicant will be able to leverage whole genome sequencing data from the ~2000 isolates that have already undergone whole genome sequencing to explore a range of projects including infection transmission chains and factors associated with individual transmission events, adaptation and parallel evolution within the CF lung and the dynamic satellite genome of chronically infecting pathogens. Many potentially impactful manuscripts are expected to come from this work.

Reporting to the Primary Investigators (PIs) Michael Parkins (Cumming School of Medicine) and Christina Thornton (Cumming School of Medicine), the post doc will be an important part of a large team conducting research into suppurative airways disease. The University of Calgary has long led infectious disease research in CF, and a wide range of highly impactful papers have come from this research group. The group will also leverage their expertise and knowledge in a wide range of other research areas ranging from bacterial evolution to population level research using wastewater.

The primary responsibility of the post doc will be analysis and interrogation of genomic data. Secondary responsibilities will include integration of genomic datasets with clinical metadata. Data analysis and visualization in support of effective oral and written communication of results will be expected. The post doc will play a key role in our team\'s efforts to publish existing and future results in peer-reviewed journals - and a significant number of high impact publications will be possible with this dataset. Accordingly, contributing to the preparation of manuscripts will be a high priority objective for this position. Additional responsibilities will include participating in and supporting the lab-based workflow described above, potentially including retrospective analysis of archived samples. The successful applicant will join a productive transdisciplinary team with supporting research funding from Cystic Fibrosis Foundation, Cystic Fibrosis Canada, Canadian Institutes of Health Research, Genome Canada, Alberta Health, Public Health Agency of Canada.

The sample archive available will enable both prospective and retrospective study design and analyses. The post doc will work as part of a large team that includes several staff with MDs and PhDs, research technicians, graduate students, and undergraduate interns such that some supervision of junior colleagues will be expected. The successful candidate will review existing literature and methodologies, analyze existing data, strategically collect and analyze additional samples, and prepare presentations and manuscripts for publication. The principal investigators will regularly review work to ensure quality and completeness and to advise on complex matters and provide feedback.

Qualifications:

Individuals should be motivated and enthusiastic about health policy research and have experience with policy, pragmatic trials, economics, implementation science, economics, statistics, or other related fields.

• PhD in molecular microbiology, genomics, bioinformatics, or a related field
• Accuracy and attention to detail
• Strong written communication skills are essential
• Experience with biostatistical approaches is essential
• Experience with microbial genomics and bioinformatics is essential, including:

• Implementing and using bioinformatic tools on the command line
• Basic programming skills in bioinformatics-relevant language (e.g., Bash, Python, R)
• Using/interacting with a high-performance computing cluster (e.g., SLURM)
• Implementation and interpretation of genomics analyses, including phylogenetics, pangenome/gene content analyses, SNP calling, etc.:

• Sequence data quality control and cleaning (e.g., FastQC, MultiQC, Trimmomatic)
• Genome assembly and annotation (e.g., Unicycler, SKESA, Trycycler, Bakta, DRAM)
• Pangenome analysis (e.g, Panaroo, PIRATE)
• SNP calling (e.g., Breseq, Snippy, GATK)
• Phylogenetics (e.g., IQ-Tree, RAxML, BEAST)
• Genomics data visualization (e.g., iTOL, ggplot2, ggtree)
• Experience with analytical methods, particularly in molecular microbiology, biostatistics, and working with nucleic acid sequences (including amplicons and genomes) is essential
• Must be able to work in a team environment and interact with a diverse range of colleagues and collaborators
• Strong verbal communication skills as well as strong listening skills are required
• Strong organizational, time management and problem-solving skills
• Must be highly goal-driven and exhibit the ability to interact effectively with internal and external stakeholders at all levels of the organization
• Able to work within a collaborative setting with others to set clear priorities while managing multiple timelines and objectives
• Must have experience in statistical analysis, visualization, and presentation of large data sets
• Evidence of a track record of peer reviewed publications will be important.

Please review the for more information prior to applying for this position.

Application Details:

If you are interested in applying, please contact Dr. Michael Parkins from the University of Calgary by sending your correspondence to . Applications will be reviewed as soon as they are received. Candidates should include the following in their application: * A brief cover letter outlining your interest in this project, detailing any additional qualifications or related experience that you have as well as your career goals

• A detailed resume
• An example of published research
• Name and contact information of at least three references

Additional Information

To learn more about postdoctoral scholar opportunities at the University of Calgary and all we have to offer, view our . For more information visit .

The University strongly recommends all faculty and staff are fully vaccinated against COVID-19.

About the University of Calgary

UCalgary is Canada\'s entrepreneurial university, located in Canada\'s most enterprising city. It is a top research university and one of the highest-ranked universities of its age. Founded in 1966, its 36,000 students experience an innovative learning environment, made rich by research, hands-on experiences and entrepreneurial thinking. It is . today at the University of Calgary. For more information, visit .

To succeed as one of Canada\'s top universities, where new ideas are created, tested and applied through first-class teaching and research, the University of Calgary needs more of the best minds in our classrooms and labs. We\'re increasing our scholarly capacity by investing in people who want to change the world, bringing the best and brightest to Calgary to form a global intellectual hub and achieve advances that matter to everyone. For more information visit .

About Calgary, Alberta

Calgary is one of the world\'s cleanest cities and has been named one of the world\'s most livable cities for years. Calgary is a city of leaders - in business, community, philanthropy and volunteerism. Calgarians benefit from the strongest economy in the nation and enjoy more days of sunshine per year than any other major Canadian city. Calgary is less than an hour\'s drive from the Rocky Mountains and boasts the most extensive urban pathway and bikeway network in North America.

The University of Calgary has launched an institution-wide committing to creating a rich, vibrant, and culturally competent campus that welcomes and supports Indigenous Peoples, encourages Indigenous community partnerships, is inclusive of Indigenous perspectives in all that we do.

As an equitable and inclusive employer, the University of Calgary recognizes that a diverse staff/faculty benefits and enriches the work, learning and research experiences of the entire campus and greater community. We are committed to removing barriers that have been historically encountered by some people in our society. We strive to recruit individuals who will further enhance our diversity and will support their academic and professional success while they are here. In particular, we encourage members of the designated groups (women, Indigenous peoples, persons with disabilities, members of visible/racialized minorities, and diverse sexual orientation and gender identities) to apply. To ensure a fair and equitable assessment, we offer accommodation at any stage during the recruitment process to applicants with disabilities. Questions regarding [diversity] EDI at UCalgary can be sent to the ( ) and requests for accommodations can be sent to Human Resources ( ).

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