Jobs

The Ecosystems and Global Change Group (www.ecosystemchange.com) at Trent University jointly led by Prof Andrew Tanentzap (Canada Research Chair in Climate Change and Northern Ecosystems) and Dr Erik Emilson (Research Scientist, Canadian Forest Service sector of Natural Resources Canada, https://glfc-wet.github.io) is recruiting a Postdoctoral Fellow to start immediately.  The initial appointment will last for two years with a possibility for renewal.

The project:  Permafrost thaw risks releasing microbes into the natural environment that have been isolated from modern ecosystems for millennia with unknown consequences for people and wildlife.  We are searching for an experienced researcher to characterise microbial community composition and functioning in thawing North American permafrost, with a particular focus on environmental pathogens and the application of single-cell sequencing approaches.  Our research group also holds large sequencing datasets from freshwaters and soils that are often coupled with untargeted metabolomics data, offering substantial opportunities for focused data mining.

The Cumming School of Medicine and Faculty of Science at the University of Calgary are accepting applications for a Postdoctoral Scholar in Bioinformatics and its application to Wastewater-Based Surveillance (WBS) of antimicrobial resistance and emerging pathogens.

The postdoc will be part of an interdisciplinary research team that uses wastewater to track the dynamics of infectious agents. We have developed an integrated surveillance network monitoring 43 municipalities, as well as several sentinel surveillance hubs including a large number of tertiary care hospitals and populations of special interest from which we collect samples 1-3x per week.  Wastewater data can be compared with population-level data and hospital-specific data drawing from a single provincial health provider – and the potential of this unique network is exceptional. To date we have amassed >2000 samples that have been processed as raw wastewater and culture enriched raw wastewater (for specific pathogens).  A parallel agriculture and agri-food network is being developed which will be further leveraged.  The postdoc will work directly with a transdisciplinary team of clinicians and researchers at the University of Calgary (Cumming School of Medicine and Faculties of Science, Engineering, and Veterinary Medicine, and Advancing Canadian Water Assets (ACWA)) and their collaborators including those at the Universities of Alberta, Athabasca and Lethbridge. The Postdoc will also have the opportunity to collaborate with public health, pharmacy, infection control, and antimicrobial stewardship experts at Alberta Health Services.

The successful applicant will join a productive transdisciplinary team with supporting research funding from NSERC, CIHR, Genome Alberta, and Alberta Health. Working with the Primary Investigators Michael Parkins and John Conly (Cumming School of Medicine, Departments of Medicine and Microbiology, Immunology & Infectious Diseases) and Casey Hubert (UCalgary Research Chair, Faculty of Science). The Postdoc will work as part of a large team that includes several HQP staff and trainees including those in graduate, undergraduate and post graduate training programs.  There will be abundant opportunities for collaboration with others interested in bioinformatics and mentorship of junior trainees.

Subject area description

Miscarriage is the most common pregnancy complication, with over 23 million pregnancies ending in miscarriage every year.  This project aims to identify fetal genetic factors (SNP and de novo copy number variants) behind miscarriage, particularly among fetuses with normal chromosome counts. The postdoc fellow will lead a project using large-scale genotyping array data from miscarried fetuses and their mothers (including calling of aneuploidies and copy number variants) and contribute to ongoing efforts in this field (GWAS, meta-analyses, etc).

The Centre for Molecular Medicine and Therapeutics at the University of British Columbia seeks applications for a Post-Doctoral Scientist in the Wasserman Lab working on the Silent Genomes Project.  The Wasserman laboratory partners with a strong genetics community to develop and apply computational (bioinformatics) methods to improve diagnosis for individuals with rare genetic disorders caused by variations in genome sequences. The Silent Genomes Project is a national collaboration focused on the establishment of an Indigenous Background Variant Library under Indigenous governance and oversight.

Based on the campus of BC Children’s Hospital, the Wasserman laboratory is the lead laboratory for the technical implementation of the Indigenous Background Variant Library, including the implementation of software pipelines for processing whole genome sequence data generated at an approved genome centre, the implementation of quality control analyses, the construction of the database to host the generated genetic data and the implementation of the interface via which the data can be accessed by approved users.  The work, while computational in focus, requires close interaction with an Indigenous governance committee, collaborators and trainees.  In addition to engineering, the Wasserman laboratory seeks to develop innovative bioinformatics methods for assessing the quality of and improving the library.  The candidate will apply computational skills to develop computationally efficient and reproducible results for the detection of genetic variants across whole genome sequences, create methods to separate shared from not shared genetic variation data from related individuals, create methods to predict the number of novel genetic variants (compared to an existing background variation database), and develop procedures for assessing the presence of structural variants, initially detected in long-read sequencing data, in short-read whole genome sequence data, and contribute to the development of scientific manuscripts, reports and funding applications.  Central to the work, is extraordinary attention to the sensitivity of the data being processed, with particular emphasis on the rights of Indigenous peoples and the central importance of adhering to the Indigenous governance procedures within the project. Experience with whole genome sequence processing and analysis, pipeline management software (e.g. Nextflow) and working with highly sensitive genetic data are strong advantages.

Organizational Status

This is a leadership role, requiring a high degree of independence, initiative and professional judgement.  The successful candidate reports to and receives guidance from Dr. W. Wasserman (Professor, Medical Genetics, Project Leader).  The successful candidate supervises staff members and possibly University students or volunteers working on Silent Genomes.  They will contribute to development of reports for oversight bodies and funding organizations.

Supervision Received

The incumbent works with wide latitude and demonstrates a high degree of independence.  They report to and receive guidance from Dr. W. Wasserman (Professor, Medical Genetics, Project Leader)

Supervision Given

The incumbent provides expertise to project team members, including  University students and other trainees participating on the Silent Genomes project.

Consequence of Error/Judgement

Lack of careful attention to protocols and regulatory and ethical guidelines could suspend the Investigator and/or University as a site for further research and/or funding. Performance must strictly conform to research protocols, Tri-Council policy statement, and standard Canadian guidelines for health research involving Indigenous People.

A high level of cultural competency and sensitivity is necessary in this position, as any insensitive actions could jeopardize our longstanding research relationship with the Indigenous communities we work with.

Errors in the dissemination of DNA sequence data or any breach of confidentiality could jeopardize this research study and Dr. Wasserman’s research program. A confidentiality agreement must be signed, stating that any identifying and/or personal information will be held in the strictest confidence.

The laboratory of Dr. Arielle Elkrief, co-Director of the CHUM Microbiome Centre is searching for a talented and self-driven Computational Biologist or Bioinformatician to join our computational team as a post-doctoral fellow. The candidate will focus on establishing computational infrastructure for analysing complex and multimodal microbiome data. The candidate will be working closely with other computational biologists, basic scientists, students, and researchers including members of the Dr. Bertrand Routy laboratory, co-Director of the CHUM Microbiome Centre.

The Elkrief lab will provide both computational support with a senior computational biologist on-staff. The candidate will be responsible for designing a data architecture to leverage and integrate in house microbiome-oncology datasets, processing, visualizing and interpreting data for multiple projects.

The lab focuses on developing novel microbiome-based therapies for people with lung cancer and melanoma treated with immunotherapy. This includes investigating the role of fecal microbial transplantation, probiotics, prebiotics, and diet in prospective clinical patient trials, with a focus on integrating multi-omic translational correlative approaches using biospecimens from patients enrolled on these trials. The specific role of the candidate will be to perform primary computational biology analyses on samples from multiple clinical trials with high potential for impact.