Bioinformatics Analyst

Institution/Company:
University of Saskatchewan
Location:
Saskatoon, SK, Canada
Job Type:
  • Staff (Full-time, permanent)
Degree Level Required:
Masters, Bachelor's
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Bioinformatics Analyst

The primary purpose of this position is to provide bioinformatics expertise, data analysis and support for health science researchers, particularly in the area of Cancer Research. This includes assistance with analysis of researcher-generated data (e.g. Next-Generation sequencing data that may include: exome, whole genome, whole genome bisulfite, RNA-seq, ChIP-seq and other types of ‘omics data). In addition, the bioinformatics analyst will assist will analyses of data from the many large public databases to help researchers find, analyze, evaluate and report data relevant to the researcher’s questions. The successful candidate will have experience analyzing publicly available and newly generated genomics and transcriptomics data in a Linux/UNIX environment. Experience interpreting results in an oncological context is highly desirable.

Responsibilities:

• Processing of researcher generated sequencing data (e.g., genomics, transcriptomics etc.) including data quality assessment, generating results using custom and established pipelines and workflows, and assisting with analysis and data interpretation. • Ensuring that data is managed efficiently, securely, and without loss or corruption through its life cycle. • Analyzing large public databases particularly those containing both ‘omics (genomics, gene expression, mutations etc.) and clinical data (e.g. survival outcomes). Some examples include: cBioportal, TCGA, META500, CPTAC, GTEx, TARGET, gnomAD, GENIE, SEER. • Providing training and support to researchers in the use of data from public databases. • Contributing to reports for basic and clinical research purposes. • Researching, implementing, and validating bioinformatic tools for specific project analyses. • Troubleshooting software and scripts. • Developing and maintaining analysis pipelines and workflows. • Documenting, communicating and training others to learn how to carry out bioinformatics analyses and the help them understand this field better. • Organizing results into clear presentations, figures, or summaries.

Qualifications:

Education: A minimum of a Bachelor of Science degree plus a graduate degree (MSc or PhD) bioinformatics, computational biology, genomics or a related discipline.

Skills and Experience: Previous experience performing processing and analyzing genomic and transcriptomic data is required. • Experience integrating data from major public sources (e.g., cBioportal, TCGA, META500, CPTAC, GTEx, TARGET, gnomAD, GENIE, SEER) to inform subsequent analyses is required. • The ideal candidate will have experience using software tools and resources (e.g., Ingenuity Pathway Analysis (IPA), Connectivity Map (CMAP, Broad Institute), KEGG Database and Pathways Analysis, Reactome Pathways Analysis, iPathwayGuide, DAVID, Innate DB, Bioconductor, XevaDB, ClinVar, PharmGKB, NIH LINCS, STRING, PPI Networks, UALCAN, KM plotter, CIBERSORT, DepMap). • The candidate must be able to work independently and as part of a team and will also have a demonstrated track record of strong technical, analytical, organizational, time-management and communication skills. • Experience with the following techniques would be considered a strong asset: • Python, R, shell scripting, Linux command line utilities • Analyzing large sequencing and ‘omics datasets • SNV and SV detection and significance prediction • Statistical methods (e.g., ANOVA, regression, clustering, survival) • Analysis of genome, exome, and targeted sequencing data • Read alignment and expression quantification • Differential expression analysis

  • How to Apply

    Interested candidates must submit a resume and cover letter to deborah.anderson@saskcancer.ca.

Additional Information

We thank all applicants, however only those selected for an interview will be contacted.

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